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commit/galaxy-central: greg: Change the import for the base message template for the tool shed to eliminate the bus error when you point your browser to the tool shed.
by Bitbucket 03 Oct '12

03 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ae683c38bdf2/ changeset: ae683c38bdf2 user: greg date: 2012-10-03 16:13:12 summary: Change the import for the base message template for the tool shed to eliminate the bus error when you point your browser to the tool shed. affected #: 1 file diff -r 7b3a7a3ea9afc3de218c7c5f2c52cdfa717ee5c5 -r ae683c38bdf2aa61403dc220e91561945a855158 templates/webapps/community/message.mako --- a/templates/webapps/community/message.mako +++ b/templates/webapps/community/message.mako @@ -1,1 +1,1 @@ -<%inherit file="/message.mako"/> +<%inherit file="../../message.mako"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: smcmanus: Cleanup
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7b3a7a3ea9af/ changeset: 7b3a7a3ea9af user: smcmanus date: 2012-10-03 00:30:08 summary: Cleanup affected #: 3 files diff -r 3d07a7800f9af46e46c1f3ad3f0fe432949f3b51 -r 7b3a7a3ea9afc3de218c7c5f2c52cdfa717ee5c5 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -321,31 +321,23 @@ log.exception( '(%s) Failed to change ownership of %s, failing' % ( job.id, self.working_directory ) ) return self.fail( job.info, stdout=stdout, stderr=stderr, exit_code=tool_exit_code ) - log.debug( "############## JobWrapper.finish: %s exit code" - % ( "None" if None == tool_exit_code else str(tool_exit_code))) # if the job was deleted, don't finish it if job.state == job.states.DELETED or job.state == job.states.ERROR: - # ERROR at this point means the job was deleted by an administrator. # SM: Note that, at this point, the exit code must be saved in case # there was an error. Errors caught here could mean that the job # was deleted by an administrator (based on old comments), but it # could also mean that a job was broken up into tasks and one of - # the tasks failed. So + # the tasks failed. So include the stderr, stdout, and exit code: return self.fail( job.info, stderr=stderr, stdout=stdout, exit_code=tool_exit_code ) # Check the tool's stdout, stderr, and exit code for errors, but only # if the job has not already been marked as having an error. # The job's stdout and stderr will be set accordingly. - log.debug( "############## JobWrapper.finish: Post-check exit code: %s/%s" - % ( ( "None" if None == tool_exit_code else str(tool_exit_code) ), - ( "None" if None == job.exit_code else str(job.exit_code) ) ) ) if job.states.ERROR != job.state: if ( self.check_tool_output( stdout, stderr, tool_exit_code, job )): job.state = job.states.OK else: job.state = job.states.ERROR - log.debug( "############## JobWrapper.finish: Post-check exit code: %s" - % ( "None" if None == tool_exit_code else str(tool_exit_code))) if self.version_string_cmd: version_filename = self.get_version_string_path() @@ -471,8 +463,6 @@ # is either incorrect or has the wrong semantics. if None != tool_exit_code: job.exit_code = tool_exit_code - log.debug( "############## JobWrapper.finish: storing %s exit code" - % ( "None" if None == job.exit_code else str(job.exit_code))) # custom post process setup inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) diff -r 3d07a7800f9af46e46c1f3ad3f0fe432949f3b51 -r 7b3a7a3ea9afc3de218c7c5f2c52cdfa717ee5c5 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -143,10 +143,7 @@ # Finish the job! try: - #job_wrapper.finish( stdout, stderr, exit_code ) - # DELETEME: This is for testing how null exit codes are handled: - log.debug( "############## Finishing job - None exit code" ) - job_wrapper.finish( stdout, stderr, None ) + job_wrapper.finish( stdout, stderr, exit_code ) except: log.exception("Job wrapper finish method failed") job_wrapper.fail("Unable to finish job", exception=True) diff -r 3d07a7800f9af46e46c1f3ad3f0fe432949f3b51 -r 7b3a7a3ea9afc3de218c7c5f2c52cdfa717ee5c5 lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -64,7 +64,7 @@ # thing as the last task to complete, which could be added later. # o if a task fails, then the job will fail and the failing task's # exit code will become the job's exit code. - job_exit_code = "" + job_exit_code = None # If we were able to get a command line, run the job. ( must be passed to tasks ) if command_line: @@ -112,17 +112,14 @@ # Deleted tasks are not included right now. # while tasks_complete is False: - log.debug( "************ Rechecking tasks" ) count_complete = 0 tasks_complete = True for tw in task_wrappers: task_state = tw.get_state() - log.debug( "***** Checking task %d: state %s" - % (tw.task_id, task_state) ) if ( model.Task.states.ERROR == task_state ): job_exit_code = tw.get_exit_code() - log.debug( "Canceling job %d: Task %s returned an error (exit code %d)" - % ( tw.job_id, tw.task_id, job_exit_code ) ) + log.debug( "Canceling job %d: Task %s returned an error" + % ( tw.job_id, tw.task_id ) ) self.cancel_job( job_wrapper, task_wrappers ) tasks_complete = True break @@ -136,8 +133,6 @@ if sleep_time < 8: sleep_time *= 2 import time - log.debug( "####################### Finished with tasks; job exit code: %d" % job_exit_code ) - job_wrapper.reclaim_ownership() # if running as the actual user, change ownership before merging. log.debug('execution finished - beginning merge: %s' % command_line) stdout, stderr = splitter.do_merge(job_wrapper, task_wrappers) @@ -164,7 +159,6 @@ # Finish the job try: - log.debug( "$$$$$$$$$$$$$$ job_exit_code before finish: %d" % job_exit_code ) job_wrapper.finish( stdout, stderr, job_exit_code ) except: log.exception("Job wrapper finish method failed") Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: smcmanus: The task runner now chooses an exit code based on the tasks' exit codes - if the tasks are successful, then the last exit code scanned is chosen, and if a task fails then the first scanned failing task's exit code is chosen. The JobWrapper's fail method also stores stdout, stderr, and the exit code if they're available, though this will currently only applies to when a Job using the task runner fails. A null/None exit code is also now supported.
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3d07a7800f9a/ changeset: 3d07a7800f9a user: smcmanus date: 2012-10-03 00:20:12 summary: The task runner now chooses an exit code based on the tasks' exit codes - if the tasks are successful, then the last exit code scanned is chosen, and if a task fails then the first scanned failing task's exit code is chosen. The JobWrapper's fail method also stores stdout, stderr, and the exit code if they're available, though this will currently only applies to when a Job using the task runner fails. A null/None exit code is also now supported. affected #: 4 files diff -r 6d45fd1d830ee85edcdc07ba93831c316102e81a -r 3d07a7800f9af46e46c1f3ad3f0fe432949f3b51 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -204,7 +204,7 @@ self.version_string_cmd = self.tool.version_string_cmd return extra_filenames - def fail( self, message, exception=False ): + def fail( self, message, exception=False, stdout="", stderr="", exit_code=None ): """ Indicate job failure by setting state and message on all output datasets. @@ -249,6 +249,20 @@ job.state = job.states.ERROR job.command_line = self.command_line job.info = message + # TODO: Put setting the stdout, stderr, and exit code in one place + # (not duplicated with the finish method). + if ( len( stdout ) > 32768 ): + stdout = stdout[:32768] + log.info( "stdout for job %d is greater than 32K, only first part will be logged to database" % job.id ) + job.stdout = stdout + if ( len( stderr ) > 32768 ): + stderr = stderr[:32768] + log.info( "stderr for job %d is greater than 32K, only first part will be logged to database" % job.id ) + job.stderr = stderr + # Let the exit code be Null if one is not provided: + if ( exit_code != None ): + job.exit_code = exit_code + self.sa_session.add( job ) self.sa_session.flush() #Perform email action even on failure. @@ -290,7 +304,7 @@ self.sa_session.add( job ) self.sa_session.flush() - def finish( self, stdout, stderr, tool_exit_code=0 ): + def finish( self, stdout, stderr, tool_exit_code=None ): """ Called to indicate that the associated command has been run. Updates the output datasets based on stderr and stdout from the command, and @@ -300,25 +314,38 @@ self.sa_session.expunge_all() job = self.get_job() + # TODO: After failing here, consider returning from the function. try: self.reclaim_ownership() except: - self.fail( job.info ) log.exception( '(%s) Failed to change ownership of %s, failing' % ( job.id, self.working_directory ) ) + return self.fail( job.info, stdout=stdout, stderr=stderr, exit_code=tool_exit_code ) + log.debug( "############## JobWrapper.finish: %s exit code" + % ( "None" if None == tool_exit_code else str(tool_exit_code))) # if the job was deleted, don't finish it if job.state == job.states.DELETED or job.state == job.states.ERROR: - #ERROR at this point means the job was deleted by an administrator. - return self.fail( job.info ) + # ERROR at this point means the job was deleted by an administrator. + # SM: Note that, at this point, the exit code must be saved in case + # there was an error. Errors caught here could mean that the job + # was deleted by an administrator (based on old comments), but it + # could also mean that a job was broken up into tasks and one of + # the tasks failed. So + return self.fail( job.info, stderr=stderr, stdout=stdout, exit_code=tool_exit_code ) # Check the tool's stdout, stderr, and exit code for errors, but only # if the job has not already been marked as having an error. # The job's stdout and stderr will be set accordingly. + log.debug( "############## JobWrapper.finish: Post-check exit code: %s/%s" + % ( ( "None" if None == tool_exit_code else str(tool_exit_code) ), + ( "None" if None == job.exit_code else str(job.exit_code) ) ) ) if job.states.ERROR != job.state: if ( self.check_tool_output( stdout, stderr, tool_exit_code, job )): job.state = job.states.OK else: job.state = job.states.ERROR + log.debug( "############## JobWrapper.finish: Post-check exit code: %s" + % ( "None" if None == tool_exit_code else str(tool_exit_code))) if self.version_string_cmd: version_filename = self.get_version_string_path() @@ -358,7 +385,6 @@ # TODO: The context['stderr'] holds stderr's contents. An error # only really occurs if the job also has an error. So check the # job's state: - #if context['stderr']: if job.states.ERROR == job.state: dataset.blurb = "error" elif dataset.has_data(): @@ -435,12 +461,18 @@ self.sa_session.flush() # Save stdout and stderr if len( job.stdout ) > 32768: - log.error( "stdout for job %d is greater than 32K, only first part will be logged to database" % job.id ) + log.info( "stdout for job %d is greater than 32K, only first part will be logged to database" % job.id ) job.stdout = job.stdout[:32768] if len( job.stderr ) > 32768: - log.error( "stderr for job %d is greater than 32K, only first part will be logged to database" % job.id ) + log.info( "stderr for job %d is greater than 32K, only first part will be logged to database" % job.id ) job.stderr = job.stderr[:32768] - job.exit_code = tool_exit_code + # The exit code will be null if there is no exit code to be set. + # This is so that we don't assign an exit code, such as 0, that + # is either incorrect or has the wrong semantics. + if None != tool_exit_code: + job.exit_code = tool_exit_code + log.debug( "############## JobWrapper.finish: storing %s exit code" + % ( "None" if None == job.exit_code else str(job.exit_code))) # custom post process setup inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) @@ -513,26 +545,27 @@ # that range, then apply the error level and add a message. # If we've reached a fatal error rule, then stop. max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR - for stdio_exit_code in self.tool.stdio_exit_codes: - if ( tool_exit_code >= stdio_exit_code.range_start and - tool_exit_code <= stdio_exit_code.range_end ): - # Tack on a generic description of the code - # plus a specific code description. For example, - # this might prepend "Job 42: Warning: Out of Memory\n". - code_desc = stdio_exit_code.desc - if ( None == code_desc ): - code_desc = "" - tool_msg = ( "%s: Exit code %d: %s" % ( - galaxy.tools.StdioErrorLevel.desc( stdio_exit_code.error_level ), - tool_exit_code, - code_desc ) ) - log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) ) - stderr = tool_msg + "\n" + stderr - max_error_level = max( max_error_level, - stdio_exit_code.error_level ) - if ( max_error_level >= - galaxy.tools.StdioErrorLevel.FATAL ): - break + if tool_exit_code != None: + for stdio_exit_code in self.tool.stdio_exit_codes: + if ( tool_exit_code >= stdio_exit_code.range_start and + tool_exit_code <= stdio_exit_code.range_end ): + # Tack on a generic description of the code + # plus a specific code description. For example, + # this might prepend "Job 42: Warning (Out of Memory)\n". + code_desc = stdio_exit_code.desc + if ( None == code_desc ): + code_desc = "" + tool_msg = ( "%s: Exit code %d (%s)" % ( + galaxy.tools.StdioErrorLevel.desc( stdio_exit_code.error_level ), + tool_exit_code, + code_desc ) ) + log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) ) + stderr = tool_msg + "\n" + stderr + max_error_level = max( max_error_level, + stdio_exit_code.error_level ) + if ( max_error_level >= + galaxy.tools.StdioErrorLevel.FATAL ): + break if max_error_level < galaxy.tools.StdioErrorLevel.FATAL: # We'll examine every regex. Each regex specifies whether @@ -1013,6 +1046,11 @@ self.sa_session.refresh( task ) return task.state + def get_exit_code( self ): + task = self.get_task() + self.sa_session.refresh( task ) + return task.exit_code + def set_runner( self, runner_url, external_id ): task = self.get_task() self.sa_session.refresh( task ) @@ -1022,7 +1060,7 @@ self.sa_session.add( task ) self.sa_session.flush() - def finish( self, stdout, stderr, tool_exit_code=0 ): + def finish( self, stdout, stderr, tool_exit_code=None ): # DBTODO integrate previous finish logic. # Simple finish for tasks. Just set the flag OK. """ @@ -1032,7 +1070,8 @@ """ # This may have ended too soon log.debug( 'task %s for job %d ended; exit code: %d' - % (self.task_id, self.job_id, tool_exit_code) ) + % (self.task_id, self.job_id, + tool_exit_code if tool_exit_code != None else -256 ) ) # default post job setup_external_metadata self.sa_session.expunge_all() task = self.get_task() diff -r 6d45fd1d830ee85edcdc07ba93831c316102e81a -r 3d07a7800f9af46e46c1f3ad3f0fe432949f3b51 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -111,11 +111,8 @@ if sleep_time < 8: # So we don't stat every second sleep_time *= 2 - # Reap the process and get the exit code. The exit code should - # only be None if the process isn't finished, but check anyway. - exit_code = proc.wait() # reap - if None == exit_code: - exit_code = 0 + # Reap the process and get the exit code. + exit_code = proc.wait() stdout_file.seek( 0 ) stderr_file.seek( 0 ) stdout = stdout_file.read( 32768 ) @@ -146,7 +143,10 @@ # Finish the job! try: - job_wrapper.finish( stdout, stderr, exit_code ) + #job_wrapper.finish( stdout, stderr, exit_code ) + # DELETEME: This is for testing how null exit codes are handled: + log.debug( "############## Finishing job - None exit code" ) + job_wrapper.finish( stdout, stderr, None ) except: log.exception("Job wrapper finish method failed") job_wrapper.fail("Unable to finish job", exception=True) diff -r 6d45fd1d830ee85edcdc07ba93831c316102e81a -r 3d07a7800f9af46e46c1f3ad3f0fe432949f3b51 lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -56,6 +56,16 @@ job_wrapper.fail( "failure preparing job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return + + # This is the job's exit code, which will depend on the tasks' + # exit code. The overall job's exit code will be one of two values: + # o if the job is successful, then the last task scanned will be + # used to determine the exit code. Note that this is not the same + # thing as the last task to complete, which could be added later. + # o if a task fails, then the job will fail and the failing task's + # exit code will become the job's exit code. + job_exit_code = "" + # If we were able to get a command line, run the job. ( must be passed to tasks ) if command_line: try: @@ -69,7 +79,9 @@ job_wrapper.fail("Job Splitting Failed, no match for '%s'" % job_wrapper.tool.parallelism) return tasks = splitter.do_split(job_wrapper) - # Not an option for now. Task objects don't *do* anything useful yet, but we'll want them tracked outside this thread to do anything. + # Not an option for now. Task objects don't *do* anything + # useful yet, but we'll want them tracked outside this thread + # to do anything. # if track_tasks_in_database: task_wrappers = [] for task in tasks: @@ -100,25 +112,31 @@ # Deleted tasks are not included right now. # while tasks_complete is False: + log.debug( "************ Rechecking tasks" ) count_complete = 0 tasks_complete = True for tw in task_wrappers: task_state = tw.get_state() + log.debug( "***** Checking task %d: state %s" + % (tw.task_id, task_state) ) if ( model.Task.states.ERROR == task_state ): - log.debug( "Canceling job %d: Task %d returned an error" - % ( tw.job_id, tw.task_id ) ) + job_exit_code = tw.get_exit_code() + log.debug( "Canceling job %d: Task %s returned an error (exit code %d)" + % ( tw.job_id, tw.task_id, job_exit_code ) ) self.cancel_job( job_wrapper, task_wrappers ) tasks_complete = True break elif not task_state in completed_states: tasks_complete = False else: + job_exit_code = tw.get_exit_code() count_complete = count_complete + 1 if tasks_complete is False: sleep( sleep_time ) if sleep_time < 8: sleep_time *= 2 import time + log.debug( "####################### Finished with tasks; job exit code: %d" % job_exit_code ) job_wrapper.reclaim_ownership() # if running as the actual user, change ownership before merging. log.debug('execution finished - beginning merge: %s' % command_line) @@ -146,7 +164,8 @@ # Finish the job try: - job_wrapper.finish( stdout, stderr ) + log.debug( "$$$$$$$$$$$$$$ job_exit_code before finish: %d" % job_exit_code ) + job_wrapper.finish( stdout, stderr, job_exit_code ) except: log.exception("Job wrapper finish method failed") job_wrapper.fail("Unable to finish job", exception=True) diff -r 6d45fd1d830ee85edcdc07ba93831c316102e81a -r 3d07a7800f9af46e46c1f3ad3f0fe432949f3b51 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -134,7 +134,7 @@ self.post_job_actions = [] self.imported = False self.handler = None - self.exit_code = 0 + self.exit_code = None # TODO: Add accessors for members defined in SQL Alchemy for the Job table and # for the mapper defined to the Job table. @@ -317,10 +317,9 @@ self.task_runner_name = None self.task_runner_external_id = None self.job = job - # SM: Using default empty strings avoids None exceptions later on. self.stdout = "" self.stderr = "" - self.exit_code = 0 + self.exit_code = None self.prepare_input_files_cmd = prepare_files_cmd def get_param_values( self, app ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: scatterplot: controls to client-side template
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6d45fd1d830e/ changeset: 6d45fd1d830e user: carlfeberhard date: 2012-10-02 23:29:06 summary: scatterplot: controls to client-side template affected #: 4 files diff -r f66f88b2f743e3b3733e00756f7655003bf1880f -r 6d45fd1d830ee85edcdc07ba93831c316102e81a static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js --- /dev/null +++ b/static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js @@ -0,0 +1,51 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-visualization-scatterplotControlForm'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; + +function program1(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <option value=\""; + foundHelper = helpers.index; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.index; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</option>\n "; + return buffer;} + +function program3(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <option value=\""; + foundHelper = helpers.index; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.index; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</option>\n "; + return buffer;} + + buffer += "\n<div id=\"loading-indicator\" style=\"display: none;\">\n <img class=\"loading-img\" src=\""; + foundHelper = helpers.loadingIndicatorImagePath; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.loadingIndicatorImagePath; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" />\n <span class=\"loading-message\"></span>\n</div>\n\n"; + buffer += "\n<div id=\"chart-settings\">\n\n "; + buffer += "\n <div id=\"x-column-input\">\n <label for=\"\">Data column for X: </label>\n <select name=\"x-column\">\n "; + stack1 = depth0.availableColumns; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </select>\n </div>\n <div id=\"y-column-input\">\n <label for=\"\">Data column for Y: </label>\n <select name=\"y-column\">\n "; + stack1 = depth0.availableColumns; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </select>\n </div>\n \n <input id=\"render-button\" type=\"button\" value=\"Draw\" />\n <div class=\"clear\"></div>\n</div>"; + return buffer;}); +})(); \ No newline at end of file diff -r f66f88b2f743e3b3733e00756f7655003bf1880f -r 6d45fd1d830ee85edcdc07ba93831c316102e81a static/scripts/templates/visualization-templates.html --- /dev/null +++ b/static/scripts/templates/visualization-templates.html @@ -0,0 +1,33 @@ +<script type="text/template" class="template-visualization" id="template-visualization-scatterplotControlForm"> + +{{! loading indicator - initially hidden }} +<div id="loading-indicator" style="display: none;"> + <img class="loading-img" src="{{loadingIndicatorImagePath}}" /> + <span class="loading-message"></span> +</div> + +{{! main controls }} +<div id="chart-settings"> + + {{! column selector containers }} + <div id="x-column-input"> + <label for="">Data column for X: </label> + <select name="x-column"> + {{#each availableColumns}} + <option value="{{index}}">{{name}}</option> + {{/each}} + </select> + </div> + <div id="y-column-input"> + <label for="">Data column for Y: </label> + <select name="y-column"> + {{#each availableColumns}} + <option value="{{index}}">{{name}}</option> + {{/each}} + </select> + </div> + + <input id="render-button" type="button" value="Draw" /> + <div class="clear"></div> +</div> +</script> diff -r f66f88b2f743e3b3733e00756f7655003bf1880f -r 6d45fd1d830ee85edcdc07ba93831c316102e81a static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -1,7 +1,8 @@ define([ "../libs/underscore", "../libs/d3", - "../mvc/base-mvc" + "../mvc/base-mvc", + "../templates/compiled/template-visualization-scatterplotControlForm" ], function(){ /* ============================================================================= @@ -389,7 +390,7 @@ * Scatterplot control UI as a backbone view * */ -var ScatterplotView = BaseView.extend( LoggableMixin ).extend({ +var ScatterplotControlForm = BaseView.extend( LoggableMixin ).extend({ //logger : console, tagName : 'form', className : 'scatterplot-settings-form', @@ -418,48 +419,31 @@ }, render : function(){ - //TODO: to template var view = this, - html = '', - columnHtml = ''; + html = ''; // build column select controls for each x, y (based on name if available) - // ugh...hafta preprocess - this.dataset.metadata_column_types = this.dataset.metadata_column_types.split( ', ' ); - _.each( this.dataset.metadata_column_types, function( type, index ){ + var formData = { + loadingIndicatorImagePath : this.loadingIndicatorImagePath, + config : this.chartConfig, + availableColumns : [] + }; + _.each( this.dataset.metadata_column_types.split( ', ' ), function( type, index ){ // use only numeric columns if( type === 'int' || type === 'float' ){ + //TODO: using 0-based indeces var name = 'column ' + index; // label with the name if available if( view.dataset.metadata_column_names ){ name = view.dataset.metadata_column_names[ index ]; } - columnHtml += '<option value="' + index + '">' + name + '</option>'; + formData.availableColumns.push({ index: index, name: name }); } }); - - // loading indicator - initially hidden - html += '<div id="loading-indicator" style="display: none;">'; - html += '<img class="loading-img" src=' + this.loadingIndicatorImagePath + ' />'; - html += '<span class="loading-message"></span>'; - html += '</div>'; - - // column selector containers - html += '<div id="x-column-input">'; - html += '<label for="">Data column for X: </label><select name="x-column">' + columnHtml + '</select>'; - html += '</div>'; - - html += '<div id="y-column-input">'; - html += '<label for="">Data column for Y: </label><select name="y-column">' + columnHtml + '</select>'; - html += '</div>'; - - html += '<input id="render-button" type="button" value="Draw" />'; - html += '<div class="clear"></div>'; - //TODO: other vals: max_vals, start_val, pagination + html = ScatterplotControlForm.templates.form( formData ); this.$el.append( html ); - this.$el.find( '#render-button' ); return this; }, @@ -509,13 +493,15 @@ url : url, dataType : 'json', success : function( response ){ + // save the endpoint (number of next line, fileptr) for this object //TODO: server sends back an endpoint, cache for next pagination request + view.endpoint = response.endpoint; + view.showLoadingIndicator( 'Rendering...' ); - // save the endpoint (number of next line, fileptr) for this object - view.endpoint = response.endpoint; view.plot.render( response.data, response.meta ); view.hideLoadingIndicator(); }, + error : function( xhr, status, error ){ view.hideLoadingIndicator(); alert( 'ERROR:' + status + '\n' + error ); @@ -523,9 +509,14 @@ }); } }); +ScatterplotControlForm.templates = CompiledTemplateLoader.getTemplates({ + 'visualization-templates.html' : { + form : 'template-visualization-scatterplotControlForm' + } +}); //============================================================================== return { - //TwoVarScatterplot : TwoVarScatterplot, - ScatterplotView : ScatterplotView + TwoVarScatterplot : TwoVarScatterplot, + ScatterplotControlForm : ScatterplotControlForm };}); \ No newline at end of file diff -r f66f88b2f743e3b3733e00756f7655003bf1880f -r 6d45fd1d830ee85edcdc07ba93831c316102e81a templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -4,18 +4,19 @@ ${parent.stylesheets()} <style type="text/css"> +/*TODO: use/move into base.less*/ +* { margin: 0px; padding: 0px; } +#chart-header { + padding : 8px; + background-color: #ebd9b2; +} .title { - margin: 0px; - padding: 8px; - background-color: #ebd9b2; - border: 2px solid #ebd9b2; } -.subtitle { - margin: 0px; - padding: 0px 8px 8px 16px; - background-color: #ebd9b2; +#chart-header .subtitle { + margin: -4px 0px 0px 4px; + padding : 0; color: white; font-size: small; } @@ -28,7 +29,7 @@ padding-top: 1em; } -#chart-settings-form > * { +#chart-settings > * { margin: 8px; } @@ -96,7 +97,7 @@ //?? hmmmm //kwargs = ${h.to_json_string( kwargs )}; - var settingsForm = new scatterplot.ScatterplotView({ + var settingsForm = new scatterplot.ScatterplotControlForm({ dataset : hda, el : $( '#chart-settings-form' ), apiDatasetsURL : apiDatasetsURL, @@ -112,8 +113,10 @@ </%def><%def name="body()"> - <h2 class="title">Scatterplot of '${hda['name']}'</h2> - <p class="subtitle">${hda['misc_info']}</p> + <div id="chart-header"> + <h2 class="title">Scatterplot of '${hda['name']}'</h2> + <p class="subtitle">${hda['misc_info']}</p> + </div><div id="chart-holder"></div><div id="chart-settings-form"></div></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: basic.py, ColumnDataProvider: altered return format to be array of column arrays (opposed to array or rows); compute min, max of each column on server; scatterplot: altered to use that format;
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f66f88b2f743/ changeset: f66f88b2f743 user: carlfeberhard date: 2012-10-02 22:37:45 summary: basic.py, ColumnDataProvider: altered return format to be array of column arrays (opposed to array or rows); compute min, max of each column on server; scatterplot: altered to use that format; affected #: 4 files diff -r 369a941393909434e0efb5c84dd831e5ab096095 -r f66f88b2f743e3b3733e00756f7655003bf1880f lib/galaxy/visualization/data_providers/basic.py --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -92,22 +92,26 @@ and self.original_dataset.metadata.comment_lines ): start_val = int( self.original_dataset.metadata.comment_lines ) + 1 - response = {} - response[ 'data' ] = data = [] - #TODO bail if columns None, not parsable, not within meta.columns # columns is an array of ints for now (should handle column names later) columns = from_json_string( columns ) - assert( all([ column < self.original_dataset.metadata.columns for column in columns ]) ),( - "column index (%d) must be less" % ( column ) + for column in columns: + assert( ( column < self.original_dataset.metadata.columns ) + and ( column >= 0 ) ),( + "column index (%d) must be positive and less" % ( column ) + " than the number of columns: %d" % ( self.original_dataset.metadata.columns ) ) - - #print columns, start_val, max_vals, skip_comments, kwargs - # alter meta by column_selectors (if any) + # set up the response, column lists + response = {} + response[ 'data' ] = data = [ [] for column in columns ] + response[ 'meta' ] = meta = [ { 'min': None, 'max': None } for column in columns ] + + column_types = [ self.original_dataset.metadata.column_types[ column ] for column in columns ] + + # function for casting by column_types def cast_val( val, type ): - """ Cast value based on type. """ + """ Cast value based on type. Return None if can't be cast """ if type == 'int': try: val = int( val ) except: return None @@ -119,21 +123,30 @@ f = open( self.original_dataset.file_name ) #TODO: add f.seek if given fptr in kwargs for count, line in enumerate( f ): + + # check line v. desired start, end if count < start_val: continue - if ( count - start_val ) >= max_vals: break fields = line.split() fields_len = len( fields ) - #TODO: this will return the wrong number of columns for abberrant lines - line_data = [ cast_val( fields[c], self.original_dataset.metadata.column_types[c] ) - for c in columns if ( c < fields_len ) ] - data.append( line_data ) + #NOTE: this will return None/null for abberrant column values (including bad indeces) + for index, column in enumerate( columns ): + column_val = None + if column < fields_len: + column_val = cast_val( fields[ column ], column_types[ index ] ) + if column_val != None: + if( meta[ index ][ 'min' ] == None + or column_val < meta[ index ][ 'min' ] ): + meta[ index ][ 'min' ] = column_val + if( meta[ index ][ 'max' ] == None + or column_val > meta[ index ][ 'max' ] ): + meta[ index ][ 'max' ] = column_val + data[ index ].append( column_val ) response[ 'endpoint' ] = dict( last_line=( count - 1 ), file_ptr=f.tell() ) f.close() return response - diff -r 369a941393909434e0efb5c84dd831e5ab096095 -r f66f88b2f743e3b3733e00756f7655003bf1880f lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -56,7 +56,7 @@ rval = dataset.get_api_value() except Exception, e: - rval = "Error in dataset API at listing contents" + rval = "Error in dataset API at listing contents: " + str( e ) log.error( rval + ": %s" % str(e), exc_info=True ) trans.response.status = 500 return rval diff -r 369a941393909434e0efb5c84dd831e5ab096095 -r f66f88b2f743e3b3733e00756f7655003bf1880f static/scripts/packed/viz/scatterplot.js --- a/static/scripts/packed/viz/scatterplot.js +++ b/static/scripts/packed/viz/scatterplot.js @@ -1,1 +1,1 @@ -define(["../libs/underscore","../libs/d3","../mvc/base-mvc"],function(){function b(f){var i=this,d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var j=Array.prototype.slice.call(arguments);j.unshift(this.toString());console.debug.apply(null,j)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(j){_.extend(this.config,j)};this.toString=function(){return this.config.id};this.translateStr=function(j,k){return"translate("+j+","+k+")"};this.rotateStr=function(k,j,l){return"rotate("+k+","+j+","+l+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(m,k,j,l){m=m||0;k=k||0;j=j||0;l=l||0;this.svg.attr("width",this.config.width+(this.config.marginRight+k)+(this.config.marginLeft+l)).attr("height",this.config.height+(this.config.marginTop+m)+(this.config.marginBottom+j)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+l,this.config.marginTop+m))};this.preprocessData=function(j){return j.slice(0,this.config.maxDataPoints)};this.setUpDomains=function(j,k){this.xMin=this.config.xMin||d3.min(j);this.xMax=this.config.xMax||d3.max(j);this.yMin=this.config.yMin||d3.min(k);this.yMax=this.config.yMax||d3.max(k)};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(j){return(String(j)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);var j=this.yAxis.selectAll("text").filter(function(n,m){return m!==0});this.yLongestLabel=d3.max(j[0].map(function(n,m){return(d3.select(n).text()).length}))||0;var k=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(k-g);if(this.config.marginLeft<k){var l=(k)-this.config.marginLeft;l=(l<0)?(0):(l);this.log("adjusting:",l);this.adjustChartDimensions(0,0,0,l)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(j){};this.glyphFinalState=function(j){};this.glyphExitState=function(j){};this.renderDatapoints=function(j,m){var l=function(o,n){return i.xScale(j[n])};var k=function(o,n){return i.yScale(m[n])};this.datapoints=this.content.selectAll(".glyph").data(j);this.datapoints.enter().append("svg:circle").attr("class","glyph").attr("cx",l).attr("cy",0).attr("r",0);this.datapoints.transition().duration(this.config.entryAnimDuration).attr("cx",l).attr("cy",k).attr("r",this.config.bubbleRadius);this.datapoints.exit().transition().duration(this.config.entryAnimDuration).attr("cy",this.config.height).attr("r",0).style("fill-opacity",0).remove()};this.render=function(j,k){this.log("renderScatterplot",j.length,k.length,this.config);j=this.preprocessData(j);k=this.preprocessData(k);this.setUpDomains(j,k);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(j,k)}}var a=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",loadingIndicatorImagePath:(galaxy_paths.get("image_path")+"/loading_large_white_bg.gif"),events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new b(this.chartConfig)},render:function(){var c=this,e="",d="";this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ");_.each(this.dataset.metadata_column_types,function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}d+='<option value="'+g+'">'+f+"</option>"}});e+='<div id="loading-indicator" style="display: none;">';e+='<img class="loading-img" src='+this.loadingIndicatorImagePath+" />";e+='<span class="loading-message"></span>';e+="</div>";e+='<div id="x-column-input">';e+='<label for="">Data column for X: </label><select name="x-column">'+d+"</select>";e+="</div>";e+='<div id="y-column-input">';e+='<label for="">Data column for Y: </label><select name="y-column">'+d+"</select>";e+="</div>";e+='<input id="render-button" type="button" value="Draw" />';e+='<div class="clear"></div>';this.$el.append(e);this.$el.find("#render-button");return this},showLoadingIndicator:function(c){c=c||"";this.$el.find("div#loading-indicator").children(".loading-message").text(c);this.$el.find("div#loading-indicator").show("fast")},hideLoadingIndicator:function(){this.$el.find("div#loading-indicator").hide("fast")},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);this.showLoadingIndicator("Fetching data...");jQuery.ajax({url:e,dataType:"json",success:function(k){d.showLoadingIndicator("Rendering...");d.endpoint=k.endpoint;d.plot.render(_.map(k.data,function(l){return l[0]}),_.map(k.data,function(l){return l[1]}));d.hideLoadingIndicator()},error:function(m,k,l){d.hideLoadingIndicator();alert("ERROR:"+k+"\n"+l)}})}});return{ScatterplotView:a}}); \ No newline at end of file +define(["../libs/underscore","../libs/d3","../mvc/base-mvc"],function(){function b(f){var i=this,d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var j=Array.prototype.slice.call(arguments);j.unshift(this.toString());console.debug.apply(null,j)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(j){_.extend(this.config,j)};this.toString=function(){return this.config.id};this.translateStr=function(j,k){return"translate("+j+","+k+")"};this.rotateStr=function(k,j,l){return"rotate("+k+","+j+","+l+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built 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j=this.yAxis.selectAll("text").filter(function(n,m){return m!==0});this.yLongestLabel=d3.max(j[0].map(function(n,m){return(d3.select(n).text()).length}))||0;var k=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(k-g);if(this.config.marginLeft<k){var l=(k)-this.config.marginLeft;l=(l<0)?(0):(l);this.log("adjusting:",l);this.adjustChartDimensions(0,0,0,l)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line 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a=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",loadingIndicatorImagePath:(galaxy_paths.get("image_path")+"/loading_large_white_bg.gif"),events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new b(this.chartConfig)},render:function(){var c=this,e="",d="";this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ");_.each(this.dataset.metadata_column_types,function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}d+='<option value="'+g+'">'+f+"</option>"}});e+='<div id="loading-indicator" style="display: none;">';e+='<img class="loading-img" src='+this.loadingIndicatorImagePath+" />";e+='<span class="loading-message"></span>';e+="</div>";e+='<div id="x-column-input">';e+='<label for="">Data column for X: </label><select name="x-column">'+d+"</select>";e+="</div>";e+='<div id="y-column-input">';e+='<label for="">Data column for Y: </label><select name="y-column">'+d+"</select>";e+="</div>";e+='<input id="render-button" type="button" value="Draw" />';e+='<div class="clear"></div>';this.$el.append(e);this.$el.find("#render-button");return this},showLoadingIndicator:function(c){c=c||"";this.$el.find("div#loading-indicator").children(".loading-message").text(c);this.$el.find("div#loading-indicator").show("fast")},hideLoadingIndicator:function(){this.$el.find("div#loading-indicator").hide("fast")},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);this.showLoadingIndicator("Fetching data...");jQuery.ajax({url:e,dataType:"json",success:function(k){d.showLoadingIndicator("Rendering...");d.endpoint=k.endpoint;d.plot.render(k.data,k.meta);d.hideLoadingIndicator()},error:function(m,k,l){d.hideLoadingIndicator();alert("ERROR:"+k+"\n"+l)}})}});return{ScatterplotView:a}}); \ No newline at end of file diff -r 369a941393909434e0efb5c84dd831e5ab096095 -r f66f88b2f743e3b3733e00756f7655003bf1880f static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -158,14 +158,16 @@ // ........................................................ data and scales this.preprocessData = function( data ){ // set a cap on the data, limit to first n points - return data.slice( 0, this.config.maxDataPoints ); + return ( data.length > this.config.maxDataPoints )? ( data.slice( 0, this.config.maxDataPoints ) ): ( data ); }; - this.setUpDomains = function( xCol, yCol ){ - this.xMin = this.config.xMin || d3.min( xCol ); - this.xMax = this.config.xMax || d3.max( xCol ); - this.yMin = this.config.yMin || d3.min( yCol ); - this.yMax = this.config.yMax || d3.max( yCol ); + this.setUpDomains = function( xCol, yCol, meta ){ + this.log( 'setUpDomains' ); + // configuration takes priority, otherwise meta (from the server) if passed, last-resort: compute it here + this.xMin = this.config.xMin || ( meta )?( meta[0].min ):( d3.min( xCol ) ); + this.xMax = this.config.xMax || ( meta )?( meta[0].max ):( d3.max( xCol ) ); + this.yMin = this.config.yMin || ( meta )?( meta[1].min ):( d3.min( yCol ) ); + this.yMax = this.config.yMax || ( meta )?( meta[1].max ):( d3.max( yCol ) ); }; this.setUpScales = function(){ @@ -352,8 +354,12 @@ //this.log( this.datapoints, 'glyphs rendered' ); }; - this.render = function( xCol, yCol ){ + this.render = function( columnData, meta ){ //pre: columns passed are numeric + //pre: at least two columns are passed + //assume: first column is x, second column is y, any remaining aren't used + var xCol = columnData[0], + yCol = columnData[1]; this.log( 'renderScatterplot', xCol.length, yCol.length, this.config ); //pre: xCol.len == yCol.len @@ -363,8 +369,8 @@ //this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); //TODO: compute min, max on server. - this.setUpDomains( xCol, yCol ); - //this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); + this.setUpDomains( xCol, yCol, meta ); + this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); this.setUpScales(); this.adjustChartDimensions(); @@ -505,12 +511,9 @@ success : function( response ){ //TODO: server sends back an endpoint, cache for next pagination request view.showLoadingIndicator( 'Rendering...' ); + // save the endpoint (number of next line, fileptr) for this object view.endpoint = response.endpoint; - view.plot.render( - // pull apart first two regardless of number of columns - _.map( response.data, function( columns ){ return columns[0]; } ), - _.map( response.data, function( columns ){ return columns[1]; } ) - ); + view.plot.render( response.data, response.meta ); view.hideLoadingIndicator(); }, error : function( xhr, status, error ){ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: scatterplot: improved adj. for varying y-axis sizes; pack scripts
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/369a94139390/ changeset: 369a94139390 user: carlfeberhard date: 2012-10-02 21:36:56 summary: scatterplot: improved adj. for varying y-axis sizes; pack scripts affected #: 8 files diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/libs/underscore.js --- a/static/scripts/packed/libs/underscore.js +++ b/static/scripts/packed/libs/underscore.js @@ -1,1 +1,1 @@ -(function(){var w=this;var k=w._;var E={};var D=Array.prototype,g=Object.prototype,r=Function.prototype;var I=D.push,o=D.slice,y=D.concat,B=D.unshift,d=g.toString,j=g.hasOwnProperty;var M=D.forEach,q=D.map,F=D.reduce,c=D.reduceRight,b=D.filter,C=D.every,p=D.some,n=D.indexOf,l=D.lastIndexOf,u=Array.isArray,f=Object.keys,G=r.bind;var N=function(O){if(O instanceof N){return O}if(!(this instanceof N)){return new N(O)}this._wrapped=O};if(typeof exports!=="undefined"){if(typeof 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f=Backbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var b=Backbone.View.extend({className:"circster",initialize:function(m){this.total_gap=m.total_gap;this.genome=m.genome;this.dataset_arc_height=m.dataset_arc_height;this.track_gap=5;this.label_arc_height=20},render:function(){var u=this,r=this.dataset_arc_height,m=u.$el.width(),t=u.$el.height(),n=Math.min(m,t)/2-this.model.get("tracks").length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),s=this.model.get("tracks");var p=k.select(u.$el[0]).append("svg").attr("width",m).attr("height",t).attr("pointer-events","all").append("svg:g").call(k.behavior.zoom().on("zoom",function(){p.attr("transform","translate("+k.event.translate+") scale("+k.event.scale+")");var v=new l(),w={};s.each(function(x){w[x.id]=[]});k.selectAll("path.chrom-data").filter(function(y,x){return v.is_visible(this,p)}).each(function(z,x){var y=$.data(this,"chrom_data");w[y.track.id].push(y.chrom)})})).attr("transform","translate("+m/2+","+t/2+")").append("svg:g");s.each(function(v,x){var z=n+x*(r+u.track_gap),w=(v.get("track_type")==="LineTrack"?g:h);var y=new w({track:v,track_index:x,radius_start:z,radius_end:z+r,genome:u.genome,total_gap:u.total_gap});y.render(p)});var q=n+s.length*(r+u.track_gap)+u.track_gap;var o=new a({track:new f(),track_index:s.length,radius_start:q,radius_end:q,genome:u.genome,total_gap:u.total_gap});o.render(p)}});var c=e.extend({initialize:function(m){this.options=m;this.options.bg_stroke="ccc";this.options.bg_fill="ccc"},render:function(r){var o=r.append("g").attr("id","parent-"+this.options.track_index);var m=this._chroms_layout(),s=this.options.radius_start,p=this.options.radius_end,t=k.svg.arc().innerRadius(s).outerRadius(p),n=o.selectAll("g").data(m).enter().append("svg:g");n.append("path").attr("d",t).style("stroke",this.options.bg_stroke).style("fill",this.options.bg_fill).append("title").text(function(v){return v.data.chrom});this.render_data(o);var u=this.options.track.get("prefs"),q=u.block_color;if(!q){q=u.color}o.selectAll("path.chrom-data").style("stroke",q).style("fill",q)},_chroms_layout:function(){var n=this.options.genome.get_chroms_info(),p=k.layout.pie().value(function(r){return r.len}).sort(null),q=p(n),m=this.options.total_gap/n.length,o=i.map(q,function(t,s){var r=t.endAngle-m;t.endAngle=(r>t.startAngle?r:t.startAngle);return t});return o},render_chrom_data:function(o,p,q,n,r,m){},render_data:function(q){var v=this,u=this._chroms_layout(),o=this.options.track,n=this.options.radius_start,s=this.options.radius_end,t=o.get_genome_wide_data(this.options.genome),r=i.zip(u,t),m=this.get_bounds(t),p=i.map(r,function(w){var x=w[0],y=w[1];return v.render_chrom_data(q,x,y,n,s,m.min,m.max)});return p}});var a=c.extend({initialize:function(m){this.options=m;this.options.bg_stroke="fff";this.options.bg_fill="fff"},render_data:function(n){var m=n.selectAll("g");m.selectAll("path").attr("id",function(o){return"label-"+o.data.chrom});m.append("svg:text").filter(function(o){return o.endAngle-o.startAngle>0.08}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(o){return"#label-"+o.data.chrom}).attr("startOffset","25%").text(function(o){return o.data.chrom})}});var d=c.extend({render_quantitative_data:function(q,w,p,t,s,o,u){var r=k.scale.linear().domain([o,u]).range([t,s]);var n=k.scale.linear().domain([0,p.length]).range([w.startAngle,w.endAngle]);var y=k.svg.line.radial().interpolate("linear").radius(function(z){return r(z[1])}).angle(function(A,z){return n(z)});var m=k.svg.area.radial().interpolate(y.interpolate()).innerRadius(r(0)).outerRadius(y.radius()).angle(y.angle());var v=q.datum(p),x=v.append("path").attr("class","chrom-data").attr("d",m);$.data(x[0][0],"chrom_data",{track:this.options.track,chrom:w.data.chrom})},get_bounds:function(){}});var h=d.extend({render_chrom_data:function(o,r,p,n,s,q,m){if(!p||typeof p==="string"){return null}return this.render_quantitative_data(o,r,p.data,n,s,q,m)},get_bounds:function(n){var m=i.map(n,function(o){if(!o||typeof o==="string"){return 0}return o.max});return{min:0,max:(m&&typeof m!=="string"?i.max(m):0)}}});var g=d.extend({render_chrom_data:function(o,r,p,n,t,q,m){var s=p.data;if(s.length===0){return}return this.render_quantitative_data(o,r,s,n,t,q,m)},get_bounds:function(n){var m=i.flatten(i.map(n,function(o){if(o){return i.map(o.data,function(q){return q[1]})}else{return 0}}));return{min:i.min(m),max:i.max(m)}}});return{CircsterView:b}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(i,k,j){var f=function(){this.initialize&&this.initialize.apply(this,arguments)};f.extend=Backbone.Model.extend;var l=Backbone.Model.extend({is_visible:function(p,m){var n=p.getBoundingClientRect(),o=$("svg")[0].getBoundingClientRect();if(n.right<0||n.left>o.right||n.bottom<0||n.top>o.bottom){return false}return true}});var e=Backbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var b=Backbone.View.extend({className:"circster",initialize:function(m){this.total_gap=m.total_gap;this.genome=m.genome;this.dataset_arc_height=m.dataset_arc_height;this.track_gap=5;this.label_arc_height=20;this.scale=1},render:function(){var v=this,s=this.dataset_arc_height,m=v.$el.width(),u=v.$el.height(),n=Math.min(m,u)/2-this.model.get("tracks").length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),t=this.model.get("tracks"),p=t.map(function(w,y){var z=n+y*(s+v.track_gap),x=(w.get("track_type")==="LineTrack"?g:h);return new x({track:w,track_index:y,radius_bounds:[z,z+s],genome:v.genome,total_gap:v.total_gap})});var q=k.select(v.$el[0]).append("svg").attr("width",m).attr("height",u).attr("pointer-events","all").append("svg:g").call(k.behavior.zoom().on("zoom",function(){var w=k.event.scale;q.attr("transform","translate("+k.event.translate+") scale("+w+")");if(v.scale!==w){if(v.zoom_drag_timeout){clearTimeout(v.zoom_drag_timeout)}v.zoom_drag_timeout=setTimeout(function(){i.each(p,function(x){x.update_scale(w)})},400)}})).attr("transform","translate("+m/2+","+u/2+")").append("svg:g");i.each(p,function(w){w.render(q)});var r=n+t.length*(s+v.track_gap)+v.track_gap;var o=new a({track:new e(),track_index:t.length,radius_bounds:[r,r],genome:v.genome,total_gap:v.total_gap});o.render(q)}});var c=f.extend({initialize:function(m){this.options=m;this.options.bg_stroke="ccc";this.options.bg_fill="ccc";this.options.chroms_layout=this._chroms_layout();this.options.data_bounds=this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome));this.options.scale=1;this.options.parent_elt=null},render:function(q){this.options.parent_elt=q.append("g").attr("id","parent-"+this.options.track_index);var p=this.options.parent_elt;var o=this.options.chroms_layout,s=k.svg.arc().innerRadius(this.options.radius_bounds[0]).outerRadius(this.options.radius_bounds[1]),m=p.selectAll("g").data(o).enter().append("svg:g");m.append("path").attr("d",s).style("stroke",this.options.bg_stroke).style("fill",this.options.bg_fill).append("title").text(function(t){return t.data.chrom});this._render_data(p);var n=this.options.track.get("prefs"),r=n.block_color;if(!r){r=n.color}p.selectAll("path.chrom-data").style("stroke",r).style("fill",r)},update_scale:function(p){var o=this.options.scale;this.options.scale=p;if(p<=o){return}var n=this,m=new l();this.options.parent_elt.selectAll("path.chrom-data").filter(function(r,q){return m.is_visible(this)}).each(function(v,s){var u=k.select(this),r=u.attr("chrom"),t=n.options.genome.get_chrom_region(r),q=n.options.track.get("data_manager").get_more_detailed_data(t,"Coverage",0,p);$.when(q).then(function(z){u.remove();n._update_data_bounds();var y=i.find(n.options.chroms_layout,function(A){return A.data.chrom===r});var w=n.options.track.get("prefs"),x=w.block_color;if(!x){x=w.color}n._render_chrom_data(n.options.parent_elt,y,z).style("stroke",x).style("fill",x)})});return n},_update_data_bounds:function(){this.options.data_bounds=this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome))},_render_data:function(p){var o=this,n=this.options.chroms_layout,m=this.options.track,s=m.get_genome_wide_data(this.options.genome),q=i.zip(n,s),r=i.map(q,function(t){var u=t[0],v=t[1];return o._render_chrom_data(p,u,v)});return p},_render_chrom_data:function(m,n,o){},_compute_path_data:function(m,n){},_chroms_layout:function(){var n=this.options.genome.get_chroms_info(),p=k.layout.pie().value(function(r){return r.len}).sort(null),q=p(n),m=this.options.total_gap/n.length,o=i.map(q,function(t,s){var r=t.endAngle-m;t.endAngle=(r>t.startAngle?r:t.startAngle);return t});return o}});var a=c.extend({initialize:function(m){this.options=m;this.options.bg_stroke="fff";this.options.bg_fill="fff";this.options.chroms_layout=this._chroms_layout()},_render_data:function(n){var m=n.selectAll("g");m.selectAll("path").attr("id",function(o){return"label-"+o.data.chrom});m.append("svg:text").filter(function(o){return o.endAngle-o.startAngle>0.08}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(o){return"#label-"+o.data.chrom}).attr("startOffset","25%").text(function(o){return o.data.chrom})}});var d=c.extend({_render_chrom_data:function(m,p,n){if(!n||typeof n==="string"||n.data.length===0){return null}var q=this._compute_path_data(p,n.data);var o=m.datum(n.data),r=o.append("path").attr("class","chrom-data").attr("chrom",p.data.chrom).attr("d",q);return r},_compute_path_data:function(o,p){var m=k.scale.linear().domain(this.options.data_bounds).range(this.options.radius_bounds);var q=k.scale.linear().domain([0,p.length]).range([o.startAngle,o.endAngle]);var n=k.svg.line.radial().interpolate("linear").radius(function(r){return m(r[1])}).angle(function(s,r){return q(r)});return k.svg.area.radial().interpolate(n.interpolate()).innerRadius(m(0)).outerRadius(n.radius()).angle(n.angle())},get_data_bounds:function(m){}});var h=d.extend({get_data_bounds:function(n){var m=i.map(n,function(o){if(!o||typeof o==="string"){return 0}return o.max});return[0,(m&&typeof m!=="string"?i.max(m):0)]}});var g=d.extend({get_data_bounds:function(n){var m=i.flatten(i.map(n,function(o){if(o){return i.map(o.data,function(q){return q[1]})}else{return 0}}));return[i.min(m),i.max(m)]}});return{CircsterView:b}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/viz/scatterplot.js --- a/static/scripts/packed/viz/scatterplot.js +++ b/static/scripts/packed/viz/scatterplot.js @@ -1,1 +1,1 @@ -define(["../libs/underscore","../libs/d3","../mvc/base-mvc"],function(){function b(e){var h=this,g=10,f=12,d=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var i=Array.prototype.slice.call(arguments);i.unshift(this.toString());console.debug.apply(null,i)}};this.log("new TwoVarScatterplot:",e);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,e);this.updateConfig=function(i){_.extend(this.config,i)};this.toString=function(){return this.config.id};this.translateStr=function(i,j){return"translate("+i+","+j+")"};this.rotateStr=function(j,i,k){return"rotate("+j+","+i+","+k+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(){this.svg.attr("width",this.config.width+(this.config.marginRight+this.config.marginLeft)).attr("height",this.config.height+(this.config.marginTop+this.config.marginBottom)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft,this.config.marginTop))};this.preprocessData=function(i){return i.slice(0,this.config.maxDataPoints)};this.setUpDomains=function(i,j){this.xMin=this.config.xMin||d3.min(i);this.xMax=this.config.xMax||d3.max(i);this.yMin=this.config.yMin||d3.min(j);this.yMax=this.config.yMax||d3.max(j)};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.log("xAxis:",this.xAxis);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}));this.log("xLongestLabel:",this.xLongestLabel);if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel);this.log("xAxisLabel:",this.xAxisLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);this.yLongestLabel=d3.max(_.map([this.yMin,this.yMax],function(j){return(String(j)).length}));this.log("yLongestLabel:",this.yLongestLabel);var i=this.yLongestLabel*g+(d);if(this.config.yAxisLabelBumpX>-(i)){this.config.yAxisLabelBumpX=-(i)}if(this.config.marginLeft<i){this.config.marginLeft=i+f;this.adjustChartDimensions()}this.log("this.config.yAxisLableBumpx, this.config.marginLeft:",this.config.yAxisLabelBumpX,this.config.marginLeft);this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel);this.log("yAxisLabel:",this.yAxisLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.log("vGridLines:",this.vGridLines);this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove();this.log("hGridLines:",this.hGridLines)};this.glyphEnterState=function(i){};this.glyphFinalState=function(i){};this.glyphExitState=function(i){};this.renderDatapoints=function(i,l){var k=function(n,m){return h.xScale(i[m])};var j=function(n,m){return h.yScale(l[m])};this.datapoints=this.content.selectAll(".glyph").data(i);this.datapoints.enter().append("svg:circle").attr("class","glyph").attr("cx",k).attr("cy",0).attr("r",0);this.datapoints.transition().duration(this.config.entryAnimDuration).attr("cx",k).attr("cy",j).attr("r",this.config.bubbleRadius);this.datapoints.exit().transition().duration(this.config.entryAnimDuration).attr("cy",this.config.height).attr("r",0).style("fill-opacity",0).remove();this.log(this.datapoints,"glyphs rendered")};this.render=function(i,j){this.log("renderScatterplot",i.length,j.length,this.config);i=this.preprocessData(i);j=this.preprocessData(j);this.log("xCol len",i.length,"yCol len",j.length);this.setUpDomains(i,j);this.log("xMin, xMax, yMin, yMax:",this.xMin,this.xMax,this.yMin,this.yMax);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(i,j)}}var a=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new b(this.chartConfig)},render:function(){var c=this,e="",d="";this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ");_.each(this.dataset.metadata_column_types,function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}d+='<option value="'+g+'">'+f+"</column>"}});e+='<div id="x-column-input">';e+='<label for="">Data column for X: </label><select name="x-column">'+d+"</select>";e+="</div>";e+='<div id="y-column-input">';e+='<label for="">Data column for Y: </label><select name="y-column">'+d+"</select>";e+="</div>";e+='<input id="render-button" type="button" value="Draw" />';e+='<div class="clear"></div>';this.$el.append(e);this.$el.find("#render-button");return this},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);jQuery.ajax({url:e,dataType:"json",success:function(k){d.endpoint=k.endpoint;d.plot.render(_.map(k.data,function(l){return l[0]}),_.map(k.data,function(l){return l[1]}))},error:function(m,k,l){alert("ERROR:"+k+"\n"+l)}})}});return{ScatterplotView:a}}); \ No newline at end of file +define(["../libs/underscore","../libs/d3","../mvc/base-mvc"],function(){function b(f){var i=this,d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var j=Array.prototype.slice.call(arguments);j.unshift(this.toString());console.debug.apply(null,j)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,bubbleRadius:4,entryAnimDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(j){_.extend(this.config,j)};this.toString=function(){return this.config.id};this.translateStr=function(j,k){return"translate("+j+","+k+")"};this.rotateStr=function(k,j,l){return"rotate("+k+","+j+","+l+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart").style("display","none");this.content=this.svg.append("svg:g").attr("class","content");this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.log("built svg:",d3.selectAll("svg"));this.adjustChartDimensions=function(m,k,j,l){m=m||0;k=k||0;j=j||0;l=l||0;this.svg.attr("width",this.config.width+(this.config.marginRight+k)+(this.config.marginLeft+l)).attr("height",this.config.height+(this.config.marginTop+m)+(this.config.marginBottom+j)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+l,this.config.marginTop+m))};this.preprocessData=function(j){return j.slice(0,this.config.maxDataPoints)};this.setUpDomains=function(j,k){this.xMin=this.config.xMin||d3.min(j);this.xMax=this.config.xMax||d3.max(j);this.yMin=this.config.yMin||d3.min(k);this.yMax=this.config.yMax||d3.max(k)};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(j){return(String(j)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);this.log("yAxis:",this.yAxis);var j=this.yAxis.selectAll("text").filter(function(n,m){return m!==0});this.yLongestLabel=d3.max(j[0].map(function(n,m){return(d3.select(n).text()).length}))||0;var k=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(k-g);if(this.config.marginLeft<k){var l=(k)-this.config.marginLeft;l=(l<0)?(0):(l);this.log("adjusting:",l);this.adjustChartDimensions(0,0,0,l)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(j){};this.glyphFinalState=function(j){};this.glyphExitState=function(j){};this.renderDatapoints=function(j,m){var l=function(o,n){return i.xScale(j[n])};var k=function(o,n){return i.yScale(m[n])};this.datapoints=this.content.selectAll(".glyph").data(j);this.datapoints.enter().append("svg:circle").attr("class","glyph").attr("cx",l).attr("cy",0).attr("r",0);this.datapoints.transition().duration(this.config.entryAnimDuration).attr("cx",l).attr("cy",k).attr("r",this.config.bubbleRadius);this.datapoints.exit().transition().duration(this.config.entryAnimDuration).attr("cy",this.config.height).attr("r",0).style("fill-opacity",0).remove()};this.render=function(j,k){this.log("renderScatterplot",j.length,k.length,this.config);j=this.preprocessData(j);k=this.preprocessData(k);this.setUpDomains(j,k);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(j,k)}}var a=BaseView.extend(LoggableMixin).extend({tagName:"form",className:"scatterplot-settings-form",loadingIndicatorImagePath:(galaxy_paths.get("image_path")+"/loading_large_white_bg.gif"),events:{"click #render-button":"renderScatterplot"},initialize:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}this.apiDatasetsURL=c.apiDatasetsURL;this.chartConfig=c.chartConfig||{};this.log("this.chartConfig:",this.chartConfig);this.plot=new b(this.chartConfig)},render:function(){var c=this,e="",d="";this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ");_.each(this.dataset.metadata_column_types,function(h,g){if(h==="int"||h==="float"){var f="column "+g;if(c.dataset.metadata_column_names){f=c.dataset.metadata_column_names[g]}d+='<option value="'+g+'">'+f+"</option>"}});e+='<div id="loading-indicator" style="display: none;">';e+='<img class="loading-img" src='+this.loadingIndicatorImagePath+" />";e+='<span class="loading-message"></span>';e+="</div>";e+='<div id="x-column-input">';e+='<label for="">Data column for X: </label><select name="x-column">'+d+"</select>";e+="</div>";e+='<div id="y-column-input">';e+='<label for="">Data column for Y: </label><select name="y-column">'+d+"</select>";e+="</div>";e+='<input id="render-button" type="button" value="Draw" />';e+='<div class="clear"></div>';this.$el.append(e);this.$el.find("#render-button");return this},showLoadingIndicator:function(c){c=c||"";this.$el.find("div#loading-indicator").children(".loading-message").text(c);this.$el.find("div#loading-indicator").show("fast")},hideLoadingIndicator:function(){this.$el.find("div#loading-indicator").hide("fast")},renderScatterplot:function(){var d=this,e=this.apiDatasetsURL+"/"+this.dataset.id+"?data_type=raw_data&",i=this.