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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Oct '14

24 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3e1209960dc6/ Changeset: 3e1209960dc6 User: erasche2 Date: 2014-10-24 16:48:54+00:00 Summary: Enable configuration of dynamic external proxy Affected #: 3 files diff -r 49996549bac445dcda93df7f1ca5010b0dddcc84 -r 3e1209960dc68b40c6c59d838b0846e457a0e6d5 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -548,6 +548,9 @@ # Enable verbose debugging of Galaxy-managed dynamic proxy. #dynamic_proxy_debug=False +# The dynamic proxy is proxied by an external proxy (e.g. apache frontend to nodejs to wrap connections in SSL) +#dynamic_proxy_external_proxy=False + # -- Logging and Debugging # Verbosity of console log messages. Acceptable values can be found here: diff -r 49996549bac445dcda93df7f1ca5010b0dddcc84 -r 3e1209960dc68b40c6c59d838b0846e457a0e6d5 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -388,6 +388,7 @@ self.dynamic_proxy_debug = string_as_bool( kwargs.get( "dynamic_proxy_debug", "False" ) ) self.dynamic_proxy_bind_port = int( kwargs.get( "dynamic_proxy_bind_port", "8800" ) ) self.dynamic_proxy_bind_ip = kwargs.get( "dynamic_proxy_bind_ip", "0.0.0.0" ) + self.dynamic_proxy_external_proxy = string_as_bool( kwargs.get( "dynamic_proxy_external_proxy", "False" ) ) # Default chunk size for chunkable datatypes -- 64k self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) ) diff -r 49996549bac445dcda93df7f1ca5010b0dddcc84 -r 3e1209960dc68b40c6c59d838b0846e457a0e6d5 lib/galaxy/web/proxy/__init__.py --- a/lib/galaxy/web/proxy/__init__.py +++ b/lib/galaxy/web/proxy/__init__.py @@ -17,7 +17,7 @@ class ProxyManager(object): def __init__( self, config ): - for option in [ "manage_dynamic_proxy", "dynamic_proxy_bind_port", "dynamic_proxy_bind_ip", "dynamic_proxy_debug" ]: + for option in [ "manage_dynamic_proxy", "dynamic_proxy_bind_port", "dynamic_proxy_bind_ip", "dynamic_proxy_debug", "dynamic_proxy_external_proxy" ]: setattr( self, option, getattr( config, option ) ) self.launch_by = "node" # TODO: Support docker if self.manage_dynamic_proxy: @@ -43,7 +43,10 @@ if ':' in host: host = host[0:host.index(':')] scheme = trans.request.scheme - proxy_url = '%s://%s:%d' % (scheme, host, self.dynamic_proxy_bind_port) + if not self.dynamic_proxy_external_proxy: + proxy_url = '%s://%s:%d' % (scheme, host, self.dynamic_proxy_bind_port) + else: + proxy_url = '%s://%s' % (scheme, host) return { 'proxy_url': proxy_url, 'proxied_port': proxy_requests.port, https://bitbucket.org/galaxy/galaxy-central/commits/4dff4b08ca02/ Changeset: 4dff4b08ca02 User: jmchilton Date: 2014-10-24 19:16:01+00:00 Summary: Merged in erasche2/galaxy-central (pull request #541) Enable configuration of dynamic external proxy Affected #: 3 files diff -r 8915d81958a3778fe538dd8cedd69dd209948189 -r 4dff4b08ca0280f1f049b13ab1694ae959385f79 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -548,6 +548,9 @@ # Enable verbose debugging of Galaxy-managed dynamic proxy. #dynamic_proxy_debug=False +# The dynamic proxy is proxied by an external proxy (e.g. apache frontend to nodejs to wrap connections in SSL) +#dynamic_proxy_external_proxy=False + # -- Logging and Debugging # Verbosity of console log messages. Acceptable values can be found here: diff -r 8915d81958a3778fe538dd8cedd69dd209948189 -r 4dff4b08ca0280f1f049b13ab1694ae959385f79 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -388,6 +388,7 @@ self.dynamic_proxy_debug = string_as_bool( kwargs.get( "dynamic_proxy_debug", "False" ) ) self.dynamic_proxy_bind_port = int( kwargs.get( "dynamic_proxy_bind_port", "8800" ) ) self.dynamic_proxy_bind_ip = kwargs.get( "dynamic_proxy_bind_ip", "0.0.0.0" ) + self.dynamic_proxy_external_proxy = string_as_bool( kwargs.get( "dynamic_proxy_external_proxy", "False" ) ) # Default chunk size for chunkable datatypes -- 64k self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) ) diff -r 8915d81958a3778fe538dd8cedd69dd209948189 -r 4dff4b08ca0280f1f049b13ab1694ae959385f79 lib/galaxy/web/proxy/__init__.py --- a/lib/galaxy/web/proxy/__init__.py +++ b/lib/galaxy/web/proxy/__init__.py @@ -17,7 +17,7 @@ class ProxyManager(object): def __init__( self, config ): - for option in [ "manage_dynamic_proxy", "dynamic_proxy_bind_port", "dynamic_proxy_bind_ip", "dynamic_proxy_debug" ]: + for option in [ "manage_dynamic_proxy", "dynamic_proxy_bind_port", "dynamic_proxy_bind_ip", "dynamic_proxy_debug", "dynamic_proxy_external_proxy" ]: setattr( self, option, getattr( config, option ) ) self.launch_by = "node" # TODO: Support docker if self.manage_dynamic_proxy: @@ -43,7 +43,10 @@ if ':' in host: host = host[0:host.index(':')] scheme = trans.request.scheme - proxy_url = '%s://%s:%d' % (scheme, host, self.dynamic_proxy_bind_port) + if not self.dynamic_proxy_external_proxy: + proxy_url = '%s://%s:%d' % (scheme, host, self.dynamic_proxy_bind_port) + else: + proxy_url = '%s://%s' % (scheme, host) return { 'proxy_url': proxy_url, 'proxied_port': proxy_requests.port, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Merged in erasche2/galaxy-central (pull request #541)
by commits-noreply＠bitbucket.org 24 Oct '14