$el.find('[name="x-column"]'),j=i.val(),g=i.children('[value="'+j+'"]').text(),h=this.$el.find('[name="y-column"]'),f=h.val(),c=h.children('[value="'+f+'"]').text();this.log(g,c);this.chartConfig.xLabel=g;this.chartConfig.yLabel=c;d.plot.updateConfig(this.chartConfig);e+=jQuery.param({columns:"["+[j,f]+"]"});this.log("url:",e);this.showLoadingIndicator("Fetching data...");jQuery.ajax({url:e,dataType:"json",success:function(k){d.showLoadingIndicator("Rendering...");d.endpoint=k.endpoint;d.plot.render(_.map(k.data,function(l){return l[0]}),_.map(k.data,function(l){return l[1]}));d.hideLoadingIndicator()},error:function(m,k,l){d.hideLoadingIndicator();alert("ERROR:"+k+"\n"+l)}})}});return{ScatterplotView:a}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/viz/sweepster.js --- a/static/scripts/packed/viz/sweepster.js +++ b/static/scripts/packed/viz/sweepster.js @@ -1,1 +1,1 @@ -define(["libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data"],function(o,f,n,h,g,d){var m=Backbone.Model.extend({defaults:{inputs:null,values:null}});var p=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(r){var q=this;this.get("tool").get("inputs").each(function(s){if(!s.get_samples()){return}s.on("change:min change:max change:num_samples",function(t){if(t.get("in_ptree")){q.set_tree_data()}},q);s.on("change:in_ptree",function(t){if(t.get("in_ptree")){q.add_param(t)}else{q.remove_param(t)}q.set_tree_data()},q)});if(r.config){_.each(r.config,function(t){var s=q.get("tool").get("inputs").find(function(u){return u.get("name")===t.name});q.add_param(s);s.set(t)})}},add_param:function(q){if(q.get("ptree_index")){return}q.set("in_ptree",true);q.set("ptree_index",this.get_tree_params().length)},remove_param:function(q){q.set("in_ptree",false);q.set("ptree_index",null);_(this.get_tree_params()).each(function(r,s){r.set("ptree_index",s+1)})},set_tree_data:function(){var r=_.map(this.get_tree_params(),function(t){return{param:t,samples:t.get_samples()}});var q=0,s=function(w,t){var y=w[t],x=y.param,v=x.get("label"),u=y.samples;if(w.length-1===t){return _.map(u,function(z){return{id:q++,name:z,param:x,value:z}})}return _.map(u,function(z){return{id:q++,name:z,param:x,value:z,children:s(w,t+1)}})};this.set("tree_data",{name:"Root",id:q++,children:(r.length!==0?s(r,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(q){return q.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(q,r){return q*r.get_samples().length},1)},get_node_settings:function(u){var s=this.get("tool").get_inputs_dict();var v=u.parent;if(v){while(v.depth!==0){s[v.param.get("name")]=v.value;v=v.parent}}var q=this,r=function(x,w){if(x.param){w[x.param.get("name")]=x.value}if(!x.children){return new m({inputs:q.get("tool").get("inputs"),values:w})}else{return _.flatten(_.map(x.children,function(y){return r(y,_.clone(w))}))}},t=r(u,s);if(!_.isArray(t)){t=[t]}return t},get_connected_nodes:function(s){var t=function(u){if(!u.children){return u}else{return _.flatten([u,_.map(u.children,function(v){return t(v)})])}};var r=[],q=s.parent;while(q){r.push(q);q=q.parent}return _.flatten([r,t(s)])},get_leaf:function(r){var s=this.get("tree_data"),q=function(t){return _.find(t,function(u){return r[u.param.get("name")]===u.value})};while(s.children){s=q(s.children)}return s},toJSON:function(){return this.get_tree_params().map(function(q){return{name:q.get("name"),min:q.get("min"),max:q.get("max"),num_samples:q.get("num_samples")}})}});var c=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:n.GenomeRegion}],initialize:function(q){if(q.track){var r=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},q.track);this.set("track",h.object_from_template(r,{},null))}},same_settings:function(q){var r=this.get("settings"),s=q.get("settings");for(var t in r){if(!s[t]||r[t]!==s[t]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var i=n.Visualization.extend({defaults:_.extend({},n.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:d.Dataset},{type:Backbone.HasOne,key:"tool",relatedModel:g.Tool},{type:Backbone.HasMany,key:"regions",relatedModel:n.GenomeRegion},{type:Backbone.HasMany,key:"tracks",relatedModel:c}],initialize:function(q){var r=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",r);this.set("parameter_tree",new p({tool:r,config:q.tree_config}))},add_track:function(q){this.get("tracks").add(q)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var l=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(q){this.canvas_manager=q.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var v=this.model.get("settings"),r=v.get("values"),t=$("<td/>").addClass("settings").appendTo(this.$el),s=$("<div/>").addClass("track-info").hide().appendTo(t);s.append($("<div/>").css("font-weight","bold").text("Track Settings"));v.get("inputs").each(function(x){s.append(x.get("label")+": "+r[x.get("name")]+"<br/>")});var q=this,w=$("<button/>").appendTo(s).text("Run on complete dataset").click(function(){s.toggle();q.trigger("run_on_dataset",v)});var u=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){s.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){q.$el.remove();$(".bs-tooltip").remove()}}]);t.prepend(u.$el);this.model.get("regions").each(function(){q.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var r=this,q=this.model.get("track"),t=this.model.get("regions"),s=this.$el.find("td.tile");if(!q){return}$.when(q.data_manager.data_is_ready()).then(function(u){t.each(function(x,w){var v=x.length()/r.TILE_LEN,z=1/v,y=r.model.get("mode");$.when(q.data_manager.get_data(x,y,v,{})).then(function(B){var A=r.canvas_manager.new_canvas();A.width=r.TILE_LEN;A.height=q.get_canvas_height(B,y,z,A.width);q.draw_tile(B,A.getContext("2d"),y,v,x,z);$(s[w]).empty().append(A)})})})}});var b=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(q){this.$el=q.tool_row;this.render()},render:function(){var r=this.model,v=r.get("type"),x=this.$el.find(".form-row-input"),t=null;x.find(":input").change(function(){r.set("value",$(this).val())});if(v==="number"){t=$(_.template(this.number_input_template,this.model.toJSON()))}else{if(v==="select"){var s=_.map(this.$el.find("select option"),function(y){return $(y).val()}),u=s.join(", ");t=$(_.template(this.select_input_template,{options:u}))}}t.insertAfter(x);var q=this,w=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){r.set("in_ptree",true);x.hide();t.show();$(this).hide();q.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){r.set("in_ptree",false);t.hide();x.show();$(this).hide();q.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(w.$el);if(r.get("in_ptree")){x.hide();q.$el.find(".icon-button.plus-button").hide()}else{q.$el.find(".icon-button.toggle").hide();t.hide()}_.each(["min","max","num_samples"],function(y){t.find("."+y).change(function(){r.set(y,parseFloat($(this).val()))})})}});var k=Backbone.View.extend({className:"tree-design",initialize:function(q){this.render()},render:function(){var s=new g.ToolFormView({model:this.model.get("tool")});s.render();this.$el.append(s.$el);var r=this,q=r.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(t){var u=new b({model:q.at(t),tool_row:$(this)})})}});var j=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(q){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var y=this.model.get_tree_params();if(!y.length){return}this.width=100*(2+y.length);this.height=15*this.model.get_num_leaves();var x=this;var w=o.layout.cluster().size([this.height,this.width-160]);var s=o.svg.diagonal().projection(function(z){return[z.y,z.x]});var q=w.nodes(this.model.get("tree_data"));var t=_.uniq(_.pluck(q,"y"));_.each(y,function(B,A){var z=t[A+1],C=$("#center").position().left;x.$el.append($("<div>").addClass("label").text(B.get("label")).css("left",z+C))});var r=o.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var v=r.selectAll("path.link").data(w.links(q)).enter().append("path").attr("class","link").attr("d",s);var u=r.selectAll("g.node").data(q).enter().append("g").attr("class","node").attr("transform",function(z){return"translate("+z.y+","+z.x+")"}).on("mouseover",function(A){var z=_.pluck(x.model.get_connected_nodes(A),"id");u.filter(function(B){return _.find(z,function(C){return C===B.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){u.style("fill","#000")});u.append("circle").attr("r",9);u.append("text").attr("dx",function(z){return z.children?-12:12}).attr("dy",3).attr("text-anchor",function(z){return z.children?"end":"start"}).text(function(z){return z.name})}});var e=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(r){this.canvas_manager=new n.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new j({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var q=this;this.model.get("tracks").each(function(s){s.get("track").view=q});this.block_color=f.get_random_color();this.reverse_strand_color=f.get_random_color([this.block_color,"#ffffff"])},render:function(){var w=new k({model:this.model.get("parameter_tree")});$("#left").append(w.$el);var z=this,t=z.model.get("regions"),x=$("<tr/>").appendTo(this.track_collection_container);t.each(function(A){x.append($("<th>").text(A.toString()))});x.children().first().attr("colspan",2);var u=$("<div>").addClass("tiles");$("#right").append(u.append(this.track_collection_container));z.model.get("tracks").each(function(A){z.add_track(A)});var y=$(this.helpText).addClass("help"),v=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".bs-tooltip").remove();y.remove()}}]);y.prepend(v.$el.css("float","right"));$("#center").append(y);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var s=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var r=["Squish","Pack"],q={};_.each(r,function(A){q[A]=function(){z.model.set("default_mode",A);z.model.get("tracks").each(function(B){B.set("mode",A)})}});make_popupmenu(s.$el.find(".chevron-expand"),q);s.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(s.$el)},run_tool_on_dataset:function(r){var q=this.model.get("tool"),t=q.get("name"),s=this.model.get("dataset");q.set_input_values(r.get("values"));$.when(q.rerun(s)).then(function(u){});show_modal("Running "+t+" on complete dataset",t+" is running on dataset '"+s.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(t){var r=this,s=this.model.get("parameter_tree");r.model.add_track(t);var q=new l({model:t,canvas_manager:r.canvas_manager});q.on("run_on_dataset",r.run_tool_on_dataset,r);r.track_collection_container.append(q.$el);q.$el.hover(function(){var v=s.get_leaf(t.get("settings").get("values"));var u=_.pluck(s.get_connected_nodes(v),"id");o.select(r.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(w){return _.find(u,function(x){return x===w.id})!==undefined}).style("fill","#f00")},function(){o.select(r.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return t},handle_node_clicks:function(){var q=this,r=this.model.get("parameter_tree"),t=this.model.get("regions"),s=o.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");s.on("click",function(z,w){var v=q.model.get("tool"),y=q.model.get("dataset"),x=r.get_node_settings(z),u=$.Deferred();if(x.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+q.model.get("tool").get("name")+" with "+x.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();u.resolve(false)}})}else{u.resolve(true)}$.when(u).then(function(A){if(!A){return}var B=_.map(x,function(C){var D=new c({settings:C,regions:t,mode:q.model.get("default_mode")});q.add_track(D);return D});_.each(B,function(D,C){setTimeout(function(){v.set_input_values(D.get("settings").get("values"));$.when(v.rerun(y,t)).then(function(F){var G=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},F.first().get("track_config")),E=h.object_from_template(G,q,null);E.data_manager.set("data_type","raw_data");E.prefs.block_color=q.block_color;E.prefs.reverse_strand_color=q.reverse_strand_color;D.set("track",E)})},C*10000)})})})}});return{SweepsterVisualization:i,SweepsterVisualizationView:e}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks","mvc/tools","mvc/data"],function(m,q,f,o,h,g,d){var n=Backbone.Model.extend({defaults:{inputs:null,values:null}});var p=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(s){var r=this;this.get("tool").get("inputs").each(function(t){if(!t.get_samples()){return}t.on("change:min change:max change:num_samples",function(u){if(u.get("in_ptree")){r.set_tree_data()}},r);t.on("change:in_ptree",function(u){if(u.get("in_ptree")){r.add_param(u)}else{r.remove_param(u)}r.set_tree_data()},r)});if(s.config){m.each(s.config,function(u){var t=r.get("tool").get("inputs").find(function(v){return v.get("name")===u.name});r.add_param(t);t.set(u)})}},add_param:function(r){if(r.get("ptree_index")){return}r.set("in_ptree",true);r.set("ptree_index",this.get_tree_params().length)},remove_param:function(r){r.set("in_ptree",false);r.set("ptree_index",null);m(this.get_tree_params()).each(function(s,t){s.set("ptree_index",t+1)})},set_tree_data:function(){var s=m.map(this.get_tree_params(),function(u){return{param:u,samples:u.get_samples()}});var r=0,t=function(x,u){var z=x[u],y=z.param,w=y.get("label"),v=z.samples;if(x.length-1===u){return m.map(v,function(A){return{id:r++,name:A,param:y,value:A}})}return m.map(v,function(A){return{id:r++,name:A,param:y,value:A,children:t(x,u+1)}})};this.set("tree_data",{name:"Root",id:r++,children:(s.length!==0?t(s,0):null)})},get_tree_params:function(){return m(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(r){return r.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(r,s){return r*s.get_samples().length},1)},get_node_settings:function(v){var t=this.get("tool").get_inputs_dict();var w=v.parent;if(w){while(w.depth!==0){t[w.param.get("name")]=w.value;w=w.parent}}var r=this,s=function(y,x){if(y.param){x[y.param.get("name")]=y.value}if(!y.children){return new n({inputs:r.get("tool").get("inputs"),values:x})}else{return m.flatten(m.map(y.children,function(z){return s(z,m.clone(x))}))}},u=s(v,t);if(!m.isArray(u)){u=[u]}return u},get_connected_nodes:function(t){var u=function(v){if(!v.children){return v}else{return m.flatten([v,m.map(v.children,function(w){return u(w)})])}};var s=[],r=t.parent;while(r){s.push(r);r=r.parent}return m.flatten([s,u(t)])},get_leaf:function(s){var t=this.get("tree_data"),r=function(u){return m.find(u,function(v){return s[v.param.get("name")]===v.value})};while(t.children){t=r(t.children)}return t},toJSON:function(){return this.get_tree_params().map(function(r){return{name:r.get("name"),min:r.get("min"),max:r.get("max"),num_samples:r.get("num_samples")}})}});var c=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:o.GenomeRegion}],initialize:function(r){if(r.track){var s=m.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},r.track);this.set("track",h.object_from_template(s,{},null))}},same_settings:function(r){var s=this.get("settings"),t=r.get("settings");for(var u in s){if(!t[u]||s[u]!==t[u]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var i=o.Visualization.extend({defaults:m.extend({},o.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:d.Dataset},{type:Backbone.HasOne,key:"tool",relatedModel:g.Tool},{type:Backbone.HasMany,key:"regions",relatedModel:o.GenomeRegion},{type:Backbone.HasMany,key:"tracks",relatedModel:c}],initialize:function(r){var s=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",s);this.set("parameter_tree",new p({tool:s,config:r.tree_config}))},add_track:function(r){this.get("tracks").add(r)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var l=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(r){this.canvas_manager=r.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var w=this.model.get("settings"),s=w.get("values"),u=$("<td/>").addClass("settings").appendTo(this.$el),t=$("<div/>").addClass("track-info").hide().appendTo(u);t.append($("<div/>").css("font-weight","bold").text("Track Settings"));w.get("inputs").each(function(y){t.append(y.get("label")+": "+s[y.get("name")]+"<br/>")});var r=this,x=$("<button/>").appendTo(t).text("Run on complete dataset").click(function(){t.toggle();r.trigger("run_on_dataset",w)});var v=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){t.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){r.$el.remove();$(".bs-tooltip").remove()}}]);u.prepend(v.$el);this.model.get("regions").each(function(){r.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var s=this,r=this.model.get("track"),u=this.model.get("regions"),t=this.$el.find("td.tile");if(!r){return}$.when(r.data_manager.data_is_ready()).then(function(v){u.each(function(y,x){var w=y.length()/s.TILE_LEN,A=1/w,z=s.model.get("mode");$.when(r.data_manager.get_data(y,z,w,{})).then(function(C){var B=s.canvas_manager.new_canvas();B.width=s.TILE_LEN;B.height=r.get_canvas_height(C,z,A,B.width);r.draw_tile(C,B.getContext("2d"),z,w,y,A);$(t[x]).empty().append(B)})})})}});var b=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(r){this.$el=r.tool_row;this.render()},render:function(){var s=this.model,w=s.get("type"),y=this.$el.find(".form-row-input"),u=null;y.find(":input").change(function(){s.set("value",$(this).val())});if(w==="number"){u=$(m.template(this.number_input_template,this.model.toJSON()))}else{if(w==="select"){var t=m.map(this.$el.find("select option"),function(z){return $(z).val()}),v=t.join(", ");u=$(m.template(this.select_input_template,{options:v}))}}u.insertAfter(y);var r=this,x=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){s.set("in_ptree",true);y.hide();u.show();$(this).hide();r.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){s.set("in_ptree",false);u.hide();y.show();$(this).hide();r.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(x.$el);if(s.get("in_ptree")){y.hide();r.$el.find(".icon-button.plus-button").hide()}else{r.$el.find(".icon-button.toggle").hide();u.hide()}m.each(["min","max","num_samples"],function(z){u.find("."+z).change(function(){s.set(z,parseFloat($(this).val()))})})}});var k=Backbone.View.extend({className:"tree-design",initialize:function(r){this.render()},render:function(){var t=new g.ToolFormView({model:this.model.get("tool")});t.render();this.$el.append(t.$el);var s=this,r=s.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(u){var v=new b({model:r.at(u),tool_row:$(this)})})}});var j=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(r){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var z=this.model.get_tree_params();if(!z.length){return}this.width=100*(2+z.length);this.height=15*this.model.get_num_leaves();var y=this;var x=q.layout.cluster().size([this.height,this.width-160]);var t=q.svg.diagonal().projection(function(A){return[A.y,A.x]});var r=x.nodes(this.model.get("tree_data"));var u=m.uniq(m.pluck(r,"y"));m.each(z,function(C,B){var A=u[B+1],D=$("#center").position().left;y.$el.append($("<div>").addClass("label").text(C.get("label")).css("left",A+D))});var s=q.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var w=s.selectAll("path.link").data(x.links(r)).enter().append("path").attr("class","link").attr("d",t);var v=s.selectAll("g.node").data(r).enter().append("g").attr("class","node").attr("transform",function(A){return"translate("+A.y+","+A.x+")"}).on("mouseover",function(B){var A=m.pluck(y.model.get_connected_nodes(B),"id");v.filter(function(C){return m.find(A,function(D){return D===C.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){v.style("fill","#000")});v.append("circle").attr("r",9);v.append("text").attr("dx",function(A){return A.children?-12:12}).attr("dy",3).attr("text-anchor",function(A){return A.children?"end":"start"}).text(function(A){return A.name})}});var e=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(s){this.canvas_manager=new o.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new j({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var r=this;this.model.get("tracks").each(function(t){t.get("track").view=r});this.block_color=f.get_random_color();this.reverse_strand_color=f.get_random_color([this.block_color,"#ffffff"])},render:function(){var x=new k({model:this.model.get("parameter_tree")});$("#left").append(x.$el);var A=this,u=A.model.get("regions"),y=$("<tr/>").appendTo(this.track_collection_container);u.each(function(B){y.append($("<th>").text(B.toString()))});y.children().first().attr("colspan",2);var v=$("<div>").addClass("tiles");$("#right").append(v.append(this.track_collection_container));A.model.get("tracks").each(function(B){A.add_track(B)});var z=$(this.helpText).addClass("help"),w=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".bs-tooltip").remove();z.remove()}}]);z.prepend(w.$el.css("float","right"));$("#center").append(z);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var t=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var s=["Squish","Pack"],r={};m.each(s,function(B){r[B]=function(){A.model.set("default_mode",B);A.model.get("tracks").each(function(C){C.set("mode",B)})}});make_popupmenu(t.$el.find(".chevron-expand"),r);t.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(t.$el)},run_tool_on_dataset:function(s){var r=this.model.get("tool"),u=r.get("name"),t=this.model.get("dataset");r.set_input_values(s.get("values"));$.when(r.rerun(t)).then(function(v){});show_modal("Running "+u+" on complete dataset",u+" is running on dataset '"+t.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(u){var s=this,t=this.model.get("parameter_tree");s.model.add_track(u);var r=new l({model:u,canvas_manager:s.canvas_manager});r.on("run_on_dataset",s.run_tool_on_dataset,s);s.track_collection_container.append(r.$el);r.$el.hover(function(){var w=t.get_leaf(u.get("settings").get("values"));var v=m.pluck(t.get_connected_nodes(w),"id");q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(x){return m.find(v,function(y){return y===x.id})!==undefined}).style("fill","#f00")},function(){q.select(s.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return u},handle_node_clicks:function(){var r=this,s=this.model.get("parameter_tree"),u=this.model.get("regions"),t=q.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");t.on("click",function(A,x){var w=r.model.get("tool"),z=r.model.get("dataset"),y=s.get_node_settings(A),v=$.Deferred();if(y.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+r.model.get("tool").get("name")+" with "+y.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();v.resolve(false)}})}else{v.resolve(true)}$.when(v).then(function(B){if(!B){return}var C=m.map(y,function(D){var E=new c({settings:D,regions:u,mode:r.model.get("default_mode")});r.add_track(E);return E});m.each(C,function(E,D){setTimeout(function(){w.set_input_values(E.get("settings").get("values"));$.when(w.rerun(z,u)).then(function(G){var H=m.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},G.first().get("track_config")),F=h.object_from_template(H,r,null);F.data_manager.set("data_type","raw_data");F.prefs.block_color=r.block_color;F.prefs.reverse_strand_color=r.reverse_strand_color;E.set("track",F)})},D*10000)})})})}});return{SweepsterVisualization:i,SweepsterVisualizationView:e}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters","viz/trackster_ui"],function(ad,y,l,v,M,ab,i,q){var r=ad.extend;var R=l.get_random_color;var ae=function(af,ah,ag){$.ajax({url:af,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(ai){show_modal("Select datasets for new tracks",ai,{Cancel:function(){hide_modal()},Add:function(){var aj=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var ak={data_type:"track_config",hda_ldda:"hda"},al=$(this).val();if($(this).attr("name")!=="id"){ak.hda_ldda="ldda"}aj[aj.length]=$.ajax({url:ah+"/"+al,data:ak,dataType:"json"})});$.when.apply($,aj).then(function(){var ak=(arguments[0] instanceof Array?$.map(arguments,function(al){return al[0]}):[arguments[0]]);ag(ak)});hide_modal()}})}})};var X=function(af){return("isResolved" in af)};var n={};var k=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this),aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){am=$(an.get(ao));if(at.offsetY<am.position().top&&!(am.hasClass("reference-track")||am.hasClass("intro"))){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};exports.moveable=m;var ac=16,H=9,E=20,B=100,J=12000,U=400,L=5000,x=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",a="Loading data...",W="Ready for display",S=10,I=20;function Y(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var s=function(ag,af,ai){if(!s.id_counter){s.id_counter=0}this.id=s.id_counter++;this.name=ai.name;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ai.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ai.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(aj){aj.stopPropagation()});var ah=this;this.container_div.hover(function(){ah.icons_div.show()},function(){ah.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};s.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".bs-tooltip").remove();af.remove()}}];r(s.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var af=this.view;this.container_div.hide(0,function(){$(this).remove();af.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,al,ak,aj,af,ai){var ah=this;this.action_icons[ag]=$("<a/>").attr("href","javascript:void(0);").attr("title",al).addClass("icon-button").addClass(ak).tooltip().click(function(){aj(ah)}).appendTo(this.icons_div);if(ai){this.action_icons[ag].hide()}},build_action_icons:function(af){var ah;for(var ag=0;ag<af.length;ag++){ah=af[ag];this.add_action_icon(ah.name,ah.title,ah.css_class,ah.on_click_fn,ah.prepend,ah.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ag,af,ah){s.call(this,ag,af,ah);this.obj_type=ah.obj_type;this.drawables=[]};r(A.prototype,s.prototype,{unpack_drawables:function(ah){this.drawables=[];var ag;for(var af=0;af<ah.length;af++){ag=p(ah[af],this.view,this);this.add_drawable(ag)}},init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_dict:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this;this.changed()},add_drawable_before:function(ah,af){this.changed();var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables.splice(ag,0,ah);return true}return false},replace_drawable:function(ah,af,ag){var ai=this.drawables.indexOf(ah);if(ai!==-1){this.drawables[ai]=af;if(ag){ah.container_div.replaceWith(af.container_div)}this.changed()}return ai},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!==-1){this.drawables.splice(af,1);ag.container=null;this.changed();return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!==-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var Q=function(ag,af,ai){r(ai,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ag,af,ai);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ai){this.unpack_drawables(ai.drawables)}if("filters" in ai){var ah=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ai.filters);ah.parent_div.replaceWith(this.filters_manager.parent_div);if(ai.filters.visible){this.setup_multitrack_filtering()}}};r(Q.prototype,s.prototype,A.prototype,{action_icons_def:[s.prototype.action_icons_def[0],s.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){$(".bs-tooltip").remove();af.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){if(af.filters_manager.visible()){af.filters_manager.clear_filters();af._restore_filter_managers()}else{af.setup_multitrack_filtering();af.request_draw(true)}af.filters_manager.toggle()}},s.prototype.action_icons_def[2]],build_container_div:function(){var af=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(af)}return af},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ah=this.drawables.length;if(ah===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ah===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ao,an,al,ar=true,aj=this.drawables[0].get_type(),af=0;for(ao=0;ao<ah;ao++){al=this.drawables[ao];if(al.get_type()!==aj){can_composite=false;break}if(al instanceof c){af++}}if(ar||af===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(af>1&&af===this.drawables.length){var at={},ag;al=this.drawables[0];for(an=0;an<al.filters_manager.filters.length;an++){ag=al.filters_manager.filters[an];at[ag.name]=[ag]}for(ao=1;ao<this.drawables.length;ao++){al=this.drawables[ao];for(an=0;an<al.filters_manager.filters.length;an++){ag=al.filters_manager.filters[an];if(ag.name in at){at[ag.name].push(ag)}}}this.filters_manager.remove_all();var ai,ak,am,ap;for(var aq in at){ai=at[aq];if(ai.length===af){ak=new i.NumberFilter({name:ai[0].name,index:ai[0].index});this.filters_manager.add_filter(ak)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].filters_manager=this.saved_filters_managers[af]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var af=0;af<this.drawables.length;af++){drawable=this.drawables[af];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var aj=[];for(var ag=0;ag<this.drawables.length;ag++){aj.push(this.drawables[ag].name)}var ah="Composite Track of "+this.drawables.length+" tracks ("+aj.join(", ")+")";var ai=new f(this.view,this.view,{name:ah,drawables:this.drawables});var af=this.container.replace_drawable(this,ai,true);ai.request_draw()},add_drawable:function(af){A.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){A.prototype.remove_drawable.call(this,af);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var af=r(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return af},request_draw:function(af,ah){for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].request_draw(af,ah)}}});var aa=function(af){r(af,{obj_type:"View"});A.call(this,"View",af.container,af);this.chrom=null;this.vis_id=af.vis_id;this.dbkey=af.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new y.CanvasManager(this.container.get(0).ownerDocument);this.reset()};ad.extend(aa.prototype,Backbone.Events);r(aa.prototype,A.prototype,{init:function(){this.requested_redraw=false;var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){ae(add_datasets_url,add_track_async_url,function(aj){ad.each(aj,function(ak){af.add_drawable(p(ak,af,af))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus();af.nav_input.autocomplete({source:function(al,aj){var am=[],ak=$.map(af.get_drawables(),function(an){return an.data_manager.search_features(al.term).success(function(ao){am=am.concat(ao)})});$.when.apply($,ak).done(function(){aj($.map(am,function(an){return{label:an[0],value:an[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX)-af.container.offset().left,width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new Z(this,{content_div:this.top_labeltrack}));this.add_label_track(new Z(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){af.resize_window()},500)});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ag,ai,af,aj){if(this.timer){clearTimeout(this.timer)}if(aj){var ah=this;this.timer=setTimeout(function(){ah.trigger("navigate",ag+":"+ai+"-"+af)},500)}else{view.trigger("navigate",ag+":"+ai+"-"+af)}},update_location:function(af,ah){this.location_span.text(commatize(af)+" - "+commatize(ah));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ah));var ag=view.chrom_select.val();if(ag!==""){this.trigger_navigate(ag,view.low,view.high,true)}},load_chroms:function(ah){ah.num=x;var af=this,ag=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){return}if(aj.reference){af.add_label_track(new C(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+x+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+x+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){var ah=this;if(!ah.chrom_data){ah.load_chroms_deferred.then(function(){ah.change_chrom(ak,ag,am)});return}if(!ak||ak==="None"){return}if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-x});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+x});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}if(ah.reference_track){ah.reference_track.init()}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}else{ah.low=0;ah.high=ah.max_high}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ai){var af=this;var ah=af.high-af.low;if(af.low-ai<af.max_low){af.low=af.max_low;af.high=af.max_low+ah}else{if(af.high-ai>af.max_high){af.high=af.max_high;af.low=af.max_high-ah}else{af.high-=ai;af.low-=ai}}af.request_redraw();var ag=af.chrom_select.val();this.trigger_navigate(ag,af.low,af.high,true)},add_drawable:function(af){A.prototype.add_drawable.call(this,af);af.init();this.changed();this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){A.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ao){var al=this,ak=(ao?[ao]:al.drawables),ah;var ag;for(var aj=0;aj<ak.length;aj++){ag=ak[aj];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[aj][1]=af;al.tracks_to_be_redrawn[aj][2]=am}}if(!this.requested_redraw){requestAnimationFrame(function(){al._redraw(an)});this.requested_redraw=true}},_redraw:function(ap){this.requested_redraw=false;var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var t=function(ah,am,ai){this.track=ah;this.name=am.name;this.params=[];var au=am.params;for(var aj=0;aj<au.length;aj++){var ao=au[aj],ag=ao.name,at=ao.label,ak=unescape(ao.html),av=ao.value,aq=ao.type;if(aq==="number"){this.params.push(new e(ag,at,ak,(ag in ai?ai[ag]:av),ao.min,ao.max))}else{if(aq==="select"){this.params.push(new O(ag,at,ak,(ag in ai?ai[ag]:av)))}else{console.log("WARNING: unrecognized tool parameter type:",ag,aq)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ax){ax.stopPropagation()}).click(function(ax){ax.stopPropagation()}).bind("dblclick",function(ax){ax.stopPropagation()});var ar=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ap=this.params;var an=this;$.each(this.params,function(ay,aB){var aA=$("<div>").addClass("param-row").appendTo(an.parent_div);var ax=$("<div>").addClass("param-label").text(aB.label).appendTo(aA);var az=$("<div/>").addClass("param-input").html(aB.html).appendTo(aA);az.find(":input").val(aB.value);$("<div style='clear: both;'/>").appendTo(aA)});this.parent_div.find("input").click(function(){$(this).select()});var aw=$("<div>").addClass("param-row").appendTo(this.parent_div);var al=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(aw);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(aw);af.click(function(){an.run_on_region()});al.click(function(){an.run_on_dataset()});if("visible" in ai&&ai.visible){this.parent_div.show()}};r(t.prototype,{update_params:function(){for(var af=0;af<this.params.length;af++){this.params[af].update_value()}},state_dict:function(){var ag={};for(var af=0;af<this.params.length;af++){ag[this.params[af].name]=this.params[af].value}ag.visible=this.parent_div.is(":visible");return ag},get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=ah});return af},get_param_values:function(){var af=[];this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();if(ag){af[af.length]=ah}});return af},run_on_dataset:function(){var af=this;af.run({target_dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ak=this.track,ah=ag.tool_id+ak.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(ak.container===view){var aj=new Q(view,view,{name:this.name});var ai=ak.container.replace_drawable(ak,aj,false);aj.container_div.insertBefore(ak.view.content_div.children()[ai]);aj.add_drawable(ak);ak.container_div.appendTo(aj.content_div);af=aj}else{af=ak.container}var al=new ak.constructor(view,af,{name:ah,hda_ldda:"hda"});al.init_for_tool_data();al.change_mode(ak.mode);al.set_filters_manager(ak.filters_manager.copy(al));al.update_icons();af.add_drawable(al);al.tiles_div.text("Starting job.");this.update_params();this.run(ag,al,function(am){al.set_dataset(new ab.Dataset(am));al.tiles_div.text("Running job.");al.init()})},run:function(af,ah,ai){af.inputs=this.get_param_values_dict();var ag=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(af),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(aj){return aj!=="pending"}});$.when(ag.go()).then(function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(z+aj.message)}else{ai(aj)}}})}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=$(ah);this.value=ai};r(O.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};r(e.prototype,O.prototype,{update_value:function(){O.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};r(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(an,aj){for(var ar=0;ar<an.length;ar++){ah=an[ar];if(ah.hidden){continue}var al="param_"+ar;var aw=ai.values[ah.key];var ay=$("<div class='form-row' />").appendTo(aj);ay.append($("<label />").attr("for",al).text(ah.label+":"));if(ah.type==="bool"){ay.append($('<input type="checkbox" />').attr("id",al).attr("name",al).attr("checked",aw))}else{if(ah.type==="text"){ay.append($('<input type="text"/>').attr("id",al).val(aw).click(function(){$(this).select()}))}else{if(ah.type==="select"){var au=$("<select />").attr("id",al);for(var ap=0;ap<ah.options.length;ap++){$("<option/>").text(ah.options[ap].label).attr("value",ah.options[ap].value).appendTo(au)}au.val(aw);ay.append(au)}else{if(ah.type==="color"){var ax=$("<div/>").appendTo(ay),at=$("<input />").attr("id",al).attr("name",al).val(aw).css("float","left").appendTo(ax).click(function(aA){$(".bs-tooltip").removeClass("in");var az=$(this).siblings(".bs-tooltip").addClass("in");az.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(az).height()/2)+($(this).height()/2)}).show();az.click(function(aB){aB.stopPropagation()});$(document).bind("click.color-picker",function(){az.hide();$(document).unbind("click.color-picker")});aA.stopPropagation()}),aq=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ax).attr("title","Set new random color").tooltip(),av=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(ax).hide(),am=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(av),ak=$("<div class='tooltip-arrow'></div>").appendTo(av),ao=$.farbtastic(am,{width:100,height:100,callback:at,color:aw});ax.append($("<div/>").css("clear","both"));(function(az){aq.click(function(){az.setColor(R())})})(ao)}else{ay.append($("<input />").attr("id",al).attr("name",al).val(aw))}}}}if(ah.help){ay.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange();this.track.changed()}}});var b=function(af,aj,ah,ag,ai){this.track=af;this.region=aj;this.low=aj.get("start");this.high=aj.get("end");this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag).height($(ag).attr("height"));this.data=ai;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(af,ak,ah,ag,ai,aj){b.call(this,af,ak,ah,ag,ai);this.max_val=aj};r(j.prototype,b.prototype);var P=function(ai,aq,aj,ah,al,at,am,au,ag,ap){b.call(this,ai,aq,aj,ah,al);this.mode=am;this.all_slotted=ag;this.feature_mapper=ap;this.has_icons=false;if(au){this.has_icons=true;var an=this;ah=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:E-1,width:ah.width}).prependTo(this.html_elt);var ao=new y.GenomeRegion({chrom:ai.view.chrom,start:this.low,end:this.high}),ar=al.length,ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ak.click(function(){an.stale=true;ai.data_manager.get_more_data(ao,ai.mode,an.resolution,{},ai.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ai.request_draw(true)}).dblclick(function(av){av.stopPropagation()});af.click(function(){an.stale=true;ai.data_manager.get_more_data(ao,ai.mode,an.resolution,{},ai.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ai.request_draw(true)}).dblclick(function(av){av.stopPropagation()})}};r(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)==="number"?Y(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(this).parents(".track-content").children(".overlay"));var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ag,af,ah){r(ah,{drag_handle_class:"draghandle"});s.call(this,ag,af,ah);this.dataset=new ab.Dataset({id:ah.dataset_id,hda_ldda:ah.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ah?ah.data_query_wait:L);this.data_manager=("data_manager" in ah?ah.data_manager:new y.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ah)||ah.resize){this.add_resize_handle()}}};r(g.prototype,s.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},s.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},s.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){if(af.filters_manager.visible()){af.filters_manager.clear_filters()}else{af.filters_manager.init_filters()}af.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(af){var ai='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ah=ad.template(ai,{track:af});var ak=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(){var am=$('select[name="regions"] option:selected').val(),ao,al=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),an=ad.map($(".bookmark"),function(ap){return new y.GenomeRegion({from_str:$(ap).children(".position").text()})});if(am==="cur"){ao=[al]}else{if(am==="bookmarks"){ao=an}else{ao=[al].concat(an)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:af.dataset_id,hda_ldda:af.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ao).toJSON())})},aj=function(al){if((al.keyCode||al.which)===27){ak()}else{if((al.keyCode||al.which)===13){ag()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ah,{No:ak,Yes:ag})}},s.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&s.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},on_resize:function(){},add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.tiles_div).css("height",aj);af.visible_height_px=(af.max_height_px===aj?0:aj);af.on_resize()}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.visible_height_px;af.changed()}).appendTo(af.container_div)},set_display_modes:function(ai,al){this.display_modes=ai;this.mode=(al?al:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ag=this,aj={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var ak=ag.display_modes[ah];aj[ak]=function(am){return function(){ag.change_mode(am);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(ak)}make_popupmenu(this.action_icons.mode_icon,aj)},build_action_icons:function(){s.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Z){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof V){return"ReadTrack"}else{if(this instanceof T){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var ag=this;ag.enabled=false;ag.tile_cache.clear();ag.data_manager.clear();ag.content_div.css("height","auto");ag.tiles_div.children().remove();ag.container_div.removeClass("nodata error pending");if(!ag.dataset_id){return}var af=$.Deferred(),ah={hda_ldda:ag.hda_ldda,data_type:this.dataset_check_type,chrom:ag.view.chrom};$.getJSON(this.dataset.url(),ah,function(ai){if(!ai||ai==="error"||ai.kind==="error"){ag.container_div.addClass("error");ag.tiles_div.text(o);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ag.tiles_div.append(aj)}}else{if(ai==="no converter"){ag.container_div.addClass("error");ag.tiles_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ag.container_div.addClass("nodata");ag.tiles_div.text(F)}else{if(ai==="pending"){ag.container_div.addClass("pending");ag.tiles_div.html(w);setTimeout(function(){ag.init()},ag.data_query_wait)}else{if(ai==="data"||ai.status==="data"){if(ai.valid_chroms){ag.valid_chroms=ai.valid_chroms;ag.update_icons()}ag.tiles_div.text(W);if(ag.view.chrom){ag.tiles_div.text("");ag.tiles_div.css("height",ag.visible_height_px+"px");ag.enabled=true;$.when(ag.predraw_init()).done(function(){af.resolve();ag.container_div.removeClass("nodata error pending");ag.request_draw()})}else{af.resolve()}}}}}}});this.update_icons();return af},predraw_init:function(){},get_drawables:function(){return this}});var N=function(ah,ag,ai){g.call(this,ah,ag,ai);var af=this;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new i.FiltersManager(this,("filters" in ai?ai.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ai&&ai.tool?new t(this,ai.tool,ai.tool_state):null);this.tile_cache=new y.Cache(S);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ai.mode){this.change_mode(ai.mode)}};r(N.prototype,s.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(af){$(".bs-tooltip").remove();af.slotters[af.view.resolution_px_b].max_rows*=2;af.request_draw(true)},hide:true}]),copy:function(af){var ag=this.to_dict();r(ag,{data_manager:this.data_manager});var ah=new this.constructor(this.view,af,ag);ah.change_mode(this.mode);ah.enabled=this.enabled;return ah},set_filters_manager:function(af){this.filters_manager=af;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show();af.action_icons.param_space_viz_icon.show()}else{af.action_icons.tools_icon.hide();af.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},before_draw:function(){},_draw:function(ag,aq){if(!this.can_draw()){return}var ao=this.view.low,ak=this.view.high,am=ak-ao,ah=this.view.container.width(),at=this.view.resolution_px_b,aj=this.view.resolution_b_px;if(this.is_overview){ao=this.view.max_low;ak=this.view.max_high;aj=(view.max_high-view.max_low)/ah;at=1/aj}this.before_draw();this.tiles_div.children().addClass("remove");var af=Math.floor(ao/(aj*U)),an=true,ar=[],al=function(au){return(au&&"track" in au)};while((af*U*aj)<ak){var ap=this.draw_helper(ag,ah,af,aj,this.tiles_div,at);if(al(ap)){ar.push(ap)}else{an=false}af+=1}if(!aq){this.tiles_div.children(".remove").removeClass("remove").remove()}var ai=this;if(an){this.tiles_div.children(".remove").remove();ai.postdraw_actions(ar,ah,at,aq)}},postdraw_actions:function(ah,ai,ak,af){var aj=false;for(var ag=0;ag<ah.length;ag++){if(ah[ag].has_icons){aj=true;break}}if(aj){for(var ag=0;ag<ah.length;ag++){tile=ah[ag];if(!tile.has_icons){tile.html_elt.css("padding-top",E)}}}},draw_helper:function(af,ar,ax,av,ak,al,at){var aq=this,aA=this._gen_tile_cache_key(ar,al,ax),ai=this._get_tile_bounds(ax,av);if(!at){at={}}var az=(af?undefined:aq.tile_cache.get_elt(aA));if(az){aq.show_tile(az,ak,al);return az}var ao=true;var aw=aq.data_manager.get_data(ai,aq.mode,av,aq.data_url_extra_params);if(X(aw)){ao=false}var am;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ai,aq.mode,av,view.reference_track.data_url_extra_params);if(X(am)){ao=false}}if(ao){r(aw,at.more_tile_data);var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}var ah=aq.view.canvas_manager.new_canvas(),ay=ai.get("start"),ag=ai.get("end"),ar=Math.ceil((ag-ay)*al)+aq.left_offset,ap=aq.get_canvas_height(aw,an,al,ar);ah.width=ar;ah.height=ap;var au=ah.getContext("2d");au.translate(this.left_offset,0);var az=aq.draw_tile(aw,au,an,av,ai,al,am);if(az!==undefined){aq.tile_cache.set_elt(aA,az);aq.show_tile(az,ak,al)}return az}var aj=$.Deferred();$.when(aw,am).then(function(){view.request_redraw(false,false,false,aq);aj.resolve()});return aj},get_canvas_height:function(af,ah,ai,ag){return this.visible_height_px},draw_tile:function(af,ag,ak,ai,aj,al,ah){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.after_show_tile(ah)},after_show_tile:function(af){this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(af,ag){var ai=Math.floor(af*U*ag),aj=Math.ceil(U*ag),ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return new y.GenomeRegion({chrom:this.view.chrom,start:ai,end:ah})},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(af,ag){return true},can_subset:function(af){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ah,ai,ak,af){var ag=this;ag.normal_postdraw_actions(ah,ai,ak,af);ag.dataset_check_type="converted_datasets_state";ag.data_query_wait=L;var aj=new l.ServerStateDeferred({url:ag.dataset_state_url,url_params:{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},interval:ag.data_query_wait,success_fn:function(al){return al!=="pending"}});$.when(aj.go()).then(function(){ag.data_manager.set("data_type","data")});ag.postdraw_actions=ag.normal_postdraw_actions}}});var Z=function(ag,af){var ah={resize:false};g.call(this,ag,af,ah);this.container_div.addClass("label-track")};r(Z.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var f=function(ag,af,aj){N.call(this,ag,af,aj);this.drawables=[];this.left_offset=0;if("drawables" in aj){var ai;for(var ah=0;ah<aj.drawables.length;ah++){ai=aj.drawables[ah];this.drawables[ah]=p(ai,ag,null);if(ai.left_offset>this.left_offset){this.left_offset=ai.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};r(f.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(af){$(".bs-tooltip").remove();af.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(af){N.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){var ah=[];for(var ag=0;ag<this.drawables.length;ag++){ah.push(this.drawables[ag].init())}var af=this;$.when.apply($,ah).then(function(){af.enabled=true;af.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:s.prototype.can_draw,draw_helper:function(ag,aw,aC,az,an,ap,ax){var av=this,aG=this._gen_tile_cache_key(aw,ap,aC),ak=this._get_tile_bounds(aC,az);if(!ax){ax={}}var aF=(ag?undefined:av.tile_cache.get_elt(aG));if(aF){av.show_tile(aF,an,ap);return aF}var ao=[],av,at=true,aA,aq;for(var aB=0;aB<this.drawables.length;aB++){av=this.drawables[aB];aA=av.data_manager.get_data(ak,av.mode,az,av.data_url_extra_params);if(X(aA)){at=false}ao.push(aA);aq=null;if(view.reference_track&&ap>view.canvas_manager.char_width_px){aq=view.reference_track.data_manager.get_data(ak,av.mode,az,view.reference_track.data_url_extra_params);if(X(aq)){at=false}}ao.push(aq)}if(at){r(aA,ax.more_tile_data);this.tile_predraw_init();var aj=av.view.canvas_manager.new_canvas(),al=av._get_tile_bounds(aC,az),aD=ak.get("start"),ah=ak.get("end"),aE=0,aw=Math.ceil((ah-aD)*ap)+this.left_offset,au=0,ai=[],aB;var af=0;for(aB=0;aB<this.drawables.length;aB++,aE+=2){av=this.drawables[aB];aA=ao[aE];var ar=av.mode;if(ar==="Auto"){ar=av.get_mode(aA);av.update_auto_mode(ar)}ai.push(ar);af=av.get_canvas_height(aA,ar,ap,aw);if(af>au){au=af}}aj.width=aw;aj.height=(ax.height?ax.height:au);aE=0;var ay=aj.getContext("2d");ay.translate(this.left_offset,0);ay.globalAlpha=0.5;ay.globalCompositeOperation="source-over";for(aB=0;aB<this.drawables.length;aB++,aE+=2){av=this.drawables[aB];aA=ao[aE];aq=ao[aE+1];aF=av.draw_tile(aA,ay,ai[aB],az,ak,ap,aq)}this.tile_cache.set_elt(aG,aF);this.show_tile(aF,an,ap);return aF}var am=$.Deferred(),av=this;$.when.apply($,ao).then(function(){view.request_redraw(false,false,false,av);am.resolve()});return am},show_group:function(){var ai=new Q(this.view,this.container,{name:this.name}),af;for(var ah=0;ah<this.drawables.length;ah++){af=this.drawables[ah];af.update_icons();ai.add_drawable(af);af.container=ai;ai.content_div.append(af.container_div)}var ag=this.container.replace_drawable(this,ai,true);ai.request_draw()},tile_predraw_init:function(){var ai=Number.MAX_VALUE,af=-ai,ag;for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];if(ag instanceof h){if(ag.prefs.min_value<ai){ai=ag.prefs.min_value}if(ag.prefs.max_value>af){af=ag.prefs.max_value}}}for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];ag.prefs.min_value=ai;ag.prefs.max_value=af}},postdraw_actions:function(ah,ak,am,ag){N.prototype.postdraw_actions.call(this,ah,ak,am,ag);var aj=-1;for(var ai=0;ai<ah.length;ai++){var af=ah[ai].html_elt.find("canvas").height();if(af>aj){aj=af}}for(var ai=0;ai<ah.length;ai++){var al=ah[ai];if(al.html_elt.find("canvas").height()!==aj){this.draw_helper(true,ak,al.index,al.resolution,al.html_elt.parent(),am,{height:aj});al.html_elt.remove()}}}});var C=function(af){N.call(this,af,{content_div:af.top_labeltrack},{resize:false});af.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new y.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};r(C.prototype,s.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:s.prototype.can_draw,draw_helper:function(aj,ah,af,ag,ak,al,ai){if(al>this.view.canvas_manager.char_width_px){return N.prototype.draw_helper.call(this,aj,ah,af,ag,ak,al,ai)}else{this.hide_contents();return null}},draw_tile:function(an,ao,aj,ai,al,ap){var ah=this;if(ap>this.view.canvas_manager.char_width_px){if(an.data===null){this.hide_contents();return}var ag=ao.canvas;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";an=an.data;for(var ak=0,am=an.length;ak<am;ak++){var af=Math.floor(ak*ap);ao.fillText(an[ak],af,10)}this.show_contents();return new b(ah,al,ai,ag,an)}this.hide_contents()}});var h=function(ah,ag,ai){var af=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ah,ag,ai);this.hda_ldda=ai.hda_ldda;this.dataset_id=ai.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:R()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ai.prefs,onchange:function(){af.set_name(af.prefs.name);af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.set_min_value(af.prefs.min_value);af.set_max_value(af.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};r(h.prototype,s.prototype,N.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(af){this.prefs.min_value=af;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(af){this.prefs.max_value=af;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.dataset.url(),{data_type:"data",stats:true,chrom:af.view.chrom,low:0,high:af.view.max_high,hda_ldda:af.hda_ldda},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min,al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div/>").text(Y(af.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(am){$(".bs-tooltip").remove();var am=parseFloat(am);if(!isNaN(am)){af.set_min_value(am)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+af.dataset_id+"_minval").prependTo(af.container_div),ai=$("<div/>").text(Y(af.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(am){$(".bs-tooltip").remove();var am=parseFloat(am);if(!isNaN(am)){af.set_max_value(am)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+af.dataset_id+"_maxval").prependTo(af.container_div)})},draw_tile:function(ao,am,ah,ag,aj,an){var af=am.canvas,ai=aj.get("start"),al=aj.get("end"),ak=new M.LinePainter(ao.data,ai,al,this.prefs,ah);ak.draw(am,af.width,af.height,an);return new b(this,aj,ag,af,ao.data)},can_subset:function(af){return false}});var u=function(ah,ag,ai){var af=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,ah,ag,ai);this.hda_ldda=ai.hda_ldda;this.dataset_id=ai.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ai.prefs,onchange:function(){af.set_name(af.prefs.name);af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.set_min_value(af.prefs.min_value);af.set_max_value(af.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};r(u.prototype,s.prototype,N.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(af){this.prefs.min_value=af;this.tile_cache.clear();this.request_draw()},set_max_value:function(af){this.prefs.max_value=af;this.tile_cache.clear();this.request_draw()},draw_tile:function(ap,an,ak,ai,ag,ao){var ah=an.canvas,af=this._get_tile_bounds(ag,ai),aj=af[0],am=af[1],al=new M.DiagonalHeatmapPainter(ap.data,aj,am,this.prefs,ak);al.draw(an,ah.width,ah.height,ao);return new b(this,ag,ai,ah,ap.data)}});var c=function(ai,ah,ak){var ag=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ai,ah,ak);var aj=R(),af=R([aj,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:af},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ak.prefs,onchange:function(){ag.set_name(ag.prefs.name);ag.tile_cache.clear();ag.set_painter_from_config();ag.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ak.hda_ldda;this.dataset_id=ak.dataset_id;this.original_dataset_id=ak.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};r(c.prototype,s.prototype,N.prototype,{set_dataset:function(af){this.dataset_id=af.get("id");this.hda_ldda=af.get("hda_ldda");this.dataset=af;this.data_manager.set("dataset",af)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(av,ap,ak,aj){N.prototype.postdraw_actions.call(this,av,aj);var ao=this,ar;if(ao.mode==="Coverage"){var ag=-1;for(ar=0;ar<av.length;ar++){var aq=av[ar].max_val;if(aq>ag){ag=aq}}for(ar=0;ar<av.length;ar++){var ax=av[ar];if(ax.max_val!==ag){ax.html_elt.remove();ao.draw_helper(true,ap,ax.index,ax.resolution,ax.html_elt.parent(),ak,{more_tile_data:{max:ag}})}}}if(ao.filters_manager){var al=ao.filters_manager.filters;for(var au=0;au<al.length;au++){al[au].update_ui_elt()}var aw=false,af,am;for(ar=0;ar<av.length;ar++){if(av[ar].data.length){af=av[ar].data[0];for(var au=0;au<al.length;au++){am=al[au];if(am.applies_to(af)&&am.min!==am.max){aw=true;break}}}}if(ao.filters_available!==aw){ao.filters_available=aw;if(!ao.filters_available){ao.filters_manager.hide()}ao.update_icons()}}this.container_div.find(".yaxislabel").remove();var ai=av[0];if(ai instanceof j){var an=(this.prefs.histogram_max?this.prefs.histogram_max:ai.max_val),ah=$("<div/>").text(an).make_text_editable({num_cols:12,on_finish:function(ay){$(".bs-tooltip").remove();var ay=parseFloat(ay);ao.prefs.histogram_max=(!isNaN(ay)?ay:null);ao.tile_cache.clear();ao.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ah)}if(ai instanceof P){var at=true;for(ar=0;ar<av.length;ar++){if(!av[ar].all_slotted){at=false;break}}if(!at){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(af){var af;if(this.mode==="Auto"){if(af==="no_detail"){af="feature spans"}else{if(af==="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,af,ai){var ag=this.view.canvas_manager.dummy_context,ah=this.slotters[aj];if(!ah||(ah.mode!==ai)){ah=new (v.FeatureSlotter)(aj,ai,B,function(ak){return ag.measureText(ak)});this.slotters[aj]=ah}return ah.slot_features(af)},get_mode:function(af){if(af.dataset_type==="summary_tree"){mode="summary_tree"}else{if(af.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>J){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(af,aj,ak,ag){if(aj==="summary_tree"||aj==="Coverage"){return this.summary_draw_height}else{var ai=this.incremental_slots(ak,af.data,aj);var ah=new (this.painter)(null,null,null,this.prefs,aj);return Math.max(ac,ah.get_required_height(ai,ag))}},draw_tile:function(ap,au,ar,av,ai,am,ah){var at=this,ag=au.canvas,aB=ai.get("start"),af=ai.get("end"),aj=this.left_offset;if(ar==="summary_tree"||ar==="Coverage"){var aD=new M.SummaryTreePainter(ap,aB,af,this.prefs);aD.draw(au,ag.width,ag.height,am);return new j(at,ai,av,ag,ap.data,ap.max)}var al=[],aq=this.slotters[am].slots;all_slotted=true;if(ap.data){var an=this.filters_manager.filters;for(var aw=0,ay=ap.data.length;aw<ay;aw++){var ak=ap.data[aw];var ax=false;var ao;for(var aA=0,aF=an.length;aA<aF;aA++){ao=an[aA];ao.update_attrs(ak);if(!ao.keep(ak)){ax=true;break}}if(!ax){al.push(ak);if(!(ak[0] in aq)){all_slotted=false}}}}var aE=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aC=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aD=new (this.painter)(al,aB,af,this.prefs,ar,aE,aC,ah);var az=null;au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";if(ap.data){az=aD.draw(au,ag.width,ag.height,am,aq);az.translation=-aj}return new P(at,ai,av,ag,ap.data,am,ar,ap.message,all_slotted,az)},data_and_mode_compatible:function(af,ag){if(ag==="Auto"){return true}else{if(ag==="Coverage"){return af.dataset_type==="summary_tree"}else{if(af.extra_info==="no_detail"||af.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(af){if(af.dataset_type==="summary_tree"||af.message||af.extra_info==="no_detail"){return false}return true}});var T=function(ag,af,ah){c.call(this,ag,af,ah);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:R()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};r(T.prototype,s.prototype,N.prototype,c.prototype);var V=function(ah,ag,aj){c.call(this,ah,ag,aj);var ai=R(),af=R([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:af},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:aj.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_icons()};r(V.prototype,s.prototype,N.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:T,ReadTrack:V,CompositeTrack:f,DrawableGroup:Q};var p=function(ah,ag,af){if("copy" in ah){return ah.copy(af)}else{var ai=ah.obj_type;if(!ai){ai=ah.track_type}return new d[ai](ag,af,ah)}};return{View:aa,DrawableGroup:Q,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:u,ReadTrack:V,VcfTrack:T,CompositeTrack:f,object_from_template:p,add_datasets:ae}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ac,x,l,u,L,aa,i){var q=ac.extend;var Q=l.get_random_color;var ad=function(ae,ag,af){$.ajax({url:ae,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(ah){show_modal("Select datasets for new tracks",ah,{Cancel:function(){hide_modal()},Add:function(){var ai=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var aj={data_type:"track_config",hda_ldda:"hda"},ak=$(this).val();if($(this).attr("name")!=="id"){aj.hda_ldda="ldda"}ai[ai.length]=$.ajax({url:ag+"/"+ak,data:aj,dataType:"json"})});$.when.apply($,ai).then(function(){var aj=(arguments[0] instanceof Array?$.map(arguments,function(ak){return ak[0]}):[arguments[0]]);af(aj)});hide_modal()}})}})};var W=function(ae){return("isResolved" in ae)};var n={};var k=function(ae,af){n[ae.attr("id")]=af};var m=function(ae,ag,ai,ah){ai=".group";var af={};n[ae.attr("id")]=ah;ae.bind("drag",{handle:"."+ag,relative:true},function(aq,ar){var ap=$(this),av=$(this).parent(),am=av.children(),ao=n[$(this).attr("id")],al,ak,at,aj,an;ak=$(this).parents(ai);if(ak.length!==0){at=ak.position().top;aj=at+ak.outerHeight();if(ar.offsetY<at){$(this).insertBefore(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable_before(ao,au);return}else{if(ar.offsetY>aj){$(this).insertAfter(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable(ao);return}}}ak=null;for(an=0;an<am.length;an++){al=$(am.get(an));at=al.position().top;aj=at+al.outerHeight();if(al.is(ai)&&this!==al.get(0)&&ar.offsetY>=at&&ar.offsetY<=aj){if(ar.offsetY-at<aj-ar.offsetY){al.find(".content-div").prepend(this)}else{al.find(".content-div").append(this)}if(ao.container){ao.container.remove_drawable(ao)}n[al.attr("id")].add_drawable(ao);return}}for(an=0;an<am.length;an++){al=$(am.get(an));if(ar.offsetY<al.position().top&&!(al.hasClass("reference-track")||al.hasClass("intro"))){break}}if(an===am.length){if(this!==am.get(an-1)){av.append(this);n[av.attr("id")].move_drawable(ao,an)}}else{if(this!==am.get(an)){$(this).insertBefore(am.get(an));n[av.attr("id")].move_drawable(ao,(ar.deltaY>0?an-1:an))}}}).bind("dragstart",function(){af["border-top"]=ae.css("border-top");af["border-bottom"]=ae.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(af)})};exports.moveable=m;var ab=16,G=9,D=20,A=100,I=12000,T=400,K=5000,w=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",R=10,H=20;function X(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var r=function(af,ae,ah){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=ah.name;this.view=af;this.container=ae;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ah.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ai){ai.stopPropagation()});var ag=this;this.container_div.hover(function(){ag.icons_div.show()},function(){ag.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){af.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure",af.config.build_form(),{Cancel:ah,OK:ae})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ae=this.view;this.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,ak,aj,ai,ae,ah){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tooltip().click(function(){ai(ag)}).appendTo(this.icons_div);if(ah){this.action_icons[af].hide()}},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend,ag.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(af,ae,ag){r.call(this,af,ae,ag);this.obj_type=ag.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ag){this.drawables=[];var af;for(var ae=0;ae<ag.length;ae++){af=p(ag[ae],this.view,this);this.add_drawable(af)}},init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw()}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},add_drawable:function(ae){this.drawables.push(ae);ae.container=this;this.changed()},add_drawable_before:function(ag,ae){this.changed();var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}this.changed()}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);af.container=null;this.changed();return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(af,ae,ah){q(ah,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,af,ae,ah);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ah){this.unpack_drawables(ah.drawables)}if("filters" in ah){var ag=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ah.filters);ag.parent_div.replaceWith(this.filters_manager.parent_div);if(ah.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters();ae._restore_filter_managers()}else{ae.setup_multitrack_filtering();ae.request_draw(true)}ae.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var an,am,ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof c){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new i.NumberFilter({name:ah[0].name,index:ah[0].index});this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].filters_manager=this.saved_filters_managers[ae]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ae=0;ae<this.drawables.length;ae++){drawable=this.drawables[ae];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ai=[];for(var af=0;af<this.drawables.length;af++){ai.push(this.drawables[af].name)}var ag="Composite Track of "+this.drawables.length+" tracks ("+ai.join(", ")+")";var ah=new f(this.view,this.view,{name:ag,drawables:this.drawables});var ae=this.container.replace_drawable(this,ah,true);ah.request_draw()},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){z.prototype.remove_drawable.call(this,ae);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ae=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ae},request_draw:function(ae,ag){for(var af=0;af<this.drawables.length;af++){this.drawables[af].request_draw(ae,ag)}}});var Z=function(ae){q(ae,{obj_type:"View"});z.call(this,"View",ae.container,ae);this.chrom=null;this.vis_id=ae.vis_id;this.dbkey=ae.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset()};ac.extend(Z.prototype,Backbone.Events);q(Z.prototype,z.prototype,{init:function(){this.requested_redraw=false;var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){ad(add_datasets_url,add_track_async_url,function(ai){ac.each(ai,function(aj){ae.add_drawable(p(aj,ae,ae))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus();ae.nav_input.autocomplete({source:function(ak,ai){var al=[],aj=$.map(ae.get_drawables(),function(am){return am.data_manager.search_features(ak.term).success(function(an){al=al.concat(an)})});$.when.apply($,aj).done(function(){ai($.map(al,function(am){return{label:am[0],value:am[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX)-ae.container.offset().left,width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ae.resize_window()},500)});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(af,ah,ae,ai){if(this.timer){clearTimeout(this.timer)}if(ai){var ag=this;this.timer=setTimeout(function(){ag.trigger("navigate",af+":"+ah+"-"+ae)},500)}else{view.trigger("navigate",af+":"+ah+"-"+ae)}},update_location:function(ae,ag){this.location_span.text(commatize(ae)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(ag));var af=view.chrom_select.val();if(af!==""){this.trigger_navigate(af,view.low,view.high,true)}},load_chroms:function(ag){ag.num=w;var ae=this,af=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){return}if(ai.reference){ae.add_label_track(new B(ae))}ae.chrom_data=ai.chrom_info;var al='<option value="">Select Chrom/Contig</option>';for(var ak=0,ah=ae.chrom_data.length;ak<ah;ak++){var aj=ae.chrom_data[ak].chrom;al+='<option value="'+aj+'">'+aj+"</option>"}if(ai.prev_chroms){al+='<option value="previous">Previous '+w+"</option>"}if(ai.next_chroms){al+='<option value="next">Next '+w+"</option>"}ae.chrom_select.html(al);ae.chrom_start_index=ai.start_index;af.resolve(ai)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){var ag=this;if(!ag.chrom_data){ag.load_chroms_deferred.then(function(){ag.change_chrom(aj,af,al)});return}if(!aj||aj==="None"){return}if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-w});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+w});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();ag.request_redraw(true);for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}if(ag.reference_track){ag.reference_track.init()}}if(af!==undefined&&al!==undefined){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}else{ag.low=0;ag.high=ag.max_high}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/ |,/g,"");var am=this,ae,ah,af=ai.split(":"),ak=af[0],al=af[1];if(al!==undefined){try{var aj=al.split("-");ae=parseInt(aj[0],10);ah=parseInt(aj[1],10)}catch(ag){return false}}am.change_chrom(ak,ae,ah)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ah){var ae=this;var ag=ae.high-ae.low;if(ae.low-ah<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+ag}else{if(ae.high-ah>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-ag}else{ae.high-=ah;ae.low-=ah}}ae.request_redraw();var af=ae.chrom_select.val();this.trigger_navigate(af,ae.low,ae.high,true)},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);ae.init();this.changed();this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){z.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(am,ae,al,an){var ak=this,aj=(an?[an]:ak.drawables),ag;var af;for(var ai=0;ai<aj.length;ai++){af=aj[ai];ag=-1;for(var ah=0;ah<ak.tracks_to_be_redrawn.length;ah++){if(ak.tracks_to_be_redrawn[ah][0]===af){ag=ah;break}}if(ag<0){ak.tracks_to_be_redrawn.push([af,ae,al])}else{ak.tracks_to_be_redrawn[ai][1]=ae;ak.tracks_to_be_redrawn[ai][2]=al}}if(!this.requested_redraw){requestAnimationFrame(function(){ak._redraw(am)});this.requested_redraw=true}},_redraw:function(ao){this.requested_redraw=false;var al=this.low,ah=this.high;if(al<this.max_low){al=this.max_low}if(ah>this.max_high){ah=this.max_high}var an=this.high-this.low;if(this.high!==0&&an<this.min_separation){ah=al+this.min_separation}this.low=Math.floor(al);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ap=13;this.overview_box.css({left:ae,width:Math.max(ap,ak)}).show();if(ak<ap){this.overview_box.css("left",ae-(ap-ak)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ak})}if(!ao){var ag,af,am;for(var ai=0,aj=this.tracks_to_be_redrawn.length;ai<aj;ai++){ag=this.tracks_to_be_redrawn[ai][0];af=this.tracks_to_be_redrawn[ai][1];am=this.tracks_to_be_redrawn[ai][2];if(ag){ag._draw(af,am)}}this.tracks_to_be_redrawn=[];for(ai=0,aj=this.label_tracks.length;ai<aj;ai++){this.label_tracks[ai]._draw()}}},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ag.dataset_id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ag,al,ah){this.track=ag;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],af=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params.push(new e(af,ar,aj,(af in ah?ah[af]:au),an.min,an.max))}else{if(ap==="select"){this.params.push(new N(af,ar,aj,(af in ah?ah[af]:au)))}else{console.log("WARNING: unrecognized tool parameter type:",af,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("param-input").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);ae.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()});if("visible" in ah&&ah.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ae=0;ae<this.params.length;ae++){this.params[ae].update_value()}},state_dict:function(){var af={};for(var ae=0;ae<this.params.length;ae++){af[this.params[ae].name]=this.params[ae].value}af.visible=this.parent_div.is(":visible");return af},get_param_values_dict:function(){var ae={};this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();ae[af]=ag});return ae},get_param_values:function(){var ae=[];this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();if(af){ae[ae.length]=ag}});return ae},run_on_dataset:function(){var ae=this;ae.run({target_dataset_id:this.track.original_dataset_id,tool_id:ae.name},null,function(af){show_modal(ae.name+" is Running",ae.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var af={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},aj=this.track,ag=af.tool_id+aj.tool_region_and_parameters_str(af.chrom,af.low,af.high),ae;if(aj.container===view){var ai=new P(view,view,{name:this.name});var ah=aj.container.replace_drawable(aj,ai,false);ai.container_div.insertBefore(aj.view.content_div.children()[ah]);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);ae=ai}else{ae=aj.container}var ak=new aj.constructor(view,ae,{name:ag,hda_ldda:"hda"});ak.init_for_tool_data();ak.change_mode(aj.mode);ak.set_filters_manager(aj.filters_manager.copy(ak));ak.update_icons();ae.add_drawable(ak);ak.tiles_div.text("Starting job.");this.update_params();this.run(af,ak,function(al){ak.set_dataset(new aa.Dataset(al));ak.tiles_div.text("Running job.");ak.init()})},run:function(ae,ag,ah){ae.inputs=this.get_param_values_dict();var af=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ae),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ai){return ai!=="pending"}});$.when(af.go()).then(function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(J)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(y+ai.message)}else{ah(ai)}}})}});var N=function(af,ae,ag,ah){this.name=af;this.label=ae;this.html=$(ag);this.value=ah};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ag,af,ai,aj,ah,ae){N.call(this,ag,af,ai,aj);this.min=ah;this.max=ae};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ae,af){L.Scaler.call(this,af);this.filter=ae};C.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ae){this.track=ae.track;this.params=ae.params;this.values={};this.restore_values((ae.saved_values?ae.saved_values:{}));this.onchange=ae.onchange};q(F.prototype,{restore_values:function(ae){var af=this;$.each(this.params,function(ag,ah){if(ae[ah.key]!==undefined){af.values[ah.key]=ae[ah.key]}else{af.values[ah.key]=ah.default_value}})},build_form:function(){var ah=this;var ae=$("<div />");var ag;function af(am,ai){for(var aq=0;aq<am.length;aq++){ag=am[aq];if(ag.hidden){continue}var ak="param_"+aq;var av=ah.values[ag.key];var ax=$("<div class='form-row' />").appendTo(ai);ax.append($("<label />").attr("for",ak).text(ag.label+":"));if(ag.type==="bool"){ax.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",av))}else{if(ag.type==="text"){ax.append($('<input type="text"/>').attr("id",ak).val(av).click(function(){$(this).select()}))}else{if(ag.type==="select"){var at=$("<select />").attr("id",ak);for(var ao=0;ao<ag.options.length;ao++){$("<option/>").text(ag.options[ao].label).attr("value",ag.options[ao].value).appendTo(at)}at.val(av);ax.append(at)}else{if(ag.type==="color"){var aw=$("<div/>").appendTo(ax),ar=$("<input />").attr("id",ak).attr("name",ak).val(av).css("float","left").appendTo(aw).click(function(az){$(".bs-tooltip").removeClass("in");var ay=$(this).siblings(".bs-tooltip").addClass("in");ay.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ay).height()/2)+($(this).height()/2)}).show();ay.click(function(aA){aA.stopPropagation()});$(document).bind("click.color-picker",function(){ay.hide();$(document).unbind("click.color-picker")});az.stopPropagation()}),ap=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aw).attr("title","Set new random color").tooltip(),au=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aw).hide(),al=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(au),aj=$("<div class='tooltip-arrow'></div>").appendTo(au),an=$.farbtastic(al,{width:100,height:100,callback:ar,color:av});aw.append($("<div/>").css("clear","both"));(function(ay){ap.click(function(){ay.setColor(Q())})})(an)}else{ax.append($("<input />").attr("id",ak).attr("name",ak).val(av))}}}}if(ag.help){ax.append($("<div class='help'/>").text(ag.help))}}}af(this.params,ae);return ae},update_from_form:function(ae){var ag=this;var af=false;$.each(this.params,function(ah,aj){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="float"){ai=parseFloat(ai)}else{if(aj.type==="int"){ai=parseInt(ai)}else{if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}}}if(ai!==ag.values[aj.key]){ag.values[aj.key]=ai;af=true}}});if(af){this.onchange();this.track.changed()}}});var b=function(ae,ai,ag,af,ah){this.track=ae;this.region=ai;this.low=ai.get("start");this.high=ai.get("end");this.resolution=ag;this.html_elt=$("<div class='track-tile'/>").append(af).height($(af).attr("height"));this.data=ah;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ae,aj,ag,af,ah,ai){b.call(this,ae,aj,ag,af,ah);this.max_val=ai};q(j.prototype,b.prototype);var O=function(ah,ap,ai,ag,ak,ar,al,at,af,ao){b.call(this,ah,ap,ai,ag,ak);this.mode=al;this.all_slotted=af;this.feature_mapper=ao;this.has_icons=false;if(at){this.has_icons=true;var am=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ag.width}).prependTo(this.html_elt);var an=new x.GenomeRegion({chrom:ah.view.chrom,start:this.low,end:this.high}),aq=ak.length,aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);aj.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()});ae.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)==="number"?X(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(this).parents(".track-content").children(".overlay"));var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(af,ae,ag){q(ag,{drag_handle_class:"draghandle"});r.call(this,af,ae,ag);this.dataset=new aa.Dataset({id:ag.dataset_id,hda_ldda:ag.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ag?ag.data_query_wait:K);this.data_manager=("data_manager" in ag?ag.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ag)||ag.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ae){ae.dynamic_tool_div.toggle();if(ae.dynamic_tool_div.is(":visible")){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ae){var ah='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ag=ac.template(ah,{track:ae});var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){var al=$('select[name="regions"] option:selected').val(),an,ak=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),am=ac.map($(".bookmark"),function(ao){return new x.GenomeRegion({from_str:$(ao).children(".position").text()})});if(al==="cur"){an=[ak]}else{if(al==="bookmarks"){an=am}else{an=[ak].concat(am)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ae.dataset_id,hda_ldda:ae.hda_ldda,regions:JSON.stringify(new Backbone.Collection(an).toJSON())})},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){af()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ag,{No:aj,Yes:af})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},on_resize:function(){},add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.tiles_div).css("height",ai);ae.visible_height_px=(ae.max_height_px===ai?0:ai);ae.on_resize()}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.values.height=ae.visible_height_px;ae.changed()}).appendTo(ae.container_div)},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof U){return"ReadTrack"}else{if(this instanceof S){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.tiles_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}var ae=$.Deferred(),ag={hda_ldda:af.hda_ldda,data_type:this.dataset_check_type,chrom:af.view.chrom};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){af.container_div.addClass("error");af.tiles_div.text(o);if(ah.message){var ai=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})});af.tiles_div.append(ai)}}else{if(ah==="no converter"){af.container_div.addClass("error");af.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){af.container_div.addClass("nodata");af.tiles_div.text(E)}else{if(ah==="pending"){af.container_div.addClass("pending");af.tiles_div.html(v);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){af.valid_chroms=ah.valid_chroms;af.update_icons()}af.tiles_div.text(V);if(af.view.chrom){af.tiles_div.text("");af.tiles_div.css("height",af.visible_height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ag,af,ah){g.call(this,ag,af,ah);var ae=this;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new i.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ah&&ah.tool?new s(this,ah.tool,ah.tool_state):null);this.tile_cache=new x.Cache(R);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.slotters[ae.view.resolution_px_b].max_rows*=2;ae.request_draw(true)},hide:true}]),copy:function(ae){var af=this.to_dict();q(af,{data_manager:this.data_manager});var ag=new this.constructor(this.view,ae,af);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},set_filters_manager:function(ae){this.filters_manager=ae;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(af){var ae=this;ae.mode=af;ae.config.values.mode=af;ae.tile_cache.clear();ae.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show();ae.action_icons.param_space_viz_icon.show()}else{ae.action_icons.tools_icon.hide();ae.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},before_draw:function(){},_draw:function(af,ap){if(!this.can_draw()){return}var an=this.view.low,aj=this.view.high,al=aj-an,ag=this.view.container.width(),ar=this.view.resolution_px_b,ai=this.view.resolution_b_px;if(this.is_overview){an=this.view.max_low;aj=this.view.max_high;ai=(view.max_high-view.max_low)/ag;ar=1/ai}this.before_draw();this.tiles_div.children().addClass("remove");var ae=Math.floor(an/(ai*T)),am=true,aq=[],ak=function(at){return(at&&"track" in at)};while((ae*T*ai)<aj){var ao=this.draw_helper(af,ag,ae,ai,this.tiles_div,ar);if(ak(ao)){aq.push(ao)}else{am=false}ae+=1}if(!ap){this.tiles_div.children(".remove").removeClass("remove").remove()}var ah=this;if(am){this.tiles_div.children(".remove").remove();ah.postdraw_actions(aq,ag,ar,ap)}},postdraw_actions:function(ag,ah,aj,ae){var ai=false;for(var af=0;af<ag.length;af++){if(ag[af].has_icons){ai=true;break}}if(ai){for(var af=0;af<ag.length;af++){tile=ag[af];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ae,aq,aw,au,aj,ak,ar){var ap=this,az=this._gen_tile_cache_key(aq,ak,aw),ah=this._get_tile_bounds(aw,au);if(!ar){ar={}}var ay=(ae?undefined:ap.tile_cache.get_elt(az));if(ay){ap.show_tile(ay,aj,ak);return ay}var an=true;var av=ap.data_manager.get_data(ah,ap.mode,au,ap.data_url_extra_params);if(W(av)){an=false}var al;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ah,ap.mode,au,view.reference_track.data_url_extra_params);if(W(al)){an=false}}if(an){q(av,ar.more_tile_data);var am=ap.mode;if(am==="Auto"){am=ap.get_mode(av);ap.update_auto_mode(am)}var ag=ap.view.canvas_manager.new_canvas(),ax=ah.get("start"),af=ah.get("end"),aq=Math.ceil((af-ax)*ak)+ap.left_offset,ao=ap.get_canvas_height(av,am,ak,aq);ag.width=aq;ag.height=ao;var at=ag.getContext("2d");at.translate(this.left_offset,0);var ay=ap.draw_tile(av,at,am,au,ah,ak,al);if(ay!==undefined){ap.tile_cache.set_elt(az,ay);ap.show_tile(ay,aj,ak)}return ay}var ai=$.Deferred();$.when(av,al).then(function(){view.request_redraw(false,false,false,ap);ai.resolve()});return ai},get_canvas_height:function(ae,ag,ah,af){return this.visible_height_px},draw_tile:function(ae,af,aj,ah,ai,ak,ag){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ag,ai,aj){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ah=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*aj;if(this.left_offset){ah-=this.left_offset}ae.css({position:"absolute",top:0,left:ah});if(ae.hasClass("remove")){ae.removeClass("remove")}else{ai.append(ae)}af.after_show_tile(ag)},after_show_tile:function(ae){this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ae,af){var ah=Math.floor(ae*T*af),ai=Math.ceil(T*af),ag=(ah+ai<=this.view.max_high?ah+ai:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:ah,end:ag})},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ae,af){return true},can_subset:function(ae){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ag,ah,aj,ae){var af=this;af.normal_postdraw_actions(ag,ah,aj,ae);af.dataset_check_type="converted_datasets_state";af.data_query_wait=K;var ai=new l.ServerStateDeferred({url:af.dataset_state_url,url_params:{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},interval:af.data_query_wait,success_fn:function(ak){return ak!=="pending"}});$.when(ai.go()).then(function(){af.data_manager.set("data_type","data")});af.postdraw_actions=af.normal_postdraw_actions}}});var Y=function(af,ae){var ag={resize:false};g.call(this,af,ae,ag);this.container_div.addClass("label-track")};q(Y.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var f=function(af,ae,ai){M.call(this,af,ae,ai);this.drawables=[];this.left_offset=0;if("drawables" in ai){var ah;for(var ag=0;ag<ai.drawables.length;ag++){ah=ai.drawables[ag];this.drawables[ag]=p(ah,af,null);if(ah.left_offset>this.left_offset){this.left_offset=ah.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ae){M.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(af,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aj=this._get_tile_bounds(aB,ay);if(!aw){aw={}}var aE=(af?undefined:au.tile_cache.get_elt(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aj,au.mode,ay,au.data_url_extra_params);if(W(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aj,au.mode,ay,view.reference_track.data_url_extra_params);if(W(ap)){ar=false}}an.push(ap)}if(ar){q(az,aw.more_tile_data);this.tile_predraw_init();var ai=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=aj.get("start"),ag=aj.get("end"),aD=0,av=Math.ceil((ag-aC)*ao)+this.left_offset,at=0,ah=[],aA;var ae=0;for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ah.push(aq);ae=au.get_canvas_height(az,aq,ao,av);if(ae>at){at=ae}}ai.width=av;ai.height=(aw.height?aw.height:at);aD=0;var ax=ai.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ah[aA],ay,aj,ao,ap)}this.tile_cache.set_elt(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},show_group:function(){var ah=new P(this.view,this.container,{name:this.name}),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ae.update_icons();ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw()},tile_predraw_init:function(){var ah=Number.MAX_VALUE,ae=-ah,af;for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];if(af instanceof h){if(af.prefs.min_value<ah){ah=af.prefs.min_value}if(af.prefs.max_value>ae){ae=af.prefs.max_value}}}for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];af.prefs.min_value=ah;af.prefs.max_value=ae}},postdraw_actions:function(ag,aj,al,af){M.prototype.postdraw_actions.call(this,ag,aj,al,af);var ai=-1;for(var ah=0;ah<ag.length;ah++){var ae=ag[ah].html_elt.find("canvas").height();if(ae>ai){ai=ae}}for(var ah=0;ah<ag.length;ah++){var ak=ag[ah];if(ak.html_elt.find("canvas").height()!==ai){this.draw_helper(true,aj,ak.index,ak.resolution,ak.html_elt.parent(),al,{height:ai});ak.html_elt.remove()}}}});var B=function(ae){M.call(this,ae,{content_div:ae.top_labeltrack},{resize:false});ae.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ai,ag,ae,af,aj,ak,ah){if(ak>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ai,ag,ae,af,aj,ak,ah)}else{this.hide_contents();return null}},draw_tile:function(am,an,ai,ah,ak,ao){var ag=this;if(ao>this.view.canvas_manager.char_width_px){if(am.data===null){this.hide_contents();return}var af=an.canvas;an.font=an.canvas.manager.default_font;an.textAlign="center";am=am.data;for(var aj=0,al=am.length;aj<al;aj++){var ae=Math.floor(aj*ao);an.fillText(am[aj],ae,10)}this.show_contents();return new b(ag,ak,ah,af,am)}this.hide_contents()}});var h=function(ag,af,ah){var ae=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:Q()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ae=this;ae.vertical_range=undefined;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.hda_ldda},function(af){ae.container_div.addClass("line-track");var ai=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ai.min,ak=ai.max;ag=Math.floor(Math.min(0,Math.max(ag,ai.mean-2*ai.sd)));ak=Math.ceil(Math.max(0,Math.min(ak,ai.mean+2*ai.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ak;$("#track_"+ae.dataset_id+"_minval").val(ae.prefs.min_value);$("#track_"+ae.dataset_id+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=$("<div/>").text(X(ae.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_min_value(al)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ae.dataset_id+"_minval").prependTo(ae.container_div),ah=$("<div/>").text(X(ae.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_max_value(al)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ae.dataset_id+"_maxval").prependTo(ae.container_div)})},draw_tile:function(an,al,ag,af,ai,am){var ae=al.canvas,ah=ai.get("start"),ak=ai.get("end"),aj=new L.LinePainter(an.data,ah,ak,this.prefs,ag);aj.draw(al,ae.width,ae.height,am);return new b(this,ai,af,ae,an.data)},can_subset:function(ae){return false}});var t=function(ag,af,ah){var ae=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;this.tile_cache.clear();this.request_draw()},draw_tile:function(ao,am,aj,ah,af,an){var ag=am.canvas,ae=this._get_tile_bounds(af,ah),ai=ae[0],al=ae[1],ak=new L.DiagonalHeatmapPainter(ao.data,ai,al,this.prefs,aj);ak.draw(am,ag.width,ag.height,an);return new b(this,af,ah,ag,ao.data)}});var c=function(ah,ag,aj){var af=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,ah,ag,aj);var ai=Q(),ae=Q([ai,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:aj.prefs,onchange:function(){af.set_name(af.prefs.name);af.tile_cache.clear();af.set_painter_from_config();af.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=aj.hda_ldda;this.dataset_id=aj.dataset_id;this.original_dataset_id=aj.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ae){this.dataset_id=ae.get("id");this.hda_ldda=ae.get("hda_ldda");this.dataset=ae;this.data_manager.set("dataset",ae)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(au,ao,aj,ai){M.prototype.postdraw_actions.call(this,au,ai);var an=this,aq;if(an.mode==="Coverage"){var af=-1;for(aq=0;aq<au.length;aq++){var ap=au[aq].max_val;if(ap>af){af=ap}}for(aq=0;aq<au.length;aq++){var aw=au[aq];if(aw.max_val!==af){aw.html_elt.remove();an.draw_helper(true,ao,aw.index,aw.resolution,aw.html_elt.parent(),aj,{more_tile_data:{max:af}})}}}if(an.filters_manager){var ak=an.filters_manager.filters;for(var at=0;at<ak.length;at++){ak[at].update_ui_elt()}var av=false,ae,al;for(aq=0;aq<au.length;aq++){if(au[aq].data.length){ae=au[aq].data[0];for(var at=0;at<ak.length;at++){al=ak[at];if(al.applies_to(ae)&&al.min!==al.max){av=true;break}}}}if(an.filters_available!==av){an.filters_available=av;if(!an.filters_available){an.filters_manager.hide()}an.update_icons()}}this.container_div.find(".yaxislabel").remove();var ah=au[0];if(ah instanceof j){var am=(this.prefs.histogram_max?this.prefs.histogram_max:ah.max_val),ag=$("<div/>").text(am).make_text_editable({num_cols:12,on_finish:function(ax){$(".bs-tooltip").remove();var ax=parseFloat(ax);an.prefs.histogram_max=(!isNaN(ax)?ax:null);an.tile_cache.clear();an.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ag)}if(ah instanceof O){var ar=true;for(aq=0;aq<au.length;aq++){if(!au[aq].all_slotted){ar=false;break}}if(!ar){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ae){var ae;if(this.mode==="Auto"){if(ae==="no_detail"){ae="feature spans"}else{if(ae==="summary_tree"){ae="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (u.FeatureSlotter)(ai,ah,A,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_mode:function(ae){if(ae.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="summary_tree"||ai==="Coverage"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ab,ag.get_required_height(ah,af))}},draw_tile:function(ao,at,aq,au,ah,al,ag){var ar=this,af=at.canvas,aA=ah.get("start"),ae=ah.get("end"),ai=this.left_offset;if(aq==="summary_tree"||aq==="Coverage"){var aC=new L.SummaryTreePainter(ao,aA,ae,this.prefs);aC.draw(at,af.width,af.height,al);return new j(ar,ah,au,af,ao.data,ao.max)}var ak=[],ap=this.slotters[al].slots;all_slotted=true;if(ao.data){var am=this.filters_manager.filters;for(var av=0,ax=ao.data.length;av<ax;av++){var aj=ao.data[av];var aw=false;var an;for(var az=0,aE=am.length;az<aE;az++){an=am[az];an.update_attrs(aj);if(!an.keep(aj)){aw=true;break}}if(!aw){ak.push(aj);if(!(aj[0] in ap)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aC=new (this.painter)(ak,aA,ae,this.prefs,aq,aD,aB,ag);var ay=null;at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";if(ao.data){ay=aC.draw(at,af.width,af.height,al,ap);ay.translation=-ai}return new O(ar,ah,au,af,ao.data,al,aq,ao.message,all_slotted,ay)},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(af==="Coverage"){return ae.dataset_type==="summary_tree"}else{if(ae.extra_info==="no_detail"||ae.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ae){if(ae.dataset_type==="summary_tree"||ae.message||ae.extra_info==="no_detail"){return false}return true}});var S=function(af,ae,ag){c.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:Q()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(S.prototype,r.prototype,M.prototype,c.prototype);var U=function(ag,af,ai){c.call(this,ag,af,ai);var ah=Q(),ae=Q([ah,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ai.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(U.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:S,ReadTrack:U,CompositeTrack:f,DrawableGroup:P};var p=function(ag,af,ae){if("copy" in ag){return ag.copy(ae)}else{var ah=ag.obj_type;if(!ah){ah=ag.track_type}return new d[ah](af,ae,ag)}};return{View:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:U,VcfTrack:S,CompositeTrack:f,object_from_template:p,add_datasets:ad}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util"],function(q,h,j){var i=function(s){return("isResolved" in s)};var e=function(s){this.default_font=s!==undefined?s:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q.extend(e.prototype,{load_pattern:function(s,w){var t=this.patterns,u=this.dummy_context,v=new Image();v.src=galaxy_paths.attributes.image_path+w;v.onload=function(){t[s]=u.createPattern(v,"repeat")}},get_pattern:function(s){return this.patterns[s]},new_canvas:function(){var s=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(s)}s.manager=this;return s}});var o=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(s){this.clear()},get_elt:function(t){var u=this.attributes.obj_cache,v=this.attributes.key_ary,s=v.indexOf(t);if(s!==-1){if(u[t].stale){v.splice(s,1);delete u[t]}else{this.move_key_to_end(t,s)}}return u[t]},set_elt:function(t,v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=this.attributes.num_elements;if(!w[t]){if(x.length>=u){var s=x.shift();delete w[s]}x.push(t)}w[t]=v;return v},move_key_to_end:function(t,s){this.attributes.key_ary.splice(s,1);this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var c=o.extend({defaults:q.extend({},o.prototype.defaults,{dataset:null,filters_manager:null,data_type:"data",data_mode_compatible:function(s,t){return true},can_subset:function(s){return false}}),data_is_ready:function(){var u=this.get("dataset"),t=$.Deferred(),s=new j.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:u.get("hda_ldda"),data_type:"state"},dataType:"json"},interval:5000,success_fn:function(v){return v!=="pending"}});$.when(s.go()).then(function(v){t.resolve(v==="ok"||v==="data")});return t},search_features:function(s){var t=this.get("dataset"),u={query:s,hda_ldda:t.get("hda_ldda"),data_type:"features"};return $.getJSON(t.url(),u)},load_data:function(A,z,t,y){var w=this.get("dataset"),v={data_type:this.get("data_type"),chrom:A.get("chrom"),low:A.get("start"),high:A.get("end"),mode:z,resolution:t,hda_ldda:w.get("hda_ldda")};$.extend(v,y);var C=this.get("filters_manager");if(C){var D=[];var s=C.filters;for(var x=0;x<s.length;x++){D.push(s[x].name)}v.filter_cols=JSON.stringify(D)}var u=this,B=$.getJSON(w.url(),v,function(E){u.set_data(A,E)});this.set_data(A,B);return B},get_data:function(y,x,u,w){var z=this.get_elt(y);if(z&&(i(z)||this.get("data_mode_compatible")(z,x))){return z}var A=this.get("key_ary"),t=this.get("obj_cache"),B,s;for(var v=0;v<A.length;v++){B=A[v];s=new f({from_str:B});if(s.contains(y)){z=t[B];if(i(z)||(this.get("data_mode_compatible")(z,x)&&this.get("can_subset")(z))){this.move_key_to_end(B,v);return z}}}return this.load_data(y,x,u,w)},set_data:function(t,s){this.set_elt(t,s)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(A,z,v,y,w){var C=this._mark_stale(A);if(!(C&&this.get("data_mode_compatible")(C,z))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var u=A.get("start");if(w===this.DEEP_DATA_REQ){$.extend(y,{start_val:C.data.length+1})}else{if(w===this.BROAD_DATA_REQ){u=(C.max_high?C.max_high:C.data[C.data.length-1][2])+1}}var B=A.copy().set("start",u);var t=this,x=this.load_data(B,z,v,y),s=$.Deferred();this.set_data(A,s);$.when(x).then(function(D){if(D.data){D.data=C.data.concat(D.data);if(D.max_low){D.max_low=C.max_low}if(D.message){D.message=D.message.replace(/[0-9]+/,D.data.length)}}t.set_data(A,D);s.resolve(D)});return s},get_more_detailed_data:function(v,x,t,w,u){var s=this._mark_stale(v);if(!s){console.log("ERROR getting more detailed data: no current data");return}if(!u){u={}}var x;if(s.dataset_type==="bigwig"){u.num_samples=s.data.length*w}else{if(s.dataset_type==="summary_tree"){u.level=s.level+1}}return this.load_data(v,x,t,u)},_mark_stale:function(t){var s=this.get_elt(t);if(!s){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString())}s.stale=true;return s},get_elt:function(s){return o.prototype.get_elt.call(this,s.toString())},set_elt:function(t,s){return o.prototype.set_elt.call(this,t.toString(),s)}});var m=c.extend({initialize:function(s){var t=new Backbone.Model();t.urlRoot=s.data_url;this.set("dataset",t)},load_data:function(u,v,s,t){console.log(u,v,s);if(s>1){return{data:null}}return c.prototype.load_data.call(this,u,v,s,t)}});var b=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(s){this.id=s.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(s){var t=q.find(this.get_chroms_info(),function(u){return u.chrom==s});return new f({chrom:t.chrom,end:t.len})}});var f=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(t){if(t.from_str){var v=t.from_str.split(":"),u=v[0],s=v[1].split("-");this.set({chrom:u,start:parseInt(s[0],10),end:parseInt(s[1],10)})}},copy:function(){return new f({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(z){var t=this.get("chrom"),y=z.get("chrom"),x=this.get("start"),v=z.get("start"),w=this.get("end"),u=z.get("end"),s;if(t&&y&&t!==y){return this.get("DIF_CHROMS")}if(x<v){if(w<v){s=this.get("BEFORE")}else{if(w<=u){s=this.get("OVERLAP_START")}else{s=this.get("CONTAINS")}}}else{if(x>u){s=this.get("AFTER")}else{if(w<=u){s=this.get("CONTAINED_BY")}else{s=this.get("OVERLAP_END")}}}return s},contains:function(s){return this.compute_overlap(s)===this.get("CONTAINS")},overlaps:function(s){return q.intersection([this.compute_overlap(s)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:f});var d=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:f}]});var p=Backbone.Collection.extend({model:d});var r=h.Dataset.extend({initialize:function(s){this.set("id",s.dataset_id);var t=new c({dataset:this});this.set("data_manager",t);var u=this.get("preloaded_data");if(u){t.set("num_elements",u.data.length);q.each(u.data,function(v){t.set_data(v.region,v)})}},get_genome_wide_data:function(s){var t=this.get("data_manager");return q.map(s.get("chroms_info").chrom_info,function(u){return t.get_elt(new f({chrom:u.chrom,start:0,end:u.len}))})}});var n=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:r}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:q.extend({},n.prototype.defaults,{bookmarks:null,viewport:null})});var a=Backbone.Model.extend({});var g=Backbone.Router.extend({initialize:function(t){this.view=t.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var s=this;s.view.on("navigate",function(u){s.navigate(u)})},change_location:function(s){this.view.go_to(s)}});return{BrowserBookmark:d,BrowserBookmarkCollection:p,Cache:o,CanvasManager:e,Genome:b,GenomeDataManager:c,GenomeRegion:f,GenomeRegionCollection:l,GenomeVisualization:k,ReferenceTrackDataManager:m,TrackBrowserRouter:g,TrackConfig:a,Visualization:n}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util"],function(q,h,j){var i=function(s){return("isResolved" in s)};var e=function(s){this.default_font=s!==undefined?s:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q.extend(e.prototype,{load_pattern:function(s,w){var t=this.patterns,u=this.dummy_context,v=new Image();v.src=galaxy_paths.attributes.image_path+w;v.onload=function(){t[s]=u.createPattern(v,"repeat")}},get_pattern:function(s){return this.patterns[s]},new_canvas:function(){var s=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(s)}s.manager=this;return s}});var o=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(s){this.clear()},get_elt:function(t){var u=this.attributes.obj_cache,v=this.attributes.key_ary,s=v.indexOf(t);if(s!==-1){if(u[t].stale){v.splice(s,1);delete u[t]}else{this.move_key_to_end(t,s)}}return u[t]},set_elt:function(t,v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=this.attributes.num_elements;if(!w[t]){if(x.length>=u){var s=x.shift();delete w[s]}x.push(t)}w[t]=v;return v},move_key_to_end:function(t,s){this.attributes.key_ary.splice(s,1);this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var c=o.extend({defaults:q.extend({},o.prototype.defaults,{dataset:null,filters_manager:null,data_type:"data",data_mode_compatible:function(s,t){return true},can_subset:function(s){return false}}),data_is_ready:function(){var u=this.get("dataset"),t=$.Deferred(),s=new j.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:u.get("hda_ldda"),data_type:"state"},dataType:"json"},interval:5000,success_fn:function(v){return v!=="pending"}});$.when(s.go()).then(function(v){t.resolve(v==="ok"||v==="data")});return t},search_features:function(s){var t=this.get("dataset"),u={query:s,hda_ldda:t.get("hda_ldda"),data_type:"features"};return $.getJSON(t.url(),u)},load_data:function(A,z,t,y){var w=this.get("dataset"),v={data_type:this.get("data_type"),chrom:A.get("chrom"),low:A.get("start"),high:A.get("end"),mode:z,resolution:t,hda_ldda:w.get("hda_ldda")};$.extend(v,y);var C=this.get("filters_manager");if(C){var D=[];var s=C.filters;for(var x=0;x<s.length;x++){D.push(s[x].name)}v.filter_cols=JSON.stringify(D)}var u=this,B=$.getJSON(w.url(),v,function(E){u.set_data(A,E)});this.set_data(A,B);return B},get_data:function(y,x,u,w){var z=this.get_elt(y);if(z&&(i(z)||this.get("data_mode_compatible")(z,x))){return z}var A=this.get("key_ary"),t=this.get("obj_cache"),B,s;for(var v=0;v<A.length;v++){B=A[v];s=new f({from_str:B});if(s.contains(y)){z=t[B];if(i(z)||(this.get("data_mode_compatible")(z,x)&&this.get("can_subset")(z))){this.move_key_to_end(B,v);return z}}}return this.load_data(y,x,u,w)},set_data:function(t,s){this.set_elt(t,s)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(A,z,v,y,w){var C=this._mark_stale(A);if(!(C&&this.get("data_mode_compatible")(C,z))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var u=A.get("start");if(w===this.DEEP_DATA_REQ){$.extend(y,{start_val:C.data.length+1})}else{if(w===this.BROAD_DATA_REQ){u=(C.max_high?C.max_high:C.data[C.data.length-1][2])+1}}var B=A.copy().set("start",u);var t=this,x=this.load_data(B,z,v,y),s=$.Deferred();this.set_data(A,s);$.when(x).then(function(D){if(D.data){D.data=C.data.concat(D.data);if(D.max_low){D.max_low=C.max_low}if(D.message){D.message=D.message.replace(/[0-9]+/,D.data.length)}}t.set_data(A,D);s.resolve(D)});return s},get_more_detailed_data:function(v,x,t,w,u){var s=this._mark_stale(v);if(!s){console.log("ERROR getting more detailed data: no current data");return}if(!u){u={}}var x;if(s.dataset_type==="bigwig"){u.num_samples=s.data.length*w}else{if(s.dataset_type==="summary_tree"){u.level=Math.min(s.level-1,2)}}return this.load_data(v,x,t,u)},_mark_stale:function(t){var s=this.get_elt(t);if(!s){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString())}s.stale=true;return s},get_elt:function(s){return o.prototype.get_elt.call(this,s.toString())},set_elt:function(t,s){return o.prototype.set_elt.call(this,t.toString(),s)}});var m=c.extend({initialize:function(s){var t=new Backbone.Model();t.urlRoot=s.data_url;this.set("dataset",t)},load_data:function(u,v,s,t){console.log(u,v,s);if(s>1){return{data:null}}return c.prototype.load_data.call(this,u,v,s,t)}});var b=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(s){this.id=s.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(s){var t=q.find(this.get_chroms_info(),function(u){return u.chrom==s});return new f({chrom:t.chrom,end:t.len})}});var f=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(t){if(t.from_str){var v=t.from_str.split(":"),u=v[0],s=v[1].split("-");this.set({chrom:u,start:parseInt(s[0],10),end:parseInt(s[1],10)})}},copy:function(){return new f({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(z){var t=this.get("chrom"),y=z.get("chrom"),x=this.get("start"),v=z.get("start"),w=this.get("end"),u=z.get("end"),s;if(t&&y&&t!==y){return this.get("DIF_CHROMS")}if(x<v){if(w<v){s=this.get("BEFORE")}else{if(w<=u){s=this.get("OVERLAP_START")}else{s=this.get("CONTAINS")}}}else{if(x>u){s=this.get("AFTER")}else{if(w<=u){s=this.get("CONTAINED_BY")}else{s=this.get("OVERLAP_END")}}}return s},contains:function(s){return this.compute_overlap(s)===this.get("CONTAINS")},overlaps:function(s){return q.intersection([this.compute_overlap(s)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:f});var d=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:f}]});var p=Backbone.Collection.extend({model:d});var r=h.Dataset.extend({initialize:function(s){this.set("id",s.dataset_id);var t=new c({dataset:this});this.set("data_manager",t);var u=this.get("preloaded_data");if(u){t.set("num_elements",u.data.length);q.each(u.data,function(v){t.set_data(v.region,v)})}},get_genome_wide_data:function(s){var t=this.get("data_manager");return q.map(s.get("chroms_info").chrom_info,function(u){return t.get_elt(new f({chrom:u.chrom,start:0,end:u.len}))})}});var n=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:r}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:q.extend({},n.prototype.defaults,{bookmarks:null,viewport:null})});var a=Backbone.Model.extend({});var g=Backbone.Router.extend({initialize:function(t){this.view=t.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var s=this;s.view.on("navigate",function(u){s.navigate(u)})},change_location:function(s){this.view.go_to(s)}});return{BrowserBookmark:d,BrowserBookmarkCollection:p,Cache:o,CanvasManager:e,Genome:b,GenomeDataManager:c,GenomeRegion:f,GenomeRegionCollection:l,GenomeVisualization:k,ReferenceTrackDataManager:m,TrackBrowserRouter:g,TrackConfig:a,Visualization:n}}); \ No newline at end of file diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -61,8 +61,9 @@ */ function TwoVarScatterplot( config ){ var plot = this, - GUESS_AT_SVG_CHAR_WIDTH = 10, - GUESS_AT_SVG_CHAR_HEIGHT = 12, + TICK_LINE_AND_PADDING = 10, + GUESS_AT_SVG_CHAR_WIDTH = 7, + GUESS_AT_SVG_CHAR_HEIGHT = 10, PADDING = 8, X_LABEL_TOO_LONG_AT = 5; @@ -135,16 +136,23 @@ this.log( 'built svg:', d3.selectAll( 'svg' ) ); - this.adjustChartDimensions = function(){ + this.adjustChartDimensions = function( top, right, bottom, left ){ + top = top || 0; + right = right || 0; + bottom = bottom || 0; + left = left || 0; this.svg - .attr( "width", this.config.width + ( this.config.marginRight + this.config.marginLeft ) ) - .attr( "height", this.config.height + ( this.config.marginTop + this.config.marginBottom ) ) + .attr( "width", this.config.width + ( this.config.marginRight + right ) + + ( this.config.marginLeft + left ) ) + .attr( "height", this.config.height + ( this.config.marginTop + top ) + + ( this.config.marginBottom + bottom ) ) // initial is hidden - show it .style( 'display', 'block' ); // move content group away from margins + //TODO: allow top, right axis this.content = this.svg.select( "g.content" ) - .attr( "transform", this.translateStr( this.config.marginLeft, this.config.marginTop ) ); + .attr( "transform", this.translateStr( this.config.marginLeft + left, this.config.marginTop + top ) ); }; // ........................................................ data and scales @@ -208,29 +216,38 @@ .orient( 'left' ); this.yAxis// = content.select( 'g#y-axis' ) .call( this.yAxisFn ); - //this.log( 'yAxis:', this.yAxis ); + this.log( 'yAxis:', this.yAxis ); - //TODO: this isn't reliable with -/+ ranges - better to go thru each tick - this.yLongestLabel = d3.max( _.map( [ this.yMin, this.yMax ], - function( number ){ return ( String( number ) ).length; } ) ); - this.log( 'yLongestLabel:', this.yLongestLabel ); + // get the tick labels for the y axis + var yTickLabels = this.yAxis.selectAll( 'text' ).filter( function( e, i ){ return i !== 0; } ); + //this.log( 'yTickLabels:', yTickLabels ); - //TODO: ugh ... so clumsy - //TODO: this isn't reliable with -/+ ranges - better to go thru each tick - var neededY = this.yLongestLabel * GUESS_AT_SVG_CHAR_WIDTH + ( PADDING ); + // get the longest label length (or 0 if no labels) + this.yLongestLabel = d3.max( + //NOTE: d3 returns an nested array - use the plain array inside ([0]) + yTickLabels[0].map( function( e, i ){ + return ( d3.select( e ).text() ).length; + }) + ) || 0; + //this.log( 'yLongestLabel:', this.yLongestLabel ); + //TODO: lose the guessing if possible + var neededY = TICK_LINE_AND_PADDING + ( this.yLongestLabel * GUESS_AT_SVG_CHAR_WIDTH ) + + PADDING + GUESS_AT_SVG_CHAR_HEIGHT; + //this.log( 'neededY:', neededY ); // increase width for yLongerStr, increase margin for y //TODO??: (or transform each number: 2k) - if( this.config.yAxisLabelBumpX > -( neededY ) ){ - this.config.yAxisLabelBumpX = -( neededY ); + this.config.yAxisLabelBumpX = -( neededY - GUESS_AT_SVG_CHAR_HEIGHT ); + if( this.config.marginLeft < neededY ){ + var adjusting = ( neededY ) - this.config.marginLeft; + adjusting = ( adjusting < 0 )?( 0 ):( adjusting ); + this.log( 'adjusting:', adjusting ); + + // update dimensions, translations + this.adjustChartDimensions( 0, 0, 0, adjusting ); } - if( this.config.marginLeft < neededY ){ - this.config.marginLeft = neededY + GUESS_AT_SVG_CHAR_HEIGHT; - // update dimensions, translations - this.adjustChartDimensions(); - } - this.log( 'this.config.yAxisLableBumpx, this.config.marginLeft:', - this.config.yAxisLabelBumpX, this.config.marginLeft ); + //this.log( 'this.config.yAxisLableBumpx, this.config.marginLeft:', + // this.config.yAxisLabelBumpX, this.config.marginLeft ); this.yAxisLabel// = yAxis.select( 'text#y-axis-label' ) .attr( 'x', this.config.yAxisLabelBumpX ) @@ -367,7 +384,7 @@ * */ var ScatterplotView = BaseView.extend( LoggableMixin ).extend({ - logger : console, + //logger : console, tagName : 'form', className : 'scatterplot-settings-form', @@ -444,12 +461,10 @@ message = message || ''; this.$el.find( 'div#loading-indicator' ).children( '.loading-message' ).text( message ); this.$el.find( 'div#loading-indicator' ).show( 'fast' ); - console.debug( 'showing:', this.$el.find( 'div#loading-indicator' ), message ); }, hideLoadingIndicator : function(){ this.$el.find( 'div#loading-indicator' ).hide( 'fast' ); - console.debug( 'hiding:', this.$el.find( 'div#loading-indicator' ) ); }, renderScatterplot : function(){ diff -r 80251cd7f94d64295ef6e64412f895d268ab988d -r 369a941393909434e0efb5c84dd831e5ab096095 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -60,9 +60,15 @@ stroke: black; shape-rendering: crispEdges; } + svg .axis text { + font-family: monospace; + font-size: 12px; +} + +svg #x-axis-label, svg #y-axis-label { font-family: sans-serif; - font-size: 12px; + font-size: 10px; } svg .glyph { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from 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commit/galaxy-central: carlfeberhard: scatterplot: loading indicators; api/datasets: minor cleanup;
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/80251cd7f94d/ changeset: 80251cd7f94d user: carlfeberhard date: 2012-10-02 19:24:26 summary: scatterplot: loading indicators; api/datasets: minor cleanup; affected #: 4 files diff -r 00681c35d987cde2200ff94c7f5510c594c904fd -r 80251cd7f94d64295ef6e64412f895d268ab988d lib/galaxy/visualization/data_providers/basic.py --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -102,6 +102,7 @@ "column index (%d) must be less" % ( column ) + " than the number of columns: %d" % ( self.original_dataset.metadata.columns ) ) + #print columns, start_val, max_vals, skip_comments, kwargs # alter meta by column_selectors (if any) diff -r 00681c35d987cde2200ff94c7f5510c594c904fd -r 80251cd7f94d64295ef6e64412f895d268ab988d lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -187,7 +187,6 @@ # Return data. data = None data_provider = trans.app.data_provider_registry.get_data_provider( trans, raw=True, original_dataset=dataset ) - print 'data_provider:', data_provider if isinstance( data_provider, ColumnDataProvider ): data = data_provider.get_data( **kwargs ) diff -r 00681c35d987cde2200ff94c7f5510c594c904fd -r 80251cd7f94d64295ef6e64412f895d268ab988d static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -181,12 +181,11 @@ this.xAxis// = content.select( 'g#x-axis' ) .attr( 'transform', this.translateStr( 0, this.config.height ) ) .call( this.xAxisFn ); - this.log( 'xAxis:', this.xAxis ); + //this.log( 'xAxis:', this.xAxis ); - //TODO: this isn't reliable with -/+ ranges - better to go thru each tick this.xLongestLabel = d3.max( _.map( [ this.xMin, this.xMax ], function( number ){ return ( String( number ) ).length; } ) ); - this.log( 'xLongestLabel:', this.xLongestLabel ); + //this.log( 'xLongestLabel:', this.xLongestLabel ); if( this.xLongestLabel >= X_LABEL_TOO_LONG_AT ){ //TODO: adjust ticks when tick labels are long - move odds down and extend tick line @@ -199,7 +198,7 @@ .attr( 'y', this.config.xAxisLabelBumpY ) .attr( 'text-anchor', 'middle' ) .text( this.config.xLabel ); - this.log( 'xAxisLabel:', this.xAxisLabel ); + //this.log( 'xAxisLabel:', this.xAxisLabel ); }; this.setUpYAxis = function(){ @@ -209,8 +208,9 @@ .orient( 'left' ); this.yAxis// = content.select( 'g#y-axis' ) .call( this.yAxisFn ); - this.log( 'yAxis:', this.yAxis ); + //this.log( 'yAxis:', this.yAxis ); + //TODO: this isn't reliable with -/+ ranges - better to go thru each tick this.yLongestLabel = d3.max( _.map( [ this.yMin, this.yMax ], function( number ){ return ( String( number ) ).length; } ) ); this.log( 'yLongestLabel:', this.yLongestLabel ); @@ -219,7 +219,7 @@ //TODO: this isn't reliable with -/+ ranges - better to go thru each tick var neededY = this.yLongestLabel * GUESS_AT_SVG_CHAR_WIDTH + ( PADDING ); - // increase width for xLongerStr, increase margin for y + // increase width for yLongerStr, increase margin for y //TODO??: (or transform each number: 2k) if( this.config.yAxisLabelBumpX > -( neededY ) ){ this.config.yAxisLabelBumpX = -( neededY ); @@ -238,7 +238,7 @@ .attr( 'text-anchor', 'middle' ) .attr( 'transform', this.rotateStr( -90, this.config.yAxisLabelBumpX, this.config.height / 2 ) ) .text( this.config.yLabel ); - this.log( 'yAxisLabel:', this.yAxisLabel ); + //this.log( 'yAxisLabel:', this.yAxisLabel ); }; // ........................................................ grid lines @@ -261,7 +261,7 @@ // remove unneeded (less ticks) this.vGridLines.exit().remove(); - this.log( 'vGridLines:', this.vGridLines ); + //this.log( 'vGridLines:', this.vGridLines ); // HORIZONTAL this.hGridLines = this.content.selectAll( 'line.h-grid-line' ) @@ -277,7 +277,7 @@ .attr( 'y2', this.yScale ); this.hGridLines.exit().remove(); - this.log( 'hGridLines:', this.hGridLines ); + //this.log( 'hGridLines:', this.hGridLines ); }; // ........................................................ data points @@ -332,7 +332,7 @@ .style( "fill-opacity", 0 ) .remove(); - this.log( this.datapoints, 'glyphs rendered' ); + //this.log( this.datapoints, 'glyphs rendered' ); }; this.render = function( xCol, yCol ){ @@ -343,11 +343,11 @@ //TODO: ^^ isn't necessarily true with current ColumnDataProvider xCol = this.preprocessData( xCol ); yCol = this.preprocessData( yCol ); - this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); + //this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); //TODO: compute min, max on server. this.setUpDomains( xCol, yCol ); - this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); + //this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); this.setUpScales(); this.adjustChartDimensions(); @@ -367,9 +367,11 @@ * */ var ScatterplotView = BaseView.extend( LoggableMixin ).extend({ - //logger : console, + logger : console, tagName : 'form', - className : 'scatterplot-settings-form', + className : 'scatterplot-settings-form', + + loadingIndicatorImagePath : ( galaxy_paths.get( 'image_path' ) + '/loading_large_white_bg.gif' ), events : { 'click #render-button' : 'renderScatterplot' @@ -397,6 +399,7 @@ var view = this, html = '', columnHtml = ''; + // build column select controls for each x, y (based on name if available) // ugh...hafta preprocess this.dataset.metadata_column_types = this.dataset.metadata_column_types.split( ', ' ); @@ -408,10 +411,16 @@ if( view.dataset.metadata_column_names ){ name = view.dataset.metadata_column_names[ index ]; } - columnHtml += '<option value="' + index + '">' + name + '</column>'; + columnHtml += '<option value="' + index + '">' + name + '</option>'; } }); + // loading indicator - initially hidden + html += '<div id="loading-indicator" style="display: none;">'; + html += '<img class="loading-img" src=' + this.loadingIndicatorImagePath + ' />'; + html += '<span class="loading-message"></span>'; + html += '</div>'; + // column selector containers html += '<div id="x-column-input">'; html += '<label for="">Data column for X: </label><select name="x-column">' + columnHtml + '</select>'; @@ -430,6 +439,18 @@ this.$el.find( '#render-button' ); return this; }, + + showLoadingIndicator : function( message ){ + message = message || ''; + this.$el.find( 'div#loading-indicator' ).children( '.loading-message' ).text( message ); + this.$el.find( 'div#loading-indicator' ).show( 'fast' ); + console.debug( 'showing:', this.$el.find( 'div#loading-indicator' ), message ); + }, + + hideLoadingIndicator : function(){ + this.$el.find( 'div#loading-indicator' ).hide( 'fast' ); + console.debug( 'hiding:', this.$el.find( 'div#loading-indicator' ) ); + }, renderScatterplot : function(){ // parse the column values for both @@ -462,19 +483,23 @@ }); this.log( 'url:', url ); + this.showLoadingIndicator( 'Fetching data...' ); jQuery.ajax({ url : url, dataType : 'json', success : function( response ){ //TODO: server sends back an endpoint, cache for next pagination request + view.showLoadingIndicator( 'Rendering...' ); view.endpoint = response.endpoint; view.plot.render( // pull apart first two regardless of number of columns _.map( response.data, function( columns ){ return columns[0]; } ), _.map( response.data, function( columns ){ return columns[1]; } ) ); + view.hideLoadingIndicator(); }, error : function( xhr, status, error ){ + view.hideLoadingIndicator(); alert( 'ERROR:' + status + '\n' + error ); } }); diff -r 00681c35d987cde2200ff94c7f5510c594c904fd -r 80251cd7f94d64295ef6e64412f895d268ab988d templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -37,12 +37,14 @@ max-width: 256px; } -#chart-settings-form [value=Draw] { - float: right; +#chart-holder { + overflow: auto; } -#chart-holder { - overflow: auto; +#chart-settings-form #loading-indicator .loading-message { + margin-left: 16px; + font-style: italic; + color: grey; } svg .grid-line { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for viewing a tool shed repository README in a changeset revision older than the tip.
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/00681c35d987/ changeset: 00681c35d987 user: greg date: 2012-10-02 17:36:20 summary: Fix for viewing a tool shed repository README in a changeset revision older than the tip. affected #: 3 files diff -r fb35591b0273945610917c178255674bba0f9a21 -r 00681c35d987cde2200ff94c7f5510c594c904fd lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1043,15 +1043,6 @@ if name == config_file: return os.path.abspath( os.path.join( root, name ) ) return None -def get_config_from_repository( app, config_file, repository, changeset_revision, dir, install_dir=None ): - """Return config_filename if it exists in some changeset of the repository using only the repository and changeset_revision.""" - if install_dir is None: - install_dir = repository.repo_path( app ) - repo_files_dir = os.path.join( install_dir, repository.name ) - repo = hg.repository( get_configured_ui(), repo_files_dir ) - ctx = get_changectx_for_changeset( repo, changeset_revision ) - config = get_config( config_file, repo, ctx, dir ) - return config def get_configured_ui(): # Configure any desired ui settings. _ui = ui.ui() @@ -1140,6 +1131,13 @@ if deleted: return 'DELETED' return None +def get_file_from_changeset_revision( app, repository, repo_files_dir, changeset_revision, file_name, dir ): + """Return file_name from the received changeset_revision of the repository manifest.""" + stripped_file_name = strip_path( file_name ) + repo = hg.repository( get_configured_ui(), repo_files_dir ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) + named_tmp_file = get_named_tmpfile_from_ctx( ctx, file_name, dir ) + return named_tmp_file def get_list_of_copied_sample_files( repo, ctx, dir ): """ Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy diff -r fb35591b0273945610917c178255674bba0f9a21 -r 00681c35d987cde2200ff94c7f5510c594c904fd lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -624,10 +624,7 @@ status = 'error' else: tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) - try: - shutil.rmtree( work_dir ) - except: - pass + remove_dir( work_dir ) trans.app.config.tool_data_path = original_tool_data_path # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) @@ -685,6 +682,12 @@ return True # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table record is not needed. return False +def remove_dir( dir ): + if os.path.exists( dir ): + try: + shutil.rmtree( dir ) + except: + pass def reset_all_metadata_on_repository( trans, id, **kwd ): def reset_all_tool_versions( trans, id, repo ): changeset_revisions = [] @@ -799,11 +802,7 @@ changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None - if os.path.exists( work_dir ): - try: - shutil.rmtree( work_dir ) - except: - pass + remove_dir( work_dir ) # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. clean_repository_metadata( trans, id, changeset_revisions ) # Set tool version information for all downloadable changeset revisions. Get the list of changeset revisions from the changelog. diff -r fb35591b0273945610917c178255674bba0f9a21 -r 00681c35d987cde2200ff94c7f5510c594c904fd lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -9,8 +9,8 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * -from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents -from galaxy.util.shed_util import get_repository_metadata_by_changeset_revision, handle_sample_files_and_load_tool_from_disk +from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_file_from_changeset_revision +from galaxy.util.shed_util import get_repository_file_contents, get_repository_metadata_by_changeset_revision, handle_sample_files_and_load_tool_from_disk from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, INITIAL_CHANGELOG_HASH, load_tool_from_config, NOT_TOOL_CONFIGS from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path from galaxy.util.shed_util import to_html_escaped, translate_string, update_repository, url_join @@ -2184,9 +2184,32 @@ repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) metadata = repository_metadata.metadata if metadata and 'readme' in metadata: - f = open( metadata[ 'readme' ], 'r' ) - raw_text = f.read() - f.close() + readme_file = str( metadata[ 'readme' ] ) + repo_files_dir = repository.repo_path + try: + f = open( readme_file, 'r' ) + raw_text = f.read() + f.close() + except IOError: + work_dir = tempfile.mkdtemp() + try: + manifest_readme_file = get_file_from_changeset_revision( trans.app, + repository, + repo_files_dir, + changeset_revision, + readme_file, + work_dir ) + f = open( manifest_readme_file, 'r' ) + raw_text = f.read() + f.close() + remove_dir( work_dir ) + except Exception, e: + raw_text = "Error locating and reading this repository's README file '%s': %s" % ( readme_file, str( e ) ) + log.debug( raw_text ) + remove_dir( work_dir ) + except Exception, e: + raw_text = "Error locating and reading this repository's README file '%s': %s" % ( readme_file, str( e ) ) + log.debug( raw_text ) readme_text = translate_string( raw_text, to_html=True ) else: readme_text = '' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Circster: show more data when zoomed in.
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fb35591b0273/ changeset: fb35591b0273 user: jgoecks date: 2012-10-02 17:17:22 summary: Circster: show more data when zoomed in. affected #: 2 files diff -r 0445cd851094b8bad61d2a96f399538f74e5db03 -r fb35591b0273945610917c178255674bba0f9a21 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -30,8 +30,7 @@ /** * A label track. */ -// FIXME: merge with tracks.js LabelTrack -var LabelTrack = Backbone.Model.extend({ +var CircsterLabelTrack = Backbone.Model.extend({ defaults: { prefs: { color: '#ccc' @@ -51,6 +50,7 @@ this.dataset_arc_height = options.dataset_arc_height; this.track_gap = 5; this.label_arc_height = 20; + this.scale = 1; }, render: function() { @@ -63,7 +63,23 @@ init_radius_start = Math.min(width, height) / 2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) - (this.label_arc_height + this.track_gap), - tracks = this.model.get('tracks'); + tracks = this.model.get('tracks'), + + // Create a renderer for each track in the visualiation. + track_renderers = tracks.map(function(track, index) { + var radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), + track_renderer_class = (track.get('track_type') === 'LineTrack' ? + CircsterBigWigTrackRenderer : + CircsterSummaryTreeTrackRenderer ); + + return new track_renderer_class({ + track: track, + track_index: index, + radius_bounds: [radius_start, radius_start + dataset_arc_height], + genome: self.genome, + total_gap: self.total_gap + }); + }); // Set up SVG element. var svg = d3.select(self.$el[0]) @@ -74,78 +90,41 @@ // Set up zooming, dragging. .append('svg:g') .call(d3.behavior.zoom().on('zoom', function() { - // Do zoom. + // Do zoom, drag. + var scale = d3.event.scale; svg.attr("transform", "translate(" + d3.event.translate + ")" + - " scale(" + d3.event.scale + ")"); + " scale(" + scale + ")"); - // Update visible elements with more data. - var utils = new SVGUtils(), - tracks_and_chroms_to_update = {}; - - tracks.each(function(t) { - tracks_and_chroms_to_update[t.id] = []; - }); - - d3.selectAll('path.chrom-data').filter(function(d, i) { - return utils.is_visible(this, svg); - }).each(function(d, i) { - var elt_data = $.data(this, 'chrom_data'); - tracks_and_chroms_to_update[elt_data.track.id].push(elt_data.chrom); - }); - - /* - _.each(_.pairs(tracks_and_chroms_to_update), function(track_and_chroms) { - var track = tracks.get(track_and_chroms[0]) - chroms = track_and_chroms[1]; - - _.each(chroms, function(chr_name) { - var chr_region = self.genome.get_chrom_region(chr_name), - data_deferred = track.get('data_manager').get_more_detailed_data(chr_region, 'Coverage', 0, d3.event.scale); - - $.when(data_deferred).then(function(data) { - console.log("got more detailed data", data); - }) - }) - - - }); - - // TODO: update tracks and chroms. - console.log(tracks_and_chroms_to_update); - */ + // Propagate scale changes to renderers. + if (self.scale !== scale) { + // Use timeout to wait for zooming/dragging to stop before rendering more detail. + if (self.zoom_drag_timeout) { + clearTimeout(self.zoom_drag_timeout); + } + self.zoom_drag_timeout = setTimeout(function() { + // Render more detail in tracks' visible elements. + _.each(track_renderers, function(renderer) { + renderer.update_scale(scale); + }); + }, 400); + } })) .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") .append('svg:g'); // -- Render each dataset in the visualization. -- - tracks.each(function(track, index) { - var radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap), - track_renderer_class = (track.get('track_type') === 'LineTrack' ? - CircsterBigWigTrackRenderer : - CircsterSummaryTreeTrackRenderer ); - - var track_renderer = new track_renderer_class({ - track: track, - track_index: index, - radius_start: radius_start, - radius_end: radius_start + dataset_arc_height, - genome: self.genome, - total_gap: self.total_gap - }); - - track_renderer.render(svg); - + _.each(track_renderers, function(renderer) { + renderer.render(svg); }); // -- Render chromosome labels. -- var radius_start = init_radius_start + tracks.length * (dataset_arc_height + self.track_gap) + self.track_gap; var chrom_labels_track = new CircsterLabelTrackRenderer({ - track: new LabelTrack(), + track: new CircsterLabelTrack(), track_index: tracks.length, - radius_start: radius_start, - radius_end: radius_start, + radius_bounds: [radius_start, radius_start], genome: self.genome, total_gap: self.total_gap }); @@ -154,27 +133,38 @@ } }); -var CircsterTrackRenderer = Base.extend( { +/** + * Renders a track in a Circster visualization. + */ +var CircsterTrackRenderer = Base.extend({ + + /* ----------------------- Public Methods ------------------------- */ initialize: function(options) { this.options = options; this.options.bg_stroke = 'ccc'; this.options.bg_fill = 'ccc'; + this.options.chroms_layout = this._chroms_layout(); + this.options.data_bounds = this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome)); + this.options.scale = 1; + this.options.parent_elt = null; }, - render: function(svg) { + /** + * Render track's data by adding SVG elements to parent. + */ + render: function(parent) { // Create track group element. - var track_group_elt = svg.append("g").attr("id", "parent-" + this.options.track_index); + this.options.parent_elt = parent.append("g").attr("id", "parent-" + this.options.track_index); + var track_parent_elt = this.options.parent_elt; // Render background arcs. - var genome_arcs = this._chroms_layout(), - radius_start = this.options.radius_start, - radius_end = this.options.radius_end, + var genome_arcs = this.options.chroms_layout, arc_gen = d3.svg.arc() - .innerRadius(radius_start) - .outerRadius(radius_end), + .innerRadius(this.options.radius_bounds[0]) + .outerRadius(this.options.radius_bounds[1]), - chroms_elts = track_group_elt.selectAll('g') + chroms_elts = track_parent_elt.selectAll('g') .data(genome_arcs).enter().append('svg:g'); // Draw arcs. @@ -185,16 +175,112 @@ .append("title").text(function(d) { return d.data.chrom; }); // Render track data. - this.render_data(track_group_elt); + this._render_data(track_parent_elt); // Apply prefs. var prefs = this.options.track.get('prefs'), block_color = prefs.block_color; if (!block_color) { block_color = prefs.color; } - track_group_elt.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); + track_parent_elt.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); }, /** + * Update renderer scale. This fetches more data if scale is increased. + */ + update_scale: function(new_scale) { + // -- Update scale and return if new scale is less than old scale. -- + + var old_scale = this.options.scale; + this.options.scale = new_scale; + if (new_scale <= old_scale) { + return; + } + + // -- Scale increased, so render visible data with more detail. -- + + var self = this, + utils = new SVGUtils(); + + // Select all chrom data and filter to operate on those that are visible. + this.options.parent_elt.selectAll('path.chrom-data').filter(function(d, i) { + return utils.is_visible(this); + }).each(function(d, i) { + // Now operating on a single path element representing chromosome data. + var path_elt = d3.select(this), + chrom = path_elt.attr('chrom'), + chrom_region = self.options.genome.get_chrom_region(chrom), + + // Get more detailde data for chrom. + data_deferred = self.options.track.get('data_manager').get_more_detailed_data(chrom_region, 'Coverage', 0, new_scale); + + // When more data is available, use new data to redraw path. + $.when(data_deferred).then(function(data) { + // Remove current data path. + path_elt.remove(); + + // Update data bounds with new data. + self._update_data_bounds(); + + // Find chromosome arc to draw data on. + var chrom_arc = _.find(self.options.chroms_layout, function(layout) { + return layout.data.chrom === chrom; + }); + + // Add new data path and apply preferences. + var prefs = self.options.track.get('prefs'), + block_color = prefs.block_color; + if (!block_color) { block_color = prefs.color; } + self._render_chrom_data(self.options.parent_elt, chrom_arc, data).style('stroke', block_color).style('fill', block_color); + }); + }); + + return self; + }, + + /* ----------------------- Internal Methods ------------------------- */ + + /** + * Update data bounds. + */ + _update_data_bounds: function() { + this.options.data_bounds = this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome)); + + // TODO: transition all paths to use the new data bounds. + }, + + /** + * Render data as elements attached to svg. + */ + _render_data: function(svg) { + var self = this, + chrom_arcs = this.options.chroms_layout, + track = this.options.track, + genome_wide_data = track.get_genome_wide_data(this.options.genome), + + // Merge chroms layout with data. + layout_and_data = _.zip(chrom_arcs, genome_wide_data), + + // Render each chromosome's data. + chroms_data_layout = _.map(layout_and_data, function(chrom_info) { + var chrom_arc = chrom_info[0], + data = chrom_info[1]; + return self._render_chrom_data(svg, chrom_arc, data); + }); + + return svg; + }, + + /** + * Render a chromosome data and attach elements to svg. + */ + _render_chrom_data: function(svg, chrom_arc, data) {}, + + /** + * Returns data for creating a path for the given data using chrom_arc and data bounds. + */ + _compute_path_data: function(chrom_arc, data) {}, + + /** * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle * separated by gaps. */ @@ -211,42 +297,6 @@ return arc; }); return chrom_arcs; - }, - - /** - * Render chromosome data and attach elements to svg. - */ - render_chrom_data: function(svg, chrom_arc, data, inner_radius, outer_radius, max) { - }, - - /** - * Render data as elements attached to svg. - */ - render_data: function(svg) { - var self = this, - chrom_arcs = this._chroms_layout(), - track = this.options.track, - r_start = this.options.radius_start, - r_end = this.options.radius_end, - - genome_wide_data = track.get_genome_wide_data(this.options.genome), - - // Merge chroms layout with data. - layout_and_data = _.zip(chrom_arcs, genome_wide_data), - - // Get min, max in data. - bounds = this.get_bounds(genome_wide_data), - - // Do dataset layout for each chromosome's data using pie layout. - chroms_data_layout = _.map(layout_and_data, function(chrom_info) { - var chrom_arc = chrom_info[0], - data = chrom_info[1]; - return self.render_chrom_data(svg, chrom_arc, data, - r_start, r_end, - bounds.min, bounds.max); - }); - - return chroms_data_layout; } }); @@ -259,18 +309,19 @@ this.options = options; this.options.bg_stroke = 'fff'; this.options.bg_fill = 'fff'; + this.options.chroms_layout = this._chroms_layout(); }, /** * Render labels. */ - render_data: function(svg) { + _render_data: function(svg) { // Add chromosome label where it will fit; an alternative labeling mechanism // would be nice for small chromosomes. var chrom_arcs = svg.selectAll('g'); chrom_arcs.selectAll('path') - .attr('id', function(d) { return 'label-' + d.data.chrom; }) + .attr('id', function(d) { return 'label-' + d.data.chrom; }); chrom_arcs.append("svg:text") .filter(function(d) { @@ -295,46 +346,56 @@ * Renders quantitative data with the form [x, value] and assumes data is equally spaced across * chromosome. Attachs a dict with track and chrom name information to DOM element. */ - render_quantitative_data: function(svg, chrom_arc, data, inner_radius, outer_radius, min, max) { + _render_chrom_data: function(svg, chrom_arc, chrom_data) { + // If no chrom data, return null. + if (!chrom_data || typeof chrom_data === "string" || chrom_data.data.length === 0) { + return null; + } + + var path_data = this._compute_path_data(chrom_arc, chrom_data.data); + + // Render data. + var parent = svg.datum(chrom_data.data), + path = parent.append('path') + .attr('class', 'chrom-data') + .attr('chrom', chrom_arc.data.chrom) + .attr('d', path_data); + + return path; + }, + + /** + * Returns data for creating a path for the given data using chrom_arc, radius bounds, and data bounds. + */ + _compute_path_data: function(chrom_arc, data) { // Radius scaler. var radius = d3.scale.linear() - .domain([min, max]) - .range([inner_radius, outer_radius]); + .domain(this.options.data_bounds) + .range(this.options.radius_bounds); // Scaler for placing data points across arc. var angle = d3.scale.linear() .domain([0, data.length]) .range([chrom_arc.startAngle, chrom_arc.endAngle]); + // Use line generator to create area. var line = d3.svg.line.radial() .interpolate("linear") .radius(function(d) { return radius(d[1]); }) .angle(function(d, i) { return angle(i); }); - var area = d3.svg.area.radial() + return d3.svg.area.radial() .interpolate(line.interpolate()) .innerRadius(radius(0)) .outerRadius(line.radius()) .angle(line.angle()); - - // Render data. - var parent = svg.datum(data), - path = parent.append("path") - .attr("class", "chrom-data") - .attr("d", area); - - // Attach dict with track and chrom info for path. - $.data(path[0][0], "chrom_data", { - track: this.options.track, - chrom: chrom_arc.data.chrom - }); }, /** - * Returns an object with min, max attributes denoting the minimum and maximum + * Returns an array with two values denoting the minimum and maximum * values for the track. */ - get_bounds: function() {} + get_data_bounds: function(data) {} }); @@ -342,29 +403,14 @@ * Layout for summary tree data in a circster visualization. */ var CircsterSummaryTreeTrackRenderer = CircsterQuantitativeTrackRenderer.extend({ - - /** - * Renders a chromosome's data. - */ - render_chrom_data: function(svg, chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { - // If no chrom data, return null. - if (!chrom_data || typeof chrom_data === "string") { - return null; - } - return this.render_quantitative_data(svg, chrom_arc, chrom_data.data, inner_radius, outer_radius, min, max); - }, - - get_bounds: function(data) { + get_data_bounds: function(data) { // Get max across data. var max_data = _.map(data, function(d) { if (!d || typeof d === 'string') { return 0; } return d.max; }); - return { - min: 0, - max: (max_data && typeof max_data !== 'string' ? _.max(max_data) : 0) - }; + return [ 0, (max_data && typeof max_data !== 'string' ? _.max(max_data) : 0) ]; } }); @@ -372,18 +418,8 @@ * Layout for BigWig data in a circster visualization. */ var CircsterBigWigTrackRenderer = CircsterQuantitativeTrackRenderer.extend({ - - /** - * Renders a chromosome's data. - */ - render_chrom_data: function(svg, chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { - var data = chrom_data.data; - if (data.length === 0) { return; } - return this.render_quantitative_data(svg, chrom_arc, data, inner_radius, outer_radius, min, max); - }, - - get_bounds: function(data) { + get_data_bounds: function(data) { // Set max across dataset by extracting all values, flattening them into a // single array, and getting the min and max. var values = _.flatten( _.map(data, function(d) { @@ -398,13 +434,11 @@ } }) ); - return { - min: _.min(values), - max: _.max(values) - }; + return [ _.min(values), _.max(values) ]; } }); +// Module exports. return { CircsterView: CircsterView }; diff -r 0445cd851094b8bad61d2a96f399538f74e5db03 -r fb35591b0273945610917c178255674bba0f9a21 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -356,7 +356,7 @@ extra_params.num_samples = cur_data.data.length * detail_multiplier; } else if (cur_data.dataset_type === 'summary_tree') { - extra_params.level = cur_data.level + 1; + extra_params.level = Math.min(cur_data.level - 1, 2); } return this.load_data(region, mode, resolution, extra_params); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Import missing utility methods from the admin controller.
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0445cd851094/ changeset: 0445cd851094 user: inithello date: 2012-10-02 16:30:38 summary: Import missing utility methods from the admin controller. affected #: 1 file diff -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c -r 0445cd851094b8bad61d2a96f399538f74e5db03 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -11,6 +11,7 @@ from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH from galaxy.util.shed_util import load_tool_from_config, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path from galaxy.web.base.controller import * +from galaxy.web.base.controllers.admin import * from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.model.item_attrs import UsesItemRatings Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for tool shed features broken due to the elimination of the ability to use the webapp param.
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c3a9547df6f1/ changeset: c3a9547df6f1 user: greg date: 2012-10-02 15:47:06 summary: Fixes for tool shed features broken due to the elimination of the ability to use the webapp param. affected #: 33 files diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -138,8 +138,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='galaxy' ) + updating_installed_repository=False ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() @@ -260,7 +259,7 @@ tool_shed_repository, self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) # Get the tool_versions from the tool shed for each tool in the installed change set. - url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( tool_shed_url, tool_shed_repository.name, self.repository_owner, installed_changeset_revision ) response = urllib2.urlopen( url ) text = response.read() diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -30,7 +30,7 @@ tool_dependencies_dict = {} repository_name = elem.get( 'name' ) changeset_revision = elem.get( 'changeset_revision' ) - url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&webapp=install_manager' % \ + url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&from_install_manager=True' % \ ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision ) try: response = urllib2.urlopen( url ) diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/tool_shed/update_manager.py --- a/lib/galaxy/tool_shed/update_manager.py +++ b/lib/galaxy/tool_shed/update_manager.py @@ -34,7 +34,7 @@ log.info( 'Transfer job restarter shutting down...' ) def check_for_update( self, repository ): tool_shed_url = get_url_from_repository_tool_shed( self.app, repository ) - url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&webapp=update_manager' % \ + url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&from_update_manager=True' % \ ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision ) try: response = urllib2.urlopen( url ) diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -297,7 +297,7 @@ # tag for any tool in the repository. break return can_generate_dependency_metadata -def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files, webapp='galaxy' ): +def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files ): """ Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make sure the files exist. @@ -602,7 +602,7 @@ tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return tool_dependencies_dict def generate_metadata_for_changeset_revision( app, repository, repository_clone_url, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False, webapp='galaxy' ): + resetting_all_metadata_on_repository=False, updating_installed_repository=False ): """ Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's @@ -695,7 +695,7 @@ if not valid: invalid_file_tups.append( ( name, error_message ) ) else: - invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths, webapp=webapp ) + invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths ) can_set_metadata = True for tup in invalid_files_and_errors_tups: if name in tup: @@ -1115,7 +1115,7 @@ return manifest_ctx, ctx_file return None, None def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): - url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( name, owner, changeset_revision ) ) + url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) ) response = urllib2.urlopen( url ) ctx_rev = response.read() response.close() diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -69,7 +69,7 @@ columns = [ UserLoginColumn( "Email", key="email", - link=( lambda item: dict( operation="information", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="information", id=item.id ) ), attach_popup=True, filterable="advanced" ), UserNameColumn( "User Name", @@ -93,18 +93,18 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Create new user", - dict( controller='admin', action='users', operation='create', webapp="community" ) ) + dict( controller='admin', action='users', operation='create' ) ) ] operations = [ grids.GridOperation( "Manage Roles and Groups", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( webapp="community", action="manage_roles_and_groups_for_user" ) ), + url_args=dict( action="manage_roles_and_groups_for_user" ) ), grids.GridOperation( "Reset Password", condition=( lambda item: not item.deleted ), allow_multiple=True, allow_popup=False, - url_args=dict( webapp="community", action="reset_user_password" ) ) + url_args=dict( action="reset_user_password" ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), @@ -119,8 +119,7 @@ return trans.user class RoleListGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same - # in the galaxy webapp. + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, role ): return role.name @@ -156,7 +155,7 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="Manage users and groups", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Manage users and groups", id=item.id ) ), attach_popup=True, filterable="advanced" ), DescriptionColumn( "Description", @@ -183,24 +182,24 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Add new role", - dict( controller='admin', action='roles', operation='create', webapp="community" ) ) + dict( controller='admin', action='roles', operation='create' ) ) ] operations = [ grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( webapp="community", action="rename_role" ) ), + url_args=dict( action="rename_role" ) ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="mark_role_deleted" ) ), + url_args=dict( action="mark_role_deleted" ) ), grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="undelete_role" ) ), + url_args=dict( action="undelete_role" ) ), grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="purge_role" ) ) ] + url_args=dict( action="purge_role" ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), @@ -213,8 +212,7 @@ return query.filter( model.Role.type != model.Role.types.PRIVATE ) class GroupListGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same - # in the galaxy webapp. + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, group ): return group.name @@ -242,7 +240,7 @@ columns = [ NameColumn( "Name", #key="name", - link=( lambda item: dict( operation="Manage users and roles", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Manage users and roles", id=item.id ) ), attach_popup=True #filterable="advanced" ), @@ -262,24 +260,24 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Add new group", - dict( controller='admin', action='groups', operation='create', webapp="community" ) ) + dict( controller='admin', action='groups', operation='create' ) ) ] operations = [ grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( webapp="community", action="rename_group" ) ), + url_args=dict( action="rename_group" ) ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="mark_group_deleted" ) ), + url_args=dict( action="mark_group_deleted" ) ), grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="undelete_group" ) ), + url_args=dict( action="undelete_group" ) ), grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="purge_group" ) ) ] + url_args=dict( action="purge_group" ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), @@ -294,12 +292,12 @@ # Override the NameColumn to include an Edit link columns[ 0 ] = CategoryListGrid.NameColumn( "Name", key="Category.name", - link=( lambda item: dict( operation="Edit", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Edit", id=item.id ) ), model_class=model.Category, attach_popup=False ) global_actions = [ grids.GridAction( "Add new category", - dict( controller='admin', action='manage_categories', operation='create', webapp="community" ) ) + dict( controller='admin', action='manage_categories', operation='create' ) ) ] class AdminRepositoryListGrid( RepositoryListGrid ): @@ -377,9 +375,7 @@ NameColumn( "Name", key="name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository_revision", - id=item.id, - webapp="community" ) ), + link=( lambda item: dict( operation="view_or_manage_repository_revision", id=item.id ) ), attach_popup=True ), RevisionColumn( "Revision", attach_popup=False ), @@ -716,7 +712,6 @@ "repository" ) ) trans.response.send_redirect( web.url_for( controller='admin', action='browse_repository_metadata', - webapp='community', message=util.sanitize_text( message ), status=status ) ) else: diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -612,8 +612,7 @@ repo_files_dir, tool_config_filename, tool, - sample_files, - webapp='community' ) + sample_files ) if invalid_files_and_errors_tups: message2 = generate_message_for_invalid_tools( invalid_files_and_errors_tups, repository, @@ -753,8 +752,7 @@ relative_install_dir=repo_dir, repository_files_dir=work_dir, resetting_all_metadata_on_repository=True, - updating_installed_repository=False, - webapp='community' ) + updating_installed_repository=False ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: # We're at the first change set in the change log. @@ -829,8 +827,7 @@ relative_install_dir=repo_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='community' ) + updating_installed_repository=False ) if metadata_dict: downloadable = is_downloadable( metadata_dict ) repository_metadata = None diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -49,7 +49,7 @@ columns = [ NameColumn( "Name", key="Category.name", - link=( lambda item: dict( operation="repositories_by_category", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="repositories_by_category", id=item.id ) ), attach_popup=False ), DescriptionColumn( "Description", key="Category.description", @@ -87,7 +87,7 @@ columns = [ CategoryListGrid.NameColumn( "Name", key="Category.name", - link=( lambda item: dict( operation="valid_repositories_by_category", id=item.id, webapp="galaxy" ) ), + link=( lambda item: dict( operation="valid_repositories_by_category", id=item.id ) ), attach_popup=False ), CategoryListGrid.DescriptionColumn( "Description", key="Category.description", @@ -136,7 +136,7 @@ rval = '<ul>' if repository.categories: for rca in repository.categories: - rval += '<li><a href="browse_repositories?operation=repositories_by_category&id=%s&webapp=community">%s</a></li>' \ + rval += '<li><a href="browse_repositories?operation=repositories_by_category&id=%s">%s</a></li>' \ % ( trans.security.encode_id( rca.category.id ), rca.category.name ) else: rval += '<li>not set</li>' @@ -173,8 +173,7 @@ NameColumn( "Name", key="name", link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="community" ) ), + id=item.id ) ), attach_popup=True ), DescriptionColumn( "Synopsis", key="description", @@ -187,7 +186,7 @@ attach_popup=False ), UserColumn( "Owner", model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), attach_popup=False, key="User.username" ), grids.CommunityRatingColumn( "Average Rating", key="rating" ), @@ -231,15 +230,14 @@ RepositoryListGrid.NameColumn( "Name", key="name", link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="community" ) ), + id=item.id ) ), attach_popup=False ), RepositoryListGrid.DescriptionColumn( "Synopsis", key="description", attach_popup=False ), RepositoryListGrid.UserColumn( "Owner", model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), attach_popup=False, key="User.username" ), RepositoryListGrid.EmailAlertsColumn( "Alert", attach_popup=False ), @@ -254,7 +252,7 @@ condition=( lambda item: not item.deleted ), async_compatible=False ) ] global_actions = [ - grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository', webapp='community' ) ) + grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository' ) ) ] class WritableRepositoryListGrid( RepositoryListGrid ): @@ -285,7 +283,7 @@ rval = '<ul>' if repository.categories: for rca in repository.categories: - rval += '<li><a href="browse_repositories?operation=valid_repositories_by_category&id=%s&webapp=galaxy">%s</a></li>' \ + rval += '<li><a href="browse_repositories?operation=valid_repositories_by_category&id=%s">%s</a></li>' \ % ( trans.security.encode_id( rca.category.id ), rca.category.name ) else: rval += '<li>not set</li>' @@ -372,9 +370,7 @@ default_sort_key = "Repository.name" columns = [ NameColumn( "Repository name", - link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="community" ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), DescriptionColumn( "Synopsis", attach_popup=False ), @@ -414,9 +410,7 @@ columns = [ col for col in MatchedRepositoryListGrid.columns ] # Override the NameColumn columns[ 0 ] = MatchedRepositoryListGrid.NameColumn( "Name", - link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="galaxy" ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ) class RepositoryController( BaseUIController, ItemRatings ): @@ -481,7 +475,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) cntrller = params.get( 'cntrller', 'repository' ) is_admin = trans.user_is_admin() invalid_tools_dict = odict() @@ -514,15 +507,12 @@ return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako', cntrller=cntrller, invalid_tools_dict=invalid_tools_dict, - webapp=webapp, message=message, status=status ) @web.expose def browse_repositories( self, trans, **kwd ): # We add params to the keyword dict in this method in order to rename the param with an "f-" prefix, simulating filtering by clicking a search # link. We have to take this approach because the "-" character is illegal in HTTP requests. - if 'webapp' not in kwd: - kwd[ 'webapp' ] = get_webapp( trans, **kwd ) if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "view_or_manage_repository": @@ -606,7 +596,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) repository = get_repository( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) @@ -619,7 +608,6 @@ metadata=metadata, commit_message=commit_message, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) @web.expose @@ -631,7 +619,7 @@ if 'f-free-text-search' in kwd: if kwd[ 'f-free-text-search' ] == 'All': # The user performed a search, then clicked the "x" to eliminate the search criteria. - new_kwd = dict( webapp='galaxy' ) + new_kwd = {} return self.valid_category_list_grid( trans, **new_kwd ) # Since we are searching valid repositories and not categories, redirect to browse_valid_repositories(). if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]: @@ -656,7 +644,6 @@ return self.valid_category_list_grid( trans, **kwd ) @web.expose def browse_valid_repositories( self, trans, **kwd ): - webapp = get_webapp( trans, **kwd ) galaxy_url = kwd.get( 'galaxy_url', None ) if 'f-free-text-search' in kwd: if 'f-Category.name' in kwd: @@ -676,7 +663,6 @@ latest_installable_changeset_revision = repository_metadata.changeset_revision return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', - webapp=webapp, repository_id=repository_id, changeset_revision=latest_installable_changeset_revision ) ) elif operation == "valid_repositories_by_category": @@ -700,12 +686,10 @@ if repository.tip != v: return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', - webapp=webapp, repository_id=trans.security.encode_id( repository.id ), changeset_revision=v ) ) url_args = dict( action='browse_valid_repositories', operation='preview_tools_in_changeset', - webapp=webapp, repository_id=repository_id ) self.valid_repository_list_grid.operations = [ grids.GridOperation( "Preview and install", url_args=url_args, @@ -745,10 +729,7 @@ shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) @web.expose def check_for_updates( self, trans, **kwd ): - """ - Handle a request from a local Galaxy instance. If the request originated with the Galaxy instances' UpdateManager, the value of 'webapp' - will be 'update_manager'. - """ + """Handle a request from a local Galaxy instance.""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -757,14 +738,13 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - webapp = get_webapp( trans, **kwd ) repository = get_repository_by_name_and_owner( trans, name, owner ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) # Default to the current changeset revision. update_to_ctx = get_changectx_for_changeset( repo, changeset_revision ) latest_changeset_revision = changeset_revision - from_update_manager = webapp == 'update_manager' + from_update_manager = kwd.get( 'from_update_manager', False ) if from_update_manager: update = 'true' no_update = 'false' @@ -923,7 +903,6 @@ message = "Repository '%s' has been created." % repository.name trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', - webapp='community', message=message, id=trans.security.encode_id( repository.id ) ) ) return trans.fill_template( '/webapps/community/repository/create_repository.mako', @@ -939,7 +918,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository, tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) @@ -952,12 +930,11 @@ tool=tool, tool_state=tool_state, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) except Exception, e: message = "Error displaying tool, probably due to a problem in the tool config. The exception is: %s." % str( e ) - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=repository_id, @@ -996,7 +973,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) @@ -1012,7 +988,7 @@ repository = get_repository( trans, repository_id ) kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision - if webapp == 'community' and ( is_admin or repository.user == trans.user ): + if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ): a = 'manage_repository' else: a = 'view_repository' @@ -1048,16 +1024,16 @@ if ok: kwd[ 'match_tuples' ] = match_tuples # Render the list view - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': # Our initial request originated from a Galaxy instance. global_actions = [ grids.GridAction( "Browse valid repositories", - dict( controller='repository', action='browse_valid_categories', webapp=webapp ) ), + dict( controller='repository', action='browse_valid_categories' ) ), grids.GridAction( "Search for valid tools", - dict( controller='repository', action='find_tools', webapp=webapp ) ), + dict( controller='repository', action='find_tools' ) ), grids.GridAction( "Search for workflows", - dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] + dict( controller='repository', action='find_workflows' ) ) ] self.install_matched_repository_list_grid.global_actions = global_actions - install_url_args = dict( controller='repository', action='find_tools', webapp=webapp ) + install_url_args = dict( controller='repository', action='find_tools' ) operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] self.install_matched_repository_list_grid.operations = operations return self.install_matched_repository_list_grid( trans, **kwd ) @@ -1071,7 +1047,6 @@ status = "error" exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/community/repository/find_tools.mako', - webapp=webapp, tool_id=self.__stringify( tool_ids ), tool_name=self.__stringify( tool_names ), tool_version=self.__stringify( tool_versions ), @@ -1083,7 +1058,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) @@ -1099,7 +1073,7 @@ repository = get_repository( trans, repository_id ) kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision - if webapp == 'community' and ( is_admin or repository.user == trans.user ): + if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ): a = 'manage_repository' else: a = 'view_repository' @@ -1136,17 +1110,16 @@ ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=[], all_workflows=True ) if ok: kwd[ 'match_tuples' ] = match_tuples - # Render the list view - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': # Our initial request originated from a Galaxy instance. global_actions = [ grids.GridAction( "Browse valid repositories", - dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), + dict( controller='repository', action='browse_valid_repositories' ) ), grids.GridAction( "Search for valid tools", - dict( controller='repository', action='find_tools', webapp=webapp ) ), + dict( controller='repository', action='find_tools' ) ), grids.GridAction( "Search for workflows", - dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] + dict( controller='repository', action='find_workflows' ) ) ] self.install_matched_repository_list_grid.global_actions = global_actions - install_url_args = dict( controller='repository', action='find_workflows', webapp=webapp ) + install_url_args = dict( controller='repository', action='find_workflows' ) operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] self.install_matched_repository_list_grid.operations = operations return self.install_matched_repository_list_grid( trans, **kwd ) @@ -1163,7 +1136,6 @@ workflow_names = [] exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/community/repository/find_workflows.mako', - webapp=webapp, workflow_name=self.__stringify( workflow_names ), exact_matches_check_box=exact_matches_check_box, message=message, @@ -1234,8 +1206,7 @@ return '' @web.expose def get_tool_dependencies( self, trans, **kwd ): - # Handle a request from a local Galaxy instance. If the request originated with the Galaxy instances' InstallManager, the value of 'webapp' - # will be 'install_manager'. + """Handle a request from a local Galaxy instance.""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1244,14 +1215,14 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - webapp = get_webapp( trans, **kwd ) repository = get_repository_by_name_and_owner( trans, name, owner ) for downloadable_revision in repository.downloadable_revisions: if downloadable_revision.changeset_revision == changeset_revision: break metadata = downloadable_revision.metadata tool_dependencies = metadata.get( 'tool_dependencies', '' ) - if webapp == 'install_manager': + from_install_manager = kwd.get( 'from_install_manager', False ) + if from_install_manager: if tool_dependencies: return tool_shed_encode( tool_dependencies ) return '' @@ -1450,7 +1421,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'error' ) - webapp = get_webapp( trans, **kwd ) repository_clone_url = generate_clone_url( trans, repository_id ) repository, tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) @@ -1461,8 +1431,7 @@ repository.repo_path, tool_config, tool, - [], - webapp=webapp ) + [] ) if invalid_file_tups: message = generate_message_for_invalid_tools( invalid_file_tups, repository, {}, as_html=True, displaying_invalid_tool=True ) elif error_message: @@ -1474,12 +1443,11 @@ tool=tool, tool_state=tool_state, is_malicious=is_malicious, - webapp=webapp, message=message, status='error' ) except Exception, e: message = "Exception thrown attempting to display tool: %s." % str( e ) - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=repository_id, @@ -1535,7 +1503,6 @@ if user.email in repository.email_alerts: email_alert_repositories.append( repository ) return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako", - webapp='community', new_repo_alert_check_box=new_repo_alert_check_box, email_alert_repositories=email_alert_repositories, message=message, @@ -1573,7 +1540,6 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', id=id, - webapp='community', message=message, status='error' ) ) if description != repository.description: @@ -1713,8 +1679,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - if 'webapp' not in kwd: - kwd[ 'webapp' ] = 'community' if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "receive email alerts": @@ -1753,7 +1717,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository = get_repository( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) @@ -1776,7 +1739,6 @@ revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, metadata=metadata, - webapp=webapp, message=message, status=status ) @web.expose @@ -2218,7 +2180,6 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) cntrller = params.get( 'cntrller', 'repository' ) - webapp = params.get( 'webapp', 'community' ) repository = get_repository( trans, id ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) metadata = repository_metadata.metadata @@ -2236,7 +2197,6 @@ changeset_revision=changeset_revision, readme_text=readme_text, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) @web.expose @@ -2245,7 +2205,6 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) - webapp = get_webapp( trans, **kwd ) repo = hg.repository( get_configured_ui(), repository.repo_path ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) @@ -2307,7 +2266,6 @@ changeset_revision_select_field=changeset_revision_select_field, revision_label=revision_label, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) @web.expose @@ -2315,7 +2273,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository = get_repository( trans, repository_id ) repo_files_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_files_dir ) @@ -2376,7 +2333,6 @@ revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -19,7 +19,7 @@ class UploadController( BaseUIController ): @web.expose - @web.require_login( 'upload', use_panels=True, webapp='community' ) + @web.require_login( 'upload', use_panels=True ) def upload( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -161,7 +161,6 @@ action='browse_repository', id=repository_id, commit_message='Deleted selected files', - webapp='community', message=message, status=status ) ) else: diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -141,7 +141,6 @@ workflow_name = kwd.get( 'workflow_name', '' ) if workflow_name: workflow_name = tool_shed_decode( workflow_name ) - webapp = kwd.get( 'webapp', 'community' ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) @@ -152,11 +151,10 @@ repository_metadata_id=repository_metadata_id, workflow_name=workflow_name, metadata=repository_metadata, - webapp=webapp, message=message, status=status ) @web.expose - def generate_workflow_image( self, trans, repository_metadata_id, workflow_name, webapp='community' ): + def generate_workflow_image( self, trans, repository_metadata_id, workflow_name ): repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) repository_id = trans.security.encode_id( repository_metadata.repository_id ) changeset_revision = repository_metadata.changeset_revision @@ -388,7 +386,6 @@ workflow_name = kwd.get( 'workflow_name', '' ) if workflow_name: workflow_name = tool_shed_decode( workflow_name ) - webapp = kwd.get( 'webapp', 'community' ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) @@ -404,8 +401,8 @@ to_file.write( to_json_string( workflow_data ) ) return open( tmp_fname ) galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - url = '%sworkflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \ - ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, tool_shed_encode( workflow_name ), webapp ) + url = '%sworkflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s' % \ + ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, tool_shed_encode( workflow_name ) ) return trans.response.send_redirect( url ) return trans.response.send_redirect( web.url_for( controller='workflow', action='view_workflow', diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -65,7 +65,7 @@ key="name", link=( lambda item: iff( item.status in [ model.ToolShedRepository.installation_status.CLONING ], None, - dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ) ), + dict( operation="manage_repository", id=item.id ) ) ), attach_popup=True ), DescriptionColumn( "Description" ), OwnerColumn( "Owner" ), @@ -410,7 +410,7 @@ def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s&webapp=galaxy' % ( galaxy_url ) ) + url = url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s' % ( galaxy_url ) ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -419,7 +419,6 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako', - webapp='galaxy', message=message, status='error' ) @web.expose @@ -429,7 +428,7 @@ repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) url = url_join( tool_shed_url, - 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ ( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) return trans.response.send_redirect( url ) @web.expose @@ -507,14 +506,14 @@ def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s&webapp=galaxy' % galaxy_url ) + url = url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s' % galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin def find_workflows_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s&webapp=galaxy' % galaxy_url ) + url = url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url ) return trans.response.send_redirect( url ) def generate_tool_path( self, repository_clone_url, changeset_revision ): """ @@ -676,7 +675,7 @@ trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) url = url_join( tool_shed_url, - '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() @@ -731,8 +730,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='galaxy' ) + updating_installed_repository=False ) tool_shed_repository.metadata = metadata_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() @@ -806,7 +804,7 @@ # Send a request to the tool shed to install the repository. tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) url = url_join( tool_shed_url, - 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s&webapp=galaxy' % \ + 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \ ( repository.name, repository.owner, repository.installed_changeset_revision, @@ -1030,7 +1028,7 @@ changeset_revisions = kwd.get( 'changeset_revisions', None ) # Get the information necessary to install each repository. url = url_join( tool_shed_url, - 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s&webapp=galaxy' % \ + 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s' % \ ( repository_ids, changeset_revisions ) ) response = urllib2.urlopen( url ) raw_text = response.read() @@ -1175,7 +1173,7 @@ repo_info_tuple = repo_info_dict[ name ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple url = url_join( tool_shed_url, - 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s' % \ ( name, repository_owner, changeset_revision ) ) response = urllib2.urlopen( url ) raw_text = response.read() @@ -1350,7 +1348,7 @@ # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset # revision to see if it was previously installed using one of them. url = url_join( tool_shed_url, - 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ ( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() @@ -1413,7 +1411,7 @@ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=True ) if metadata and 'readme' in metadata: url = url_join( tool_shed_url, - 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s' % \ ( repository.name, repository.owner, repository.installed_changeset_revision ) ) response = urllib2.urlopen( url ) raw_text = response.read() @@ -1448,8 +1446,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='galaxy' ) + updating_installed_repository=False ) repository.metadata = metadata_dict trans.sa_session.add( repository ) trans.sa_session.flush() @@ -1506,7 +1503,7 @@ repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) url = url_join( tool_shed_url, - 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( repository.name, repository.owner, repository.changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() @@ -1625,8 +1622,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - webapp='galaxy' ) + updating_installed_repository=True ) repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision @@ -1676,7 +1672,6 @@ changeset_revision=repository.changeset_revision, readme_text=readme_text, is_malicious=is_malicious, - webapp='galaxy', message=message, status=status ) @web.expose @@ -1685,7 +1680,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository = get_repository( trans, repository_id ) repository_metadata = repository.metadata tool_metadata = {} diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1026,7 +1026,6 @@ """ url = kwd.get( 'url', '' ) workflow_text = kwd.get( 'workflow_text', '' ) - webapp = get_webapp( trans, **kwd ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) import_button = kwd.get( 'import_button', False ) @@ -1056,8 +1055,8 @@ import_button = True if tool_shed_url and not import_button: # Use urllib (send another request to the tool shed) to retrieve the workflow. - workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \ - ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp ) + workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&open_for_url=true' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ) ) response = urllib2.urlopen( workflow_url ) workflow_text = response.read() response.close() @@ -1137,7 +1136,7 @@ for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): if shed_url.endswith( '/' ): shed_url = shed_url.rstrip( '/' ) - url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, url_for( '/', qualified=True ), webapp ) + url = '%s/repository/find_tools?galaxy_url=%s' % ( shed_url, url_for( '/', qualified=True ) ) if missing_tool_tups: url += '&tool_id=' for missing_tool_tup in missing_tool_tups: @@ -1155,7 +1154,6 @@ action = 'index' return trans.response.send_redirect( web.url_for( controller='admin', action=action, - webapp='galaxy', message=message, status=status ) ) else: @@ -1164,8 +1162,8 @@ if tool_shed_url: # We've received the textual representation of a workflow from a Galaxy tool shed. message = "Workflow <b>%s</b> imported successfully." % workflow.name - url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ - ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message ) + url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&message=%s' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), message ) return trans.response.send_redirect( url ) elif installed_repository_file: # The workflow was read from a file included with an installed tool shed repository. diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -48,19 +48,19 @@ <div class="toolSectionBody"><div class="toolSectionBg"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories', webapp='community' )}">Browse all repositories</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories' )}">Browse all repositories</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories', webapp='community' )}">Reset selected metadata</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories' )}">Reset selected metadata</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata', webapp='community' )}">Browse metadata</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata' )}">Browse metadata</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='admin', webapp='community' )}">Browse invalid tools</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='admin' )}">Browse invalid tools</a></div></div></div> @@ -70,7 +70,7 @@ <div class="toolSectionBody"><div class="toolSectionBg"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories', webapp='community' )}">Manage categories</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories' )}">Manage categories</a></div></div></div> @@ -81,13 +81,13 @@ <div class="toolSectionBody"><div class="toolSectionBg"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='users', webapp='community' )}">Manage users</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='users' )}">Manage users</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='groups', webapp='community' )}">Manage groups</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='groups' )}">Manage groups</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='roles', webapp='community' )}">Manage roles</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='roles' )}">Manage roles</a></div></div></div> @@ -95,7 +95,7 @@ Statistics </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='regenerate_statistics', webapp='community' )}">View shed statistics</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='regenerate_statistics' )}">View shed statistics</a></div></div></div> @@ -104,7 +104,7 @@ <%def name="center_panel()"><% - center_url = h.url_for( action='center', webapp='community' ) + center_url = h.url_for( action='center' ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/admin/statistics.mako --- a/templates/webapps/community/admin/statistics.mako +++ b/templates/webapps/community/admin/statistics.mako @@ -7,7 +7,7 @@ <div class="toolForm"><div class="toolFormTitle">Tool shed statistics generated on ${trans.app.shed_counter.generation_time}</div> - <form name="regenerate_statistics" id="regenerate_statistics" action="${h.url_for( controller='admin', action='regenerate_statistics', webapp='community' )}" method="post" > + <form name="regenerate_statistics" id="regenerate_statistics" action="${h.url_for( controller='admin', action='regenerate_statistics' )}" method="post" ><div class="form-row"><table class="grid"><tr> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -64,10 +64,10 @@ </%def> ## Repositories tab. - ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index', webapp='community' ) )} + ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index' ) )} ## Admin tab. - ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index', webapp='community' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} + ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} ## Help tab. <% @@ -85,9 +85,9 @@ ## User tabs. <% # Menu for user who is not logged in. - menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login', webapp='community' ), "galaxy_main" ] ] + menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] if app.config.allow_user_creation: - menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user', webapp='community' ), "galaxy_main" ] ) + menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) extra_class = "loggedout-only" visible = ( trans.user == None ) tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) @@ -101,12 +101,12 @@ if app.config.remote_user_logout_href: menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) else: - menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='community' ), "galaxy_main" ] ) - logout_url = h.url_for( controller='/user', action='logout', webapp='community' ) + menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) + logout_url = h.url_for( controller='/user', action='logout' ) menu_options.append( [ 'Logout', logout_url, "_top" ] ) menu_options.append( None ) if app.config.use_remote_user: - menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='community' ), "galaxy_main" ] ) + menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] ) extra_class = "loggedin-only" visible = ( trans.user != None ) diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/common/view_readme.mako --- a/templates/webapps/community/common/view_readme.mako +++ b/templates/webapps/community/common/view_readme.mako @@ -3,7 +3,7 @@ <%namespace file="/webapps/community/common/common.mako" import="render_readme" /><% - if webapp == 'community': + if trans.webapp.name == 'community': is_admin = trans.user_is_admin() is_new = repository.is_new can_contact_owner = trans.user and trans.user != repository.user @@ -22,43 +22,43 @@ <br/><br/><ul class="manage-table-actions"> - %if webapp == 'community': + %if trans.webapp.name == 'community': <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: - <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">Rate repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz', webapp=webapp )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2', webapp=webapp )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip', webapp=webapp )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> %endif </div> %else: %if cntrller=='repository': - <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', operation='preview_tools_in_changeset', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Preview tools for install</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', operation='preview_tools_in_changeset', id=trans.security.encode_id( repository.id ) )}">Preview tools for install</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -50,10 +50,10 @@ </div><div class="toolSectionBody"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for valid tools</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows', webapp='community' )}">Search for workflows</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div></div> %endif @@ -62,7 +62,7 @@ All Repositories </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a></div> %if trans.user: <div class="toolSectionPad"></div> @@ -70,20 +70,20 @@ My Repositories and Tools </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='repositories_i_own', webapp='community' )}">Repositories I own</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='repositories_i_own' )}">Repositories I own</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='writable_repositories', webapp='community' )}">My writable repositories</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='writable_repositories' )}">My writable repositories</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository', webapp='community' )}">My invalid tools</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository' )}">My invalid tools</a></div><div class="toolSectionPad"></div><div class="toolSectionTitle"> Available Actions </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository', webapp='community' )}">Create new repository</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository' )}">Create new repository</a></div> %else: <div class="toolSectionPad"></div> @@ -91,7 +91,7 @@ Available Actions </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='/user', action='login', webapp='community' )}">Login to create a repository</a> + <a target="galaxy_main" href="${h.url_for( controller='/user', action='login' )}">Login to create a repository</a></div> %endif </div> @@ -102,9 +102,9 @@ <%def name="center_panel()"><% if trans.app.config.require_login and not trans.user: - center_url = h.url_for( controller='user', action='login', message=message, status=status, webapp='community' ) + center_url = h.url_for( controller='user', action='login', message=message, status=status ) else: - center_url = h.url_for( controller='repository', action='browse_categories', message=message, status=status, webapp='community' ) + center_url = h.url_for( controller='repository', action='browse_categories', message=message, status=status ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/browse_invalid_tools.mako --- a/templates/webapps/community/repository/browse_invalid_tools.mako +++ b/templates/webapps/community/repository/browse_invalid_tools.mako @@ -20,7 +20,7 @@ <% repository_id, repository_name, repository_owner, changeset_revision = repository_tup %><tr><td> - <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision )}"> ${invalid_tool_config} </a></td> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/browse_repository.mako --- a/templates/webapps/community/repository/browse_repository.mako +++ b/templates/webapps/community/repository/browse_repository.mako @@ -65,23 +65,23 @@ <br/><br/><ul class="manage-table-actions"> %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -83,7 +83,7 @@ hg clone <a href="${clone_str}">${clone_str}</a></%def> -<%def name="render_repository_items( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )"> +<%def name="render_repository_items( repository_metadata_id, metadata, can_set_metadata=False )"><% from galaxy.tool_shed.encoding_util import tool_shed_encode %> %if metadata or can_set_metadata: <p/> @@ -184,10 +184,10 @@ <tr><td><div style="float:left;" class="menubutton split popup" id="tool-${index}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">${tool_dict[ 'name' ]}</a> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision )}">${tool_dict[ 'name' ]}</a></div><div popupmenu="tool-${index}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ], webapp=webapp )}">View tool metadata</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View tool metadata</a></div></td><td>${tool_dict[ 'description' ]}</td> @@ -232,7 +232,7 @@ %for invalid_tool_config in invalid_tool_configs: <tr><td> - <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision )}"> ${invalid_tool_config} </a></td> @@ -274,7 +274,7 @@ %><tr><td> - <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp )}">${workflow_name}</a> + <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) )}">${workflow_name}</a></td><td> %if steps: diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/contact_owner.mako --- a/templates/webapps/community/repository/contact_owner.mako +++ b/templates/webapps/community/repository/contact_owner.mako @@ -31,26 +31,26 @@ <br/><br/><ul class="manage-table-actions"> %if is_new and can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/find_tools.mako --- a/templates/webapps/community/repository/find_tools.mako +++ b/templates/webapps/community/repository/find_tools.mako @@ -10,11 +10,11 @@ %><%inherit file="${inherit(context)}"/> -%if webapp == 'galaxy': +%if trans.webapp.name == 'galaxy': <br/><br/><ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></li></ul> %endif @@ -32,7 +32,7 @@ strings if these types of search strings are entered in more than one field. </div><div style="clear: both"></div> - <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}" method="post" > + <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools' )}" method="post" ><div class="form-row"><label>Tool id:</label><input name="tool_id" type="textfield" value="${tool_id}" size="40"/> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/find_workflows.mako --- a/templates/webapps/community/repository/find_workflows.mako +++ b/templates/webapps/community/repository/find_workflows.mako @@ -10,11 +10,11 @@ %><%inherit file="${inherit(context)}"/> -%if webapp == 'galaxy': +%if trans.webapp.name == 'galaxy': <br/><br/><ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a></li> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a></li> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a></ul> %endif @@ -30,7 +30,7 @@ Comma-separated strings may be entered to expand search criteria. </div><div style="clear: both"></div> - <form name="find_workflows" id="find_workflows" action="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}" method="post" > + <form name="find_workflows" id="find_workflows" action="${h.url_for( controller='repository', action='find_workflows' )}" method="post" ><div style="clear: both"></div><div class="form-row"><label>Workflow name:</label> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -42,30 +42,30 @@ <br/><br/><ul class="manage-table-actions"> %if is_new and can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_reset_all_metadata: - <a class="action-button" href="${h.url_for( controller='repository', action='reset_all_metadata', id=trans.security.encode_id( repository.id ), webapp='community' )}">Reset all repository metadata</a> + <a class="action-button" href="${h.url_for( controller='repository', action='reset_all_metadata', id=trans.security.encode_id( repository.id ) )}">Reset all repository metadata</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> @@ -276,7 +276,7 @@ <div class="toolFormBody"> %if display_reviews: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False, webapp='community' )}"><label>Hide Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a></div><table class="grid"><thead> @@ -303,7 +303,7 @@ </table> %else: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True, webapp='community' )}"><label>Display Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a></div> %endif </div> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -36,15 +36,15 @@ <br/><br/><ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div></ul> @@ -79,4 +79,4 @@ </div></div><p/> -${render_repository_items( repository_metadata_id, metadata, webapp=webapp )} +${render_repository_items( repository_metadata_id, metadata )} diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/rate_repository.mako --- a/templates/webapps/community/repository/rate_repository.mako +++ b/templates/webapps/community/repository/rate_repository.mako @@ -72,29 +72,29 @@ <br/><br/><ul class="manage-table-actions"> %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -121,46 +121,46 @@ <br/><br/><ul class="manage-table-actions"> - %if webapp == 'galaxy': + %if trans.webapp.name == 'galaxy': <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Browse repository</a></li></div><li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="tool_shed-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %else: %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -50,13 +50,13 @@ %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">Browse or delete repository files</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> %endif </div></ul> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_changelog.mako --- a/templates/webapps/community/repository/view_changelog.mako +++ b/templates/webapps/community/repository/view_changelog.mako @@ -45,24 +45,24 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_changeset.mako --- a/templates/webapps/community/repository/view_changeset.mako +++ b/templates/webapps/community/repository/view_changeset.mako @@ -46,27 +46,27 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -11,8 +11,8 @@ can_rate = not is_new and trans.user and repository.user != trans.user can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) - can_browse_contents = webapp == 'community' and not is_new - can_view_change_log = webapp == 'community' and not is_new + can_browse_contents = trans.webapp.name == 'community' and not is_new + can_view_change_log = trans.webapp.name == 'community' and not is_new if can_push: browse_label = 'Browse or delete repository tip files' else: @@ -37,44 +37,44 @@ <br/><br/><ul class="manage-table-actions"> - %if webapp == 'community': + %if trans.webapp.name == 'community': %if is_new and can_upload: - <li><a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a></li> + <li><a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a></li> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: - <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">Rate repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz', webapp=webapp )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2', webapp=webapp )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip', webapp=webapp )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif %else: - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %endif </ul> @@ -87,7 +87,7 @@ <div class="toolForm"><div class="toolFormTitle">Repository revision</div><div class="toolFormBody"> - <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), webapp=webapp )}" method="post" > + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"><% if changeset_revision == repository.tip: @@ -117,7 +117,7 @@ <div class="form-row"><label>Name:</label> %if can_browse_contents: - <a href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${repository.name}</a> + <a href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${repository.name}</a> %else: ${repository.name} %endif @@ -132,7 +132,7 @@ <div class="form-row"><label>Revision:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${revision_label}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> %else: ${revision_label} %endif @@ -157,7 +157,7 @@ %endif </div></div> -${render_repository_items( repository_metadata_id, metadata, webapp=webapp )} +${render_repository_items( repository_metadata_id, metadata )} %if repository.categories: <p/><div class="toolForm"> @@ -172,12 +172,12 @@ </div></div> %endif -%if webapp == 'community' and trans.user and trans.app.config.smtp_server: +%if trans.webapp.name == 'community' and trans.user and trans.app.config.smtp_server: <p/><div class="toolForm"><div class="toolFormTitle">Notification on update</div><div class="toolFormBody"> - <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), webapp=webapp )}" method="post" > + <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"><label>Receive email alerts:</label> ${alerts_check_box.get_html()} @@ -214,7 +214,7 @@ <div class="toolFormBody"> %if display_reviews: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False, webapp=webapp )}"><label>Hide Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a></div><table class="grid"><thead> @@ -241,7 +241,7 @@ </table> %else: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True, webapp=webapp )}"><label>Display Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a></div> %endif </div> diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -12,10 +12,10 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) - can_browse_contents = webapp == 'community' and not is_new + can_browse_contents = trans.webapp.name == 'community' and not is_new can_rate = repository.user != trans.user can_manage = is_admin or repository.user == trans.user - can_view_change_log = webapp == 'community' and not is_new + can_view_change_log = trans.webapp.name == 'community' and not is_new if can_push: browse_label = 'Browse or delete repository tip files' else: @@ -34,43 +34,43 @@ <br/><br/><ul class="manage-table-actions"> - %if webapp == 'galaxy': + %if trans.webapp.name == 'galaxy': <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Browse repository</a></li></div><li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="tool_shed-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %else: %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> @@ -126,7 +126,7 @@ </div><div class="form-row"><label>Name:</label> - <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_metadata_dict[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">${tool_metadata_dict[ 'name' ]}</a> + <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_metadata_dict[ 'tool_config' ], changeset_revision=changeset_revision )}">${tool_metadata_dict[ 'name' ]}</a><div style="clear: both"></div></div> %if 'description' in tool_metadata_dict: diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_workflow.mako --- a/templates/webapps/community/repository/view_workflow.mako +++ b/templates/webapps/community/repository/view_workflow.mako @@ -7,7 +7,7 @@ from galaxy.web.framework.helpers import time_ago from galaxy.tool_shed.encoding_util import tool_shed_encode - in_tool_shed = webapp == 'community' + in_tool_shed = trans.webapp.name == 'community' is_admin = trans.user_is_admin() is_new = repository.is_new can_manage = is_admin or trans.user == repository.user @@ -34,8 +34,8 @@ %><%inherit file="${inherit(context)}"/> -<%def name="render_workflow( repository_metadata_id, workflow_name, webapp )"> - <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp ) %> +<%def name="render_workflow( repository_metadata_id, workflow_name )"> + <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> @@ -43,32 +43,32 @@ <ul class="manage-table-actions"> %if in_tool_shed: %if is_new and can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> @@ -80,14 +80,14 @@ %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp )}">Import workflow to local Galaxy</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install repository to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) )}">Import workflow to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install repository to local Galaxy</a></li></div><li><a class="action-button" id="toolshed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="toolshed-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %endif </ul> @@ -105,4 +105,4 @@ </div><br clear="left"/> -${render_workflow( repository_metadata_id, workflow_name, webapp )} +${render_workflow( repository_metadata_id, workflow_name )} diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/user/manage_email_alerts.mako --- a/templates/webapps/community/user/manage_email_alerts.mako +++ b/templates/webapps/community/user/manage_email_alerts.mako @@ -4,10 +4,10 @@ <br/><br/><ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='repository', action='multi_select_email_alerts', cntrller='repository', webapp=webapp )}">Manage repository alerts</a> + <a class="action-button" href="${h.url_for( controller='repository', action='multi_select_email_alerts', cntrller='repository' )}">Manage repository alerts</a></li><li> - <a class="action-button" href="${h.url_for( controller='user', action='index', cntrller='repository', webapp=webapp )}">User preferences</a> + <a class="action-button" href="${h.url_for( controller='user', action='index', cntrller='repository' )}">User preferences</a></li></ul> @@ -17,7 +17,7 @@ <div class="toolForm"><div class="toolFormTitle">Email alerts for new repositories</div> - <form name="new_repo_alert" id="new_repo_alert" action="${h.url_for( controller='repository', action='manage_email_alerts', webapp=webapp )}" method="post" > + <form name="new_repo_alert" id="new_repo_alert" action="${h.url_for( controller='repository', action='manage_email_alerts' )}" method="post" ><div class="form-row"><label>New repository alert:</label> ${new_repo_alert_check_box.get_html()} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fix some UI framework issues.
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4bdb9214efd6/ changeset: 4bdb9214efd6 user: jgoecks date: 2012-10-02 04:53:21 summary: Fix some UI framework issues. affected #: 3 files diff -r 55e7d7008efee2c5622f2505612265a9593ae992 -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 static/scripts/libs/underscore.js --- a/static/scripts/libs/underscore.js +++ b/static/scripts/libs/underscore.js @@ -1,7 +1,10 @@ -// Underscore.js 1.4.0 -// http://underscorejs.org +// Underscore.js 1.3.1 // (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc. -// Underscore may be freely distributed under the MIT license. +// Underscore is freely distributable under the MIT license. +// Portions of Underscore are inspired or borrowed from Prototype, +// Oliver Steele's Functional, and John Resig's Micro-Templating. +// For all details and documentation: +// http://documentcloud.github.com/underscore (function() { @@ -21,9 +24,7 @@ var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype; // Create quick reference variables for speed access to core prototypes. - var push = ArrayProto.push, - slice = ArrayProto.slice, - concat = ArrayProto.concat, + var slice = ArrayProto.slice, unshift = ArrayProto.unshift, toString = ObjProto.toString, hasOwnProperty = ObjProto.hasOwnProperty; @@ -45,11 +46,7 @@ nativeBind = FuncProto.bind; // Create a safe reference to the Underscore object for use below. - var _ = function(obj) { - if (obj instanceof _) return obj; - if (!(this instanceof _)) return new _(obj); - this._wrapped = obj; - }; + var _ = function(obj) { return new wrapper(obj); }; // Export the Underscore object for **Node.js**, with // backwards-compatibility for the old `require()` API. If we're in @@ -65,7 +62,7 @@ } // Current version. - _.VERSION = '1.4.0'; + _.VERSION = '1.3.1'; // Collection Functions // -------------------- @@ -74,11 +71,12 @@ // Handles objects with the built-in `forEach`, arrays, and raw objects. // Delegates to **ECMAScript 5**'s native `forEach` if available. var each = _.each = _.forEach = function(obj, iterator, context) { + if (obj == null) return; if (nativeForEach && obj.forEach === nativeForEach) { obj.forEach(iterator, context); } else if (obj.length === +obj.length) { for (var i = 0, l = obj.length; i < l; i++) { - if (iterator.call(context, obj[i], i, obj) === breaker) return; + if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return; } } else { for (var key in obj) { @@ -93,10 +91,12 @@ // Delegates to **ECMAScript 5**'s native `map` if available. _.map = _.collect = function(obj, iterator, context) { var results = []; + if (obj == null) return results; if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context); each(obj, function(value, index, list) { results[results.length] = iterator.call(context, value, index, list); }); + if (obj.length === +obj.length) results.length = obj.length; return results; }; @@ -104,6 +104,7 @@ // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available. _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) { var initial = arguments.length > 2; + if (obj == null) obj = []; if (nativeReduce && obj.reduce === nativeReduce) { if (context) iterator = _.bind(iterator, context); return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator); @@ -124,26 +125,14 @@ // Delegates to **ECMAScript 5**'s native `reduceRight` if available. _.reduceRight = _.foldr = function(obj, iterator, memo, context) { var initial = arguments.length > 2; + if (obj == null) obj = []; if (nativeReduceRight && obj.reduceRight === nativeReduceRight) { if (context) iterator = _.bind(iterator, context); - return arguments.length > 2 ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator); + return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator); } - var length = obj.length; - if (length !== +length) { - var keys = _.keys(obj); - length = keys.length; - } - each(obj, function(value, index, list) { - index = keys ? keys[--length] : --length; - if (!initial) { - memo = obj[index]; - initial = true; - } else { - memo = iterator.call(context, memo, obj[index], index, list); - } - }); - if (!initial) throw new TypeError('Reduce of empty array with no initial value'); - return memo; + var reversed = _.toArray(obj).reverse(); + if (context && !initial) iterator = _.bind(iterator, context); + return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator); }; // Return the first value which passes a truth test. Aliased as `detect`. @@ -163,6 +152,7 @@ // Aliased as `select`. _.filter = _.select = function(obj, iterator, context) { var results = []; + if (obj == null) return results; if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context); each(obj, function(value, index, list) { if (iterator.call(context, value, index, list)) results[results.length] = value; @@ -173,6 +163,7 @@ // Return all the elements for which a truth test fails. _.reject = function(obj, iterator, context) { var results = []; + if (obj == null) return results; each(obj, function(value, index, list) { if (!iterator.call(context, value, index, list)) results[results.length] = value; }); @@ -183,13 +174,13 @@ // Delegates to **ECMAScript 5**'s native `every` if available. // Aliased as `all`. _.every = _.all = function(obj, iterator, context) { - iterator || (iterator = _.identity); var result = true; + if (obj == null) return result; if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context); each(obj, function(value, index, list) { if (!(result = result && iterator.call(context, value, index, list))) return breaker; }); - return !!result; + return result; }; // Determine if at least one element in the object matches a truth test. @@ -198,6 +189,7 @@ var any = _.some = _.any = function(obj, iterator, context) { iterator || (iterator = _.identity); var result = false; + if (obj == null) return result; if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context); each(obj, function(value, index, list) { if (result || (result = iterator.call(context, value, index, list))) return breaker; @@ -205,10 +197,11 @@ return !!result; }; - // Determine if the array or object contains a given value (using `===`). - // Aliased as `include`. - _.contains = _.include = function(obj, target) { + // Determine if a given value is included in the array or object using `===`. + // Aliased as `contains`. + _.include = _.contains = function(obj, target) { var found = false; + if (obj == null) return found; if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1; found = any(obj, function(value) { return value === target; @@ -220,7 +213,7 @@ _.invoke = function(obj, method) { var args = slice.call(arguments, 2); return _.map(obj, function(value) { - return (_.isFunction(method) ? method : value[method]).apply(value, args); + return (_.isFunction(method) ? method || value : value[method]).apply(value, args); }); }; @@ -229,25 +222,9 @@ return _.map(obj, function(value){ return value[key]; }); }; - // Convenience version of a common use case of `filter`: selecting only objects - // with specific `key:value` pairs. - _.where = function(obj, attrs) { - if (_.isEmpty(attrs)) return []; - return _.filter(obj, function(value) { - for (var key in attrs) { - if (attrs[key] !== value[key]) return false; - } - return true; - }); - }; - // Return the maximum element or (element-based computation). - // Can't optimize arrays of integers longer than 65,535 elements. - // See: https://bugs.webkit.org/show_bug.cgi?id=80797 _.max = function(obj, iterator, context) { - if (!iterator && _.isArray(obj) && obj[0] === +obj[0] && obj.length < 65535) { - return Math.max.apply(Math, obj); - } + if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj); if (!iterator && _.isEmpty(obj)) return -Infinity; var result = {computed : -Infinity}; each(obj, function(value, index, list) { @@ -259,9 +236,7 @@ // Return the minimum element (or element-based computation). _.min = function(obj, iterator, context) { - if (!iterator && _.isArray(obj) && obj[0] === +obj[0] && obj.length < 65535) { - return Math.min.apply(Math, obj); - } + if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj); if (!iterator && _.isEmpty(obj)) return Infinity; var result = {computed : Infinity}; each(obj, function(value, index, list) { @@ -273,107 +248,81 @@ // Shuffle an array. _.shuffle = function(obj) { - var rand; - var index = 0; - var shuffled = []; - each(obj, function(value) { - rand = _.random(index++); - shuffled[index - 1] = shuffled[rand]; - shuffled[rand] = value; + var shuffled = [], rand; + each(obj, function(value, index, list) { + if (index == 0) { + shuffled[0] = value; + } else { + rand = Math.floor(Math.random() * (index + 1)); + shuffled[index] = shuffled[rand]; + shuffled[rand] = value; + } }); return shuffled; }; - // An internal function to generate lookup iterators. - var lookupIterator = function(value) { - return _.isFunction(value) ? value : function(obj){ return obj[value]; }; - }; - // Sort the object's values by a criterion produced by an iterator. - _.sortBy = function(obj, value, context) { - var iterator = lookupIterator(value); + _.sortBy = function(obj, iterator, context) { return _.pluck(_.map(obj, function(value, index, list) { return { value : value, - index : index, criteria : iterator.call(context, value, index, list) }; }).sort(function(left, right) { - var a = left.criteria; - var b = right.criteria; - if (a !== b) { - if (a > b || a === void 0) return 1; - if (a < b || b === void 0) return -1; - } - return left.index < right.index ? -1 : 1; + var a = left.criteria, b = right.criteria; + return a < b ? -1 : a > b ? 1 : 0; }), 'value'); }; - // An internal function used for aggregate "group by" operations. - var group = function(obj, value, context, behavior) { + // Groups the object's values by a criterion. Pass either a string attribute + // to group by, or a function that returns the criterion. + _.groupBy = function(obj, val) { var result = {}; - var iterator = lookupIterator(value); + var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; }; each(obj, function(value, index) { - var key = iterator.call(context, value, index, obj); - behavior(result, key, value); + var key = iterator(value, index); + (result[key] || (result[key] = [])).push(value); }); return result; }; - // Groups the object's values by a criterion. Pass either a string attribute - // to group by, or a function that returns the criterion. - _.groupBy = function(obj, value, context) { - return group(obj, value, context, function(result, key, value) { - (_.has(result, key) ? result[key] : (result[key] = [])).push(value); - }); - }; - - // Counts instances of an object that group by a certain criterion. Pass - // either a string attribute to count by, or a function that returns the - // criterion. - _.countBy = function(obj, value, context) { - return group(obj, value, context, function(result, key, value) { - if (!_.has(result, key)) result[key] = 0; - result[key]++; - }); - }; - - // Use a comparator function to figure out the smallest index at which - // an object should be inserted so as to maintain order. Uses binary search. - _.sortedIndex = function(array, obj, iterator, context) { - iterator = iterator == null ? _.identity : lookupIterator(iterator); - var value = iterator.call(context, obj); + // Use a comparator function to figure out at what index an object should + // be inserted so as to maintain order. Uses binary search. + _.sortedIndex = function(array, obj, iterator) { + iterator || (iterator = _.identity); var low = 0, high = array.length; while (low < high) { - var mid = (low + high) >>> 1; - iterator.call(context, array[mid]) < value ? low = mid + 1 : high = mid; + var mid = (low + high) >> 1; + iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid; } return low; }; // Safely convert anything iterable into a real, live array. - _.toArray = function(obj) { - if (!obj) return []; - if (obj.length === +obj.length) return slice.call(obj); - return _.values(obj); + _.toArray = function(iterable) { + if (!iterable) return []; + if (iterable.toArray) return iterable.toArray(); + if (_.isArray(iterable)) return slice.call(iterable); + if (_.isArguments(iterable)) return slice.call(iterable); + return _.values(iterable); }; // Return the number of elements in an object. _.size = function(obj) { - return (obj.length === +obj.length) ? obj.length : _.keys(obj).length; + return _.toArray(obj).length; }; // Array Functions // --------------- // Get the first element of an array. Passing **n** will return the first N - // values in the array. Aliased as `head` and `take`. The **guard** check - // allows it to work with `_.map`. - _.first = _.head = _.take = function(array, n, guard) { + // values in the array. Aliased as `head`. The **guard** check allows it to work + // with `_.map`. + _.first = _.head = function(array, n, guard) { return (n != null) && !guard ? slice.call(array, 0, n) : array[0]; }; - // Returns everything but the last entry of the array. Especially useful on + // Returns everything but the last entry of the array. Especcialy useful on // the arguments object. Passing **n** will return all the values in // the array, excluding the last N. The **guard** check allows it to work with // `_.map`. @@ -391,12 +340,12 @@ } }; - // Returns everything but the first entry of the array. Aliased as `tail` and `drop`. - // Especially useful on the arguments object. Passing an **n** will return - // the rest N values in the array. The **guard** + // Returns everything but the first entry of the array. Aliased as `tail`. + // Especially useful on the arguments object. Passing an **index** will return + // the rest of the values in the array from that index onward. The **guard** // check allows it to work with `_.map`. - _.rest = _.tail = _.drop = function(array, n, guard) { - return slice.call(array, (n == null) || guard ? 1 : n); + _.rest = _.tail = function(array, index, guard) { + return slice.call(array, (index == null) || guard ? 1 : index); }; // Trim out all falsy values from an array. @@ -404,21 +353,13 @@ return _.filter(array, function(value){ return !!value; }); }; - // Internal implementation of a recursive `flatten` function. - var flatten = function(input, shallow, output) { - each(input, function(value) { - if (_.isArray(value)) { - shallow ? push.apply(output, value) : flatten(value, shallow, output); - } else { - output.push(value); - } - }); - return output; - }; - // Return a completely flattened version of an array. _.flatten = function(array, shallow) { - return flatten(array, shallow, []); + return _.reduce(array, function(memo, value) { + if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value)); + memo[memo.length] = value; + return memo; + }, []); }; // Return a version of the array that does not contain the specified value(s). @@ -429,28 +370,28 @@ // Produce a duplicate-free version of the array. If the array has already // been sorted, you have the option of using a faster algorithm. // Aliased as `unique`. - _.uniq = _.unique = function(array, isSorted, iterator, context) { - var initial = iterator ? _.map(array, iterator, context) : array; - var results = []; - var seen = []; - each(initial, function(value, index) { - if (isSorted ? (!index || seen[seen.length - 1] !== value) : !_.contains(seen, value)) { - seen.push(value); - results.push(array[index]); + _.uniq = _.unique = function(array, isSorted, iterator) { + var initial = iterator ? _.map(array, iterator) : array; + var result = []; + _.reduce(initial, function(memo, el, i) { + if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) { + memo[memo.length] = el; + result[result.length] = array[i]; } - }); - return results; + return memo; + }, []); + return result; }; // Produce an array that contains the union: each distinct element from all of // the passed-in arrays. _.union = function() { - return _.uniq(concat.apply(ArrayProto, arguments)); + return _.uniq(_.flatten(arguments, true)); }; // Produce an array that contains every item shared between all the - // passed-in arrays. - _.intersection = function(array) { + // passed-in arrays. (Aliased as "intersect" for back-compat.) + _.intersection = _.intersect = function(array) { var rest = slice.call(arguments, 1); return _.filter(_.uniq(array), function(item) { return _.every(rest, function(other) { @@ -462,8 +403,8 @@ // Take the difference between one array and a number of other arrays. // Only the elements present in just the first array will remain. _.difference = function(array) { - var rest = concat.apply(ArrayProto, slice.call(arguments, 1)); - return _.filter(array, function(value){ return !_.contains(rest, value); }); + var rest = _.flatten(slice.call(arguments, 1)); + return _.filter(array, function(value){ return !_.include(rest, value); }); }; // Zip together multiple lists into a single array -- elements that share @@ -472,27 +413,10 @@ var args = slice.call(arguments); var length = _.max(_.pluck(args, 'length')); var results = new Array(length); - for (var i = 0; i < length; i++) { - results[i] = _.pluck(args, "" + i); - } + for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i); return results; }; - // Converts lists into objects. Pass either a single array of `[key, value]` - // pairs, or two parallel arrays of the same length -- one of keys, and one of - // the corresponding values. - _.object = function(list, values) { - var result = {}; - for (var i = 0, l = list.length; i < l; i++) { - if (values) { - result[list[i]] = values[i]; - } else { - result[list[i][0]] = list[i][1]; - } - } - return result; - }; - // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**), // we need this function. Return the position of the first occurrence of an // item in an array, or -1 if the item is not included in the array. @@ -500,25 +424,23 @@ // If the array is large and already in sort order, pass `true` // for **isSorted** to use binary search. _.indexOf = function(array, item, isSorted) { - var i = 0, l = array.length; + if (array == null) return -1; + var i, l; if (isSorted) { - if (typeof isSorted == 'number') { - i = (isSorted < 0 ? Math.max(0, l + isSorted) : isSorted); - } else { - i = _.sortedIndex(array, item); - return array[i] === item ? i : -1; - } + i = _.sortedIndex(array, item); + return array[i] === item ? i : -1; } - if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item, isSorted); - for (; i < l; i++) if (array[i] === item) return i; + if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item); + for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i; return -1; }; // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available. - _.lastIndexOf = function(array, item, fromIndex) { - if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item, fromIndex); - var i = (fromIndex != null ? fromIndex : array.length); - while (i--) if (array[i] === item) return i; + _.lastIndexOf = function(array, item) { + if (array == null) return -1; + if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item); + var i = array.length; + while (i--) if (i in array && array[i] === item) return i; return -1; }; @@ -592,7 +514,7 @@ // it with the arguments supplied. _.delay = function(func, wait) { var args = slice.call(arguments, 2); - return setTimeout(function(){ return func.apply(null, args); }, wait); + return setTimeout(function(){ return func.apply(func, args); }, wait); }; // Defers a function, scheduling it to run after the current call stack has @@ -604,46 +526,39 @@ // Returns a function, that, when invoked, will only be triggered at most once // during a given window of time. _.throttle = function(func, wait) { - var context, args, timeout, throttling, more, result; + var context, args, timeout, throttling, more; var whenDone = _.debounce(function(){ more = throttling = false; }, wait); return function() { context = this; args = arguments; var later = function() { timeout = null; - if (more) { - result = func.apply(context, args); - } + if (more) func.apply(context, args); whenDone(); }; if (!timeout) timeout = setTimeout(later, wait); if (throttling) { more = true; } else { - throttling = true; - result = func.apply(context, args); + func.apply(context, args); } whenDone(); - return result; + throttling = true; }; }; // Returns a function, that, as long as it continues to be invoked, will not // be triggered. The function will be called after it stops being called for - // N milliseconds. If `immediate` is passed, trigger the function on the - // leading edge, instead of the trailing. - _.debounce = function(func, wait, immediate) { - var timeout, result; + // N milliseconds. + _.debounce = function(func, wait) { + var timeout; return function() { var context = this, args = arguments; var later = function() { timeout = null; - if (!immediate) result = func.apply(context, args); + func.apply(context, args); }; - var callNow = immediate && !timeout; clearTimeout(timeout); timeout = setTimeout(later, wait); - if (callNow) result = func.apply(context, args); - return result; }; }; @@ -654,9 +569,7 @@ return function() { if (ran) return memo; ran = true; - memo = func.apply(this, arguments); - func = null; - return memo; + return memo = func.apply(this, arguments); }; }; @@ -665,8 +578,7 @@ // conditionally execute the original function. _.wrap = function(func, wrapper) { return function() { - var args = [func]; - push.apply(args, arguments); + var args = [func].concat(slice.call(arguments, 0)); return wrapper.apply(this, args); }; }; @@ -688,9 +600,7 @@ _.after = function(times, func) { if (times <= 0) return func(); return function() { - if (--times < 1) { - return func.apply(this, arguments); - } + if (--times < 1) { return func.apply(this, arguments); } }; }; @@ -708,23 +618,7 @@ // Retrieve the values of an object's properties. _.values = function(obj) { - var values = []; - for (var key in obj) if (_.has(obj, key)) values.push(obj[key]); - return values; - }; - - // Convert an object into a list of `[key, value]` pairs. - _.pairs = function(obj) { - var pairs = []; - for (var key in obj) if (_.has(obj, key)) pairs.push([key, obj[key]]); - return pairs; - }; - - // Invert the keys and values of an object. The values must be serializable. - _.invert = function(obj) { - var result = {}; - for (var key in obj) if (_.has(obj, key)) result[obj[key]] = key; - return result; + return _.map(obj, _.identity); }; // Return a sorted list of the function names available on the object. @@ -747,26 +641,6 @@ return obj; }; - // Return a copy of the object only containing the whitelisted properties. - _.pick = function(obj) { - var copy = {}; - var keys = concat.apply(ArrayProto, slice.call(arguments, 1)); - each(keys, function(key) { - if (key in obj) copy[key] = obj[key]; - }); - return copy; - }; - - // Return a copy of the object without the blacklisted properties. - _.omit = function(obj) { - var copy = {}; - var keys = concat.apply(ArrayProto, slice.call(arguments, 1)); - for (var key in obj) { - if (!_.contains(keys, key)) copy[key] = obj[key]; - } - return copy; - }; - // Fill in a given object with default properties. _.defaults = function(obj) { each(slice.call(arguments, 1), function(source) { @@ -791,16 +665,19 @@ return obj; }; - // Internal recursive comparison function for `isEqual`. - var eq = function(a, b, aStack, bStack) { + // Internal recursive comparison function. + function eq(a, b, stack) { // Identical objects are equal. `0 === -0`, but they aren't identical. // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal. if (a === b) return a !== 0 || 1 / a == 1 / b; // A strict comparison is necessary because `null == undefined`. if (a == null || b == null) return a === b; // Unwrap any wrapped objects. - if (a instanceof _) a = a._wrapped; - if (b instanceof _) b = b._wrapped; + if (a._chain) a = a._wrapped; + if (b._chain) b = b._wrapped; + // Invoke a custom `isEqual` method if one is provided. + if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b); + if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a); // Compare `[[Class]]` names. var className = toString.call(a); if (className != toString.call(b)) return false; @@ -830,15 +707,14 @@ if (typeof a != 'object' || typeof b != 'object') return false; // Assume equality for cyclic structures. The algorithm for detecting cyclic // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`. - var length = aStack.length; + var length = stack.length; while (length--) { // Linear search. Performance is inversely proportional to the number of // unique nested structures. - if (aStack[length] == a) return bStack[length] == b; + if (stack[length] == a) return true; } // Add the first object to the stack of traversed objects. - aStack.push(a); - bStack.push(b); + stack.push(a); var size = 0, result = true; // Recursively compare objects and arrays. if (className == '[object Array]') { @@ -848,24 +724,20 @@ if (result) { // Deep compare the contents, ignoring non-numeric properties. while (size--) { - if (!(result = eq(a[size], b[size], aStack, bStack))) break; + // Ensure commutative equality for sparse arrays. + if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break; } } } else { - // Objects with different constructors are not equivalent, but `Object`s - // from different frames are. - var aCtor = a.constructor, bCtor = b.constructor; - if (aCtor !== bCtor && !(_.isFunction(aCtor) && (aCtor instanceof aCtor) && - _.isFunction(bCtor) && (bCtor instanceof bCtor))) { - return false; - } + // Objects with different constructors are not equivalent. + if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false; // Deep compare objects. for (var key in a) { if (_.has(a, key)) { // Count the expected number of properties. size++; // Deep compare each member. - if (!(result = _.has(b, key) && eq(a[key], b[key], aStack, bStack))) break; + if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break; } } // Ensure that both objects contain the same number of properties. @@ -877,20 +749,18 @@ } } // Remove the first object from the stack of traversed objects. - aStack.pop(); - bStack.pop(); + stack.pop(); return result; - }; + } // Perform a deep comparison to check if two objects are equal. _.isEqual = function(a, b) { - return eq(a, b, [], []); + return eq(a, b, []); }; // Is a given array, string, or object empty? // An "empty" object has no enumerable own-properties. _.isEmpty = function(obj) { - if (obj == null) return true; if (_.isArray(obj) || _.isString(obj)) return obj.length === 0; for (var key in obj) if (_.has(obj, key)) return false; return true; @@ -898,7 +768,7 @@ // Is a given value a DOM element? _.isElement = function(obj) { - return !!(obj && obj.nodeType === 1); + return !!(obj && obj.nodeType == 1); }; // Is a given value an array? @@ -912,36 +782,35 @@ return obj === Object(obj); }; - // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp. - each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp'], function(name) { - _['is' + name] = function(obj) { - return toString.call(obj) == '[object ' + name + ']'; - }; - }); - - // Define a fallback version of the method in browsers (ahem, IE), where - // there isn't any inspectable "Arguments" type. + // Is a given variable an arguments object? + _.isArguments = function(obj) { + return toString.call(obj) == '[object Arguments]'; + }; if (!_.isArguments(arguments)) { _.isArguments = function(obj) { return !!(obj && _.has(obj, 'callee')); }; } - // Optimize `isFunction` if appropriate. - if (typeof (/./) !== 'function') { - _.isFunction = function(obj) { - return typeof obj === 'function'; - }; - } - - // Is a given object a finite number? - _.isFinite = function(obj) { - return _.isNumber(obj) && isFinite(obj); + // Is a given value a function? + _.isFunction = function(obj) { + return toString.call(obj) == '[object Function]'; }; - // Is the given value `NaN`? (NaN is the only number which does not equal itself). + // Is a given value a string? + _.isString = function(obj) { + return toString.call(obj) == '[object String]'; + }; + + // Is a given value a number? + _.isNumber = function(obj) { + return toString.call(obj) == '[object Number]'; + }; + + // Is the given value `NaN`? _.isNaN = function(obj) { - return _.isNumber(obj) && obj != +obj; + // `NaN` is the only value for which `===` is not reflexive. + return obj !== obj; }; // Is a given value a boolean? @@ -949,6 +818,16 @@ return obj === true || obj === false || toString.call(obj) == '[object Boolean]'; }; + // Is a given value a date? + _.isDate = function(obj) { + return toString.call(obj) == '[object Date]'; + }; + + // Is the given value a regular expression? + _.isRegExp = function(obj) { + return toString.call(obj) == '[object RegExp]'; + }; + // Is a given value equal to null? _.isNull = function(obj) { return obj === null; @@ -959,8 +838,7 @@ return obj === void 0; }; - // Shortcut function for checking if an object has a given property directly - // on itself (in other words, not on a prototype). + // Has own property? _.has = function(obj, key) { return hasOwnProperty.call(obj, key); }; @@ -981,65 +859,20 @@ }; // Run a function **n** times. - _.times = function(n, iterator, context) { + _.times = function (n, iterator, context) { for (var i = 0; i < n; i++) iterator.call(context, i); }; - // Return a random integer between min and max (inclusive). - _.random = function(min, max) { - if (max == null) { - max = min; - min = 0; - } - return min + (0 | Math.random() * (max - min + 1)); + // Escape a string for HTML interpolation. + _.escape = function(string) { + return (''+string).replace(/&/g, '&').replace(/</g, '<').replace(/>/g, '>').replace(/"/g, '"').replace(/'/g, ''').replace(/\//g,'/'); }; - // List of HTML entities for escaping. - var entityMap = { - escape: { - '&': '&', - '<': '<', - '>': '>', - '"': '"', - "'": ''', - '/': '/' - } - }; - entityMap.unescape = _.invert(entityMap.escape); - - // Regexes containing the keys and values listed immediately above. - var entityRegexes = { - escape: new RegExp('[' + _.keys(entityMap.escape).join('') + ']', 'g'), - unescape: new RegExp('(' + _.keys(entityMap.unescape).join('|') + ')', 'g') - }; - - // Functions for escaping and unescaping strings to/from HTML interpolation. - _.each(['escape', 'unescape'], function(method) { - _[method] = function(string) { - if (string == null) return ''; - return ('' + string).replace(entityRegexes[method], function(match) { - return entityMap[method][match]; - }); - }; - }); - - // If the value of the named property is a function then invoke it; - // otherwise, return it. - _.result = function(object, property) { - if (object == null) return null; - var value = object[property]; - return _.isFunction(value) ? value.call(object) : value; - }; - - // Add your own custom functions to the Underscore object. + // Add your own custom functions to the Underscore object, ensuring that + // they're correctly added to the OOP wrapper as well. _.mixin = function(obj) { each(_.functions(obj), function(name){ - var func = _[name] = obj[name]; - _.prototype[name] = function() { - var args = [this._wrapped]; - push.apply(args, arguments); - return result.call(this, func.apply(_, args)); - }; + addToWrapper(name, _[name] = obj[name]); }); }; @@ -1062,72 +895,41 @@ // When customizing `templateSettings`, if you don't want to define an // interpolation, evaluation or escaping regex, we need one that is // guaranteed not to match. - var noMatch = /(.)^/; + var noMatch = /.^/; - // Certain characters need to be escaped so that they can be put into a - // string literal. - var escapes = { - "'": "'", - '\\': '\\', - '\r': 'r', - '\n': 'n', - '\t': 't', - '\u2028': 'u2028', - '\u2029': 'u2029' + // Within an interpolation, evaluation, or escaping, remove HTML escaping + // that had been previously added. + var unescape = function(code) { + return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'"); }; - var escaper = /\\|'|\r|\n|\t|\u2028|\u2029/g; - // JavaScript micro-templating, similar to John Resig's implementation. // Underscore templating handles arbitrary delimiters, preserves whitespace, // and correctly escapes quotes within interpolated code. - _.template = function(text, data, settings) { - settings = _.defaults({}, settings, _.templateSettings); - - // Combine delimiters into one regular expression via alternation. - var matcher = new RegExp([ - (settings.escape || noMatch).source, - (settings.interpolate || noMatch).source, - (settings.evaluate || noMatch).source - ].join('|') + '|$', 'g'); - - // Compile the template source, escaping string literals appropriately. - var index = 0; - var source = "__p+='"; - text.replace(matcher, function(match, escape, interpolate, evaluate, offset) { - source += text.slice(index, offset) - .replace(escaper, function(match) { return '\\' + escapes[match]; }); - source += - escape ? "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'" : - interpolate ? "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'" : - evaluate ? "';\n" + evaluate + "\n__p+='" : ''; - index = offset + match.length; - }); - source += "';\n"; - - // If a variable is not specified, place data values in local scope. - if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n'; - - source = "var __t,__p='',__j=Array.prototype.join," + - "print=function(){__p+=__j.call(arguments,'');};\n" + - source + "return __p;\n"; - - try { - var render = new Function(settings.variable || 'obj', '_', source); - } catch (e) { - e.source = source; - throw e; - } - - if (data) return render(data, _); - var template = function(data) { - return render.call(this, data, _); + _.template = function(str, data) { + var c = _.templateSettings; + var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' + + 'with(obj||{}){__p.push(\'' + + str.replace(/\\/g, '\\\\') + .replace(/'/g, "\\'") + .replace(c.escape || noMatch, function(match, code) { + return "',_.escape(" + unescape(code) + "),'"; + }) + .replace(c.interpolate || noMatch, function(match, code) { + return "'," + unescape(code) + ",'"; + }) + .replace(c.evaluate || noMatch, function(match, code) { + return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('"; + }) + .replace(/\r/g, '\\r') + .replace(/\n/g, '\\n') + .replace(/\t/g, '\\t') + + "');}return __p.join('');"; + var func = new Function('obj', '_', tmpl); + if (data) return func(data, _); + return function(data) { + return func.call(this, data, _); }; - - // Provide the compiled function source as a convenience for precompilation. - template.source = 'function(' + (settings.variable || 'obj') + '){\n' + source + '}'; - - return template; }; // Add a "chain" function, which will delegate to the wrapper. @@ -1135,15 +937,29 @@ return _(obj).chain(); }; - // OOP + // The OOP Wrapper // --------------- + // If Underscore is called as a function, it returns a wrapped object that // can be used OO-style. This wrapper holds altered versions of all the // underscore functions. Wrapped objects may be chained. + var wrapper = function(obj) { this._wrapped = obj; }; + + // Expose `wrapper.prototype` as `_.prototype` + _.prototype = wrapper.prototype; // Helper function to continue chaining intermediate results. - var result = function(obj) { - return this._chain ? _(obj).chain() : obj; + var result = function(obj, chain) { + return chain ? _(obj).chain() : obj; + }; + + // A method to easily add functions to the OOP wrapper. + var addToWrapper = function(name, func) { + wrapper.prototype[name] = function() { + var args = slice.call(arguments); + unshift.call(args, this._wrapped); + return result(func.apply(_, args), this._chain); + }; }; // Add all of the Underscore functions to the wrapper object. @@ -1152,35 +968,32 @@ // Add all mutator Array functions to the wrapper. each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) { var method = ArrayProto[name]; - _.prototype[name] = function() { - var obj = this._wrapped; - method.apply(obj, arguments); - if ((name == 'shift' || name == 'splice') && obj.length === 0) delete obj[0]; - return result.call(this, obj); + wrapper.prototype[name] = function() { + var wrapped = this._wrapped; + method.apply(wrapped, arguments); + var length = wrapped.length; + if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0]; + return result(wrapped, this._chain); }; }); // Add all accessor Array functions to the wrapper. each(['concat', 'join', 'slice'], function(name) { var method = ArrayProto[name]; - _.prototype[name] = function() { - return result.call(this, method.apply(this._wrapped, arguments)); + wrapper.prototype[name] = function() { + return result(method.apply(this._wrapped, arguments), this._chain); }; }); - _.extend(_.prototype, { + // Start chaining a wrapped Underscore object. + wrapper.prototype.chain = function() { + this._chain = true; + return this; + }; - // Start chaining a wrapped Underscore object. - chain: function() { - this._chain = true; - return this; - }, - - // Extracts the result from a wrapped and chained object. - value: function() { - return this._wrapped; - } - - }); + // Extracts the result from a wrapped and chained object. + wrapper.prototype.value = function() { + return this._wrapped; + }; }).call(this); diff -r 55e7d7008efee2c5622f2505612265a9593ae992 -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 static/scripts/viz/sweepster.js --- a/static/scripts/viz/sweepster.js +++ b/static/scripts/viz/sweepster.js @@ -3,8 +3,8 @@ * genomic visualization. */ -define(["libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks", "mvc/tools", "mvc/data"], - function(d3, util, visualization, tracks, tools, data) { +define(["libs/underscore", "libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks", "mvc/tools", "mvc/data"], + function(_, d3, util, visualization, tracks, tools, data) { /** * A collection of tool input settings. Object is useful for keeping a list of settings diff -r 55e7d7008efee2c5622f2505612265a9593ae992 -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,7 +1,7 @@ define( ["libs/underscore", "viz/visualization", "viz/trackster/util", "viz/trackster/slotting", "viz/trackster/painters", "mvc/data", - "viz/trackster/filters", "viz/trackster_ui" ], - function( _, visualization, util, slotting, painters, data, filters_mod, trackster_ui_mod ) { + "viz/trackster/filters" ], + function( _, visualization, util, slotting, painters, data, filters_mod ) { var extend = _.extend; var get_random_color = util.get_random_color; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: afgane: Fix workflow API imports
by Bitbucket 02 Oct '12

02 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/55e7d7008efe/ changeset: 55e7d7008efe user: afgane date: 2012-10-02 03:03:00 summary: Fix workflow API imports affected #: 1 file diff -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 -r 55e7d7008efee2c5622f2505612265a9593ae992 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -8,9 +8,10 @@ from sqlalchemy import desc from galaxy import util from galaxy import web -from galaxy.tools.parameters import visit_input_values, DataToolParameter +from galaxy import model +from galaxy.tools.parameters import visit_input_values, DataToolParameter, RuntimeValue from galaxy.web.base.controller import BaseAPIController, url_for -from galaxy.workflow.modules import module_factory +from galaxy.workflow.modules import module_factory, ToolModule from galaxy.jobs.actions.post import ActionBox from galaxy.model.item_attrs import UsesAnnotations @@ -344,7 +345,7 @@ def _workflow_from_dict( self, trans, data, source=None ): """ - RPARK: copied from galaxy.web.controllers.workflows.py + RPARK: copied from galaxy.webapps.galaxy.controllers.workflows.py Creates a workflow from a dict. Created workflow is stored in the database and returned. """ # Put parameters in workflow mode @@ -388,7 +389,7 @@ # Stick this in the step temporarily step.temp_input_connections = step_dict['input_connections'] # Save step annotation. - annotation = step_dict[ 'annotation' ] + #annotation = step_dict[ 'annotation' ] #if annotation: #annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) # ------------------------------------------ # @@ -398,7 +399,7 @@ # Unpack and add post-job actions. post_job_actions = step_dict.get( 'post_job_actions', {} ) for name, pja_dict in post_job_actions.items(): - pja = PostJobAction( pja_dict[ 'action_type' ], + model.PostJobAction( pja_dict[ 'action_type' ], step, pja_dict[ 'output_name' ], pja_dict[ 'action_arguments' ] ) # Second pass to deal with connections between steps Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: fixes and improvements to (alt)history - now renders history controls; fix to popupmenu parent parameter; pack scripts
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3164ba737fd4/ changeset: 3164ba737fd4 user: carlfeberhard date: 2012-10-02 00:25:35 summary: fixes and improvements to (alt)history - now renders history controls; fix to popupmenu parent parameter; pack scripts affected #: 19 files diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -173,11 +173,19 @@ states = states.split( "," ) for encoded_id, state in zip( ids, states ): try: + # assume encoded and decode to int id = int( trans.app.security.decode_id( encoded_id ) ) except: + # fallback to non-encoded id id = int( encoded_id ) + + # fetch new data for that id data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) + + # if the state has changed, if data.state != state: + + # find out if we need to force a refresh on this data job_hda = data while job_hda.copied_from_history_dataset_association: job_hda = job_hda.copied_from_history_dataset_association @@ -187,12 +195,15 @@ if tool: force_history_refresh = tool.force_history_refresh if not job_hda.visible: - force_history_refresh = True + force_history_refresh = True + + # add the new state html for the item, the refresh option and the new state, map to the id rval[encoded_id] = { "state": data.state, "html": unicode( trans.fill_template( "root/history_item.mako", data=data, hid=data.hid ), 'utf-8' ), "force_history_refresh": force_history_refresh } + return rval @web.json diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -196,7 +196,7 @@ } }); // locate the element with the id corresponding to the menu's popupmenu attr - var box = $( "#" + menu.attr( 'popupmenu' ) ); + var box = $( parent ).find( "#" + menu.attr( 'popupmenu' ) ); // For menus with clickable link text, make clicking on the link go through instead // of activating the popup menu diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -69,6 +69,72 @@ } }; +// ============================================================================= +/** Global string localization object (and global short form alias) + * set with either: + * GalaxyLocalization.setLocalizedString( original, localized ) + * GalaxyLocalization.setLocalizedString({ original1 : localized1, original2 : localized2 }) + * get with either: + * _l( original ) + */ +//TODO: move to Galaxy.Localization (maybe galaxy.base.js) +var GalaxyLocalization = jQuery.extend({}, { + aliasName : '_l', + localizedStrings : {}, + + setLocalizedString : function( str_or_obj, localizedString ){ + // pass in either two strings (english, translated) or an obj (map) of english : translated attributes + //console.debug( this + '.setLocalizedString:', str_or_obj, localizedString ); + var self = this; + + // DRY non-duplicate assignment function + var setStringIfNotDuplicate = function( original, localized ){ + // do not set if identical - strcmp expensive but should only happen once per page per word + if( original !== localized ){ + self.localizedStrings[ original ] = localized; + } + }; + + if( jQuery.type( str_or_obj ) === "string" ){ + setStringIfNotDuplicate( str_or_obj, localizedString ); + + } else if( jQuery.type( str_or_obj ) === "object" ){ + jQuery.each( str_or_obj, function( key, val ){ + //console.debug( 'key=>val', key, '=>', val ); + // could recurse here but no reason + setStringIfNotDuplicate( key, val ); + }); + + } else { + throw( 'Localization.setLocalizedString needs either a string or object as the first argument,' + + ' given: ' + str_or_obj ); + } + }, + + localize : function( strToLocalize ){ + //console.debug( this + '.localize:', strToLocalize ); + // return the localized version if it's there, the strToLocalize if not + var retStr = strToLocalize; + if( _.has( this.localizedStrings, strToLocalize ) ){ + //console.debug( 'found' ); + retStr = this.localizedStrings[ strToLocalize ]; + } + //console.debug( 'returning:', retStr ); + return retStr; + }, + + toString : function(){ return 'GalaxyLocalization'; } +}); + +// global localization alias +window[ GalaxyLocalization.aliasName ] = function( str ){ return GalaxyLocalization.localize( str ); }; + +//TEST: setLocalizedString( string, string ), _l( string ) +//TEST: setLocalizedString( hash ), _l( string ) +//TEST: setLocalizedString( string === string ), _l( string ) +//TEST: _l( non assigned string ) + + //============================================================================== /** diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -6,71 +6,47 @@ Backbone.js implementation of history panel TODO: - replicate then refactor (could be the wrong order) + meta: + require.js + convert function comments to jsDoc style, complete comments + move inline styles into base.less + watch the magic strings + watch your globals - fix: - tags - annotations - _render_displayApps - _render_downloadButton - widget building (popupmenu, etc.) - history.mako js: updater, etc. - have info bodies prev. opened, redisplay on refresh + all: + add classes, ids on empty divs + incorporate relations? + events (local/ui and otherwise) + have info bodies prev. opened, redisplay on refresh + transfer history.mako js: + updater, etc. + create viz icon + trackster + scatterplot + phylo-viz + on ready: + delete function + check_transfer_status (running->ok) + quota meter update + + historyItemView: + poly HistoryItemView (and HistoryView?) on: for_editing, display_structured, trans.user + don't draw body until it's first unhide event + HIview state transitions (eg. upload -> ok), curr: build new, delete old, place new (in render) + move visualizations menu + include phyloviz - don't draw body until it's first unhide event - all history.mako js -> this - HIview state transitions (eg. upload -> ok), curr: build new, delete old, place new (in render) - History (meta controls : collapse all, rename, annotate, etc. - see history.js.120823.bak) - events (local/ui and otherwise) - HistoryCollection: (collection of History: 'Saved Histories') + History: + renaming broken + tags rendering broken (url?) + annotation (url?) + meta controls : collapse all, rename, annotate, etc. + + collection: + show_deleted, show_hidden (thru js - no refresh) + - ?move IconButtonViews -> templates? - - convert function comments to jsDoc style, complete comments - collection -> show_deleted, show_hidden - poly HistoryItemView on: for_editing, display_structured, trans.user - incorporate relations? - localization - template helper {{#local}} calls _l() - - move inline styles into base.less - add classes, ids on empty divs - watch the magic strings ============================================================================= */ - -//============================================================================== -// jq plugin? -//?? into template? I dunno: need to handle variadic keys, remove empty attrs (href="") -//TODO: not happy with this (a 4th rendering/templating system!?) or it being global -function linkHTMLTemplate( config, tag ){ - // Create an anchor (or any tag) using any config params passed in - //NOTE!: send class attr as 'classes' to avoid res. keyword collision (jsLint) - if( !config ){ return '<a></a>'; } - tag = tag || 'a'; - - var template = [ '<' + tag ]; - for( key in config ){ - var val = config[ key ]; - if( val === '' ){ continue; } - switch( key ){ - case 'text': continue; - case 'classes': - // handle keyword class which is also an HTML attr name - key = 'class'; - val = ( config.classes.join )?( config.classes.join( ' ' ) ):( config.classes ); - //note: lack of break (fall through) - default: - template.push( [ ' ', key, '="', val, '"' ].join( '' ) ); - } - } - template.push( '>' ); - if( 'text' in config ){ template.push( config.text ); } - template.push( '</' + tag + '>' ); - - return template.join( '' ); -} - -//============================================================================== //TODO: use initialize (or validate) to check purged AND deleted -> purged XOR deleted var HistoryItem = BaseModel.extend( LoggableMixin ).extend({ // a single HDA model @@ -292,7 +268,6 @@ var deleteBtnData = { title : 'Delete', href : this.model.get( 'delete_url' ), - target : 'galaxy_main', id : 'historyItemDeleter-' + this.model.get( 'id' ), icon_class : 'delete' }; @@ -329,8 +304,7 @@ var primaryActionButtons = $( '<div/>' ).attr( 'id', 'primary-actions-' + this.model.get( 'id' ) ), view = this; _.each( buttonRenderingFuncs, function( fn ){ - var render_return = fn.call( view ); - primaryActionButtons.append( render_return ); + primaryActionButtons.append( fn.call( view ) ); }); return primaryActionButtons; }, @@ -342,8 +316,7 @@ // return either: a single download icon-button (if there are no meta files) // or a popupmenu with links to download assoc. meta files (if there are meta files) var downloadLinkHTML = HistoryItemView.templates.downloadLinks( this.model.toJSON() ); - this.log( '_render_downloadButton, downloadLinkHTML:', downloadLinkHTML ); - + //this.log( this + '_render_downloadButton, downloadLinkHTML:', downloadLinkHTML ); return $( downloadLinkHTML ); }, @@ -447,7 +420,7 @@ // ................................................................................ other elements _render_tagArea : function(){ - if( this.model.get( 'retag_url' ) ){ return null; } + if( !this.model.get( 'retag_url' ) ){ return null; } //TODO: move to mvc/tags.js return $( HistoryItemView.templates.tagArea( this.model.toJSON() ) ); }, @@ -464,14 +437,14 @@ var displayAppsDiv = $( '<div/>' ).addClass( 'display-apps' ); if( !_.isEmpty( this.model.get( 'display_types' ) ) ){ - this.log( this + 'display_types:', this.model.get( 'display_types' ) ); + //this.log( this + 'display_types:', this.model.get( 'display_types' ) ); //TODO:?? does this ever get used? displayAppsDiv.append( HistoryItemView.templates.displayApps({ displayApps : this.model.toJSON().display_types }) ); } if( !_.isEmpty( this.model.get( 'display_apps' ) ) ){ - this.log( this + 'display_apps:', this.model.get( 'display_apps' ) ); + //this.log( this + 'display_apps:', this.model.get( 'display_apps' ) ); displayAppsDiv.append( HistoryItemView.templates.displayApps({ displayApps : this.model.toJSON().display_apps }) ); @@ -655,9 +628,10 @@ // Show or hide tag area; if showing tag area and it's empty, fill it. if( tagArea.is( ":hidden" ) ){ - if( !tagElt.html() ){ + if( !jQuery.trim( tagElt.html() ) ){ // Need to fill tag element. $.ajax({ + //TODO: the html from this breaks a couple of times url: this.model.get( 'ajax_get_tag_url' ), error: function() { alert( "Tagging failed" ); }, success: function(tag_elt_html) { @@ -688,7 +662,7 @@ // Show or hide annotation area; if showing annotation area and it's empty, fill it. if ( annotationArea.is( ":hidden" ) ){ - if( !annotationElem.html() ){ + if( !jQuery.trim( annotationElem.html() ) ){ // Need to fill annotation element. $.ajax({ url: this.model.get( 'ajax_get_annotation_url' ), @@ -762,6 +736,7 @@ //============================================================================== var History = BaseModel.extend( LoggableMixin ).extend({ + //TODO: bind change events from items and collection to this (itemLengths, states) // uncomment this out see log messages //logger : console, @@ -770,7 +745,8 @@ defaults : { id : '', name : '', - state : '', + state : '', + //TODO:?? change these to a list of encoded ids? state_details : { discarded : 0, empty : 0, @@ -781,15 +757,51 @@ running : 0, setting_metadata: 0, upload : 0 - } + }, + + // maybe security issues... + userIsAdmin : false, + userRoles : [], + //TODO: hardcoded + + //TODO: wire this to items + itemsLength : 0, + showDeleted : false, + showHidden : false, + + diskSize : 0, + deleted : false, + + // tagging_common.mako: render_individual_tagging_element(user=trans.get_user(), + // tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") + tags : [], + annotation : null, + message : null, + quotaMsg : false, + + baseURL : null, + hideDeletedURL : null, + hideHiddenURL : null, + tagURL : null, + annotateURL : null }, initialize : function( data, history_datasets ){ - this.log( this + '.initialize', data, history_datasets ); + //this.log( this + '.initialize', data, history_datasets ); this.items = new HistoryCollection(); }, + toJSON : function(){ + // unfortunately, bb doesn't call 'get' to form the JSON meaning computed vals from get aren't used, so... + // a simple example of override and super call + var json = Backbone.Model.prototype.toJSON.call( this ); + json.itemsLength = this.items.length; + //this.log( this + '.json:', json ); + return json; + }, + loadDatasetsAsHistoryItems : function( datasets ){ + //TODO: add via ajax - multiple datasets at once // adds the given dataset/Item data to historyItems // and updates this.state based on their states //pre: datasets is a list of objs @@ -799,12 +811,12 @@ stateDetails = this.get( 'state_details' ); _.each( datasets, function( dataset, index ){ - self.log( 'loading dataset: ', dataset, index ); + //self.log( 'loading dataset: ', dataset, index ); // create an item sending along the history_id as well var historyItem = new HistoryItem( _.extend( dataset, { history_id: selfID } ) ); - self.log( 'as History:', historyItem ); + //self.log( 'as History:', historyItem ); self.items.add( historyItem ); // add item's state to running totals in stateDetails @@ -864,28 +876,42 @@ // direct attachment to existing element el : 'body.historyPage', - initialize : function(){ - this.log( this + '.initialize' ); + initialize : function(){ + this.log( this + '.initialize:', this ); this.itemViews = []; var parent = this; this.model.items.each( function( item ){ var itemView = new HistoryItemView({ model: item }); parent.itemViews.push( itemView ); }); - //itemViews.reverse(); }, - render : function(){ - this.log( this + '.render' ); + render : function(){ + this.$el.append( HistoryView.templates.historyPanel( this.model.toJSON() ) ); + this.log( this + ' rendered from template:', this.$el ); - // render to temp, move all at once, remove temp holder + // set up aliases + this.itemsDiv = this.$el.find( '#' + this.model.get( 'id' ) + '-datasets' ); + + //TODO: set up widgets, tooltips, etc. + + if( this.model.items.length ){ + // render to temp, move all at once, remove temp holder + var tempDiv = this._render_items(); + this.itemsDiv.append( tempDiv.children() ); + tempDiv.remove(); + } + }, + + _render_items : function(){ + var div = $( '<div/>' ), + view = this; //NOTE!: render in reverse (newest on top) via prepend (instead of append) - var tempDiv = $( '<div/>' ); - _.each( this.itemViews, function( view ){ - tempDiv.prepend( view.render() ); + _.each( this.itemViews, function( itemView ){ + view.log( view + '.render_items:', itemView ); + div.prepend( itemView.render() ); }); - this.$el.append( tempDiv.children() ); - tempDiv.remove(); + return div; }, toString : function(){ @@ -893,6 +919,13 @@ return 'HistoryView(' + nameString + ')'; } }); +//HistoryItemView.templates = InDomTemplateLoader.getTemplates({ +HistoryView.templates = CompiledTemplateLoader.getTemplates({ + 'history-templates.html' : { + historyPanel : 'template-history-historyPanel' + } +}); + //============================================================================== diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -157,79 +157,10 @@ } }); -// ============================================================================= -/** Global string localization object (and global short form alias) - * set with either: - * GalaxyLocalization.setLocalizedString( original, localized ) - * GalaxyLocalization.setLocalizedString({ original1 : localized1, original2 : localized2 }) - * get with either: - * _l( original ) - */ -//TODO: move to Galaxy.Localization -var GalaxyLocalization = jQuery.extend({}, { - aliasName : '_l', - localizedStrings : {}, - - setLocalizedString : function( str_or_obj, localizedString ){ - // pass in either two strings (english, translated) or an obj (map) of english : translated attributes - //console.debug( this + '.setLocalizedString:', str_or_obj, localizedString ); - var self = this; - - // DRY non-duplicate assignment function - var setStringIfNotDuplicate = function( original, localized ){ - // do not set if identical - strcmp expensive but should only happen once per page per word - if( original !== localized ){ - self.localizedStrings[ original ] = localized; - } - }; - - if( jQuery.type( str_or_obj ) === "string" ){ - setStringIfNotDuplicate( str_or_obj, localizedString ); - - } else if( jQuery.type( str_or_obj ) === "object" ){ - jQuery.each( str_or_obj, function( key, val ){ - //console.debug( 'key=>val', key, '=>', val ); - // could recurse here but no reason - setStringIfNotDuplicate( key, val ); - }); - - } else { - throw( 'Localization.setLocalizedString needs either a string or object as the first argument,' + - ' given: ' + str_or_obj ); - } - }, - - localize : function( strToLocalize ){ - //console.debug( this + '.localize:', strToLocalize ); - // return the localized version if it's there, the strToLocalize if not - // try/catch cheaper than if in - try { - //var localized = this.localizedStrings[ strToLocalize ]; - //return localized; - return this.localizedStrings[ strToLocalize ]; - } catch( err ){ - //TODO??: potentially problematic catch all - //console.error( err ); - return strToLocalize; - } - }, - - toString : function(){ return 'GalaxyLocalization'; } -}); -// global localization alias -window[ GalaxyLocalization.aliasName ] = function( str ){ return GalaxyLocalization.localize( str ); }; 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a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return 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BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){return(this.logger)?(this.logger.log.apply(this,arguments)):(undefined)}};var TemplateLoader=_.extend({},LoggableMixin,{getTemplateLoadFn:function(){throw ("There is no templateLoadFn. Make sure you're using a subclass of TemplateLoader")},getTemplates:function(d,e){e=e||false;this.log(this,"getTemplates:",d,", forceReload:",e);var c={},a=this,b=this.getTemplateLoadFn();if(!d){return c}jQuery.each(d,function(f,g){jQuery.each(g,function(h,i){a.log(a+", templateFile:",f,"templateName:",h,", templateID:",i);c[h]=b.call(a,f,h,i)})});return c}});var CompiledTemplateLoader=_.extend({},TemplateLoader,{getTemplateLoadFn:function(){return this.loadCompiledHandlebarsTemplate},loadCompiledHandlebarsTemplate:function(b,a,c){this.log("getInDomTemplates, templateFile:",b,"templateName:",a,", templateID:",c);if(!Handlebars.templates||!Handlebars.templates[c]){throw ("Template not found: Handlebars."+c+". Check your h.templates() call in the mako file that rendered this page")}this.log("found template function:",c);return Handlebars.templates[c]}});var InDomTemplateLoader=_.extend({},TemplateLoader,{compileTemplate:function(a){if(!Handlebars||!Handlebars.compile){throw ("No Handlebars.compile found. You may only have Handlebars.runtime loaded.Include handlebars.full for this to work")}this.log("compiling template:",a);return Handlebars.compile(a)},findTemplateInDom:function(b,a,c){return $("script#"+c).last()},getTemplateLoadFn:function(){return this.loadInDomTemplate},loadInDomTemplate:function(b,a,c){this.log("getInDomTemplate, templateFile:",b,"templateName:",a,", templateID:",c);var d=this.findTemplateInDom(b,a,c);if(!d||!d.length){throw ("Template not found within the DOM: "+c+". 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Make sure you're using a subclass of TemplateLoader")},getTemplates:function(d,e){e=e||false;this.log(this,"getTemplates:",d,", forceReload:",e);var c={},a=this,b=this.getTemplateLoadFn();if(!d){return c}jQuery.each(d,function(f,g){jQuery.each(g,function(h,i){a.log(a+", templateFile:",f,"templateName:",h,", templateID:",i);c[h]=b.call(a,f,h,i)})});return c}});var CompiledTemplateLoader=_.extend({},TemplateLoader,{getTemplateLoadFn:function(){return this.loadCompiledHandlebarsTemplate},loadCompiledHandlebarsTemplate:function(b,a,c){this.log("getInDomTemplates, templateFile:",b,"templateName:",a,", templateID:",c);if(!Handlebars.templates||!Handlebars.templates[c]){throw ("Template not found: Handlebars."+c+". 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HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model)},render:function(){var c=this.model.get("id"),b=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+c);var a=$("<div/>").attr("id","historyItem-"+c).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+b);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});make_popup_menus(a);this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),target:"galaxy_main",id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){var e=d.call(a);b.append(e)});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HistoryItemView.templates.downloadLinks(this.model.toJSON());this.log("_render_downloadButton, downloadLinkHTML:",a);return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){this.log(this+"display_types:",this.model.get("display_types"));a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_types}))}if(!_.isEmpty(this.model.get("display_apps"))){this.log(this+"display_apps:",this.model.get("display_apps"));a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_apps}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!a.html()){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!c.html()){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"common-templates.html":{warningMsg:"template-warningmessagesmall"},"history-templates.html":{messages:"template-history-warning-messages",titleLink:"template-history-titleLink",hdaSummary:"template-history-hdaSummary",downloadLinks:"template-history-downloadLinks",failedMetadata:"template-history-failedMetaData",tagArea:"template-history-tagArea",annotationArea:"template-history-annotationArea",displayApps:"template-history-displayApps"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0}},initialize:function(b,a){this.log(this+".initialize",b,a);this.items=new HistoryCollection()},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){a.log("loading dataset: ",f,e);var h=new HistoryItem(_.extend(f,{history_id:b}));a.log("as History:",h);a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize");this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.log(this+".render");var a=$("<div/>");_.each(this.itemViews,function(b){a.prepend(b.render())});this.$el.append(a.children());a.remove()},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}}); \ No newline at end of file +var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model)},render:function(){var c=this.model.get("id"),b=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+c);var a=$("<div/>").attr("id","historyItem-"+c).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+b);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});make_popup_menus(a);this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HistoryItemView.templates.downloadLinks(this.model.toJSON());return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_types}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_apps}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"common-templates.html":{warningMsg:"template-warningmessagesmall"},"history-templates.html":{messages:"template-history-warning-messages",titleLink:"template-history-titleLink",hdaSummary:"template-history-hdaSummary",downloadLinks:"template-history-downloadLinks",failedMetadata:"template-history-failedMetaData",tagArea:"template-history-tagArea",annotationArea:"template-history-annotationArea",displayApps:"template-history-displayApps"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0},userIsAdmin:false,userRoles:[],itemsLength:0,showDeleted:false,showHidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false,baseURL:null,hideDeletedURL:null,hideHiddenURL:null,tagURL:null,annotateURL:null},initialize:function(b,a){this.items=new HistoryCollection()},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);a.itemsLength=this.items.length;return a},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){var h=new HistoryItem(_.extend(f,{history_id:b}));a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize:",this);this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.$el.append(HistoryView.templates.historyPanel(this.model.toJSON()));this.log(this+" rendered from template:",this.$el);this.itemsDiv=this.$el.find("#"+this.model.get("id")+"-datasets");if(this.model.items.length){var a=this._render_items();this.itemsDiv.append(a.children());a.remove()}},_render_items:function(){var b=$("<div/>"),a=this;_.each(this.itemViews,function(c){a.log(a+".render_items:",c);b.prepend(c.render())});return b},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryView.templates=CompiledTemplateLoader.getTemplates({"history-templates.html":{historyPanel:"template-history-historyPanel"}}); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=$(Handlebars.partials.iconButton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});IconButtonView.templates={iconButton:Handlebars.partials.iconButton};var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(c){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",c.attributes.title).addClass("icon-button menu-button").addClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_click);if(c.attributes.tooltip_config){b.tooltip(c.attributes.tooltip_config)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var GalaxyLocalization=jQuery.extend({},{aliasName:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(b){try{return this.localizedStrings[b]}catch(a){return b}},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.aliasName]=function(a){return GalaxyLocalization.localize(a)}; \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=$(Handlebars.partials.iconButton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});IconButtonView.templates={iconButton:Handlebars.partials.iconButton};var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(c){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",c.attributes.title).addClass("icon-button menu-button").addClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_click);if(c.attributes.tooltip_config){b.tooltip(c.attributes.tooltip_config)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}}); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/packed/templates/compiled/helpers-common-templates.js --- a/static/scripts/packed/templates/compiled/helpers-common-templates.js +++ b/static/scripts/packed/templates/compiled/helpers-common-templates.js @@ -1,1 +1,1 @@ -Handlebars.registerPartial("clearFloatDiv",function(a){return'<div class="clear"></div>'});Handlebars.registerHelper("warningmessagesmall",function(a){return'<div class="warningmessagesmall"><strong>'+a.fn(this)+"</strong></div>"});Handlebars.registerPartial("iconButton",function(c,b){var a="";a+=(c.enabled)?("<a"):("<span");if(c.title){a+=' title="'+c.title+'"'}a+=' class="icon-button';if(c.isMenuButton){a+=" menu-button"}if(c.title){a+=" tooltip"}a+=" "+c.icon_class;if(!c.enabled){a+="_disabled"}a+='"';if(c.id){a+=' id="'+c.id+'"'}a+=' href="'+((c.href)?(c.href):("javascript:void(0);"))+'"';if(c.target){a+=' target="'+c.target+'"'}if(!c.visible){a+=' style="display: none;"'}a+=">"+((c.enabled)?("</a>"):("</span>"));return a}); \ No newline at end of file +Handlebars.registerPartial("clearFloatDiv",function(a){return'<div class="clear"></div>'});Handlebars.registerHelper("warningmessagesmall",function(a){return'<div class="warningmessagesmall"><strong>'+a.fn(this)+"</strong></div>"});Handlebars.registerHelper("local",function(a){return _l(a.fn(this))});Handlebars.registerPartial("iconButton",function(c,b){var a="";a+=(c.enabled)?("<a"):("<span");if(c.title){a+=' title="'+c.title+'"'}a+=' class="icon-button';if(c.isMenuButton){a+=" menu-button"}if(c.title){a+=" tooltip"}a+=" "+c.icon_class;if(!c.enabled){a+="_disabled"}a+='"';if(c.id){a+=' id="'+c.id+'"'}a+=' href="'+((c.href)?(c.href):("javascript:void(0);"))+'"';if(c.target){a+=' target="'+c.target+'"'}if(!c.visible){a+=' style="display: none;"'}a+=">"+((c.enabled)?("</a>"):("</span>"));return a}); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/packed/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/packed/templates/compiled/template-history-downloadLinks.js +++ b/static/scripts/packed/templates/compiled/template-history-downloadLinks.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(s,r){var p="",q,o;p+='\n<div popupmenu="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a class="action-button" href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'">Download Dataset</a>\n <a>Additional Files</a>\n ';q=s.meta_files;q=f.each.call(s,q,{hash:{},inverse:m.noop,fn:m.program(2,d,r)});if(q||q===0){p+=q}p+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n</div>\n';return p}function d(s,r){var p="",q,o;p+='\n <a class="action-button" href="';o=f.meta_download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_download_url;q=typeof q===h?q():q}p+=i(q)+'">Download ';o=f.meta_file_type;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_file_type;q=typeof q===h?q():q}p+=i(q)+"</a>\n ";return p}function n(p,o){return'\n<a href="" title="Download" class="icon-button disk tooltip"></a>\n'}c=l.meta_files;c=f["if"].call(l,c,{hash:{},inverse:m.program(4,n,j),fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(s,r){var p="",q,o;p+='\n<div popupmenu="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a class="action-button" href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'">Download Dataset</a>\n <a>Additional Files</a>\n ';q=s.meta_files;q=f.each.call(s,q,{hash:{},inverse:m.noop,fn:m.program(2,d,r)});if(q||q===0){p+=q}p+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n</div>\n';return p}function d(s,r){var p="",q,o;p+='\n <a class="action-button" href="';o=f.meta_download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_download_url;q=typeof q===h?q():q}p+=i(q)+'">Download ';o=f.meta_file_type;if(o){q=o.call(s,{hash:{}})}else{q=s.meta_file_type;q=typeof q===h?q():q}p+=i(q)+"</a>\n ";return p}function n(s,r){var p="",q,o;p+='\n<a href="';o=f.download_url;if(o){q=o.call(s,{hash:{}})}else{q=s.download_url;q=typeof q===h?q():q}p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n';return p}c=l.meta_files;c=f["if"].call(l,c,{hash:{},inverse:m.program(4,n,j),fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})(); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/packed/templates/compiled/template-history-historyPanel.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(k,C,A,s,J){A=A||k.helpers;var B="",o,n,y=this,f="function",c=A.blockHelperMissing,e=this.escapeExpression;function u(L,K){return"refresh"}function t(L,K){return"collapse all"}function r(O,N){var L="",M,K;L+='\n <div style="width: 40px; float: right; white-space: nowrap;">\n <a id="history-tag" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button tags tooltip" target="galaxy_main" href="';K=A.tagURL;if(K){M=K.call(O,{hash:{}})}else{M=O.tagURL;M=typeof M===f?M():M}L+=e(M)+'"></a>\n <a id="history-annotate" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="';K=A.annotateURL;if(K){M=K.call(O,{hash:{}})}else{M=O.annotateURL;M=typeof M===f?M():M}L+=e(M)+'"></a>\n </div>\n ';return L}function q(L,K){return"Edit history tags"}function m(L,K){return"Edit history annotation"}function I(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideDeletedURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideDeletedURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function H(L,K){return"hide deleted"}function G(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideHiddenURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideHiddenURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function F(L,K){return"hide hidden"}function E(O,N){var L="",M,K;L+="\n ";L+='\n <div id="history-size" style="position: absolute; top: 3px; right: 0px;">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+'</div>\n <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">';K=A.name;if(K){M=K.call(O,{hash:{}})}else{M=O.name;M=typeof M===f?M():M}L+=e(M)+"</div>\n \n ";return L}function D(O,N){var L="",M,K;L+='\n <div id="history-size">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+"</div>\n ";return L}function p(O,N){var L="",M,K;L+="\n";K=A.warningmessagesmall;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}else{M=O.warningmessagesmall;M=typeof M===f?M():M}if(!A.warningmessagesmall){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}if(M||M===0){L+=M}L+="\n";return L}function l(N,M){var L,K;K=A.local;if(K){L=K.call(N,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}else{L=N.local;L=typeof L===f?L():L}if(!A.local){L=c.call(N,L,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}if(L||L===0){return L}else{return""}}function j(L,K){return"You are currently viewing a deleted history!"}function i(N,M){var K="",L;K+="\n";K+='\n<div style="margin: 0px 5px 10px 5px">\n\n <div id="history-tag-area" style="display: none">\n <b>Tags:</b>\n ';K+="\n ";K+='\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';L=N.annotation;L=A["if"].call(N,L,{hash:{},inverse:y.program(27,g,M),fn:y.program(25,h,M)});if(L||L===0){K+=L}K+="\n </div>\n </div>\n </div>\n</div>\n";return K}function h(O,N){var L="",M,K;L+="\n ";K=A.annotation;if(K){M=K.call(O,{hash:{}})}else{M=O.annotation;M=typeof M===f?M():M}L+=e(M)+"\n ";return L}function g(L,K){return"\n <em>Describe or add notes to history</em>\n "}function d(O,N){var L="",M,K;L+='\n<div id="message-container">\n <div class="';K=A.status;if(K){M=K.call(O,{hash:{}})}else{M=O.status;M=typeof M===f?M():M}L+=e(M)+'message">\n ';K=A.message;if(K){M=K.call(O,{hash:{}})}else{M=O.message;M=typeof M===f?M():M}L+=e(M)+"\n </div><br />\n</div>\n";return L}function z(L,K){return'\n <div id="quota-message" class="errormessage">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n <br/>\n '}function x(O,N){var L="",M,K;L+='\n<div id="';K=A.id;if(K){M=K.call(O,{hash:{}})}else{M=O.id;M=typeof M===f?M():M}L+=e(M)+'-datasets" class="history-datasets-list">\n ';L+="\n</div>\n\n";return L}function w(O,N){var L="",M,K;L+='\n<div class="infomessagesmall" id="emptyHistoryMessage">\n';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(36,v,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(36,v,N)})}if(M||M===0){L+=M}L+="\n</div>\n";return L}function v(L,K){return"Your history is empty. Click 'Get Data' on the left pane to start"}B+='<div id="top-links" class="historyLinks">\n <a title="';n=A.local;if(n){o=n.call(C,{hash:{},inverse:y.noop,fn:y.program(1,u,J)})}else{o=C.local;o=typeof o===f?o():o}if(!A.local){o=c.call(C,o,{hash:{},inverse:y.noop,fn:y.program(1,u,J)})}if(o||o===0){B+=o}B+='" class="icon-button arrow-circle tooltip" href="';n=A.baseURL;if(n){o=n.call(C,{hash:{}})}else{o=C.baseURL;o=typeof o===f?o():o}B+=e(o)+"\"></a>\n <a title='";n=A.local;if(n){o=n.call(C,{hash:{},inverse:y.noop,fn:y.program(3,t,J)})}else{o=C.local;o=typeof o===f?o():o}if(!A.local){o=c.call(C,o,{hash:{},inverse:y.noop,fn:y.program(3,t,J)})}if(o||o===0){B+=o}B+="' class='icon-button toggle tooltip' href='#' style=\"display: none\"></a>\n ";o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(5,r,J)});if(o||o===0){B+=o}B+='\n</div>\n<div class="clear"></div>\n\n';B+="\n";o=C.showDeleted;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(10,I,J)});if(o||o===0){B+=o}B+="\n\n";o=C.showHidden;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(13,G,J)});if(o||o===0){B+=o}B+="\n\n";B+='\n<div id="history-name-area" class="historyLinks">\n <div id="history-name-container" style="position: relative;">\n ';o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.program(18,D,J),fn:y.program(16,E,J)});if(o||o===0){B+=o}B+='\n </div> \n</div>\n<div style="clear: both;"></div>\n\n';o=C.deleted;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(20,p,J)});if(o||o===0){B+=o}B+="\n\n";B+="\n";B+="\n";o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(24,i,J)});if(o||o===0){B+=o}B+="\n\n";o=C.message;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(29,d,J)});if(o||o===0){B+=o}B+='\n\n<div id="quota-message-container">\n ';o=C.over_quota;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(31,z,J)});if(o||o===0){B+=o}B+="\n</div>\n\n";o=C.itemsLength;o=A["if"].call(C,o,{hash:{},inverse:y.program(35,w,J),fn:y.program(33,x,J)});if(o||o===0){B+=o}return B})})(); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/packed/templates/compiled/tool_search.js --- a/static/scripts/packed/templates/compiled/tool_search.js +++ b/static/scripts/packed/templates/compiled/tool_search.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_search=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<input type="text" name="query" value="';g=d.search_hint_string;if(g){c=g.call(l,{hash:{}})}else{c=l.search_hint_string;c=typeof c===f?c():c}h+=i(c)+'" id="tool-search-query" autocomplete="off" class="search-query parent-width" />\n<a id="search-clear-btn" class="icon-button cross-circle tooltip" title="clear search (esc)"></a>\n<img src="';g=d.spinner_url;if(g){c=g.call(l,{hash:{}})}else{c=l.spinner_url;c=typeof c===f?c():c}h+=i(c)+'" id="search-spinner" class="search-spinner"/>';return h})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_search=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<input type="text" name="query" value="';g=d.search_hint_string;if(g){c=g.call(l,{hash:{}})}else{c=l.search_hint_string;c=typeof c===f?c():c}h+=i(c)+'" id="tool-search-query" autocomplete="off" class="search-query parent-width" />\n<a id="search-clear-btn" class="tooltip" title="clear search (esc)"></a>\n<img src="';g=d.spinner_url;if(g){c=g.call(l,{hash:{}})}else{c=l.spinner_url;c=typeof c===f?c():c}h+=i(c)+'" id="search-spinner" class="search-spinner"/>';return h})})(); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/templates/common-templates.html --- a/static/scripts/templates/common-templates.html +++ b/static/scripts/templates/common-templates.html @@ -14,6 +14,15 @@ }); </script> +<script type="text/javascript" class="helper-common" id="helper-local"> +/** Calls _l (from base-mvc.js) to localize strings (if poosible) + * This helper is specifically for localization within templates + */ +Handlebars.registerHelper( 'local', function( options ){ + return _l( options.fn( this ) ); +}); +</script> + <script type="text/template" class="template-common" id="template-warningmessagesmall"> {{! renders a warning in a (mostly css) highlighted, iconned warning box }} <div class="warningmessagesmall"><strong>{{{ warning }}}</strong></div> diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/templates/compiled/helpers-common-templates.js --- a/static/scripts/templates/compiled/helpers-common-templates.js +++ b/static/scripts/templates/compiled/helpers-common-templates.js @@ -8,6 +8,12 @@ Handlebars.registerHelper( 'warningmessagesmall', function( options ){ return '<div class="warningmessagesmall"><strong>' + options.fn( this ) + '</strong></div>' }); +/** Calls _l (from base-mvc.js) to localize strings (if poosible) + * This helper is specifically for localization within templates + */ +Handlebars.registerHelper( 'local', function( options ){ + return _l( options.fn( this ) ); +}); /** Renders a glx style icon-button (see IconButton in mvc/ui.js) * can be used in either of the following ways: * within a template: {{> iconButton buttonData}} diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/templates/compiled/template-history-downloadLinks.js +++ b/static/scripts/templates/compiled/template-history-downloadLinks.js @@ -45,8 +45,13 @@ function program4(depth0,data) { - - return "\n<a href=\"\" title=\"Download\" class=\"icon-button disk tooltip\"></a>\n";} + var buffer = "", stack1, foundHelper; + buffer += "\n<a href=\""; + foundHelper = helpers.download_url; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.download_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" title=\"Download\" class=\"icon-button disk tooltip\"></a>\n"; + return buffer;} stack1 = depth0.meta_files; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(4, program4, data),fn:self.program(1, program1, data)}); diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/templates/compiled/template-history-historyPanel.js --- /dev/null +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -0,0 +1,272 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; + +function program1(depth0,data) { + + + return "refresh";} + +function program3(depth0,data) { + + + return "collapse all";} + +function program5(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <div style=\"width: 40px; float: right; white-space: nowrap;\">\n <a id=\"history-tag\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\""; + foundHelper = helpers.tagURL; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.tagURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"></a>\n <a id=\"history-annotate\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\""; + foundHelper = helpers.annotateURL; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.annotateURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"></a>\n </div>\n "; + return buffer;} +function program6(depth0,data) { + + + return "Edit history tags";} + +function program8(depth0,data) { + + + return "Edit history annotation";} + +function program10(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n<div class=\"historyLinks\">\n <a href=\""; + foundHelper = helpers.hideDeletedURL; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.hideDeletedURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</a>\n</div>\n"; + return buffer;} +function program11(depth0,data) { + + + return "hide deleted";} + +function program13(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n<div class=\"historyLinks\">\n <a href=\""; + foundHelper = helpers.hideHiddenURL; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.hideHiddenURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</a>\n</div>\n"; + return buffer;} +function program14(depth0,data) { + + + return "hide hidden";} + +function program16(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n "; + buffer += "\n <div id=\"history-size\" style=\"position: absolute; top: 3px; right: 0px;\">"; + foundHelper = helpers.diskSize; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.diskSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div id=\"history-name\" style=\"margin-right: 50px;\" class=\"tooltip editable-text\" title=\"Click to rename history\">"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n \n "; + return buffer;} + +function program18(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <div id=\"history-size\">"; + foundHelper = helpers.diskSize; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.diskSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n "; + return buffer;} + +function program20(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n"; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n"; + return buffer;} +function program21(depth0,data) { + + var stack1, foundHelper; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }} +function program22(depth0,data) { + + + return "You are currently viewing a deleted history!";} + +function program24(depth0,data) { + + var buffer = "", stack1; + buffer += "\n"; + buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <b>Tags:</b>\n "; + buffer += "\n "; + buffer += "\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; + stack1 = depth0.annotation; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(27, program27, data),fn:self.program(25, program25, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n </div>\n </div>\n</div>\n"; + return buffer;} +function program25(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.annotation; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.annotation; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\n "; + return buffer;} + +function program27(depth0,data) { + + + return "\n <em>Describe or add notes to history</em>\n ";} + +function program29(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n<div id=\"message-container\">\n <div class=\""; + foundHelper = helpers.status; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "message\">\n "; + foundHelper = helpers.message; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\n </div><br />\n</div>\n"; + return buffer;} + +function program31(depth0,data) { + + + return "\n <div id=\"quota-message\" class=\"errormessage\">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n <br/>\n ";} + +function program33(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n<div id=\""; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "-datasets\" class=\"history-datasets-list\">\n "; + buffer += "\n</div>\n\n"; + return buffer;} + +function program35(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\">\n"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(36, program36, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(36, program36, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</div>\n"; + return buffer;} +function program36(depth0,data) { + + + return "Your history is empty. Click 'Get Data' on the left pane to start";} + + buffer += "<div id=\"top-links\" class=\"historyLinks\">\n <a title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\" class=\"icon-button arrow-circle tooltip\" href=\""; + foundHelper = helpers.baseURL; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.baseURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"></a>\n <a title='"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "' class='icon-button toggle tooltip' href='#' style=\"display: none\"></a>\n "; + stack1 = depth0.userRoles; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</div>\n<div class=\"clear\"></div>\n\n"; + buffer += "\n"; + stack1 = depth0.showDeleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + stack1 = depth0.showHidden; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + buffer += "\n<div id=\"history-name-area\" class=\"historyLinks\">\n <div id=\"history-name-container\" style=\"position: relative;\">\n "; + stack1 = depth0.userRoles; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(18, program18, data),fn:self.program(16, program16, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div> \n</div>\n<div style=\"clear: both;\"></div>\n\n"; + stack1 = depth0.deleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + buffer += "\n"; + buffer += "\n"; + stack1 = depth0.userRoles; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(24, program24, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + stack1 = depth0.message; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(29, program29, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n<div id=\"quota-message-container\">\n "; + stack1 = depth0.over_quota; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</div>\n\n"; + stack1 = depth0.itemsLength; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(35, program35, data),fn:self.program(33, program33, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + return buffer;}); +})(); \ No newline at end of file diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -64,7 +64,7 @@ <a href="{{download_url}}" title="Download" class="icon-button disk tooltip"></a></div> {{else}} -<a href="" title="Download" class="icon-button disk tooltip"></a> +<a href="{{download_url}}" title="Download" class="icon-button disk tooltip"></a> {{/if}} </script> @@ -96,3 +96,112 @@ <br /> {{/each}} </script> + + +<script type="text/template" class="template-history" id="template-history-historyPanel"> +<div id="top-links" class="historyLinks"> + <a title="{{#local}}refresh{{/local}}" class="icon-button arrow-circle tooltip" href="{{baseURL}}"></a> + <a title='{{#local}}collapse all{{/local}}' class='icon-button toggle tooltip' href='#' style="display: none"></a> + {{#if userRoles}} + <div style="width: 40px; float: right; white-space: nowrap;"> + <a id="history-tag" title="{{#local}}Edit history tags{{/local}}" + class="icon-button tags tooltip" target="galaxy_main" href="{{tagURL}}"></a> + <a id="history-annotate" title="{{#local}}Edit history annotation{{/local}}" + class="icon-button annotate tooltip" target="galaxy_main" href="{{annotateURL}}"></a> + </div> + {{/if}} +</div> +<div class="clear"></div> + +{{! TODO: move to js with no reload - use each with historyLinks }} +{{#if showDeleted}} +<div class="historyLinks"> + <a href="{{hideDeletedURL}}">{{#local}}hide deleted{{/local}}</a> +</div> +{{/if}} + +{{#if showHidden}} +<div class="historyLinks"> + <a href="{{hideHiddenURL}}">{{#local}}hide hidden{{/local}}</a> +</div> +{{/if}} + +{{! history name (if any) }} +<div id="history-name-area" class="historyLinks"> + <div id="history-name-container" style="position: relative;"> + {{#if userRoles}} + {{! TODO: factor out conditional css }} + <div id="history-size" style="position: absolute; top: 3px; right: 0px;">{{diskSize}}</div> + <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">{{name}}</div> + + {{else}} + <div id="history-size">{{diskSize}}</div> + {{/if}} + </div> +</div> +<div style="clear: both;"></div> + +{{#if deleted}} +{{#warningmessagesmall}}{{#local}}You are currently viewing a deleted history!{{/local}}{{/warningmessagesmall}} +{{/if}} + +{{! tags and annotations }} +{{! TODO: wire these to js events }} +{{#if userRoles}} +{{! TODO: move inline styles out }} +<div style="margin: 0px 5px 10px 5px"> + + <div id="history-tag-area" style="display: none"> + <b>Tags:</b> + {{! load via js render_individual_tagging_element }} + {{! render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") }} + </div> + + <div id="history-annotation-area" style="display: none"> + <strong>Annotation / Notes:</strong> + <div id="history-annotation-container"> + <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> + {{#if annotation}} + {{annotation}} + {{else}} + <em>Describe or add notes to history</em> + {{/if}} + </div> + </div> + </div> +</div> +{{/if}} + +{{#if message}} +<div id="message-container"> + <div class="{{status}}message"> + {{message}} + </div><br /> +</div> +{{/if}} + +<div id="quota-message-container"> + {{#if over_quota}} + <div id="quota-message" class="errormessage"> + You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. + </div> + <br/> + {{/if}} +</div> + +{{#if itemsLength}} +<div id="{{id}}-datasets" class="history-datasets-list"> + {{! NOTE: HistoryItemViews will be appended here }} +</div> + +{{else}}{{! no history items }} +<div class="infomessagesmall" id="emptyHistoryMessage"> +{{#local}}Your history is empty. Click 'Get Data' on the left pane to start{{/local}} +</div> +{{/if}} +</script> + + + diff -r 78f37cb76a5f981febf36b8119278c59d2319e91 -r 3164ba737fd44f0ec842d6f2d743563d18d1dd74 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -97,15 +97,16 @@ # edit attr button if for_editing: if not( hda.deleted or hda.purged ): - edit_url = h.url_for( controller='dataset', action='edit', dataset_id=encoded_data_id ) + edit_url = h.url_for( controller='dataset', action='edit', + dataset_id=encoded_data_id ) add_to_data( edit_url=edit_url ) # delete button if for_editing and not ( deleted or dataset_purged or purged ): - add_to_data( delete_url=h.url_for( controller='dataset', action='delete', dataset_id=encoded_data_id, - ##TODO: loose end - show_deleted_on_refresh=show_deleted - )) + delete_url = h.url_for( controller='dataset', action='delete', + dataset_id=encoded_data_id, + show_deleted_on_refresh=show_deleted ) + add_to_data( delete_url=delete_url ) # ................................................................ primary actions (error, info, download) # download links (hda and associated meta files) @@ -127,7 +128,21 @@ # error report if for_editing: #NOTE: no state == 'error' check - add_to_data( report_error_url=h.url_for( h.url_for( controller='dataset', action='errors', id=encoded_data_id ) ) ) + ##TODO: has to have an _UN_ encoded id + #report_error_url = h.url_for( controller='dataset', action='errors', id=encoded_data_id ) + report_error_url = h.url_for( controller='dataset', action='errors', id=hda.id ) + add_to_data( report_error_url=report_error_url ) + + # info/params + show_params_url = h.url_for( controller='dataset', action='show_params', dataset_id=encoded_data_id ) + add_to_data( show_params_url=show_params_url ) + + # rerun + if for_editing: + ##TODO: has to have an _UN_ encoded id + #rerun_url = h.url_for( controller='tool_runner', action='rerun', id=encoded_data_id ) + rerun_url = h.url_for( controller='tool_runner', action='rerun', id=hda.id ) + add_to_data( rerun_url=rerun_url ) # visualizations if hda.ext in app.datatypes_registry.get_available_tracks(): @@ -265,39 +280,61 @@ %></%def> - +##TODO: remove after filling tags.js +<%namespace file="../tagging_common.mako" import="render_individual_tagging_element" /><%def name="context_to_js()"><% ##print 'context', context, dir( context ) ##print 'context.kwargs', context.kwargs ##print 'history:', history - user_is_admin = trans.user_is_admin() - user_roles = trans.get_current_user_roles() - prepped_hdas = [ - prep_hda( hda, True ) for hda in datasets ] + ##TODO: move to API + for_editing = True context_dict = { 'history' : { - 'id' : trans.security.encode_id( history.id ), - 'name' : history.name + 'id' : trans.security.encode_id( history.id ), + 'name' : history.name, + + 'status' : status, + 'showDeleted' : show_deleted, + 'showHidden' : show_hidden, + 'quotaMsg' : over_quota, + 'message' : message, ##'go outside' + + 'deleted' : history.deleted, + 'diskSize' : history.get_disk_size( nice_size=True ), + + ## maybe security issues... + 'userIsAdmin' : trans.user_is_admin(), + 'userRoles' : [ role.get_api_value() for role in trans.get_current_user_roles() ], + + ##tagging_common.mako: render_individual_tagging_element(user=trans.get_user(), + ## tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") + 'tags' : [], + ##TODO: broken - of course + ##TODO: remove after filling tags.js + ##'tagHTML' : render_individual_tagging_element( + ## user=trans.get_user(), + ## tagged_item=history, + ## elt_context="history.mako", + ## use_toggle_link=False, + ## input_size="20"), + ##TODO:?? h.to_unicode( annotation ) | h + 'annotation' : h.to_unicode( annotation ), + + ##TODO: broken + 'baseURL' : h.url_for( 'history', show_deleted=show_deleted ), + 'hideDeletedURL' : h.url_for( 'history', show_deleted=False ), + 'hideHiddenURL' : h.url_for( 'history', show_hidden=False ), + 'tagURL' : h.url_for( controller='history', action='tag' ), + 'annotateURL' : h.url_for( controller='history', action='annotate' ) }, - 'annotation' : annotation, - 'hdas' : prepped_hdas, - 'hdaId' : hda_id, - 'showDeleted' : show_deleted, - 'showHidden' : show_hidden, - 'quotaMsg' : over_quota, - 'message' : message, - 'status' : status, + 'hdas' : [ prep_hda( hda, for_editing ) for hda in datasets ], # some of these may be unneeded when all is said and done... - 'forEditing' : True, - - ## maybe security issues... - 'userIsAdmin' : user_is_admin, - 'userRoles' : [ role.get_api_value() for role in user_roles ], - + 'hdaId' : hda_id, + 'forEditing' : for_editing, } %> ${ h.to_json_string( context_dict ) } @@ -307,9 +344,7 @@ ${parent.javascripts()} ${h.js( - "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", - ##"libs/handlebars.full", - "galaxy.autocom_tagging", + "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", "mvc/base-mvc", "mvc/ui" )} @@ -324,15 +359,12 @@ "template-history-downloadLinks", "template-history-tagArea", "template-history-annotationArea", - "template-history-displayApps" + "template-history-displayApps", + + "template-history-historyPanel" )} - ## if using in-dom templates they need to go here (before the Backbone classes are defined) - ##NOTE: it's impossible(?) to include _ templates in this way bc they use identical delims as mako - ## (without altering Underscore.templateSettings) - ##<%include file="../../static/scripts/templates/common-templates.html" /> - ##<%include file="../../static/scripts/templates/history-templates.html" /> - + ##TODO: fix: curr hasta be _after_ h.templates - move somehow ${h.js( "mvc/history" ##"mvc/tags", "mvc/annotations" @@ -345,40 +377,34 @@ // Init. on document load. var pageData = ${context_to_js()}; - - //USE_MOCK_DATA = true; - USE_CURR_DATA = true; + if( console && console.debug ){ + window.pageData = pageData; + + ##_.each( pageData.hdas, function( hda ){ + ## console.debug( hda ); + ##}); + } // on ready + USE_CURR_DATA = true; $(function(){ if( console && console.debug ){ console.debug( 'using backbone.js in history panel' ); } - if( window.USE_MOCK_DATA ){ - if( console && console.debug ){ console.debug( '\t using mock data' ); } - createMockHistoryData(); - return; - - //TODO: handle empty history - } else if ( window.USE_CURR_DATA ){ - if( console && console.debug ){ console.debug( '\t using current history data' ); } + if ( window.USE_CURR_DATA ){ + // Navigate to a dataset. + if( pageData.hdaId ){ + self.location = "#" + pageData.hdaId; + } + glx_history = new History( pageData.history ).loadDatasetsAsHistoryItems( pageData.hdas ); glx_history_view = new HistoryView({ model: glx_history }); glx_history_view.render(); return; + + } else { + // sandbox } - - // sandbox here - // testing iconButton - //ibm = new IconButton({ - // icon_class : 'information', - // on_click : function( event ){ console.debug( 'blerg' ); }, - //}); - //mockObj = { one : 1 }; - //ibv = new IconButtonView({ model : ibm }); - //new_click = function( event ){ console.debug( mockObj.one ); } - //$( 'body' ).append( ibv.render().$el ); - }); </script> @@ -387,7 +413,8 @@ <%def name="stylesheets()"> ${parent.stylesheets()} ${h.css("base", "history", "autocomplete_tagging" )} - <style>" + <style> + ## TODO: move to base.less .historyItemBody { display: none; } @@ -425,164 +452,4 @@ ${_('Galaxy History')} </%def> -<body class="historyPage"></body> - -<script type="text/javascript"> -function createMockHistoryData(){ - mockHistory = {}; - mockHistory.data = { - - template : { - id : 'a799d38679e985db', - name : 'template', - data_type : 'fastq', - file_size : 226297533, - genome_build : '?', - metadata_data_lines : 0, - metadata_dbkey : '?', - metadata_sequences : 0, - misc_blurb : '215.8 MB', - misc_info : 'uploaded fastq file (misc_info)', - model_class : 'HistoryDatasetAssociation', - download_url : '', - state : 'ok', - visible : true, - deleted : false, - purged : false, - - hid : 0, - //TODO: move to history - for_editing : true, - //for_editing : false, - - //?? not needed - //can_edit : true, - //can_edit : false, - - accessible : true, - - //TODO: move into model functions (build there (and cache?)) - //!! be careful with adding these accrd. to permissions - //!! IOW, don't send them via template/API if the user doesn't have perms to use - //!! (even if they don't show up) - undelete_url : '', - purge_url : '', - unhide_url : '', - - display_url : 'example.com/display', - edit_url : 'example.com/edit', - delete_url : 'example.com/delete', - - show_params_url : 'example.com/show_params', - rerun_url : 'example.com/rerun', - - retag_url : 'example.com/retag', - annotate_url : 'example.com/annotate', - - peek : [ - '<table cellspacing="0" cellpadding="3"><tr><th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th><th>5.MAPQ</th><th>6.CIGAR</th><th>7.MRNM</th><th>8.MPOS</th><th>9.ISIZE</th><th>10.SEQ</th><th>11.QUAL</th><th>12.OPT</th></tr>', - '<tr><td colspan="100%">@SQ SN:gi|87159884|ref|NC_007793.1| LN:2872769</td></tr>', - '<tr><td colspan="100%">@PG ID:bwa PN:bwa VN:0.5.9-r16</td></tr>', - '<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 73 gi|87159884|ref|NC_007793.1| 2720169 37 101M = 2720169 0 NAATATGACATTATTTTCAAAACAGCTGAAAATTTAGACGTACCGATTTATCTACATCCCGCGCCAGTTAACAGTGACATTTATCAATCATACTATAAAGG !!!!!!!!!!$!!!$!!!!!$!!!!!!$!$!$$$!!$!!$!!!!!!!!!!!$!</td></tr>', - '<tr><td colspan="100%">!!!$!$!$$!!$$!!$!!!!!!!!!!!!!!!!!!!!!!!!!!$!!$!! XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0A100</td></tr>', - '<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 133 gi|87159884|ref|NC_007793.1| 2720169 0 * = 2720169 0 NAAACTGTGGCTTCGTTNNNNNNNNNNNNNNNGTGANNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNCNAANNNNNNNNNNNNNNNNNNNNN !!!!!!!!!!!!$!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>', - '<tr><td colspan="100%">!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>', - '</table>' - ].join( '' ) - } - - }; - _.extend( mockHistory.data, { - - notAccessible : - _.extend( _.clone( mockHistory.data.template ), - { accessible : false }), - - //deleted, purged, visible - deleted : - _.extend( _.clone( mockHistory.data.template ), - { deleted : true, - delete_url : '', - purge_url : 'example.com/purge', - undelete_url : 'example.com/undelete' }), - purgedNotDeleted : - _.extend( _.clone( mockHistory.data.template ), - { purged : true, - delete_url : '' }), - notvisible : - _.extend( _.clone( mockHistory.data.template ), - { visible : false, - unhide_url : 'example.com/unhide' }), - - hasDisplayApps : - _.extend( _.clone( mockHistory.data.template ), - { display_apps : { - 'display in IGB' : { - Web: "/display_application/63cd3858d057a6d1/igb_bam/Web", - Local: "/display_application/63cd3858d057a6d1/igb_bam/Local" - } - } - } - ), - canTrackster : - _.extend( _.clone( mockHistory.data.template ), - { trackster_urls : { - 'data-url' : "example.com/trackster-data", - 'action-url' : "example.com/trackster-action", - 'new-url' : "example.com/trackster-new" - } - } - ), - zeroSize : - _.extend( _.clone( mockHistory.data.template ), - { file_size : 0 }), - - hasMetafiles : - _.extend( _.clone( mockHistory.data.template ), { - download_meta_urls : { - 'bam_index' : "example.com/bam-index" - } - }), - - //states - upload : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.UPLOAD }), - queued : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.QUEUED }), - running : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.RUNNING }), - empty : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.EMPTY }), - error : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.ERROR, - report_error_url: 'example.com/report_err' }), - discarded : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.DISCARDED }), - setting_metadata : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.SETTING_METADATA }), - failed_metadata : - _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.FAILED_METADATA }) -/* -*/ - }); - - //mockHistory.views.deleted.logger = console; - mockHistory.items = {}; - mockHistory.views = {}; - for( key in mockHistory.data ){ - mockHistory.items[ key ] = new HistoryItem( mockHistory.data[ key ] ); - mockHistory.items[ key ].set( 'name', key ); - mockHistory.views[ key ] = new HistoryItemView({ model : mockHistory.items[ key ] }); - //console.debug( 'view: ', mockHistory.views[ key ] ); - $( 'body' ).append( mockHistory.views[ key ].render() ); - } -} -</script> \ No newline at end of file +<body class="historyPage"></body> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: admin: another import fix
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/78f37cb76a5f/ changeset: 78f37cb76a5f user: james_taylor date: 2012-10-01 22:55:29 summary: admin: another import fix affected #: 1 file diff -r 3c8f65f7e1a4f4217499f2369907a75a8dbcb4e9 -r 78f37cb76a5f981febf36b8119278c59d2319e91 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -4,6 +4,7 @@ from galaxy.model.orm import * from galaxy.util import inflector +from galaxy.web.form_builder import CheckboxField class Admin( object ): # Override these Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Handle unavailable tool shed when checking for updates to installed tool shed repositories at Galaxy server startup.
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3c8f65f7e1a4/ changeset: 3c8f65f7e1a4 user: greg date: 2012-10-01 22:31:25 summary: Handle unavailable tool shed when checking for updates to installed tool shed repositories at Galaxy server startup. affected #: 1 file diff -r 348ae95c02cca1d6d1b446738631ecbcf76c810a -r 3c8f65f7e1a4f4217499f2369907a75a8dbcb4e9 lib/galaxy/tool_shed/update_manager.py --- a/lib/galaxy/tool_shed/update_manager.py +++ b/lib/galaxy/tool_shed/update_manager.py @@ -36,9 +36,13 @@ tool_shed_url = get_url_from_repository_tool_shed( self.app, repository ) url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&webapp=update_manager' % \ ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision ) - response = urllib2.urlopen( url ) - text = response.read() - response.close() + try: + response = urllib2.urlopen( url ) + text = response.read() + response.close() + except Exception, e: + # The required tool shed may be unavailable. + text = 'False' return string_as_bool( text ) def shutdown( self ): self.running = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: removing webapp parameter from admin templates, fixing an import and some linting errors
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/348ae95c02cc/ changeset: 348ae95c02cc user: james_taylor date: 2012-10-01 22:16:50 summary: removing webapp parameter from admin templates, fixing an import and some linting errors affected #: 14 files diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -1,8 +1,10 @@ -from datetime import date, datetime, timedelta +from datetime import datetime, timedelta -from galaxy import config, tools, web, util +from galaxy import web, util from galaxy.model.orm import * +from galaxy.util import inflector + class Admin( object ): # Override these user_list_grid = None @@ -296,7 +298,6 @@ @web.expose @web.require_admin def mark_role_deleted( self, trans, **kwd ): - params = util.Params( kwd ) id = kwd.get( 'id', None ) if not id: message = "No role ids received for deleting" @@ -319,7 +320,6 @@ @web.expose @web.require_admin def undelete_role( self, trans, **kwd ): - params = util.Params( kwd ) id = kwd.get( 'id', None ) if not id: message = "No role ids received for undeleting" @@ -358,7 +358,6 @@ # - DefaultHistoryPermissions where role_id == Role.id # - GroupRoleAssociations where role_id == Role.id # - DatasetPermissionss where role_id == Role.id - params = util.Params( kwd ) id = kwd.get( 'id', None ) if not id: message = "No role ids received for purging" @@ -608,7 +607,6 @@ @web.expose @web.require_admin def undelete_group( self, trans, **kwd ): - params = util.Params( kwd ) id = kwd.get( 'id', None ) if not id: message = "No group ids received for undeleting" @@ -642,7 +640,6 @@ def purge_group( self, trans, **kwd ): # This method should only be called for a Group that has previously been deleted. # Purging a deleted Group simply deletes all UserGroupAssociations and GroupRoleAssociations. - params = util.Params( kwd ) id = kwd.get( 'id', None ) if not id: message = "No group ids received for purging" diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/dataset_security/group/group.mako --- a/templates/admin/dataset_security/group/group.mako +++ b/templates/admin/dataset_security/group/group.mako @@ -51,7 +51,6 @@ <div class="toolFormTitle">Group '${group.name}'</div><div class="toolFormBody"><form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='manage_users_and_roles_for_group', id=trans.security.encode_id( group.id ) )}" method="post" > - <input name="webapp" type="hidden" value="${webapp}" size=40"/><div class="form-row"><div style="float: left; margin-right: 10px;"><label>Roles associated with '${group.name}'</label> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/dataset_security/group/group_create.mako --- a/templates/admin/dataset_security/group/group_create.mako +++ b/templates/admin/dataset_security/group/group_create.mako @@ -57,7 +57,6 @@ <div class="toolFormBody"><form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='create_group' )}" method="post" ><div class="form-row"> - <input name="webapp" type="hidden" value="${webapp}" size=40"/><label>Name:</label><input name="name" type="textfield" value="${name}" size=40"/></div> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/dataset_security/group/group_rename.mako --- a/templates/admin/dataset_security/group/group_rename.mako +++ b/templates/admin/dataset_security/group/group_rename.mako @@ -10,7 +10,6 @@ <div class="toolFormBody"><form name="library" action="${h.url_for( controller='admin', action='rename_group' )}" method="post" ><div class="form-row"> - <input name="webapp" type="hidden" value="${webapp}" size=40"/><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"><input type="text" name="name" value="${group.name}" size="40"/> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/dataset_security/role/role.mako --- a/templates/admin/dataset_security/role/role.mako +++ b/templates/admin/dataset_security/role/role.mako @@ -51,7 +51,6 @@ <div class="toolFormTitle">Role '${role.name}'</div><div class="toolFormBody"><form name="associate_role_user_group" id="associate_role_user_group" action="${h.url_for( action='manage_users_and_groups_for_role', id=trans.security.encode_id( role.id ) )}" method="post" > - <input name="webapp" type="hidden" value="${webapp}" size=40"/><div class="form-row"><div style="float: left; margin-right: 10px;"><label>Users associated with '${role.name}'</label> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/dataset_security/role/role_create.mako --- a/templates/admin/dataset_security/role/role_create.mako +++ b/templates/admin/dataset_security/role/role_create.mako @@ -57,7 +57,6 @@ <div class="toolFormBody"><form name="associate_role_group_user" id="associate_role_group_user" action="${h.url_for( action='create_role' )}" method="post" ><div class="form-row"> - <input name="webapp" type="hidden" value="${webapp}" size=40"/><label>Name:</label><input name="name" type="textfield" value="${name}" size=40"/></div> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/dataset_security/role/role_rename.mako --- a/templates/admin/dataset_security/role/role_rename.mako +++ b/templates/admin/dataset_security/role/role_rename.mako @@ -10,7 +10,6 @@ <div class="toolFormBody"><form name="library" action="${h.url_for( controller='admin', action='rename_role' )}" method="post" ><div class="form-row"> - <input name="webapp" type="hidden" value="${webapp}" size=40"/><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"><input type="text" name="name" value="${role.name}" size="40"/> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/quota/quota.mako --- a/templates/admin/quota/quota.mako +++ b/templates/admin/quota/quota.mako @@ -51,7 +51,6 @@ <div class="toolFormTitle">Quota '${name}'</div><div class="toolFormBody"><form name="associate_quota_user_group" id="associate_quota_user_group" action="${h.url_for( action='manage_users_and_groups_for_quota', id=id )}" method="post" > - <input name="webapp" type="hidden" value="${webapp}" size=40"/><div class="form-row"><div style="float: left; margin-right: 10px;"><label>Users associated with '${name}'</label> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/quota/quota_create.mako --- a/templates/admin/quota/quota_create.mako +++ b/templates/admin/quota/quota_create.mako @@ -66,7 +66,6 @@ <div class="toolFormBody"><form name="associate_quota_group_user" id="associate_quota_group_user" action="${h.url_for( action='create_quota' )}" method="post" ><div class="form-row"> - <input name="webapp" type="hidden" value="${webapp}" size=40"/><label>Name:</label><input name="name" type="textfield" value="${name}" size=40"/></div> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/quota/quota_edit.mako --- a/templates/admin/quota/quota_edit.mako +++ b/templates/admin/quota/quota_edit.mako @@ -26,7 +26,6 @@ <div class="toolFormTitle">Change quota amount</div><div class="toolFormBody"><form name="library" action="${h.url_for( controller='admin', action='edit_quota' )}" method="post" > - <input name="webapp" type="hidden" value="${webapp}"/><input name="id" type="hidden" value="${id}"/><div class="form-row"><label>Amount</label> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/quota/quota_rename.mako --- a/templates/admin/quota/quota_rename.mako +++ b/templates/admin/quota/quota_rename.mako @@ -19,7 +19,6 @@ <div class="toolFormBody"><form name="library" action="${h.url_for( controller='admin', action='rename_quota' )}" method="post" ><div class="form-row"> - <input name="webapp" type="hidden" value="${webapp}" size=40"/><label>Name:</label><div style="float: left; width: 250px; margin-right: 10px;"><input type="text" name="name" value="${name}" size="40"/> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/quota/quota_set_default.mako --- a/templates/admin/quota/quota_set_default.mako +++ b/templates/admin/quota/quota_set_default.mako @@ -28,7 +28,6 @@ <div class="toolFormTitle">Set quota default</div><div class="toolFormBody"><form name="set_quota_default" id="set_quota_default" action="${h.url_for( action='set_quota_default' )}" method="post" > - <input name="webapp" type="hidden" value="${webapp}" size=40"/><input name="id" type="hidden" value="${id}"/><div class="form-row"><label>Is this quota a default for a class of users (if yes, what type)?</label> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/user/reset_password.mako --- a/templates/admin/user/reset_password.mako +++ b/templates/admin/user/reset_password.mako @@ -9,7 +9,6 @@ <div class="toolFormTitle">Reset password for users</div><div class="toolFormBody"><form name="form" action="${h.url_for( controller='admin', action='reset_user_password' )}" method="post" > - <input name="webapp" type="hidden" value="${webapp}" size=40"/><input type="hidden" name="id" value="${id}" size="40"> %for user in users: <div class="form-row"> diff -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf -r 348ae95c02cca1d6d1b446738631ecbcf76c810a templates/admin/user/user.mako --- a/templates/admin/user/user.mako +++ b/templates/admin/user/user.mako @@ -76,7 +76,6 @@ </div></div><div class="form-row"> - <input type="hidden" name="webapp" value="${webapp}"/><input type="submit" name="user_roles_groups_edit_button" value="Save"/></div></form> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: james_taylor: test framework: no longer pass webapp argument to requests
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2e0d02ea0aaf/ changeset: 2e0d02ea0aaf user: james_taylor date: 2012-10-01 21:24:36 summary: test framework: no longer pass webapp argument to requests affected #: 2 files diff -r cda0af45c3d3bd4fa9e62b37b5cc91f5272a0178 -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -835,12 +835,11 @@ self.assertTrue( genome_build == dbkey ) # Functions associated with user accounts - def create( self, cntrller='user', email='test(a)bx.psu.edu', password='testuser', username='admin-user', webapp='galaxy', redirect='' ): + def create( self, cntrller='user', email='test(a)bx.psu.edu', password='testuser', username='admin-user', redirect='' ): # HACK: don't use panels because late_javascripts() messes up the twill browser and it # can't find form fields (and hence user can't be logged in). self.visit_url( "%s/user/create?cntrller=%s&use_panels=False" % ( self.url, cntrller ) ) tc.fv( '1', 'email', email ) - tc.fv( '1', 'webapp', webapp ) tc.fv( '1', 'redirect', redirect ) tc.fv( '1', 'password', password ) tc.fv( '1', 'confirm', password ) @@ -945,17 +944,16 @@ self.visit_url( "%s/%s" % ( self.url, url ) ) self.check_page_for_string( 'Default history permissions have been changed.' ) self.home() - def login( self, email='test(a)bx.psu.edu', password='testuser', username='admin-user', webapp='galaxy', redirect='' ): + def login( self, email='test(a)bx.psu.edu', password='testuser', username='admin-user', redirect='' ): # test(a)bx.psu.edu is configured as an admin user previously_created, username_taken, invalid_username = \ - self.create( email=email, password=password, username=username, webapp=webapp, redirect=redirect ) + self.create( email=email, password=password, username=username, redirect=redirect ) if previously_created: # The acount has previously been created, so just login. # HACK: don't use panels because late_javascripts() messes up the twill browser and it # can't find form fields (and hence user can't be logged in). self.visit_url( "%s/user/login?use_panels=False" % self.url ) tc.fv( '1', 'email', email ) - tc.fv( '1', 'webapp', webapp ) tc.fv( '1', 'redirect', redirect ) tc.fv( '1', 'password', password ) tc.submit( 'login_button' ) @@ -1221,13 +1219,12 @@ # Dataset Security stuff # Tests associated with users def create_new_account_as_admin( self, email='test4(a)bx.psu.edu', password='testuser', - username='regular-user4', webapp='galaxy', redirect='' ): + username='regular-user4', redirect='' ): """Create a new account for another user""" # HACK: don't use panels because late_javascripts() messes up the twill browser and it # can't find form fields (and hence user can't be logged in). self.visit_url( "%s/user/create?cntrller=admin" % self.url ) tc.fv( '1', 'email', email ) - tc.fv( '1', 'webapp', webapp ) tc.fv( '1', 'redirect', redirect ) tc.fv( '1', 'password', password ) tc.fv( '1', 'confirm', password ) diff -r cda0af45c3d3bd4fa9e62b37b5cc91f5272a0178 -r 2e0d02ea0aaf51301582671740c9281a1a8e15cf test/functional/test_admin_features.py --- a/test/functional/test_admin_features.py +++ b/test/functional/test_admin_features.py @@ -29,7 +29,6 @@ previously_created, username_taken, invalid_username = self.create_new_account_as_admin( email='diff(a)you.com', password=password, username='admin-user', - webapp='galaxy', redirect='' ) if not username_taken: raise AssertionError, "The public name (%s) is already being used by another user, but no error was displayed" \ @@ -39,14 +38,12 @@ previously_created, username_taken, invalid_username = self.create_new_account_as_admin( email='diff(a)you.com', password=password, username='h', - webapp='galaxy', redirect='' ) if not invalid_username: raise AssertionError, "The public name (%s) is is invalid, but no error was displayed" % username previously_created, username_taken, invalid_username = self.create_new_account_as_admin( email=email, password=password, username='regular-user3', - webapp='galaxy', redirect='' ) # Get the user object for later tests global regular_user3 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Handle unavailable main Galaxy tool shed when checking for migrated tools.
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cda0af45c3d3/ changeset: cda0af45c3d3 user: greg date: 2012-10-01 21:04:52 summary: Handle unavailable main Galaxy tool shed when checking for migrated tools. affected #: 2 files diff -r 4ccb8691639233bb99b4f3e3ebb9b9eacf4c9461 -r cda0af45c3d3bd4fa9e62b37b5cc91f5272a0178 lib/galaxy/tool_shed/migrate/check.py --- a/lib/galaxy/tool_shed/migrate/check.py +++ b/lib/galaxy/tool_shed/migrate/check.py @@ -43,6 +43,8 @@ db_schema = schema.ControlledSchema( engine, migrate_repository ) latest_tool_migration_script_number = migrate_repository.versions.latest if latest_tool_migration_script_number != db_schema.version: + # The default behavior is that the tool shed is down. + tool_shed_accessible = False if app.new_installation: # New installations will not be missing tools, so we don't need to worry about them. missing_tool_configs_dict = odict() @@ -51,8 +53,12 @@ if tool_panel_configs: # The missing_tool_configs_dict contents are something like: # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]} - missing_tool_configs_dict = check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) + tool_shed_accessible, missing_tool_configs_dict = check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) else: + # It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but + # we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in + # the database. + tool_shed_accessible = True missing_tool_configs_dict = odict() have_tool_dependencies = False for k, v in missing_tool_configs_dict.items(): @@ -63,79 +69,82 @@ if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file: config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' ) if not app.config.running_functional_tests: - # Automatically update the value of the migrate_tools.version database table column. - cmd = 'sh manage_tools.sh%s upgrade' % config_arg - proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) - return_code = proc.wait() - output = proc.stdout.read( 32768 ) - if return_code != 0: - raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) - elif missing_tool_configs_dict: - if len( tool_panel_configs ) == 1: - plural = '' - tool_panel_config_file_names = tool_panel_configs[ 0 ] - else: - plural = 's' - tool_panel_config_file_names = ', '.join( tool_panel_configs ) - msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" - msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" - msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be\n" - msg += "automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" - msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" - msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n" - msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names ) - msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n" - msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n" - msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location\n' - msg += "setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n" - msg += "you execute the installation process if appropriate. The configured location must be outside of the Galaxy installation\n" - msg += "directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within\n" - msg += "the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using mercurial's\n" - msg += "clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly\n" - msg += "configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed\n" - msg += "repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following\n" - msg += "URL for details.\n\nhttp://mercurial.selenic.com/wiki/.hgignore\n\n" - if have_tool_dependencies: - msg += "The following tool dependencies can also optionally be installed (see the option flag in the command below). If you\n" - msg += "choose to install them (recommended), they will be installed within the location specified by the 'tool_dependency_dir'\n" - msg += "setting in your main Galaxy configuration file (e.g., uninverse_wsgi.ini).\n" - processed_tool_dependencies = [] + if tool_shed_accessible: + # Automatically update the value of the migrate_tools.version database table column. + cmd = 'sh manage_tools.sh%s upgrade' % config_arg + proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) + return_code = proc.wait() + output = proc.stdout.read( 32768 ) + if return_code != 0: + raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) + elif missing_tool_configs_dict: + if len( tool_panel_configs ) == 1: + plural = '' + tool_panel_config_file_names = tool_panel_configs[ 0 ] + else: + plural = 's' + tool_panel_config_file_names = ', '.join( tool_panel_configs ) + msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" + msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" + msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be\n" + msg += "automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" + msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" + msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n" + msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names ) + msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n" + msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n" + msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location\n' + msg += "setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n" + msg += "you execute the installation process if appropriate. The configured location must be outside of the Galaxy installation\n" + msg += "directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within\n" + msg += "the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using mercurial's\n" + msg += "clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly\n" + msg += "configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed\n" + msg += "repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following\n" + msg += "URL for details.\n\nhttp://mercurial.selenic.com/wiki/.hgignore\n\n" + if have_tool_dependencies: + msg += "The following tool dependencies can also optionally be installed (see the option flag in the command below). If you\n" + msg += "choose to install them (recommended), they will be installed within the location specified by the 'tool_dependency_dir'\n" + msg += "setting in your main Galaxy configuration file (e.g., uninverse_wsgi.ini).\n" + processed_tool_dependencies = [] + for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(): + for tool_dependencies_tup in tool_dependencies: + if tool_dependencies_tup not in processed_tool_dependencies: + msg += "------------------------------------\n" + msg += "Tool Dependency\n" + msg += "------------------------------------\n" + msg += "Name: %s, Version: %s, Type: %s\n" % ( tool_dependencies_tup[ 0 ], + tool_dependencies_tup[ 1 ], + tool_dependencies_tup[ 2 ] ) + if tool_dependencies_tup[ 3 ]: + msg += "Requirements and installation information:\n" + msg += "%s\n" % tool_dependencies_tup[ 3 ] + else: + msg += "\n" + msg += "------------------------------------\n" + processed_tool_dependencies.append( tool_dependencies_tup ) + msg += "\n" + msg += "%s" % output.replace( 'done', '' ) + msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n" + msg += "sh ./scripts/migrate_tools/%04d_tools.sh\n" % latest_tool_migration_script_number + msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n" + if have_tool_dependencies: + msg += "The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies'\n" + msg += "option to the above command like this:\n\n" + msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n" + msg += "sh ./scripts/migrate_tools/%04d_tools.sh install_dependencies\n" % latest_tool_migration_script_number + msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n" + msg += "Tool dependencies can be installed after the repositories have been installed as well.\n\n" + msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" + msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" + msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" + msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names ) for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(): - for tool_dependencies_tup in tool_dependencies: - if tool_dependencies_tup not in processed_tool_dependencies: - msg += "------------------------------------\n" - msg += "Tool Dependency\n" - msg += "------------------------------------\n" - msg += "Name: %s, Version: %s, Type: %s\n" % ( tool_dependencies_tup[ 0 ], - tool_dependencies_tup[ 1 ], - tool_dependencies_tup[ 2 ] ) - if tool_dependencies_tup[ 3 ]: - msg += "Requirements and installation information:\n" - msg += "%s\n" % tool_dependencies_tup[ 3 ] - else: - msg += "\n" - msg += "------------------------------------\n" - processed_tool_dependencies.append( tool_dependencies_tup ) - msg += "\n" - msg += "%s" % output.replace( 'done', '' ) - msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n" - msg += "sh ./scripts/migrate_tools/%04d_tools.sh\n" % latest_tool_migration_script_number - msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n" - if have_tool_dependencies: - msg += "The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies'\n" - msg += "option to the above command like this:\n\n" - msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n" - msg += "sh ./scripts/migrate_tools/%04d_tools.sh install_dependencies\n" % latest_tool_migration_script_number - msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n" - msg += "Tool dependencies can be installed after the repositories have been installed as well.\n\n" - msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" - msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" - msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" - msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names ) - for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(): - msg += "%s\n" % missing_tool_config - msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n" - raise Exception( msg ) + msg += "%s\n" % missing_tool_config + msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n" + raise Exception( msg ) + else: + log.debug( "The main Galaxy tool shed is not currently available, so skipped tool migration %s until next server startup" % db_schema.version ) else: log.info( "At migrate_tools version %d" % db_schema.version ) diff -r 4ccb8691639233bb99b4f3e3ebb9b9eacf4c9461 -r cda0af45c3d3bd4fa9e62b37b5cc91f5272a0178 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -21,6 +21,8 @@ root = tree.getroot() tool_shed = root.get( 'name' ) tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ) + # The default behavior is that the tool shed is down. + tool_shed_accessible = False if tool_shed_url: for elem in root: if elem.tag == 'repository': @@ -30,36 +32,44 @@ changeset_revision = elem.get( 'changeset_revision' ) url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&webapp=install_manager' % \ ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision ) - response = urllib2.urlopen( url ) - text = response.read() - response.close() - if text: - tool_dependencies_dict = tool_shed_decode( text ) - for dependency_key, requirements_dict in tool_dependencies_dict.items(): - tool_dependency_name = requirements_dict[ 'name' ] - tool_dependency_version = requirements_dict[ 'version' ] - tool_dependency_type = requirements_dict[ 'type' ] - tool_dependency_readme = requirements_dict.get( 'readme', '' ) - tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) ) - for tool_elem in elem.findall( 'tool' ): - migrated_tool_configs_dict[ tool_elem.get( 'file' ) ] = tool_dependencies - # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. - missing_tool_configs_dict = odict() - for tool_panel_config in tool_panel_configs: - tree = util.parse_xml( tool_panel_config ) - root = tree.getroot() - for elem in root: - if elem.tag == 'tool': - missing_tool_configs_dict = check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ) - elif elem.tag == 'section': - for section_elem in elem: - if section_elem.tag == 'tool': - missing_tool_configs_dict = check_tool_tag_set( section_elem, migrated_tool_configs_dict, missing_tool_configs_dict ) + try: + response = urllib2.urlopen( url ) + text = response.read() + response.close() + tool_shed_accessible = True + except Exception, e: + # Tool shed may be unavailable - we have to set tool_shed_accessible since we're looping. + tool_shed_accessible = False + print "The URL\n%s\nraised the exception:\n%s\n" % ( url, str( e ) ) + if tool_shed_accessible: + if text: + tool_dependencies_dict = tool_shed_decode( text ) + for dependency_key, requirements_dict in tool_dependencies_dict.items(): + tool_dependency_name = requirements_dict[ 'name' ] + tool_dependency_version = requirements_dict[ 'version' ] + tool_dependency_type = requirements_dict[ 'type' ] + tool_dependency_readme = requirements_dict.get( 'readme', '' ) + tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) ) + for tool_elem in elem.findall( 'tool' ): + migrated_tool_configs_dict[ tool_elem.get( 'file' ) ] = tool_dependencies + if tool_shed_accessible: + # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. + missing_tool_configs_dict = odict() + for tool_panel_config in tool_panel_configs: + tree = util.parse_xml( tool_panel_config ) + root = tree.getroot() + for elem in root: + if elem.tag == 'tool': + missing_tool_configs_dict = check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ) + elif elem.tag == 'section': + for section_elem in elem: + if section_elem.tag == 'tool': + missing_tool_configs_dict = check_tool_tag_set( section_elem, migrated_tool_configs_dict, missing_tool_configs_dict ) else: exception_msg = '\n\nThe entry for the main Galaxy tool shed at %s is missing from the %s file. ' % ( tool_shed, app.config.tool_sheds_config ) exception_msg += 'The entry for this tool shed must always be available in this file, so re-add it before attempting to start your Galaxy server.\n' raise Exception( exception_msg ) - return missing_tool_configs_dict + return tool_shed_accessible, missing_tool_configs_dict def check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ): file_path = elem.get( 'file', None ) if file_path: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: pgcleanup: Print a useful message if no options are given.
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4ccb86916392/ changeset: 4ccb86916392 user: natefoo date: 2012-10-01 19:45:37 summary: pgcleanup: Print a useful message if no options are given. affected #: 1 file diff -r 844e566f36acc3d94856a55c0d4d4dcf291f8b81 -r 4ccb8691639233bb99b4f3e3ebb9b9eacf4c9461 scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -76,6 +76,11 @@ self.options.sequence = [ x.strip() for x in self.options.sequence.split(',') ] + if self.options.sequence == ['']: + print "Error: At least one action must be specified in the action sequence\n" + parser.print_help() + sys.exit(0) + def __setup_logging(self): format = "%(funcName)s %(levelname)s %(asctime)s %(message)s" if self.options.debug: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Handle the case where a tool dependency definition changed in a tool shed repository and the new definition was pulled to a Galaxy installed repository when the Galaxy admin got updates for the repository.
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/844e566f36ac/ changeset: 844e566f36ac user: greg date: 2012-10-01 18:24:53 summary: Handle the case where a tool dependency definition changed in a tool shed repository and the new definition was pulled to a Galaxy installed repository when the Galaxy admin got updates for the repository. affected #: 5 files diff -r de2c99ce5f749582c3ce3bfb02422588c70b1a06 -r 844e566f36acc3d94856a55c0d4d4dcf291f8b81 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3077,10 +3077,16 @@ self.error_message = error_message @property def can_install( self ): - return self.status in [ self.installation_status.NEVER_INSTALLED, self.installation_status.UNINSTALLED ] + return self.status in [ self.installation_status.NEVER_INSTALLED, self.installation_status.UNINSTALLED ] @property def can_uninstall( self ): - return self.status in [ self.installation_status.ERROR, self.installation_status.INSTALLED ] + return self.status in [ self.installation_status.ERROR, self.installation_status.INSTALLED ] + @property + def can_update( self ): + return self.status in [ self.installation_status.NEVER_INSTALLED, + self.installation_status.INSTALLED, + self.installation_status.ERROR, + self.installation_status.UNINSTALLED ] @property def in_error_state( self ): return self.status == self.installation_status.ERROR diff -r de2c99ce5f749582c3ce3bfb02422588c70b1a06 -r 844e566f36acc3d94856a55c0d4d4dcf291f8b81 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -138,6 +138,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, + updating_installed_repository=False, webapp='galaxy' ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) diff -r de2c99ce5f749582c3ce3bfb02422588c70b1a06 -r 844e566f36acc3d94856a55c0d4d4dcf291f8b81 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -528,7 +528,6 @@ status=app.model.ToolDependency.installation_status.NEVER_INSTALLED, set_status=set_status ) tool_dependency_objects.append( tool_dependency ) - elif tool_dependency_type == 'set_environment': for env_elem in elem: # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> @@ -603,13 +602,19 @@ tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return tool_dependencies_dict def generate_metadata_for_changeset_revision( app, repository, repository_clone_url, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, webapp='galaxy' ): + resetting_all_metadata_on_repository=False, updating_installed_repository=False, webapp='galaxy' ): """ Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's disk files, so the value of repository_files_dir will not always be repository.repo_path (it could be an absolute path to a temporary directory containing a clone). If it is an absolute path, the value of relative_install_dir must contain repository.repo_path. """ + if updating_installed_repository: + # Keep the original tool shed repository metadata if setting metadata on a repository installed into a local Galaxy instance for which + # we have pulled updates. + original_repository_metadata = repository.metadata + else: + original_repository_metadata = None readme_file_names = get_readme_file_names( repository.name ) metadata_dict = {} invalid_file_tups = [] @@ -724,7 +729,11 @@ # This step must be done after metadata for tools has been defined. tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', files_dir ) if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) + metadata_dict = generate_tool_dependency_metadata( app, + repository, + tool_dependencies_config, + metadata_dict, + original_repository_metadata=original_repository_metadata ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs # Reset the value of the app's tool_data_path and tool_data_table_config_path to their respective original values. @@ -747,11 +756,16 @@ if requirements_dict: tool_dependencies_dict[ dependency_key ] = requirements_dict return tool_dependencies_dict -def generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ): +def generate_tool_dependency_metadata( app, repository, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): """ If the combination of name, version and type of each element is defined in the <requirement> tag for at least one tool in the repository, then update the received metadata_dict with information from the parsed tool_dependencies_config. """ + if original_repository_metadata: + # Keep a copy of the original tool dependencies dictionary in the metadata. + original_tool_dependencies_dict = original_repository_metadata.get( 'tool_dependencies', None ) + else: + original_tool_dependencies_dict = None try: tree = ElementTree.parse( tool_dependencies_config ) except Exception, e: @@ -770,6 +784,10 @@ if tool_dependencies_dict: metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict if tool_dependencies_dict: + if original_tool_dependencies_dict: + # We're generating metadata on an update pulled to a tool shed repository installed into a Galaxy instance, so handle changes to + # tool dependencies appropriately. + handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_tool_dependencies_dict, tool_dependencies_dict ) metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict return metadata_dict def generate_tool_guid( repository_clone_url, tool ): @@ -1470,6 +1488,24 @@ # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( app ) return repository_tools_tups +def handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_dependency_dict, new_dependency_dict ): + """ + This method is called when a Galaxy admin is getting updates for an installed tool shed repository in order to cover the case where an + existing tool dependency was changed (e.g., the version of the dependency was changed) but the tool version for which it is a dependency + was not changed. In this case, we only want to determine if any of the dependency information defined in original_dependency_dict was + changed in new_dependency_dict. We don't care if new dependencies were added in new_dependency_dict since they will just be treated as + missing dependencies for the tool. + """ + updated_tool_dependency_names = [] + deleted_tool_dependency_names = [] + for original_dependency_key, original_dependency_val_dict in original_dependency_dict.items(): + if original_dependency_key not in new_dependency_dict: + updated_tool_dependency = update_existing_tool_dependency( app, repository, original_dependency_val_dict, new_dependency_dict ) + if updated_tool_dependency: + updated_tool_dependency_names.append( updated_tool_dependency.name ) + else: + deleted_tool_dependency_names.append( original_dependency_val_dict[ 'name' ] ) + return updated_tool_dependency_names, deleted_tool_dependency_names def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups, sample_files_copied ): """ Inspect each tool to see if it has any input parameters that are dynamically generated select lists that depend on a .loc file. @@ -1862,21 +1898,28 @@ trans.app.toolbox.write_integrated_tool_panel_config_file() def remove_tool_dependency( trans, tool_dependency ): dependency_install_dir = tool_dependency.installation_directory( trans.app ) - try: - shutil.rmtree( dependency_install_dir ) - removed = True - error_message = '' - log.debug( "Removed tool dependency installation directory: %s" % str( dependency_install_dir ) ) - except Exception, e: - removed = False - error_message = "Error removing tool dependency installation directory %s: %s" % ( str( dependency_install_dir ), str( e ) ) - log.debug( error_message ) + removed, error_message = remove_tool_dependency_installation_directory( dependency_install_dir ) if removed: tool_dependency.status = trans.model.ToolDependency.installation_status.UNINSTALLED tool_dependency.error_message = None trans.sa_session.add( tool_dependency ) trans.sa_session.flush() return removed, error_message +def remove_tool_dependency_installation_directory( dependency_install_dir ): + if os.path.exists( dependency_install_dir ): + try: + shutil.rmtree( dependency_install_dir ) + removed = True + error_message = '' + log.debug( "Removed tool dependency installation directory: %s" % str( dependency_install_dir ) ) + except Exception, e: + removed = False + error_message = "Error removing tool dependency installation directory %s: %s" % ( str( dependency_install_dir ), str( e ) ) + log.debug( error_message ) + else: + removed = True + error_message = '' + return removed, error_message def reset_tool_data_tables( app ): # Reset the tool_data_tables to an empty dictionary. app.tool_data_tables.data_tables = {} @@ -1925,7 +1968,7 @@ translated.append( '' ) return ''.join( translated ) def to_html_str( text ): - """Translates the characters in text to sn html string""" + """Translates the characters in text to an html string""" translated = [] for c in text: if c in VALID_CHARS: @@ -1954,6 +1997,63 @@ else: translated_string = '' return translated_string +def update_existing_tool_dependency( app, repository, original_dependency_dict, new_dependencies_dict ): + """ + Update an exsiting tool dependency whose definition was updated in a change set pulled by a Galaxy administrator when getting updates + to an installed tool shed repository. The original_dependency_dict is a single tool dependency definition, an example of which is: + {"name": "bwa", + "readme": "\\nCompiling BWA requires zlib and libpthread to be present on your system.\\n ", + "type": "package", + "version": "0.6.2"} + The new_dependencies_dict is the dictionary generated by the generate_tool_dependency_metadata method. + """ + new_tool_dependency = None + original_name = original_dependency_dict[ 'name' ] + original_type = original_dependency_dict[ 'type' ] + original_version = original_dependency_dict[ 'version' ] + # Locate the appropriate tool_dependency associated with the repository. + tool_dependency = None + for tool_dependency in repository.tool_dependencies: + if tool_dependency.name == original_name and tool_dependency.type == original_type and tool_dependency.version == original_version: + break + if tool_dependency and tool_dependency.can_update: + dependency_install_dir = tool_dependency.installation_directory( app ) + removed_from_disk, error_message = remove_tool_dependency_installation_directory( dependency_install_dir ) + if removed_from_disk: + sa_session = app.model.context.current + new_dependency_name = None + new_dependency_type = None + new_dependency_version = None + for new_dependency_key, new_dependency_val_dict in new_dependencies_dict.items(): + # Match on name only, hopefully this will be enough! + if original_name == new_dependency_val_dict[ 'name' ]: + new_dependency_name = new_dependency_val_dict[ 'name' ] + new_dependency_type = new_dependency_val_dict[ 'type' ] + new_dependency_version = new_dependency_val_dict[ 'version' ] + break + if new_dependency_name and new_dependency_type and new_dependency_version: + # Update all attributes of the tool_dependency record in the database. + log.debug( "Updating tool dependency '%s' with type '%s' and version '%s' to have new type '%s' and version '%s'." % \ + ( str( tool_dependency.name ), + str( tool_dependency.type ), + str( tool_dependency.version ), + str( new_dependency_type ), + str( new_dependency_version ) ) ) + tool_dependency.type = new_dependency_type + tool_dependency.version = new_dependency_version + tool_dependency.status = app.model.ToolDependency.installation_status.UNINSTALLED + tool_dependency.error_message = None + sa_session.add( tool_dependency ) + sa_session.flush() + new_tool_dependency = tool_dependency + else: + # We have no new tool dependency definition based on a matching dependency name, so remove the existing tool dependency record + # from the database. + log.debug( "Deleting tool dependency with name '%s', type '%s' and version '%s' from the database since it is no longer defined." % \ + ( str( tool_dependency.name ), str( tool_dependency.type ), str( tool_dependency.version ) ) ) + sa_session.delete( tool_dependency ) + sa_session.flush() + return new_tool_dependency def update_repository( repo, ctx_rev=None ): """ Update the cloned repository to changeset_revision. It is critical that the installed repository is updated to the desired diff -r de2c99ce5f749582c3ce3bfb02422588c70b1a06 -r 844e566f36acc3d94856a55c0d4d4dcf291f8b81 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -753,6 +753,7 @@ relative_install_dir=repo_dir, repository_files_dir=work_dir, resetting_all_metadata_on_repository=True, + updating_installed_repository=False, webapp='community' ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: @@ -828,6 +829,7 @@ relative_install_dir=repo_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, + updating_installed_repository=False, webapp='community' ) if metadata_dict: downloadable = is_downloadable( metadata_dict ) diff -r de2c99ce5f749582c3ce3bfb02422588c70b1a06 -r 844e566f36acc3d94856a55c0d4d4dcf291f8b81 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -731,6 +731,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, + updating_installed_repository=False, webapp='galaxy' ) tool_shed_repository.metadata = metadata_dict trans.sa_session.add( tool_shed_repository ) @@ -1447,6 +1448,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, + updating_installed_repository=False, webapp='galaxy' ) repository.metadata = metadata_dict trans.sa_session.add( repository ) @@ -1566,8 +1568,7 @@ # Filter tool dependencies to only those that are installed. tool_dependencies_for_uninstallation = [] for tool_dependency in tool_dependencies: - if tool_dependency.status in [ trans.model.ToolDependency.installation_status.INSTALLED, - trans.model.ToolDependency.installation_status.ERROR ]: + if tool_dependency.can_uninstall: tool_dependencies_for_uninstallation.append( tool_dependency ) for tool_dependency in tool_dependencies_for_uninstallation: uninstalled, error_message = remove_tool_dependency( trans, tool_dependency ) @@ -1616,14 +1617,16 @@ repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) pull_repository( repo, repository_clone_url, latest_ctx_rev ) update_repository( repo, latest_ctx_rev ) + tool_shed = clean_tool_shed_url( tool_shed_url ) # Update the repository metadata. - tool_shed = clean_tool_shed_url( tool_shed_url ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, repository_clone_url=repository_clone_url, relative_install_dir=relative_install_dir, repository_files_dir=None, - resetting_all_metadata_on_repository=False ) + resetting_all_metadata_on_repository=False, + updating_installed_repository=True, + webapp='galaxy' ) repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: smcmanus: Store exit_code in database for jobs and tasks
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/de2c99ce5f74/ changeset: de2c99ce5f74 user: smcmanus date: 2012-10-01 17:42:10 summary: Store exit_code in database for jobs and tasks affected #: 1 file diff -r 035583d94b11200276aed333a859b8e49b64429f -r de2c99ce5f749582c3ce3bfb02422588c70b1a06 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -440,6 +440,7 @@ if len( job.stderr ) > 32768: log.error( "stderr for job %d is greater than 32K, only first part will be logged to database" % job.id ) job.stderr = job.stderr[:32768] + job.exit_code = tool_exit_code # custom post process setup inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) @@ -1060,9 +1061,9 @@ if len( stderr ) > 32768: log.error( "stderr for job %d is greater than 32K, only first part will be logged to database" % task.id ) task.stderr = stderr[:32768] + task.exit_code = tool_exit_code task.command_line = self.command_line self.sa_session.flush() - log.debug( 'task %d ended' % self.task_id ) def cleanup( self ): # There is no task cleanup. The job cleans up for all tasks. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Missed a file in the previous commit.
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/035583d94b11/ changeset: 035583d94b11 user: inithello date: 2012-10-01 16:13:34 summary: Missed a file in the previous commit. affected #: 1 file diff -r 8d7397d2c59bb15a710f45013ca1faf8c91326e7 -r 035583d94b11200276aed333a859b8e49b64429f test-data/hg19chrX_midpart.fasta --- a/test-data/hg19chrX_midpart.fasta +++ /dev/null @@ -1,751 +0,0 @@ ->chrX_part -TCTGTTAGACTCACTCAGGACTGTATGAGCATCACCTGTGCTGCACTGTG -ACTTTACAGATATTAACGAAGAATCCTCAAGGATCTGTGTTTCGGAGGCA -ATCTGGTGACCAGCAGCATTCTCAGCATTCAAATGATGACCCTCAAAATA -GGCAGTAGCATTTTTATCTGCTCTGTCATTGGCTACAAAAGACGGCACCA -CTGGTACTGATCTTGGTAGCTGATATTCAGGAGAAAGGCTGACCAAGGGT -GTATATATGCTGGTGTACTGGGGCAAACCTGGTAACACATTTATGTATGC -TGGCGATGTCCGGGTGTTATCAAATCTCTGGAAAGGAAGATACGTACAGT -ATCCTGTGACCAAATGGGATTGAGCCCAATAAGTTGGTTTCACATCCTCA -AGAACCGGTTTGGGAGAATTAGAGGAGACTCGCTTGTAATTTGCATCCTC -AGAGCCTGGTTTGGGAGAATTAGAAGAGAACCCTTTGGGTTTCCCATCCT -CAGAAACTTGTCTAGAAGAATTATCGGATACTGGTTTGGCCTTCACATCT -TCACAAGCTGGCTTGGGAGAATTTGCAGACAAAGGTTTGGGTTTCACATC -TTCAGAAGCTGGTGCTGAAGATGAACCTGATACTGGTTTAGACTTTACAT -CTGGTTTAAATTCCCTAGCAGCTGAATTAAGTGGTAGTTTAACTTGTAAA -TACTCTCCTGCTTTTGAAATGTCTTCTACTTTTGTTTTAATGTTTTTCTT -CTTTCTTTTTTTCTTGAGCCGTGATGCAACTTTCTTCAATGCAATACAGT -TGTCAATCACAACAAAACGGGGACATCCCAAGAGAAAAGATTTTAAACCT -CCTGCTTTTTCTAGTATTGGTCGAGTTTCTTCTGGGAAAAACTCATATTC -TTCAGAGAACATCTTGTGACTCATGTCCAAGGGACCATGTTCCTCCAACA -ACTGAGAGAAGTAATCATATAGAGTTGAACATTTTTGTTTTGGGTTCATG -TCCCATAGCTTCTTATTGCGGACAACATATTCATTACTGTGTTGGTCATA -GAGAGCTTCAAATTCTTCTACGTCTTGCCGAAGATGGTCAGGCACTGCAA -ATGGGCCTGCAGTATCTGAATTTTGATTGCTATGGTCTTCACTTGAAGTG -ATGATCTCATTATTTGGAGTTACTGAAGTTGTTCCAGACCCAACTAACAT -AGGCTTTGAATCCTTTGGTTTCTTTTTCTTGCCTTTGTTTTTCACCTTGG -TAGAACTAAACGGTGCTTCGCCACTGTCTTGTTTCCTTAACACAGTACAG -CGGCTGTCCATTATATCAAAGAATTCATCTAAAGCACTATGTAATGCTGG -GAACTTGTCTCTGTGTTCTTCTAGCAGCCATATTAAACAGCGGGCTTCCT -TCGATGATGTTGGCTCAAAGAAATAATCAAGTTGCTTTCCTTCTATAGAG -TCTAGTTTGTGACCATATTTCTCATTCCAGAGGAAAGTCATGATGCTAAA -ATCAAGCTGTTTAAGAGATGCTTCATACCGAGAAAAGAAAGGTCCTGTGG -CATCTAAGCCAAAGCTATTAAGTTTTCGGATCCAGGCGGCTAATTTGGGC -TCCACTTCTTTAAGCTCACTCAAAACATGCAGAAATATTCTTGTCTTTAC -TCTGTTCTTTTCTTGAATCAAGTGACGAATAACATAGTCCACTGCTTCAT -TTAGAAAATTTCTGCTTGAAAAACAGGTTGTATAGTCCTCTGTGCTCAAA -ACTTTCCAAGAAAGTAATTCTTTGAGAAGCGTGGCTGTATTCCATATGCC -GGATTTAATCTTGTCAGCATACTGCTTTATACACTGTAGAATTCTGTCAT -CAAGGAACTGACAATGCTGAACATTGTCTACAGTTTCTTTCTGCTCTTCG -TTTTTGGGTGGATTACTTTCTCTTAAGTCCTCCTCCATTCTTTCTTGTGC -TAATTTTTTTGCTTCTTTTTTTTGGATCTTTCTCTTCAATTTTTTGTCTT -CTTTCAGTCTTAGTTTCTCTAGGCTAGAACATTTCTGTTTCAGAATAGGT -CTTGGAGGAACCTTTTCTTTTATGACCTTGTGTTCAAATTCACATTTAAC -TTGACCACCACTGCTGAAGATGATAATCTTAGAAATGACACCTTCACAGT -CAGGGGTAAGACATATTCCTTGTAGAAAATCCTTGTCAATTTTATCATTA -AAGGTTGTGGTTTTTAACTTCTTCCAGCAATTCATGTGAAATTCTATTTT -ACAGTACTGGCAACAGCTGATGCGTATAAAACCCTTAAAGTCTGGATCAG -TTATGTATATCTGGATCTTAGAATATCCACAGCACTTCTGATAGCAACAA -ATGGCATCTGGCACTGGAGGGAACTTGCATTCTTCAACAAATTTCTCTAA -CAGCATCTTTATTTTTTCTGGCTGAGACTCTTCAATAATCACATTACTTG -TGGGCCAAGTTAACACTCCAGGAAGACGATAAATCAAGGTTCTTGCTTTC -TCAAAGTGATTGAGAGCTTCTAGAAATCTGTTTTTTTTCAAATATACTTT -TCCAATTCCACAGTAGGCCAAGCAATCAAGTCCCTCATTGTGGTAGTGTT -CAATAATCCTCTTAAACTGGTTTTCAGCTTCAGATAGTTCTTCAGGCTGT -CCTATTCCAAGGAGTGAAATGGCAAGTCCATAGACAACCAAGACATAGTT -AATCATGGCCAGATTCAATTGCTTTATTTTTTGAGGATCTAAACCATTCA -GCAACTCTGTAAAGGCATGTGCGGCACTGCGGCAACGCTGCTCCAATAAG -GCTGTATAGCCATCTTGAATTAAGCTTCTCAGCATTGTCATTATATTAGC -AAAATCCTGGTGTGCACCTCTGGAAGATTTAGAAAACTGTTTCTCCAAGA -TGTTCTTCAAATCTGCTGGTAAAGTCAATTGTGAACTAGAACTGAACTTT -TCTGATTCATTGTTTCGAGATTTTTGTTTTCCTTTATGTTTCGGAGGCTG -ACTTGATGGTGGTGAAAATTCAGGATGACAGTCACAATCATCTACCATCA -ATGCCTCATCCATCACCTTTAGATTCTGATTACCACCGTTAGCCATTTCG -TGATTAATTTTTCTGAAATCTCTTTCCTTCTCCACAAAGTTAAGTGAAGT -ACTAAATACAGGTGCTGATAAACTCCTAGGTGTGTAGGCCCTGTTTTCAT -AAAAGGCTTTAATTGGATTCTTATTTGCTGTTCGACCTTGTAGGTCTTCT -ATTTGTTTTTGTAACTTTACATGCTGCTGAATTAGATCCTTGATTCCCTC -AGGGTCATTTTTACAGAGTTTTTGAGCTGTTATGTTTGCTTGCAGGGCCC -AGTTATATTCCCCCAGCATAGAAAGAGCATCACAATAACGATAATGACCC -TTTGGCCAAGTGTTCTTCAGAATAGTGGCTCTCTTTCCATCACCAAGTGC -ATTTCTAAACTGTCCAGTACGAAGAAAACAAAGAGCTCGGTTACCATAAA -GAAGGTGGTTTTCAGGTCTATATTCAATGGCTCTGGTGTAATAGATAATA -GCTATATCAAATCTTTCTTTGGAAAACTCTTCATTTCCTTTCATTTTCAT -TAGTTCTCCTTGCTCTATACAATCCATACAACTTTGGGTTTTAAGTTCTT -CAAGCAAATTGCAGTCTTCCATTACAATTTTAGTTATGTGGTACTTGTAT -TCAGTAAAGAAAATACTTAACATAGGCCAACAATTGTCAATTGATCCTAA -TTTAGTTAGAATTGTTACATCGCCTGCATATTTTATCCAATTCAGAGCTT -CTTCCATTGCCAAGATTTTATTTTCTATTTTATAACCAATTCTCAATAAG -CCTCCAATAAGGAGTGAATCATTAGCAGCTTTCTTTGCCAAATCCACAAT -ATCTTCCATCAACTCAAGATGTTGTAATCTCTTCAAATTTATCTCGGAAG -CACGTGAATTGTTGGCGTCCACACAGGGATGCAATCGTGATATTACAGAA -CTGTTTTGATGTTGAAACAGAAGTGGCCAGAAGATGTTTATTTTAATGGC -ATCACAATAATCTTGCAGGACAGAAATTGGTTTACTACACCATATACTGC -AGATGTCAAATTCTAAATTCCTCTCACTTTGGACATAATCTTTATATTGC -TTACCCACCCCATCACAGTAAAGCTGAGTCACACGAACATAATCATCGGT -CATAAATTCAGCAGCAAAGACACAATCGTCCACGTAAGGGCAATCTTCTA -ACAAGGCATAATCCGCCATAGTGAAATCTCCCTCAGCAAAATTGTCCGTG -ATGCACAAGTCACGCACACACGGAGGGGTGTGGAAGGCCCCGCTCCCCTG -GCATCTCGGCTGCAGCGGGACCAGGTAACACATCCGGGAGCCCGGCCGCG -CGCCGGGTGTGCACTCACCCGGGCCTGCCGCCCGCGAGCCTGGGACGCAG -GCATccgccgccgccgccgccgccaccgccgccgccgccgcggccgccgc -cgcagcagccgccgctgccgccgccgccgccgctgctgccgctgccgctt -ccgccgccgccgccgccacctccgGCCCTCTACGTCAGCGGACGGTGGGA -GGGAGCGAGTGCTTTTAACTGTTTCGGTGTCAATACTGACCACAGTCATT -ATTTTCTCCGGCTGTACTTTAAAGTCTTAATGGTTGAAGCCATGTATCCT -TTGCCCACAGACCAGAGGAAGGGGAACCAGGTTCTTTCAGGAAAGTGCAT -GGGGGATGCCTCTCTCTCATCATGTCCCCTGACTCCCAGGTGTAATCATA -ATCTCCTCATGGAAGTGCCAGGCACATAGAGAGTGCTCTTCCTGCTGCCT -CCACTCCTGCTAGACAGAGCCCTGTCAAGGTCATCCTAAGGGCTGGGATC -CACTAACAGCTTTGACCTTAAAGCAGAGTCTGATATTGGGGATGTCATTT -CTTCACTCTGATGTACTAATTTTTTTTTTTATCTATACGCTGATGAGAGG -CTGCTCAGACACCTGCAAATTAGCATCACACTCCCCTAGGTTCTCTAGCA -AGATATTCTGGGAGGAAAACCTCTGAATCTTATTTCTACCTGTTGCTCAA -GGAAGGGACTGTTTCCAAAGAAAATCACAGTCGTATACAGGGGAGCTTTT -CTGTGTCCCTTTTTCTCCTTTGTTCCTTTTCCCCTCTCTCTCTTTTAATG -GCACCCATTTCTTCCCATCACTTAGAATCACTGAGAATCTTTTTTTACCC -TGGCTTATAAATTGTGTAGAATTCCTGTAAAGTATGGTGCTCCTTTGTCT -GTTTCCATTGTCTCTGACCTAATTTTTGACTGACTGGCCATTTACCTGAT -CCACTTtaaaagccaggagaactgtgttctcatttcagaagaaactgtgt -taccctggccagttttcttcccttttctgggattcatttcatctgtaaaa -tggggggCGGGGGTTGACCATCCTGGGTTCTATCTGGAGGTCGATGGGAG -TCAGagagagagctctgacatggtgatgcagggccttgaactccactcac -agctctgctgctaacctagcatgtgatttagttctagtccctttccactt -ctgagcctcagttccccatctAAGCAGCCATGACTGACAAGGGAGAAGTC -TTAGACTCCCACAAATGAGGACCTTGATCCCCTAACATGACTGTGTGTTC -ATAAGACCCGTATCCTCTGATCTTGAGCAGATAGAGCCTTTTCTTATCCT -CTGGATTGCTTCTTGGAAATGGCTGTAGCGAAAGCCTCTTCTTTTGTGCT -TGATACTTTATTTTCCCAGGTAAGCTCCCTCTACCTTTGTCCTGGGGCAT -GTATTTATGGATATTTTAGTTAGAAAAAGCTATCAATTAGTGTAATTAGC -TTATTGTCACCTTCAATCTTGACCCTCTCCCTGCACTGTCCCCTACCCAC -CTCAGGTTCTCTCTTATTTTAACTTAGTGAGCAGAGCTCCTGGCTGCATC -ACCATAGCAACCAGCAGCTAGGACCTATTAAGCCATGATGAGTCATTAGA -CATCTAAGCTGATTATAGAGTCCAGAATGTTAACTGCAGAAGAGATGCTG -AAAGAAGGAAAATGAGGCAGATCTTAACCTACAAACAAGTAGACAACAGA -GTAGCTGAGTGCTTCAAACTATCCCCGACCTGGATGCCATGGGCGCTATG -GGCCTGGGTGTCAACACCTTGGCATGTACCCTCAGCCACCAGACCAGAGG -GAGGGGCACCAGGCCCATTCTCTTCCCAGGGAAGTAATTCTGGACACCTT -CCTGCCAACATGCTCCAAGTAGATGGATTTGAGTCTGGATTTTTCAATGG -GCAGTACCAATTACTGAGTTCATCCTGAGTCCTACTCCTAATCTAGTGAC -ACATTTCCTTATCTTTCAACTTTCCATAGAAGTTTCTTAAATGAAAAAGG -GCATTTTTTTTTTTACTTGTTTGAAACTCTCTTTTCCCAGTCAGTTCCCC -TGCTGCCTTGGCCTGTATTTGTGGCCTGTTAAATTTAAAAGTCTATCAGT -TAGTCTAATTAGGATATTCAAATTTTAATTATTTTCCCTTCTCCACATGG -GCAGCCACCCACCCTTCTTTTATTCTCTCTTTTTATTTCATTTAGGGAAA -AAAGCTCTTGGCAGGATTGCTATAGAAACCAGCCACCAGGCAGACTAGGC -CATTGTGCTTCTGGACACTGATACTCAAAGCTGATTATGGGTCTGGAAGC -TTGCATGGCTGAGCAAGACTGATGGAGTTAAGACAAAGAGGGTCTCAGCT -ACAGAGAAGGGGAAAATAAGCACCTCAGAACTTTAGACAAACCTCAGCCC -TACCTTTATCTTTGCCCCTGTATGCTTCATGGAAGAAAAAAGTTAGAATG -AGGAAGGCTGTCCCCTATTAAAGATGAATGTCTGGGTTGACATCAGAACT -TGTGCCCTTAGGCTAACCCTGCCATGACGACAAACCCACACCTGTGAACA -TGTCATTTTCACTGAGTATCCCTAGTTCCTATTAAATTACCTGGCATATA -CTTAAGGTTCTCATAGTGCTTGGTGCTCAGCAATTCTGTAAGACAGAGCA -CTACTAGTGAGAGCACACTGAGACTACCTTGGAACATGAGCAAGTGAAGA -CTTCCTAACACACTGGATTTTTCTGGGAAATGACACTAATGAAAGCCTCT -GCTATGTGCTCTAAGGCTCCCTGTTTGCAATTTACCTCCCCTGCCTTCTG -GCAGTGGTGGTGTAAATGCCTGGTGGAGGGGCTTTGAAAGCTGTTAGTCA -CTGAAGTACCTAAGTGTATTAGGCTATTATTGCCTTCAAGGATTTTCCCC -TGGTCCCACAATGCACCCCTGTCTACATTAACAGGCTCCCACTCATTTAC -ACTGGGAGAGCAGTGCTCCTGGACACATTGCCATAGCAACCAGAAGCCAG -ACAGAGTAGGAGGGTGAGCCAGACATTTGACAGCAAAGGTTAGTGGAGTA -TCTGTTGGAGAGGGGCTGACTCTTAGGAGGAAAATACCTTATCTCTCAGC -TGCAGAGAAATAGGCCACTAGGCCCCTCAGTGTTCCAACACCATCCCCTC -CCCATCCTCCATCCCCATGCCTCCAGATGAGGAGTAGTCAGAATGAGTTT -TGTTTTATCTGGAGGCCAAGGCCTGTGTTTTATCAGAATAGGTATCCTTT -GCCCCGAAGCCGGTCAAGGGAACCAGGTACCACATACTTCCTCCTACGCC -ACCTTGTTACCAAACTAACACCCATGAGTGAACATATGCTCCAAATGTGt -gttcccatgactgcatctcctgtgcctagaatagtgtcaagtatatggca -gTGCAACTTTctgcacttcccctgtctactcactccattgcagttcacac -cttatcatttgcagaattccatttactactggaatacccactgtattagt -ctgtcctcatgctgctaataaagacatacccgagactggacaatttacaa -cagaaagaggtttaatggacttacagtttcttgtggctggggaggcctca -caatcacagctgaagatgaaaggcacatctcacatagtggcagacaagag -aagagagcttgtgcagggaaacttctctttttaaaaccatcagatcttgt -gagacttattcattatcatgaagaacagcacaggaaagaactgcccccat -gattcaattacctcctaacgggtccctcccacaacatgtgggaattcaag -atgagatttgggtaaggacacagccaaaccatatcagccacagtctcaac -tgatgacactgagaacatgaaagtaaaggaatagcctttaaaaacttctc -acttccatgcatctgcaacttgatactctgctttccctttcatcactatg -gataaactctctacattcctatgaaaacccatacctaccgttggccacta -gattacaccccttcttgactattcaatgcatggtcccagcaatgctgtct -gtgctctttgccacatcatcaatttacctttatgtactggatgattccca -tcagtacacaaagattccacaagtctcccttgcaacaacaacaacaaaac -caacaagaaagaaacaaaacaccctaccttaactgtacaacccactccac -ctactgcatcatctctgtacaccaaacttcctcaaaaatcattatgtggt -cttgatttgttcacttatgtactctcatttttttcttgaacccaccctag -tcaagcttttatcccccactccatggaaatagctcaagatccccaaataa -cctgcatattgttaaacctagtgattatttctcaggctggtcttacttga -ctgaaaagtagaatttgacacaattgatcacttcctcctccttgtaatac -tttcctcacttaatttacaggacatttctgtctcttggttgtgcttctgc -ttcagtgtctgccatttttcagagtcatggctagttactcctcactgctt -tgacctcttcacCCTGCTAGAAGCTATTAGTCAAAACATAAGTTTTTATT -TAGCCAATTGAAGGTGTGTAACATAGGACTGTGGTTGTCAGAATGGAAAC -CACTTGGGCCTTCATATAGGTGGCTGAAGAAATTTATCCAAGCAAGAGAT -AGCATCAGGTCCTGGGCTAACAGCTTTCTGGTTGGGAAAGACCCCCAACA -CCTGCCTTCATTCAGTGAGACAATTGTATGACTCACCTGCAGTAATGTGC -AGGTTAAAGGTAACGAGTTGAACTTGTAGCTTGCCCCTCTCTCACTACAT -AAACTCCTTTCTTCTCTCTGGAAGGAGTTCAGTTTCCAGCAGAGGTGATG -ACAGATTAACAGATTCCAGTTTAAAAAGTGCTATAACCCTGAAGGGGGTG -GGGTATGTTGGTAGATAAGAGAAGTTAGATCTTTAATAAATCCCACAAAT -TATTCTGGGCAATTTATTTACTGAGAATTTTTAACTCTCAAGTGTTAAGA -TTTTCCTAGATAATCATTTGTTTAATTCAGGTTTTCAAAAGCATTTACTT -CAGACTCCTTTTATTCTCTTAATTTCTTTTCTATTGCTGTTTTAAAAACA -AACAAAAAAAATACTTAGTGACTCAATTAAAAAATATTATTGGTGAGGGG -ATGAAGCACAGTTTCAAAGAGTTACAAATTAAAAATATTAATTGGCATCT -GAATTGCAAGAATCCATTTACCTCCACTCTCTAAGCTCTAATGATGTTTG -TGTCCCCAAGTCAAGTTCCAAAGTAACCATTATTCCCAATAGGTAAAATT -CCTCTGACCTCTGGTCCTGTTGAACCTTAAGGCTTACCATAAAATTGCTT -CAAATTGCAAGAAATGAGCGTGGAATTCTTCCCTCCCCCTAGCCAAGGCC -TGTTCTAGTTACAACCAACAGTCGATAAATCCCAGTGCTTCTCCCATAGT -CCCAACCCTCTCGTGCACTCTCACTACCTCATTGAGGGCTTTGGAGTTTC -CAGGATACAGCATACGAGTCTTACCAAAATCCCAGATGGGGCACCTCTCA -GTCATAACTTAAGAAGATGCTCTCAGATCTTGACTCCCAGATTCAGCCCA -GACTCACTATGATCTTGAAGTGCCTTGTGAACTTTAACAAATGGCCCATC -CTGTCCCCAGTCTCTGGTGCATAAACTGTTTCCCACATCAATCACGAGCA -CAGGTTCTATGCCATCCAACACTGCATTGTTCCTTGACATGTTTTTTTTT -TTTGTTTGTGCAGTCAACACATAATTGATGAGGCACATTCTACATGACAG -GCACTACACAAGAGACTGAGGGGTGAACTGATTAGCACCCTGCCCCTTTG -GTGACCTGTTAAGATATAATAATAATGGTCATACTGAGCTCTGAGAGTAA -AATAAAAACAGCAGTACACTCAGGAGGGGCCAAAAATATTCCATTCCTTC -CTTCCCCATCAACTTTTTATTTGTGGATCCTCAAGGCCGAATGATCCTGG -AAGACCCCTGTCTGCATAAAGACATTTATTTGTGGCCTTTCATTTCAAGT -AATTGAGTTTTGATATCTATACCAAACAAAGAAACGTCCAGACCCCCATC -ACATTATAGCTTCCCCTAAACAGTTGTTTGCAACAAACAGGTTCAGTAAG -TGACCAGTTATAAGATTAATATATAAGAAAATAGCTTTCCAGTGACTAAA -ATCCAGCTGGAAGGGCAAGGAAGTTTTACTTCATTACTGCATCTCCTAAG -AAGCTTACTAAGTCTCTGTTTCCCAAATATGTGAAAAGCAATAAGTTGCT -TCTAGGGTAAGAAGCAATAATGTATGTGTATGGAATGAACTGGCATTCAC -CTGAAGCTCAATAAAAGTTATTCCCTTCCCTTTGGAAAAAAAAAACCCAG -TTCTCAAGGTGGGACTACAGAAAATGTTTGCTTTTCATCAATTCTTTAGG -TAATTTTGAGCTTCATCTTGGGGCTGAGAATTTGGGTCAGGACCTATTGA -GAATAGCCACCACTCACCTCAAAAGAGATCACATCAGGAGGTTCATAATC -TGTTTCTATCTTTCAAGTATTCTTATTGCTTTTTCACATTTCTCTTTCAG -TACCTTACAATGGAAATATGGGCATTTCATAAAACAGAACGAGATAGTCA -TGTGCACAGCATTATCAGGGCCAAGCTTTGGAAAAATGGACTCTGATATT -CAGGACAATATCCTTAGCAAAGGGCAATTTTGATTCTCAAACGCGGACCA -GCAAAGTGCTTTGCAGTCTAATGATCCAAGCCTACCTCCAGTTTTTCTTT -TGACATCTGAAGCCTTGAACTGATTCCGGTTGCAACCACTTTACAATGAA -GGTTTTAAAATCCCTAACACACAATTCTATCAACCCTTACTCTTCAATCA -GTCAAGTACCCTACGTTTCCAATCCTAGAAATTAGGCTGCCTCCATTCCC -TGATATATAGAATGCTTTCAAATTTATAATCCAGTGCCAAGTCTTGCTTC -CATCCCTGACTTTTTTACTTTCTTAAGAATCAGAAACCATGAAGAATTCT -GGGCCCCTTGCTGATCAGCACAGTGCTATGAGAATTTCACAAGCCAAGGA -CAGTACAGATCCAGAAATCCTGTTTTATAAACTGTGTCAAGATTCAAAGT -CCATTTTCttttttattattattatactttaagttctagggtacatatgc -acaacgtgcaggtttgttacatatgtatacatgcgcccttttggtatgct -gcacccattaactcatcatttactctaggtatatctcctaatgctacacc -tcccccctccccccaccccacggcaggcccccgtgtgtgatgttccccat -gctgtgtccaagtgttctcattgttcagttcccacctatgagtgagaaca -tgcggtgtttagttttttgtccttgccatagtttgctgagaatgatggtt -tccagcttcatccatgtccttgcaaaggacatgaactcatccttttttat -ggctgcatactattccatggtgtatatgtgccacattttcttaatcaggt -ctatcattgatggacatttgggttggttccaagtctgtgatattgtgaat -agtgtcacaataaacatatgtgtgcatgtgtctttatagcagcaggattt -ataatcctttgggtatatactcagtaatgggatggcttggtcaaatggaa -tttctagttctagatccttgaggaatcgccacactgtcttccacaatggt -tgaactagtttacagtcccaccaacagtgtaaaagtgctcctatttctcc -acatcctctccagcaccttttgtttcctggcttgttaatgattggcattc -taactgttgtgagatggtatttcattgtggttttgatttgcgtttctctg -atggccagtgatgatcagtattttttcatgtgtctgttggctgccgatcc -cacagaaatacaaagtaccatcagagaatactataaacacctcaacgcaa -ataaactagaaaatctagaaaaatggataaattcctcgacatatacaccc -tcccaagactaaaccaggaagaagttgaatccctgaatagaccaataaca -ggctctgaaattgaggcaataatgaatatgctaccaacccaaaaaagtcc -aggaccagaggcattcacagccgaattctaccagaggtacaaagaggagc -tggtaccattccttctgaaaccattccaatcaatagaaaaagagggaatc -ctccctaactcattttatgaggccagcatcatccttattccaaagcatgg -cagagacaaagcaaaacaaaagagaattttagaccaatatccctgatgaa -catcgacgcaaaaatcctcaataaaatcctggcaaactgaatccagcagc -acatcaaaaagcttatccaccatgatcaagttggcttcatccctgggata -caaggctggttcaacatatgcaaatcaataaacataatccatcatataaa -cagaatcaaagacaaaaaccacatgattatctcaatagatgcagaaaagg -cctttgacacaattcaacagcccttcatgctaaaaactctcaataaacta -ggtattcatgggatgtatctcaaaataataagagctatttatgacaaacc -cacagccaatgccataatgaatgggcagaaactggaagcattccctttga -aaactggcacaagacagggatgccctctctcaccactcctattcaacata -gtgttggaagttctggccagggcaatcaggcaggagaaagaaatacaggc -tattcaattaggaaaagaggaagtcaaattgtccctgtttgcagatgaca -tgattgtatatttagaaaaccccatcatctcagcccaaaatctccttaag -ctgataagcaacttcaacaaagtctcaggatacaaaatcaacgtgcaaaa -atcacaagcattcatatacaccaataacagacaaacagggagccaaatta -tgagtgaattctcaAAGTCCATTTTCttttttttaaatattattatacaa -gtttaatatataGTCAAATGCACAACAATTTATCCTCTGGATTGGGAACA -AGAGATTTCTAGACATCTCAGCTTTAGCCAGTTTATTATACACCTACTGC -TTCATAGTTGAGTTCTTCCAGAATATCTGTTAGAACCCCTGATAGCATAC -TATTTTGTGATGAGATAAATACTTTAAAAATTATATGATCACAGTAGCAT -GGAATGACATTTCCTTAATGCTATGTTTGAGGGCCTTTTTCTTGTTTCTG -CTAGTAGAATCTGTTCTACCATTACTTATATACAAACATTATTTATTGCC -AACATGATACACATTATATGGTGTGGATCCAGTAAATATTTGTAAATTAA -CTGATTTGGCACCCCACAATATCTCAAGACATGAGATTTAAGAAGAAAAG -AGCTTGACTAGTAAACCTGGTAGAGAAAATGCCTTTATACAGTTAGTATA -TCCCACAATACTATCAACAAGTAGATTGGATTTTATTGTTATAACAGAAT -TGAGTGAGATTGTGAATAATAAGAAAGTTGAGTTGTGGTGCATTGTCCTT -AGAAGTTTCCTTCCTTTCTTTCCTTCTGTTCAGTGTTGTGACCTCAAATA -AGGGGCACAGATGCCTCCTCGGGCAGCTTGGGGCAAGTGATCTACTTTCT -TTTTTTTTTCTTTTTTAAAAttttattattattatactttaagttttagg -gtacatgtgcacaacgtgcaggtttgttacatatgtatacatgtgccctt -ttggtgtgctgcacctattaactcatcattaagcattaggtatatctcct -aatgctatccctcctcactccccccaccccaccacagtccccggtgtgta -atgttccccttcctgtgtccatgtattctgattgttcaattcccacctat -gagtgagaacatgcggtgtttggttttttgtccttgtgatagtttgctga -gaatgatggtttgcagcttcatccatgtccccacaaaggacatgaactca -tcattttttatggctgcatagtattccatggtgtatatgtgccacatttt -cttaatccagtctatcattgttggacatttgggttggttccaagtctttg -ctattgtgaatagtgctgcaataaacgtacgtgtgcatgtgtctttatag -cagcaggatttataatcctttgggtatatactcagtaatgagatggctgg -gtcaaatggtatttctagttctagatccctgaggaatcgccacaccgact -tccacaatggttgagctagttcacagtcccaccaacagtgtaaaagtgtt -cctatttctccacatcctctccagcacctgttgtttcctgactttttaat -gatcaccattctaactggtgtgagatggtactcattgtggttttgatttg -catttctctgatggccagtgatgatgagcattttttcatgtgtcttttgg -ctccataaatgtcttcttttgagaagtgtctgttcatatccttcgtccac -tttttgatggggttgtttgtttttttcttgtaaatttgtttgagttcatt -gtagattctagatattagccctttgtcagatgagtaggttgtgccatccc -catcaagctaccaatgactttcttcacagaattggaaaaaacttctttaa -agttcatatggaaccaaaaaagagcccgcattgccaagtcaatcctaagc -caaaatatcaaagctggaggcatcatgctacctgacttcaaactatacta -caaggttacagtctgacacacagagctagtgaaatttaggcagagcaact -gcacaggcatgtgcagagaccaggagccttagatacttgggctttctggg -ctcccctaaaaaagtagttgcaactcaagcaaagcaggaacagacccccg -tacataccctaggaaagaggctgaatccagggggccaagcagcaacagtc -tacaggccccacttccatggcatctcacaggataagacccagtggcttgg -aattccagccaggcaccggtagtagtgttacacctctctgagacagagct -cctgtggagaggggccaggggccaacctccatctttgctgtttggacaac -tttgctgtttcagccttcgagctttggagagtccaagccaaccgggggtg -gaagggactcctgagcacagcacaactgctctgtgaaaatgtggccagtc -tgcttctttaaatgggtccctgatcccattccttctcactgggtgggacc -tcccaactagggtctccagccacccccaccactgttatctggctaaacag -ttttgaaacctccttaggatagagctcccagagagaaaagtgaaccgaca -tctttgctgtttgtgtgacaaccattccagccttcaggttttggagagtc -caagctgaccaggggagaaagggattacccaacacagcacagctgttata -caaaaacatggctagactgctgtttaaaacaagtttccaatcccgttcct -cctcactaggcaggacctcccaaccagaacctccagccaccctcgagggt -gttctttggccaacagagatccgaatacttcctcagttggagctcccaag -gggaggggcaggcctccatctttgctctttgggtgacttagctgtttcac -ccttttcgctttgagattctgaggtgacaaaaggctgaagcagacaccca -gcacagcagagctgctctatgaaaacatggcaagactgatttttaaagca -agtctctgatcctattcctcctcactggaggtgacctcccaactggggtc -tccagccagctccttcagatgcattcaggctggcaaaaagtccatacctc -cctgggatggaggtcccagagggaggggcaggttgccatttttactgttt -tgcagcctttggtggtaatacctccaggtaccagaaactccaaggtgact -agcaactggagtgggcatccagcataccacagcaatccggcaaagaaaat -gtctagcctgttacattggtatctgtttccatatctcatcaccaggcaag -tcttccagacctgggcctccagccatcatctgccagagatactgagccag -tagcaactttacaactccctggacagagtttccaggggcaactgaaagtc -tttctaccactgcctctgtagtggacctgtctttgctaaccttggactaa -caaaggagtaaaaaccctacctaagtgccttatccacacctccaacaagc -tgcagttgacccaagaagaggaggccagtttgtctccaatgggtcctaca -caccccctgctgctcatcaccagacaaggaacccctggcttgggcccaca -gcacaaaccctccatcctaggctgatttcactgcacaattgctgacccac -atttctctggggtggagcccccaggaggcaagcaaagtggtggcacagca -agccagctgatatggagcccagagggtttagtgttggagcatctgtagtg -gagtgtggccaggtacggccatccctcttggctcagcttgctcccataag -agacttcagacctaggggaatggtcagatctgatctctgccatgcagtct -tgcacaccagatggggctgatccaacctgagcactccttggtctcctggc -ctctttcagggtttcaccctggacactccagcttacaaggcagtcttgga -tgccctggggacacacaccttaccttctgcactagtagactgcgcctgat -cagtggagagtgccaaaaatgtggcccctatggccctgcacagcctgcat -attccatcctcatactgcagctttcctcaagtccatggcaactctccaca -tccctttgctggcacctgtctgcatgagtaggttttgcttcacatgctct -gccaacacacgggattgcagtacacccccaccacctccactgaacaccaa -tgaagatgaagccttagtgggcacagagccagcaagccccacccccacca -gcacctagcccctgtgctaatgctgcacagagaacaaggtatcctcccac -accccgagtgatcactcctgcttgcagggaacaaagaaggcacccagacc -tgtgctggccaacaaccttccaaaagccaataccacctccactgcaacag -tgcacacaatcttcagcaggggctttctgctccccaccacccccagctgc -ctagcctctgccactgtggtaaatgcctgcaggaaggcaggtacccctgt -atttgctaacactcttgctgcagctgctgcacattgggccccacagcaca -gtggactgcaaacctcatggaccagagaacaaagtcagggccccagagtt -agcatatgtaggccaggggttgggagctgagcactggccccctaaaagct -ttctgaaatgaagccatttggctgaatcaaacttgtacctcaatcaaacc -atcaaggtcatgaataaaagaaaagaaaagaaaagaaaagaaaagaaaag -aaacccagccaaaggtcagcaacctcaaagattgtaggtacataaaccca -caaatatgagaaagaatcagtgcaagaacacaaaaaactcaaaaagccag -agtgccttctttcctacaaatgaccatatcacctgtccagcaagggttca -caaccaggctgaggctgagatggctgaaatgacagaagtagatttcagaa -catgaacaggaatgaagttcattgagctacaagagtacattgtgacccac -tgcaagaaagctaaaaattatgataaaacattgcaggagctgacagacaa -aatagccagtatacagaagaacacaattgacctgacagagctaaaaacac -actacaagaattttataattctatcacatgtattaatagcagaatagacc -aaatggaggagtctcagagcttgaatactgtctttttgaaataagacagg -cagacaagaatagagaaaaaagaataaaaagaaatgaacagagcctccaa -gaaatatggaattatgtaaagagattgaatctatgacgggctggtgtacc -tgaaagagatggggagaatggaaccaacttggaaaacatattttaggata -ttatccatgagaatgtccccaatgtagctaggaaggccaacatacaaatt -caggaaatactgagaaccccagtaagatataccacaagaagatcatcccc -aagacacaatcatcagattctccaaggttgaaatgaatgagaaaaatgtt -aaagacagctagagacaaagctcaggtcatctacaaaaggaagcccattg -gactaaaagtggatttctcagctaaaaccctacaagccagaagagatttg -gggctaatattcaacactcttaaagaaaagaaattcaaaccaagaatttc -atatctggccaaactaaacttcataagcaaaggagaaatcagatcttttt -cagacaagcaaatgctgagggaaattgttaccaccagatctgtcttacaa -gaactcctgaaggaagcacccaatatgcaaaggaaagactgttaccagcc -actacaaaaacacactgaattacacagtccagtgacactataaatcaacc -acataaacaagtctgcaaaataaccagccagcattatgatgacaagataa -aagacatatcaatactaaagttgaatgtaaatgggatacatgccccaatt -aaaggtcacagagtgtcaagctggataaagagccaaggcccattgctatg -ttgccctcaagtgacccatctcacgtgtaatgacacacactggctcaaaa -taaagggatggagaaataccaaccaagcaaatggaaaacataaaaacaat -cctagtttctgacaaaacagaatttaaaacaacaaagatcaaagaagaca -aagaagggcatcatataatggtaaagggttcagttgacaaagataatcta -gccattctaaatatatatgcactcaacacaggagcacccagtttcataaa -gcaagtacatagagactttcaaagagtcttagactcccactcaataacag -tgggagactttaacaccctacagacaatattagttcaatcattgagacag -aatattaacaatgatattcaggacttgaactcagcactggatcaaatgga -cctgatagttatctccacaacttttgacctcaaaccaacagaatatacat -tattctcatcaacacattgcacttactctaaaatcaatcatataatcaga -agtaaaacactccttagcaaacgtaagataactcaaatcataacaaacag -tctctcagaacacaatgcaatcaaattcaaaatgaagattaagaaattta -ctcagaactgtacaattacatggaaattgaataacctgctcctagatgac -ttttgagtaaataatgaaattaaggcagaaaccaatatggtttttgacac -taatggaacaaagagacaacataccagaatctctgggacacagctaaggc -agtgttaagaggaaaatttatagcactaactgcccatgttaaaaagttag -aaggatctctagttaacaacctaatgtcacaactaaaagaattagagagc -caagagaaaacatattttaaagctagcagatgataagaaataaccaaaat -tagagctgaactaaagaatataggcattaaaaaaacattcagaagatcaa -agaatccaggagctttttttttttgaaaaaattaattaaatagatagact -gctagctagatcaataaagaagaaaagagaaaagactcacgtaagaatgg -cgtgaacccgagaggtggagctggcagtgagccgagatcgtgccactgca -ctctagcctgggtgacagagcgagactccttctcaaaaaaaaaaaaaaaa -aaaaaggaaatgacaagggggatattaccactggcaccacagaaatacaa -acaaccatcagaaaatattattaattcctctatgtacataaactagaaaa -tctataagaaatggataaattcctgggcacatacaccctcccaagactga -accaggaagaaattgaaccgttaaacaaacccataatgagttctgaaatt -gagacagtaataaatagtctacgaaccaaaaaaagctcaggaccagaaag -attcacagctgaattctaccagatgtacaaagaagagccagtgccattcc -cactgaagctattcaaaaaatggaaaagaagggactcctctgtaactcat -gctatggggccttcctaactgatgttattggtctgaaaacttcagaccag -tattcagcatcatcctgatgccaaaacctgtaagagatactacaaaaaaa -gaaaacttcagagcaatattttttatgaatatcaatgcaaaaattcacca -caaaatactaggaaactgaatccagcagcacatcaaaaagcttatccacc -aggatcaagtaggttttatccctgggattcaaggtttgttcaaaatatgc -aaatcaataaatgcaattcatcacataaacagagctaaaaacaaaaacca -catgattagctcaatagatgcagaaaaagctttaaaaaaaatttaatatc -tcttcatgttaaaaactctcaataaattatatattgaaagaacatacctc -aaaattataagagccatttattgcaaacccacaggcaatatactgaatgg -gcaaaagctggaagcattccccttgaaagccggcagaagacaaggatgct -ctttctcaccactcctattcaacataatattggaagtcctggccagcgca -atcaggcaagagaaagaaagaagggacattcaaaataggaagagaggaac -tcaaattatccctttttgcaggcgatatgatcctatatctagaaaattct -atcatctcagcccaaaagcttcttaagctgaaaaacagcttcagcaaagt -cttaggatacaaaatcaatgtgcaaaaatcactaacattcctataccaac -aacagtcaagctgagagccaaatcaagaatgaactttcaatcactattgt -cacaagaaagaataaaatacctagcaatacagcttactaggaaggtgaaa -ggtctctacaaggagaactacagaccactgctcaaagaaatcagagatga -cacaaatgaatgaaaaatatttcattcattcattcattcatggataggaa -gaatcaatgtctctaaaatggccatattgcccaaagcaatttatagattc -actgctgttcttatttttaaagccattgagattcttcacagagctagaaa -gactattttaaaaaccacatgaacagagctagaaaaaactattttaaaaa -tcacatggaaagaaaaagcacaagtggttaaggaaattttaagcagaaag -aacaaagcctgaggcattacaccacctgaatttaaactactctacagggt -tacagtaaccaaaacagcatagtactggcacaaaaatagacacataggcc -aatggaacagaatggagaatccagaaaaaaagaccacacccctacaacta -cctgatctttgacaaacttgacaaaaacaagcaatggggaaaggattccc -tattcaataaataatgctagtgtaactggctaggtggatgcagatgattg -aaaccggactccttctttacactatatacaaaattaactcaagatgtatt -aaaaatacttaaatataaaactgaaaacaagaaaaaccttgaaagtcaac -ataggcaatgtcattcggggcataggcatggtcaaataattcatgacaaa -aatgacaaaatcaattgcaaccaaagcaaaaattgacaaatgggaactaa -ttaaactaaagagcttctgcacagcaaaataaaccatcagcagaataaag -agacaacctaaagaatgggagaaaatgtttgcaaactatgcatctgataa -aggtctgctattcagcatctataaggaacttaaataaatttacaagaaaa -aaaacaaactcattaaaaagttggcaaaggacatgaacaggcaattatca -agagaagacgtacgtgtggccaaaaactgtatgaaggaaagctcaacatc -actgatcattagattaatgcaaatcaaaatcacaatgagataccgtgtca -caccagtcagaatgtctattattaaaaagtcaaaaataatggatactggc -gaagttgtgaaaaaaaggaatgcttatacaattttggtaggagtgtacat -tcattcaaccattgtggatgacagtttggttattcctcaaagacctaaag -acagaaatactacttgacccagcaatcccattactgggtatatacacaaa -gagatatacatcattctattataaagacacatgcatgcatatatattatt -gcagccactattcacaatactaaagatatgaaatcaatctaaatgaccat -cagtgatagactggataaagaaaatgtggtacatatgtagcatggaatac -tatgcagccataaaaaacccaaaattacgtcctttgcaagtacatggatg -gagctggaggacattatcctcagtatactaatgctggagcagaaaaccaa -gcaccacatgttctcacttataagtgacagctaaatgatgagaacacatg -gacacatagaggggaacaatacacactggggtctatcagaaggtgaagat -tgggaggagggagatgatcaggaaaactaactaatggatactaggcttaa -tacctgaatgatgaaataatctgtacaccaaaccccccatgacccaagtt -tacctatgtaataagcctgcacatgtattcctcaacttaaaaattaaaaa -taaaTATATAgaaaaaaagaagtcacaaaagacaatataatgcatgtctc -cttttatatgaaatgtctagaatagaataatttatggatacagaaagtat -acttatggttgcctaggtctcaagaaagaagtgaatggggagtgattgct -aatggatatgggttttatttttgtaatgactaaaatgttctaaataagat -tgtgatgatggttgtacaagtctgtaaatacactgataaccattgaatta -tacactttaaataggccaataacatagtatgtgaattatatctcaataaa -gcagttaaaaTACATAAAAAGAATAATAGATTTTCATGTTCCTTTACACT -AGCTATTGGCTTGCCGACTGGTGTTTTCAAATCCTGTTGATTCAAGTGCA -AATGTATATGCATCACTCTGGGTTTTCTCTAGAAAATATTTGCTATGACC -TTAAAACTTTGTGTATCTTCTGACCCTGAAGATGTTGTCTAATGGAAATT -ATTGTAAGGCAATAGTCGTTTATGAGAACAAAGTTTTTACTCTCATAATG -CTTATCACAGTGATACCCTGCAAAATTATTAAAACATAAAACATATCATT -TCTGTTGCAAGAAGAAATGATAGAACAGCTCTAAAATGTAAATATATGTC -TCCATGAGACGATAGCAGTAGCTTAGAAATCAATGTGGAgacaggattaa -tcacctgccaagtaaagatcccctgggccatgagtaatcagcaacaatat -ccaggcagtacagtactttccatgggccttgggttagacacagagactta -atagcttcagatttgacccagcacattcccagctctggtggctatgcggg -aaagactctttctgcttgaggaaatatgagaaaagagtaaaggggacttt -gtcttgcagcttggataccagcttggccacagtgaggtagagcaccaaga -gggcaattgggtttttcaataccaggcactggtttgtggaaggcatttat -gaaacttcccttgtacagagggtaactcgcttcctggaagggagggttcc -agtccaggcagtactcaccatggtcctggggtggtggtggccagagagag -aaactccaattcttgtgaaaaggggaagaaagggtaggaatggctttctc -ttgtggcttgggtgccacctcagccacagtaaaccagggtaccaggtaga -ttcctaagattgctgattccaggctctggctcctggatgacaattctgga -cttgcctgaaaatgggaacttgccaacttgtagggatggacagaagcctg -gctggctttgctacctgctgattatacagctctagaagtttgagcagacg -taggtgttaggtagatcattgttaccatgggccttaggggagaaacagcc -ccttgctggcttcaggtttgagcaagcacagttcaagtgatggtggccac -aagggttctaatgtccctcttccccaagctccaggcagctctgcaagaca -gaggctccatttatttggaagaaagtaagaaaagggaacaagagcctttg -ccttgtaatacagagaattcctttggattgtacccaagaccaccaaggcg -gtacatctactactcttcaagagtcatggcattactgtgcttggggtacc -tcctaatgcagatatggctgcagtggccagaaacttagattacaaaaccc -aagtcccttcaaatacctcgaaagactttccaagaagaatgggtacaaac -aatcccagactataaagactacaataaatactcaactcttcaatgtccag -acatcaaggaatatccacaaacataaacaacaagactaacctggaaacat -ggccttaccaaacagcctaaataaggcaccagggagcaatcctagagaga -gagacatgtgacatctttgaaagagaatgaaaaataattgttttgaggaa -agtgaacgaaattcaagatatcacagaggaaaaattccgaatactatccg -ataaatttaacaaaaagaatgaaataagtgaaaagaatcaagcagaaaat -ctggagctgaaaaataccattgcaatacggaagaatgcatcactctctct -ctttttttttcttttttttaattatactttaagttttagggtacacgtgc -acaatatgcagatttgttacatatgtatacatgtgccatgttggtgtgct -gcaacaccatggaatactatgcagccataaaaaaggatgagttcatgtcc -tttttagggacatagatgaagctggaaaccatcattctcagcaaactatc -gcaaggacaaaaaaccaaacaccgcatgttctcactcataggtgggaatc -gaacaatgagaacacatggacacaggaaggggagcatcactctctcttac -cagcaaaactgatcaatcagaggaaagaaatgctgagcctggagacaggt -tatttgaaaatacacagtcagaggagacaaaagaaaagagaataaaaaag -aatgaagcacacctacaggatctagagaataaccttaaaagggcaaatcc -gtggtattgatcttaaacaggaggtagagaaatagatggggatagaaagt -tcattcaaaatgatgataacagaagatttcccaaaaccacagaaaaatat -caatatttaaatagaagtacaagcagatttaacccaaagaagactacctc -aaggcaattaatactcaaacacccaaagatcaaagggtcttaatagaaac -aagagaaaaaaataacatataatggagcttcaatatgtctggcagcagat -tttttagcagaaattttataggccatgagagaatgacatgacataacata -tttaaaatgctaaaggaaaaaaTCATGCATCATTTTTTTTAAGTTTTCAC -CCTAGTCTCCTTTTATATTTTATAttattttattttattatactttaagt -tttagggtacatgtgcacaatgtgcaggttagttacatatgtacacatgt -gccatgctggtgtgctgcacccattaactcatcatttagcattaagtata -tctcctaaagctatccctcccccatccccccaccccacaacagtccccag -agtgtgatgttccctttcctgtgtccatgtgttctcattgttcaattccc -acctatgagtgagaacatgcggtgtttggttttttgttcttgcgatagtt -tactgagaatgatgatttccaatttcatccatgtccctacaaaggacatg -aactcaccattttttatggctgcatagtattccacggtgtatatgtgcca -cattttcttaatccagtctatcattgttggacatttgggttggttccaag -tctttgctatcgtgaatagtgccgcaataaacatacgtgtgcatgtgtct -ttatagcagcatgatttatagtcctttgggtatgtacccagtaatgggat -ggctgggtcaaatggtatttctagttctagatccctgaggaatcgccaca -ctgacttccagaatggttgaactagtttacagtcccaccaacagtgtaaa -agtgttcttatttctccacatcctctccagcacctgttttttcctgactt -tttaatgattgccattctaactggtgtgagatggtatctcattgtggttt -tgatttgcatttctctgatggccagtgatggtgagcattttttcatgtgt 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-ctggtctctatgcacacatgcaagcaatggtggtgcagcaggagtgggca -gggtgtgctcacatacagagtagtggcatagtggggtgcatacataaatg -catgctggcagggaagggagttgaggtcaaccagcatgcacatgcactga -caaagcaatgtcaggggtagctgtgggcaaatttgtgctgccaaaggggc -acagaggaggctgtagttgggggagtgtgtgggtgggcttgtgtgcacca -gtagaagctgctctgctggagctctgcaaatgtgaggcatggtctgtcag -tgcaggaactgtgatgtgtgtctccaggaggcattccagctgggcaccca -aggctgcactgcaagcatgtgcactaggggagtaaaggtgagccttgggg -gatggacatccctggctgtactccactgacgacactcacacaccaaatcc -cttgggttccacactggctggtcttctgcctctaccacttctctaagcag -ctctgcctgccactacaagtgtccatgcaggttagggggtctcctgctgc -cagaattccagagatccatggtgtgggcaggttgctcctcacctgctcaa -cttaccttttccctgggagtggctggtggccaggaacaagtcccagtgca -tggaagtcccttgcagggttcccaccttcctttctctatagcccagcatc -tgagtcttccctccatcaattctcattgtctttcctccaaatatatgctt -ggagtgtgccaggcttcccaatgtcctagtctcttggtggcagatatttc -acttggctgcactgagtgagccaccttgccTATAATTTTTagaaggcttt -taactagatattatctcatttatccatttttgctttggttgtctgtgctt -gtgaggtactactcgaatctttgcctagtccagtgtcttggagaatttct -gtgatattttcttgtagtagttttatagtttgaagtgttagatAATAATC -AGACTCAACAAATGGCAGAATTCACAATTAATGAAACACACAATAGTAGA -TCAATGTAAAAATAACTTTAAAGATAAATCTGGTTTAAATATTGAAAGAG -ACGAAAAAGGGACTGTAATTTGTAAGACAAGAACAGGAATCTTCTTTAAC -AATAAGGTATATTTTAAAAAAGAAACAACTGGAAATTTTATAAATGAAAC -AGGTATGCACTGAAATAAAACCATTAATAGATTGCTCATATATTTCGACA -GAGTCAAGGCTGAGTATTGAGTTAGAACACAGATTAgacaggggtcacat -ctaattcatccctgtaccccagtgtctaatacaATAAGGCCAACATATAA -CAAGTGTTTCAAAATTGCTTATTAAATTGAACTGGGTAAGTGGTCTTCAG -ATAGGCCAGACATCTCTGGGCTTCTCCAGTGTATAGGGGTTTCAGGGGGG -CAGGACAGCCTCAAGTGGAACTACCTGAGGGCTGGGCAGAGCTGGGTGTG -GTTCCTCGTGGGTGGAGTAGGCAATAAAGGCTATCTAGAAAAGAGGTACT -GGCTTTACCATTCACCTCAGGGACTAACTAGTTTGTTCCCTCTCAGAGCT -GGAGAGTGAATTATCTTCATTCAGCACATGTCTGGCTACTATTCATCCTC -CCCGTGTCAAAGAtacttaaagtagtgaaaacagatcttattcagtaact -actaacaatgctgaaaaaagctgagctccattccaatttgtgcaaaggtg -gtttgggcattttaaagggagaatgatgttgggggctgagtagagtcaga -gaagtgaaaactacaaaatattggtcagtgtaaatgcactgtgtttaggc -catctgtgtttgttagccggcagttatcaaagttaggatttgtccttcca -cagagactggaagacagggttcctatctttcttgattacatttcaaagaa -atggctctcaggtccttgggagagacatttctaaattgtaagagatacat -attcactgtaataagcccttttaaataagtgctctaaaaaagggaggtca -gggtcttatcatcagattttggcaagaacaaacagtatattttcctggca -gcattgaactttctcaggcagtcattttagtggggtttggggtcaattat -agggacccagccttaggctgtgagaaaccatgctagagtttagttagttc -ccttactactacaggggtttggacagaagtgttagttccaggagttctgc -agttctcCCCTGTTAGAAACTCTAAGGATGTCCATGGCTATATTTATGTG -ACAAAACATTATATAAATGGTTGATGTTAACAACCTGCCAAAGATTATTT -TTCTTACTCCCTCCCTCCTAGGCCTTTTGCAACCCCCACCCCCATTACAG -AGAAAGGGGAACAATCCTGTGTGCAACCAGCTCTCCATACCTGGCCCCCA -CAGCTGGATCTCAGGGTGATCTCCTTTACCACCTGGAATGATAAATACCT -TCTTCCAGGACAGCAGCCCTCTTTATCTTGCAGAAGGAGGCAATCCAGGC -TGGGTCCTTCGCCAGGGTACCATTTTCCTGCAGCCTCTACAGGAAAATAA -GCTCGTCTGAGCTGTGGCCTGAGCAGGTCAAGTCTTCAGTAGAGAGGTCA -ACTTTAGAAACAATGGCTATTCTTGTGTCTTCCCTTTCTCTATCCTCCTT -CCCTTCTATATTACCAAAGAAGTGAACACTTAGAGGACAGAAACTTTATC -CTGTCTAGCCCATGCCAAAGAAGATGTTCTCAAGAGAAGAACAGTTTGAA -AGAGGCTGCTTGGACCTTAGGCCTCAGCTCCCAACTCCCTCCCTAACTCT -TTCCCCTTAGAAAGGAAATCATCCTCACTGACTGAAGCCCTGAGTGGCAA -GTCAGCAGGTGGTTTCCTGTAGGACACTGAGGTCTGCTTAAATAGACCAC -CCATATGCTTCCATAAAAATATCTTGTGTATTGGAGTCTACAAATAATAT -ATTCTTGATGCACCTAAACCTCACTAATTCATAACCACCTGGGGTTAACA -TTTGCCTGAAGTATTTTCTAAAGAAAACAAAGACTAGTGATTCTAACAAC -CCAGATGTTGTTTGACTTCAGCTACCCAGGTGTTGACAAGTAGTAGTTTT -AAAAGCAGTTGTATGGCATGGAAATATCACTAGACTAAGATACAACTGGT -TTGGGTCACAGTTCTGAAATCATCAAATGGTAGATATGTGACTGGGATTT -TCTATCAATTTATTGAAAACAGCATTAAGTggcctagaaagatgtgagta -actttcccaagttcacacagctagtaagtgacagaaaaagtaccgtccag -atctagagttcttaaccattccaaatatattgccccatccTTATCAGGTG -CTTGTTTATTCCTATGGTTTCTAGAGAGCAAAAGTATTAATATTTCAGGG -TACACTTTTTTGCAACTTTTTTTGGCAACTATCTTCAAATCCTGCCTGCA -GAGAATTCCTAAAGATATTGTTGAGCACTCATTGAGATGGAAGACAAACC -CTGTTCAACGAGAAATCTTACTGTCTGGAGATCCCCTCTAAGAAAGAAGA -AGGAGACTGCAGGGGTCTTGTCTGAACATGAAAGACACTTATGAGTTGGt -ctagattgtcagtattggaggatttaggggcagcaatccttggggcaggg -ggaatttccttgaaatccacatatgccagtctagctcagcttttgcttgg Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- 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commit/galaxy-central: inithello: Removed unused test files.
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8d7397d2c59b/ changeset: 8d7397d2c59b user: inithello date: 2012-10-01 16:06:15 summary: Removed unused test files. affected #: 11 files Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Remove the bwa wrappers from the repository.
by Bitbucket 01 Oct '12

01 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d3ce9d2dcbca/ changeset: d3ce9d2dcbca user: inithello date: 2012-10-01 15:24:33 summary: Remove the bwa wrappers from the repository. affected #: 3 files diff -r e86e9e97daf8f4b682cfe1fe5c12c8a408fd9cc3 -r d3ce9d2dcbca9b79292773968754697c50d761a9 tools/sr_mapping/bwa_color_wrapper.xml --- a/tools/sr_mapping/bwa_color_wrapper.xml +++ /dev/null @@ -1,482 +0,0 @@ -<tool id="bwa_color_wrapper" name="Map with BWA for SOLiD" version="1.0.2"> - <description></description> - <parallelism method="basic"></parallelism> - <command interpreter="python"> - bwa_wrapper.py - --threads="4" - --color-space - - ## reference source - --fileSource=$genomeSource.refGenomeSource - #if $genomeSource.refGenomeSource == "history": - ##build index on the fly - --ref="${genomeSource.ownFile}" - --dbkey=$dbkey - #else: - ##use precomputed indexes - --ref="${genomeSource.indices.fields.path}" - --do_not_build_index - #end if - - ## input file(s) - --input1=$paired.input1 - #if $paired.sPaired == "paired": - --input2=$paired.input2 - #end if - - ## output file - --output=$output - - ## run parameters - --genAlignType=$paired.sPaired - --params=$params.source_select - #if $params.source_select != "pre_set": - --maxEditDist=$params.maxEditDist - --fracMissingAligns=$params.fracMissingAligns - --maxGapOpens=$params.maxGapOpens - --maxGapExtens=$params.maxGapExtens - --disallowLongDel=$params.disallowLongDel - --disallowIndel=$params.disallowIndel - --seed=$params.seed - --maxEditDistSeed=$params.maxEditDistSeed - --mismatchPenalty=$params.mismatchPenalty - --gapOpenPenalty=$params.gapOpenPenalty - --gapExtensPenalty=$params.gapExtensPenalty - --suboptAlign="${params.suboptAlign}" - --noIterSearch=$params.noIterSearch - --outputTopN=$params.outputTopN - --outputTopNDisc=$params.outputTopNDisc - --maxInsertSize=$params.maxInsertSize - --maxOccurPairing=$params.maxOccurPairing - #if $params.readGroup.specReadGroup == "yes" - --rgid="$params.readGroup.rgid" - --rgcn="$params.readGroup.rgcn" - --rgds="$params.readGroup.rgds" - --rgdt="$params.readGroup.rgdt" - --rgfo="$params.readGroup.rgfo" - --rgks="$params.readGroup.rgks" - --rglb="$params.readGroup.rglb" - --rgpg="$params.readGroup.rgpg" - --rgpi="$params.readGroup.rgpi" - --rgpl="$params.readGroup.rgpl" - --rgpu="$params.readGroup.rgpu" - --rgsm="$params.readGroup.rgsm" - #end if - #end if - - ## suppress output SAM header - --suppressHeader=$suppressHeader - </command> - <requirements> - <requirement type="package">bwa</requirement> - </requirements> - <inputs> - <conditional name="genomeSource"> - <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select a reference genome"> - <options from_data_table="bwa_indexes_color"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available for the selected input dataset" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> - </when> - </conditional> - <conditional name="paired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="input1" type="data" format="fastqcssanger" label="FASTQ file (Nucleotide-space recoded from color-space)"> - <help>Convert color-space data to nucleotide-space (see help section below for steps). Must have Sanger-scaled quality values with ASCII offset 33</help> - </param> - </when> - <when value="paired"> - <param name="input1" type="data" format="fastqcssanger" label="Forward FASTQ file (Nucleotide-space recoded from color-space)" help="Must have Sanger-scaled quality values with ASCII offset 33"> - <help>Convert color-space data to nucleotide-space (see help section below for steps). Must have Sanger-scaled quality values with ASCII offset 33</help> - </param> - <param name="input2" type="data" format="fastqcssanger" label="Reverse FASTQ file (Nucleotide-space recoded from color-space)" help="Must have Sanger-scaled quality values with ASCII offset 33"> - <help>Convert color-space data to nucleotide-space (see help section below for steps). Must have Sanger-scaled quality values with ASCII offset 33</help> - </param> - </when> - </conditional> - <conditional name="params"> - <param name="source_select" type="select" label="BWA settings to use" help="For most mapping needs use Commonly Used settings. If you want full control use Full Parameter List"> - <option value="pre_set">Commonly Used</option> - <option value="full">Full Parameter List</option> - </param> - <when value="pre_set" /> - <when value="full"> - <param name="maxEditDist" type="integer" value="0" label="Maximum edit distance (aln -n)" help="Enter this value OR a fraction of missing alignments, not both" /> - <param name="fracMissingAligns" type="float" value="0.04" label="Fraction of missing alignments given 2% uniform base error rate (aln -n)" help="Enter this value OR maximum edit distance, not both" /> - <param name="maxGapOpens" type="integer" value="1" label="Maximum number of gap opens (aln -o)" /> - <param name="maxGapExtens" type="integer" value="-1" label="Maximum number of gap extensions (aln -e)" help="-1 for k-difference mode (disallowing long gaps)" /> - <param name="disallowLongDel" type="integer" value="16" label="Disallow long deletion within [value] bp towards the 3'-end (aln -d)" /> - <param name="disallowIndel" type="integer" value="5" label="Disallow insertion/deletion within [value] bp towards the end (aln -i)" /> - <param name="seed" type="integer" value="-1" label="Number of first subsequences to take as seed (aln -l)" help="Enter -1 for infinity" /> - <param name="maxEditDistSeed" type="integer" value="2" label="Maximum edit distance in the seed (aln -k)" /> - <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /> - <param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" /> - <param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" /> - <param name="suboptAlign" type="integer" optional="True" label="Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /> - <param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" /> - <param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" /> - <param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" /> - <param name="maxInsertSize" type="integer" value="500" label="Maximum insert size for a read pair to be considered as being mapped properly (sampe -a)" help="For paired-end reads only. Only used when there are not enough good alignments to infer the distribution of insert sizes" /> - <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing (sampe -o)" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing" /> - <conditional name="readGroup"> - <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)"> - <option value="yes">Yes</option> - <option value="no" selected="True">No</option> - </param> - <when value="yes"> - <param name="rgid" type="text" size="25" label="Read group identiﬁer (ID). Each @RG line must have a unique ID. The value of ID is used in the RG -tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group -IDs may be modiﬁed when merging SAM ﬁles in order to handle collisions." /> - <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" /> - <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" /> - <param name="rgdt" type="text" size="25" label="Date that run was produced (DT)" help="Optional. ISO8601 format date or date/time, like YYYY-MM-DD" /> - <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each -ﬂow of each read." help="Optional. Multi-base ﬂows are encoded in IUPAC format, and non-nucleotide ﬂows by -various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" /> - <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" help="Optional" /> - <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" /> - <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" /> - <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" /> - <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, -SOLID, HELICOS, IONTORRENT and PACBIO" /> - <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identiﬁer (e.g. ﬂowcell-barcode.lane for Illumina or slide for SOLiD)" /> - <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" /> - </when> - <when value="no" /> - </conditional> - </when> - </conditional> - <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" /> - </inputs> - <outputs> - <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> - <actions> - <conditional name="genomeSource.refGenomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="bwa_indexes_color" column="1"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="genomeSource.indices" column="0" /> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="genomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> - </data> - </outputs> - <tests> - <test> -  - <param name="refGenomeSource" value="history" /> - <param name="ownFile" value="hg19chrX_midpart.fasta" /> - <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in4.fastqcssanger" ftype="fastqcssanger" /> - <param name="source_select" value="pre_set" /> - <param name="suppressHeader" value="false" /> - <output name="output" file="bwa_wrapper_out4.sam" ftype="sam" sort="True" lines_diff="2" /> - </test> - <test> -  - <param name="refGenomeSource" value="indexed" /> - <param name="indices" value="equCab2chrM" /> - <param name="sPaired" value="paired" /> - <param name="input1" value="bwa_wrapper_in5.fastqcssanger" ftype="fastqcssanger" /> - <param name="input2" value="bwa_wrapper_in6.fastqcssanger" ftype="fastqcssanger" /> - <param name="source_select" value="pre_set" /> - <param name="suppressHeader" value="true" /> - <output name="output" file="bwa_wrapper_out5.sam" ftype="sam" sort="True" /> - </test> - <test> -  - <param name="refGenomeSource" value="indexed" /> - <param name="indices" value="hg19chrX_midpart" /> - <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in4.fastqcssanger" ftype="fastqcssanger" /> - <param name="source_select" value="full" /> - <param name="maxEditDist" value="0" /> - <param name="fracMissingAligns" value="0.04" /> - <param name="maxGapOpens" value="1" /> - <param name="maxGapExtens" value="-1" /> - <param name="disallowLongDel" value="16" /> - <param name="disallowIndel" value="5" /> - <param name="seed" value="-1" /> - <param name="maxEditDistSeed" value="2" /> - <param name="mismatchPenalty" value="3" /> - <param name="gapOpenPenalty" value="11" /> - <param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="" /> - <param name="noIterSearch" value="true" /> - <param name="outputTopN" value="3" /> - <param name="outputTopNDisc" value="10" /> - <param name="maxInsertSize" value="500" /> - <param name="maxOccurPairing" value="100000" /> - <param name="specReadGroup" value="yes" /> - <param name="rgid" value="474747" /> - <param name="rgcn" value="" /> - <param name="rgds" value="description" /> - <param name="rgdt" value="2011-03-14" /> - <param name="rgfo" value="" /> - <param name="rgks" value="" /> - <param name="rglb" value="lib-child-1-A" /> - <param name="rgpg" value="" /> - <param name="rgpi" value="200" /> - <param name="rgpl" value="SOLID" /> - <param name="rgpu" value="" /> - <param name="rgsm" value="child-1" /> - <param name="suppressHeader" value="false" /> - <output name="output" file="bwa_wrapper_out6.sam" ftype="sam" sort="True" lines_diff="2" /> - </test> - <test> -  - <param name="refGenomeSource" value="history" /> - <param name="ownFile" value="chr_m.fasta" /> - <param name="sPaired" value="paired" /> - <param name="input1" value="bwa_wrapper_in5.fastqcssanger" ftype="fastqcssanger" /> - <param name="input2" value="bwa_wrapper_in6.fastqcssanger" ftype="fastqcssanger" /> - <param name="source_select" value="full" /> - <param name="maxEditDist" value="0" /> - <param name="fracMissingAligns" value="0.04" /> - <param name="maxGapOpens" value="1" /> - <param name="maxGapExtens" value="-1" /> - <param name="disallowLongDel" value="16" /> - <param name="disallowIndel" value="5" /> - <param name="seed" value="-1" /> - <param name="maxEditDistSeed" value="2" /> - <param name="mismatchPenalty" value="3" /> - <param name="gapOpenPenalty" value="11" /> - <param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="" /> - <param name="noIterSearch" value="true" /> - <param name="outputTopN" value="3" /> - <param name="outputTopNDisc" value="10" /> - <param name="maxInsertSize" value="100" /> - <param name="maxOccurPairing" value="2" /> - <param name="specReadGroup" value="no" /> - <param name="suppressHeader" value="false" /> - <output name="output" file="bwa_wrapper_out7.sam" ftype="sam" sort="True" lines_diff="2" /> - </test> - </tests> - <help> - -**What it does** - -BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-60. - ------- - -**Know what you are doing** - -.. class:: warningmark - -There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. - - .. __: http://bio-bwa.sourceforge.net/ - ------- - -**Input formats** - -BWA accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files, set to either FASTQ Sanger or FASTQ Color Space Sanger as appropriate. - -If you have Color Space Sanger, it must be converted to nucleotide-space first. To do this, use the Manipulate FASTQ tool under NGS: QC and manipulation, with the following settings: - Manipulate reads on Sequence Content, choosing Change Adapter Base, and having the text box empty. - Manipulate reads on Sequence Content, doing a String Translate from "01234." to "ACGTN". - - ------- - -**A Note on Built-in Reference Genomes** - -The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY. - ------- - -**Outputs** - -The output is in SAM format, and has the following columns:: - - Column Description - -------- -------------------------------------------------------- - 1 QNAME Query (pair) NAME - 2 FLAG bitwise FLAG - 3 RNAME Reference sequence NAME - 4 POS 1-based leftmost POSition/coordinate of clipped sequence - 5 MAPQ MAPping Quality (Phred-scaled) - 6 CIGAR extended CIGAR string - 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME) - 8 MPOS 1-based Mate POSition - 9 ISIZE Inferred insert SIZE - 10 SEQ query SEQuence on the same strand as the reference - 11 QUAL query QUALity (ASCII-33 gives the Phred base quality) - 12 OPT variable OPTional fields in the format TAG:VTYPE:VALU - -The flags are as follows:: - - Flag Description - ------ ------------------------------------- - 0x0001 the read is paired in sequencing - 0x0002 the read is mapped in a proper pair - 0x0004 the query sequence itself is unmapped - 0x0008 the mate is unmapped - 0x0010 strand of the query (1 for reverse) - 0x0020 strand of the mate - 0x0040 the read is the first read in a pair - 0x0080 the read is the second read in a pair - 0x0100 the alignment is not primary - -It looks like this (scroll sideways to see the entire example):: - - QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT - HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh - HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh - -------- - -**BWA settings** - -All of the options have a default value. You can change any of them. All of the options in BWA have been implemented here. - ------- - -**BWA parameter list** - -This is an exhaustive list of BWA options: - -For **aln**:: - - -n NUM Maximum edit distance if the value is INT, or the fraction of missing - alignments given 2% uniform base error rate if FLOAT. In the latter - case, the maximum edit distance is automatically chosen for different - read lengths. [0.04] - -o INT Maximum number of gap opens [1] - -e INT Maximum number of gap extensions, -1 for k-difference mode - (disallowing long gaps) [-1] - -d INT Disallow a long deletion within INT bp towards the 3'-end [16] - -i INT Disallow an indel within INT bp towards the ends [5] - -l INT Take the first INT subsequence as seed. If INT is larger than the - query sequence, seeding will be disabled. For long reads, this option - is typically ranged from 25 to 35 for '-k 2'. [inf] - -k INT Maximum edit distance in the seed [2] - -t INT Number of threads (multi-threading mode) [1] - -M INT Mismatch penalty. BWA will not search for suboptimal hits with a score - lower than (bestScore-misMsc). [3] - -O INT Gap open penalty [11] - -E INT Gap extension penalty [4] - -c Reverse query but not complement it, which is required for alignment - in the color space. - -R Proceed with suboptimal alignments even if the top hit is a repeat. By - default, BWA only searches for suboptimal alignments if the top hit is - unique. Using this option has no effect on accuracy for single-end - reads. It is mainly designed for improving the alignment accuracy of - paired-end reads. However, the pairing procedure will be slowed down, - especially for very short reads (~32bp). - -N Disable iterative search. All hits with no more than maxDiff - differences will be found. This mode is much slower than the default. - -For **samse**:: - - -n INT Maximum number of alignments to output in the XA tag for reads paired - properly. If a read has more than INT hits, the XA tag will not be - written. [3] - -r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null] - -For **sampe**:: - - -a INT Maximum insert size for a read pair to be considered as being mapped - properly. Since version 0.4.5, this option is only used when there - are not enough good alignment to infer the distribution of insert - sizes. [500] - -n INT Maximum number of alignments to output in the XA tag for reads paired - properly. If a read has more than INT hits, the XA tag will not be - written. [3] - -N INT Maximum number of alignments to output in the XA tag for disconcordant - read pairs (excluding singletons). If a read has more than INT hits, - the XA tag will not be written. [10] - -o INT Maximum occurrences of a read for pairing. A read with more - occurrences will be treated as a single-end read. Reducing this - parameter helps faster pairing. [100000] - -r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null] - -For specifying the read group in **samse** or **sampe**, use the following:: - - @RG Read group. Unordered multiple @RG lines are allowed. - ID Read group identiﬁer. Each @RG line must have a unique ID. The value of - ID is used in the RG tags of alignment records. Must be unique among all - read groups in header section. Read group IDs may be modiﬁed when - merging SAM ﬁles in order to handle collisions. - CN Name of sequencing center producing the read. - DS Description. - DT Date the run was produced (ISO8601 date or date/time). - FO Flow order. The array of nucleotide bases that correspond to the - nucleotides used for each flow of each read. Multi-base flows are encoded - in IUPAC format, and non-nucleotide flows by various other characters. - Format : /\*|[ACMGRSVTWYHKDBN]+/ - KS The array of nucleotide bases that correspond to the key sequence of each read. - LB Library. - PG Programs used for processing the read group. - PI Predicted median insert size. - PL Platform/technology used to produce the reads. Valid values : CAPILLARY, - LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO. - PU Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for - SOLiD). Unique identiﬁer. - SM Sample. Use pool name where a pool is being sequenced. - - </help> -</tool> - - diff -r e86e9e97daf8f4b682cfe1fe5c12c8a408fd9cc3 -r d3ce9d2dcbca9b79292773968754697c50d761a9 tools/sr_mapping/bwa_wrapper.py --- a/tools/sr_mapping/bwa_wrapper.py +++ /dev/null @@ -1,342 +0,0 @@ -#!/usr/bin/env python - -""" -Runs BWA on single-end or paired-end data. -Produces a SAM file containing the mappings. -Works with BWA version 0.5.9. - -usage: bwa_wrapper.py [options] - -See below for options -""" - -import optparse, os, shutil, subprocess, sys, tempfile - -def stop_err( msg ): - sys.stderr.write( '%s\n' % msg ) - sys.exit() - -def check_is_double_encoded( fastq ): - # check that first read is bases, not one base followed by numbers - bases = [ 'A', 'C', 'G', 'T', 'a', 'c', 'g', 't', 'N' ] - nums = [ '0', '1', '2', '3' ] - for line in file( fastq, 'rb'): - if not line.strip() or line.startswith( '@' ): - continue - if len( [ b for b in line.strip() if b in nums ] ) > 0: - return False - elif line.strip()[0] in bases and len( [ b for b in line.strip() if b in bases ] ) == len( line.strip() ): - return True - else: - raise Exception, 'First line in first read does not appear to be a valid FASTQ read in either base-space or color-space' - raise Exception, 'There is no non-comment and non-blank line in your FASTQ file' - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to use' ) - parser.add_option( '-c', '--color-space', dest='color_space', action='store_true', help='If the input files are SOLiD format' ) - parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' ) - parser.add_option( '-f', '--input1', dest='fastq', help='The (forward) fastq file to use for the mapping' ) - parser.add_option( '-F', '--input2', dest='rfastq', help='The reverse fastq file to use for mapping if paired-end data' ) - parser.add_option( '-u', '--output', dest='output', help='The file to save the output (SAM format)' ) - parser.add_option( '-g', '--genAlignType', dest='genAlignType', help='The type of pairing (single or paired)' ) - parser.add_option( '-p', '--params', dest='params', help='Parameter setting to use (pre_set or full)' ) - parser.add_option( '-s', '--fileSource', dest='fileSource', help='Whether to use a previously indexed reference sequence or one form history (indexed or history)' ) - parser.add_option( '-n', '--maxEditDist', dest='maxEditDist', help='Maximum edit distance if integer' ) - parser.add_option( '-m', '--fracMissingAligns', dest='fracMissingAligns', help='Fraction of missing alignments given 2% uniform base error rate if fraction' ) - parser.add_option( '-o', '--maxGapOpens', dest='maxGapOpens', help='Maximum number of gap opens' ) - parser.add_option( '-e', '--maxGapExtens', dest='maxGapExtens', help='Maximum number of gap extensions' ) - parser.add_option( '-d', '--disallowLongDel', dest='disallowLongDel', help='Disallow a long deletion within specified bps' ) - parser.add_option( '-i', '--disallowIndel', dest='disallowIndel', help='Disallow indel within specified bps' ) - parser.add_option( '-l', '--seed', dest='seed', help='Take the first specified subsequences' ) - parser.add_option( '-k', '--maxEditDistSeed', dest='maxEditDistSeed', help='Maximum edit distance to the seed' ) - parser.add_option( '-M', '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty' ) - parser.add_option( '-O', '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty' ) - parser.add_option( '-E', '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' ) - parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', default=None, help='Proceed with suboptimal alignments even if the top hit is a repeat' ) - parser.add_option( '-N', '--noIterSearch', dest='noIterSearch', help='Disable iterative search' ) - parser.add_option( '-T', '--outputTopN', dest='outputTopN', help='Maximum number of alignments to output in the XA tag for reads paired properly' ) - parser.add_option( '', '--outputTopNDisc', dest='outputTopNDisc', help='Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)' ) - parser.add_option( '-S', '--maxInsertSize', dest='maxInsertSize', help='Maximum insert size for a read pair to be considered mapped good' ) - parser.add_option( '-P', '--maxOccurPairing', dest='maxOccurPairing', help='Maximum occurrences of a read for pairings' ) - parser.add_option( '', '--rgid', dest='rgid', help='Read group identifier' ) - parser.add_option( '', '--rgcn', dest='rgcn', help='Sequencing center that produced the read' ) - parser.add_option( '', '--rgds', dest='rgds', help='Description' ) - parser.add_option( '', '--rgdt', dest='rgdt', help='Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)' ) - parser.add_option( '', '--rgfo', dest='rgfo', help='Flow order' ) - parser.add_option( '', '--rgks', dest='rgks', help='The array of nucleotide bases that correspond to the key sequence of each read' ) - parser.add_option( '', '--rglb', dest='rglb', help='Library name' ) - parser.add_option( '', '--rgpg', dest='rgpg', help='Programs used for processing the read group' ) - parser.add_option( '', '--rgpi', dest='rgpi', help='Predicted median insert size' ) - parser.add_option( '', '--rgpl', dest='rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT' and 'PACBIO' ], help='Platform/technology used to produce the reads' ) - parser.add_option( '', '--rgpu', dest='rgpu', help='Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)' ) - parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' ) - parser.add_option( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' ) - parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" ) - parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) - parser.add_option( '-I', '--illumina1.3', dest='illumina13qual', help='Input FASTQ files have Illuina 1.3 quality scores' ) - (options, args) = parser.parse_args() - - # output version # of tool - try: - tmp = tempfile.NamedTemporaryFile().name - tmp_stdout = open( tmp, 'wb' ) - proc = subprocess.Popen( args='bwa 2>&1', shell=True, stdout=tmp_stdout ) - tmp_stdout.close() - returncode = proc.wait() - stdout = None - for line in open( tmp_stdout.name, 'rb' ): - if line.lower().find( 'version' ) >= 0: - stdout = line.strip() - break - if stdout: - sys.stdout.write( 'BWA %s\n' % stdout ) - else: - raise Exception - except: - sys.stdout.write( 'Could not determine BWA version\n' ) - - # check for color space fastq that's not double-encoded and exit if appropriate - if options.color_space: - if not check_is_double_encoded( options.fastq ): - stop_err( 'Your file must be double-encoded (it must be converted from "numbers" to "bases"). See the help section for details' ) - if options.genAlignType == 'paired': - if not check_is_double_encoded( options.rfastq ): - stop_err( 'Your reverse reads file must also be double-encoded (it must be converted from "numbers" to "bases"). See the help section for details' ) - - fastq = options.fastq - if options.rfastq: - rfastq = options.rfastq - - # set color space variable - if options.color_space: - color_space = '-c' - else: - color_space = '' - - # make temp directory for placement of indices - tmp_index_dir = tempfile.mkdtemp() - tmp_dir = tempfile.mkdtemp() - # index if necessary - if options.fileSource == 'history' and not options.do_not_build_index: - ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) - ref_file_name = ref_file.name - ref_file.close() - os.symlink( options.ref, ref_file_name ) - # determine which indexing algorithm to use, based on size - try: - size = os.stat( options.ref ).st_size - if size <= 2**30: - indexingAlg = 'is' - else: - indexingAlg = 'bwtsw' - except: - indexingAlg = 'is' - indexing_cmds = '%s -a %s' % ( color_space, indexingAlg ) - cmd1 = 'bwa index %s %s' % ( indexing_cmds, ref_file_name ) - try: - tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name - tmp_stderr = open( tmp, 'wb' ) - proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp, 'rb' ) - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if returncode != 0: - raise Exception, stderr - except Exception, e: - # clean up temp dirs - if os.path.exists( tmp_index_dir ): - shutil.rmtree( tmp_index_dir ) - if os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - stop_err( 'Error indexing reference sequence. ' + str( e ) ) - else: - ref_file_name = options.ref - if options.illumina13qual: - illumina_quals = "-I" - else: - illumina_quals = "" - - # set up aligning and generate aligning command options - if options.params == 'pre_set': - aligning_cmds = '-t %s %s %s' % ( options.threads, color_space, illumina_quals ) - gen_alignment_cmds = '' - else: - if options.maxEditDist != '0': - editDist = options.maxEditDist - else: - editDist = options.fracMissingAligns - if options.seed != '-1': - seed = '-l %s' % options.seed - else: - seed = '' - if options.suboptAlign: - suboptAlign = '-R "%s"' % ( options.suboptAlign ) - else: - suboptAlign = '' - if options.noIterSearch == 'true': - noIterSearch = '-N' - else: - noIterSearch = '' - aligning_cmds = '-n %s -o %s -e %s -d %s -i %s %s -k %s -t %s -M %s -O %s -E %s %s %s %s %s' % \ - ( editDist, options.maxGapOpens, options.maxGapExtens, options.disallowLongDel, - options.disallowIndel, seed, options.maxEditDistSeed, options.threads, - options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty, - suboptAlign, noIterSearch, color_space, illumina_quals ) - if options.genAlignType == 'paired': - gen_alignment_cmds = '-a %s -o %s' % ( options.maxInsertSize, options.maxOccurPairing ) - if options.outputTopNDisc: - gen_alignment_cmds += ' -N %s' % options.outputTopNDisc - else: - gen_alignment_cmds = '' - if options.rgid: - if not options.rglb or not options.rgpl or not options.rgsm: - stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' ) - readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm ) - if options.rgcn: - readGroup += '\tCN:%s' % options.rgcn - if options.rgds: - readGroup += '\tDS:%s' % options.rgds - if options.rgdt: - readGroup += '\tDT:%s' % options.rgdt - if options.rgfo: - readGroup += '\tFO:%s' % options.rgfo - if options.rgks: - readGroup += '\tKS:%s' % options.rgks - if options.rgpg: - readGroup += '\tPG:%s' % options.rgpg - if options.rgpi: - readGroup += '\tPI:%s' % options.rgpi - if options.rgpu: - readGroup += '\tPU:%s' % options.rgpu - gen_alignment_cmds += ' -r "%s"' % readGroup - if options.outputTopN: - gen_alignment_cmds += ' -n %s' % options.outputTopN - # set up output files - tmp_align_out = tempfile.NamedTemporaryFile( dir=tmp_dir ) - tmp_align_out_name = tmp_align_out.name - tmp_align_out.close() - tmp_align_out2 = tempfile.NamedTemporaryFile( dir=tmp_dir ) - tmp_align_out2_name = tmp_align_out2.name - tmp_align_out2.close() - # prepare actual aligning and generate aligning commands - cmd2 = 'bwa aln %s %s %s > %s' % ( aligning_cmds, ref_file_name, fastq, tmp_align_out_name ) - cmd2b = '' - if options.genAlignType == 'paired': - cmd2b = 'bwa aln %s %s %s > %s' % ( aligning_cmds, ref_file_name, rfastq, tmp_align_out2_name ) - cmd3 = 'bwa sampe %s %s %s %s %s %s >> %s' % ( gen_alignment_cmds, ref_file_name, tmp_align_out_name, tmp_align_out2_name, fastq, rfastq, options.output ) - else: - cmd3 = 'bwa samse %s %s %s %s >> %s' % ( gen_alignment_cmds, ref_file_name, tmp_align_out_name, fastq, options.output ) - # perform alignments - buffsize = 1048576 - try: - # need to nest try-except in try-finally to handle 2.4 - try: - # align - try: - tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name - tmp_stderr = open( tmp, 'wb' ) - proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp, 'rb' ) - stderr = '' - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if returncode != 0: - raise Exception, stderr - except Exception, e: - raise Exception, 'Error aligning sequence. ' + str( e ) - # and again if paired data - try: - if cmd2b: - tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name - tmp_stderr = open( tmp, 'wb' ) - proc = subprocess.Popen( args=cmd2b, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp, 'rb' ) - stderr = '' - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if returncode != 0: - raise Exception, stderr - except Exception, e: - raise Exception, 'Error aligning second sequence. ' + str( e ) - # generate align - try: - tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name - tmp_stderr = open( tmp, 'wb' ) - proc = subprocess.Popen( args=cmd3, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp, 'rb' ) - stderr = '' - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if returncode != 0: - raise Exception, stderr - except Exception, e: - raise Exception, 'Error generating alignments. ' + str( e ) - # remove header if necessary - if options.suppressHeader == 'true': - tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir) - tmp_out_name = tmp_out.name - tmp_out.close() - try: - shutil.move( options.output, tmp_out_name ) - except Exception, e: - raise Exception, 'Error moving output file before removing headers. ' + str( e ) - fout = file( options.output, 'w' ) - for line in file( tmp_out.name, 'r' ): - if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ): - fout.write( line ) - fout.close() - # check that there are results in the output file - if os.path.getsize( options.output ) > 0: - sys.stdout.write( 'BWA run on %s-end data' % options.genAlignType ) - else: - raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.' - except Exception, e: - stop_err( 'The alignment failed.\n' + str( e ) ) - finally: - # clean up temp dir - if os.path.exists( tmp_index_dir ): - shutil.rmtree( tmp_index_dir ) - if os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - -if __name__=="__main__": __main__() diff -r e86e9e97daf8f4b682cfe1fe5c12c8a408fd9cc3 -r d3ce9d2dcbca9b79292773968754697c50d761a9 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml +++ /dev/null @@ -1,474 +0,0 @@ -<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.3"> - <description></description> - <parallelism method="basic"></parallelism> - <command interpreter="python"> - bwa_wrapper.py - --threads="4" - - #if $input1.ext == "fastqillumina": - --illumina1.3 - #end if - - ## reference source - --fileSource=$genomeSource.refGenomeSource - #if $genomeSource.refGenomeSource == "history": - ##build index on the fly - --ref="${genomeSource.ownFile}" - --dbkey=$dbkey - #else: - ##use precomputed indexes - --ref="${genomeSource.indices.fields.path}" - --do_not_build_index - #end if - - ## input file(s) - --input1=$paired.input1 - #if $paired.sPaired == "paired": - --input2=$paired.input2 - #end if - - ## output file - --output=$output - - ## run parameters - --genAlignType=$paired.sPaired - --params=$params.source_select - #if $params.source_select != "pre_set": - --maxEditDist=$params.maxEditDist - --fracMissingAligns=$params.fracMissingAligns - --maxGapOpens=$params.maxGapOpens - --maxGapExtens=$params.maxGapExtens - --disallowLongDel=$params.disallowLongDel - --disallowIndel=$params.disallowIndel - --seed=$params.seed - --maxEditDistSeed=$params.maxEditDistSeed - --mismatchPenalty=$params.mismatchPenalty - --gapOpenPenalty=$params.gapOpenPenalty - --gapExtensPenalty=$params.gapExtensPenalty - --suboptAlign="${params.suboptAlign}" - --noIterSearch=$params.noIterSearch - --outputTopN=$params.outputTopN - --outputTopNDisc=$params.outputTopNDisc - --maxInsertSize=$params.maxInsertSize - --maxOccurPairing=$params.maxOccurPairing - #if $params.readGroup.specReadGroup == "yes" - --rgid="$params.readGroup.rgid" - --rgcn="$params.readGroup.rgcn" - --rgds="$params.readGroup.rgds" - --rgdt="$params.readGroup.rgdt" - --rgfo="$params.readGroup.rgfo" - --rgks="$params.readGroup.rgks" - --rglb="$params.readGroup.rglb" - --rgpg="$params.readGroup.rgpg" - --rgpi="$params.readGroup.rgpi" - --rgpl="$params.readGroup.rgpl" - --rgpu="$params.readGroup.rgpu" - --rgsm="$params.readGroup.rgsm" - #end if - #end if - - ## suppress output SAM header - --suppressHeader=$suppressHeader - </command> - <requirements> - <requirement type="package">bwa</requirement> - </requirements> - <inputs> - <conditional name="genomeSource"> - <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select a reference genome"> - <options from_data_table="bwa_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> - </when> - </conditional> - <conditional name="paired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="input1" type="data" format="fastqsanger,fastqillumina" label="FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" /> - </when> - <when value="paired"> - <param name="input1" type="data" format="fastqsanger,fastqillumina" label="Forward FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" /> - <param name="input2" type="data" format="fastqsanger,fastqillumina" label="Reverse FASTQ file" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" /> - </when> - </conditional> - <conditional name="params"> - <param name="source_select" type="select" label="BWA settings to use" help="For most mapping needs use Commonly Used settings. If you want full control use Full Parameter List"> - <option value="pre_set">Commonly Used</option> - <option value="full">Full Parameter List</option> - </param> - <when value="pre_set" /> - <when value="full"> - <param name="maxEditDist" type="integer" value="0" label="Maximum edit distance (aln -n)" help="Enter this value OR a fraction of missing alignments, not both" /> - <param name="fracMissingAligns" type="float" value="0.04" label="Fraction of missing alignments given 2% uniform base error rate (aln -n)" help="Enter this value OR maximum edit distance, not both" /> - <param name="maxGapOpens" type="integer" value="1" label="Maximum number of gap opens (aln -o)" /> - <param name="maxGapExtens" type="integer" value="-1" label="Maximum number of gap extensions (aln -e)" help="-1 for k-difference mode (disallowing long gaps)" /> - <param name="disallowLongDel" type="integer" value="16" label="Disallow long deletion within [value] bp towards the 3'-end (aln -d)" /> - <param name="disallowIndel" type="integer" value="5" label="Disallow insertion/deletion within [value] bp towards the end (aln -i)" /> - <param name="seed" type="integer" value="-1" label="Number of first subsequences to take as seed (aln -l)" help="Enter -1 for infinity" /> - <param name="maxEditDistSeed" type="integer" value="2" label="Maximum edit distance in the seed (aln -k)" /> - <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /> - <param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" /> - <param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" /> - <param name="suboptAlign" type="integer" optional="True" label="Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /> - <param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" /> - <param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" /> - <param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" /> - <param name="maxInsertSize" type="integer" value="500" label="Maximum insert size for a read pair to be considered as being mapped properly (sampe -a)" help="For paired-end reads only. Only used when there are not enough good alignments to infer the distribution of insert sizes" /> - <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing (sampe -o)" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing" /> - <conditional name="readGroup"> - <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)"> - <option value="yes">Yes</option> - <option value="no" selected="True">No</option> - </param> - <when value="yes"> - <param name="rgid" type="text" size="25" label="Read group identiﬁer (ID). Each @RG line must have a unique ID. The value of ID is used in the RG -tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group -IDs may be modiﬁed when merging SAM ﬁles in order to handle collisions." /> - <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read (CN)" help="Optional" /> - <param name="rgds" type="text" size="25" label="Description (DS)" help="Optional" /> - <param name="rgdt" type="text" size="25" label="Date that run was produced (DT)" help="Optional. ISO8601 format date or date/time, like YYYY-MM-DD" /> - <param name="rgfo" type="text" size="25" label="Flow order (FO). The array of nucleotide bases that correspond to the nucleotides used for each -ﬂow of each read." help="Optional. Multi-base ﬂows are encoded in IUPAC format, and non-nucleotide ﬂows by -various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" /> - <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" help="Optional" /> - <param name="rglb" type="text" size="25" label="Library name (LB)" help="Required if RG specified" /> - <param name="rgpg" type="text" size="25" label="Programs used for processing the read group (PG)" help="Optional" /> - <param name="rgpi" type="text" size="25" label="Predicted median insert size (PI)" help="Optional" /> - <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, -SOLID, HELICOS, IONTORRENT and PACBIO" /> - <param name="rgpu" type="text" size="25" label="Platform unit (PU)" help="Optional. Unique identiﬁer (e.g. ﬂowcell-barcode.lane for Illumina or slide for SOLiD)" /> - <param name="rgsm" type="text" size="25" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" /> - </when> - <when value="no" /> - </conditional> - </when> - </conditional> - <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" /> - </inputs> - <outputs> - <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> - <actions> - <conditional name="genomeSource.refGenomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="bwa_indexes" column="1"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="genomeSource.indices" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="genomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> - </data> - </outputs> - <tests> - <test> -  - <param name="refGenomeSource" value="indexed" /> - <param name="indices" value="phiX" /> - <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in1.fastqsanger" ftype="fastqsanger" /> - <param name="source_select" value="pre_set" /> - <param name="suppressHeader" value="true" /> - <output name="output" file="bwa_wrapper_out1.sam" ftype="sam" sort="True" /> - </test> - <test> -  - <param name="refGenomeSource" value="history" /> - <param name="ownFile" value="phiX.fasta" /> - <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in1.fastqsanger" ftype="fastqsanger" /> - <param name="source_select" value="full" /> - <param name="maxEditDist" value="0" /> - <param name="fracMissingAligns" value="0.04" /> - <param name="maxGapOpens" value="1" /> - <param name="maxGapExtens" value="-1" /> - <param name="disallowLongDel" value="16" /> - <param name="disallowIndel" value="5" /> - <param name="seed" value="-1" /> - <param name="maxEditDistSeed" value="2" /> - <param name="mismatchPenalty" value="3" /> - <param name="gapOpenPenalty" value="11" /> - <param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="" /> - <param name="noIterSearch" value="true" /> - <param name="outputTopN" value="3" /> - <param name="outputTopNDisc" value="10" /> - <param name="maxInsertSize" value="500" /> - <param name="maxOccurPairing" value="100000" /> - <param name="specReadGroup" value="no" /> - <param name="suppressHeader" value="true" /> - <output name="output" file="bwa_wrapper_out2.sam" ftype="sam" sort="True" /> - </test> - <test> -  - <param name="refGenomeSource" value="indexed" /> - <param name="indices" value="phiX" /> - <param name="sPaired" value="paired" /> - <param name="input1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" /> - <param name="input2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" /> - <param name="source_select" value="full" /> - <param name="maxEditDist" value="0" /> - <param name="fracMissingAligns" value="0.04" /> - <param name="maxGapOpens" value="1" /> - <param name="maxGapExtens" value="-1" /> - <param name="disallowLongDel" value="16" /> - <param name="disallowIndel" value="5" /> - <param name="seed" value="-1" /> - <param name="maxEditDistSeed" value="2" /> - <param name="mismatchPenalty" value="3" /> - <param name="gapOpenPenalty" value="11" /> - <param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="" /> - <param name="noIterSearch" value="true" /> - <param name="outputTopN" value="3" /> - <param name="outputTopNDisc" value="10" /> - <param name="maxInsertSize" value="500" /> - <param name="maxOccurPairing" value="100000" /> - <param name="specReadGroup" value="yes" /> - <param name="rgid" value="abcdefg" /> - <param name="rgcn" value="" /> - <param name="rgds" value="descrip" /> - <param name="rgdt" value="2010-11-01" /> - <param name="rgfo" value="" /> - <param name="rgks" value="" /> - <param name="rglb" value="lib-mom-A" /> - <param name="rgpg" value="" /> - <param name="rgpi" value="400" /> - <param name="rgpl" value="ILLUMINA" /> - <param name="rgpu" value="" /> - <param name="rgsm" value="mom" /> - <param name="suppressHeader" value="false" /> - <output name="output" file="bwa_wrapper_out3.sam" ftype="sam" sort="True" lines_diff="2" /> - </test> - <test> -  - <param name="refGenomeSource" value="history" /> -  - <param name="ownFile" value="phiX.fasta" /> - <param name="sPaired" value="paired" /> - <param name="input1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" /> - <param name="input2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" /> - <param name="source_select" value="preSet" /> - <param name="suppressHeader" value="true" /> - <output name="output" file="bwa_wrapper_out8.sam" ftype="sam" sort="True" /> - </test> - </tests> - <help> - -**What it does** - -BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-60. - ------- - -**Know what you are doing** - -.. class:: warningmark - -There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. - - .. __: http://bio-bwa.sourceforge.net/ - ------- - -**Input formats** - -BWA accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*) or Illumina FASTQ format (galaxy type *fastqillumina*). Use the FASTQ Groomer to prepare your files. - ------- - -**A Note on Built-in Reference Genomes** - -The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY. - ------- - -**Outputs** - -The output is in SAM format, and has the following columns:: - - Column Description - -------- -------------------------------------------------------- - 1 QNAME Query (pair) NAME - 2 FLAG bitwise FLAG - 3 RNAME Reference sequence NAME - 4 POS 1-based leftmost POSition/coordinate of clipped sequence - 5 MAPQ MAPping Quality (Phred-scaled) - 6 CIGAR extended CIGAR string - 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME) - 8 MPOS 1-based Mate POSition - 9 ISIZE Inferred insert SIZE - 10 SEQ query SEQuence on the same strand as the reference - 11 QUAL query QUALity (ASCII-33 gives the Phred base quality) - 12 OPT variable OPTional fields in the format TAG:VTYPE:VALU - -The flags are as follows:: - - Flag Description - ------ ------------------------------------- - 0x0001 the read is paired in sequencing - 0x0002 the read is mapped in a proper pair - 0x0004 the query sequence itself is unmapped - 0x0008 the mate is unmapped - 0x0010 strand of the query (1 for reverse) - 0x0020 strand of the mate - 0x0040 the read is the first read in a pair - 0x0080 the read is the second read in a pair - 0x0100 the alignment is not primary - -It looks like this (scroll sideways to see the entire example):: - - QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT - HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh - HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh - -------- - -**BWA settings** - -All of the options have a default value. You can change any of them. All of the options in BWA have been implemented here. - ------- - -**BWA parameter list** - -This is an exhaustive list of BWA options: - -For **aln**:: - - -n NUM Maximum edit distance if the value is INT, or the fraction of missing - alignments given 2% uniform base error rate if FLOAT. In the latter - case, the maximum edit distance is automatically chosen for different - read lengths. [0.04] - -o INT Maximum number of gap opens [1] - -e INT Maximum number of gap extensions, -1 for k-difference mode - (disallowing long gaps) [-1] - -d INT Disallow a long deletion within INT bp towards the 3'-end [16] - -i INT Disallow an indel within INT bp towards the ends [5] - -l INT Take the first INT subsequence as seed. If INT is larger than the - query sequence, seeding will be disabled. For long reads, this option - is typically ranged from 25 to 35 for '-k 2'. [inf] - -k INT Maximum edit distance in the seed [2] - -t INT Number of threads (multi-threading mode) [1] - -M INT Mismatch penalty. BWA will not search for suboptimal hits with a score - lower than (bestScore-misMsc). [3] - -O INT Gap open penalty [11] - -E INT Gap extension penalty [4] - -c Reverse query but not complement it, which is required for alignment - in the color space. - -R Proceed with suboptimal alignments even if the top hit is a repeat. By - default, BWA only searches for suboptimal alignments if the top hit is - unique. Using this option has no effect on accuracy for single-end - reads. It is mainly designed for improving the alignment accuracy of - paired-end reads. However, the pairing procedure will be slowed down, - especially for very short reads (~32bp). - -N Disable iterative search. All hits with no more than maxDiff - differences will be found. This mode is much slower than the default. - -For **samse**:: - - -n INT Maximum number of alignments to output in the XA tag for reads paired - properly. If a read has more than INT hits, the XA tag will not be - written. [3] - -r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null] - -For **sampe**:: - - -a INT Maximum insert size for a read pair to be considered as being mapped - properly. Since version 0.4.5, this option is only used when there - are not enough good alignment to infer the distribution of insert - sizes. [500] - -n INT Maximum number of alignments to output in the XA tag for reads paired - properly. If a read has more than INT hits, the XA tag will not be - written. [3] - -N INT Maximum number of alignments to output in the XA tag for disconcordant - read pairs (excluding singletons). If a read has more than INT hits, - the XA tag will not be written. [10] - -o INT Maximum occurrences of a read for pairing. A read with more - occurrences will be treated as a single-end read. Reducing this - parameter helps faster pairing. [100000] - -r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null] - -For specifying the read group in **samse** or **sampe**, use the following:: - - @RG Read group. Unordered multiple @RG lines are allowed. - ID Read group identiﬁer. Each @RG line must have a unique ID. The value of - ID is used in the RG tags of alignment records. Must be unique among all - read groups in header section. Read group IDs may be modiﬁed when - merging SAM ﬁles in order to handle collisions. - CN Name of sequencing center producing the read. - DS Description. - DT Date the run was produced (ISO8601 date or date/time). - FO Flow order. The array of nucleotide bases that correspond to the - nucleotides used for each ﬂow of each read. Multi-base ﬂows are encoded - in IUPAC format, and non-nucleotide ﬂows by various other characters. - Format : /\*|[ACMGRSVTWYHKDBN]+/ - KS The array of nucleotide bases that correspond to the key sequence of each read. - LB Library. - PG Programs used for processing the read group. - PI Predicted median insert size. - PL Platform/technology used to produce the reads. Valid values : CAPILLARY, - LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO. - PU Platform unit (e.g. ﬂowcell-barcode.lane for Illumina or slide for - SOLiD). Unique identiﬁer. - SM Sample. Use pool name where a pool is being sequenced. - - </help> -</tool> - - Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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