24 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4dff4b08ca02/ Changeset: 4dff4b08ca02 User: jmchilton Date: 2014-10-24 19:16:01+00:00 Summary: Merged in erasche2/galaxy-central (pull request #541) Enable configuration of dynamic external proxy Affected #: 3 files diff -r 8915d81958a3778fe538dd8cedd69dd209948189 -r 4dff4b08ca0280f1f049b13ab1694ae959385f79 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -548,6 +548,9 @@ # Enable verbose debugging of Galaxy-managed dynamic proxy. #dynamic_proxy_debug=False +# The dynamic proxy is proxied by an external proxy (e.g. apache frontend to nodejs to wrap connections in SSL) +#dynamic_proxy_external_proxy=False + # -- Logging and Debugging # Verbosity of console log messages. Acceptable values can be found here: diff -r 8915d81958a3778fe538dd8cedd69dd209948189 -r 4dff4b08ca0280f1f049b13ab1694ae959385f79 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -388,6 +388,7 @@ self.dynamic_proxy_debug = string_as_bool( kwargs.get( "dynamic_proxy_debug", "False" ) ) self.dynamic_proxy_bind_port = int( kwargs.get( "dynamic_proxy_bind_port", "8800" ) ) self.dynamic_proxy_bind_ip = kwargs.get( "dynamic_proxy_bind_ip", "0.0.0.0" ) + self.dynamic_proxy_external_proxy = string_as_bool( kwargs.get( "dynamic_proxy_external_proxy", "False" ) ) # Default chunk size for chunkable datatypes -- 64k self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) ) diff -r 8915d81958a3778fe538dd8cedd69dd209948189 -r 4dff4b08ca0280f1f049b13ab1694ae959385f79 lib/galaxy/web/proxy/__init__.py --- a/lib/galaxy/web/proxy/__init__.py +++ b/lib/galaxy/web/proxy/__init__.py @@ -17,7 +17,7 @@ class ProxyManager(object): def __init__( self, config ): - for option in [ "manage_dynamic_proxy", "dynamic_proxy_bind_port", "dynamic_proxy_bind_ip", "dynamic_proxy_debug" ]: + for option in [ "manage_dynamic_proxy", "dynamic_proxy_bind_port", "dynamic_proxy_bind_ip", "dynamic_proxy_debug", "dynamic_proxy_external_proxy" ]: setattr( self, option, getattr( config, option ) ) self.launch_by = "node" # TODO: Support docker if self.manage_dynamic_proxy: @@ -43,7 +43,10 @@ if ':' in host: host = host[0:host.index(':')] scheme = trans.request.scheme - proxy_url = '%s://%s:%d' % (scheme, host, self.dynamic_proxy_bind_port) + if not self.dynamic_proxy_external_proxy: + proxy_url = '%s://%s:%d' % (scheme, host, self.dynamic_proxy_bind_port) + else: + proxy_url = '%s://%s' % (scheme, host) return { 'proxy_url': proxy_url, 'proxied_port': proxy_requests.port, 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: martenson: fix to css propagating library TR styles to the whole app
by commits-noreply＠bitbucket.org 24 Oct '14

24 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8915d81958a3/ Changeset: 8915d81958a3 User: martenson Date: 2014-10-24 17:48:51+00:00 Summary: fix to css propagating library TR styles to the whole app Affected #: 3 files diff -r 49996549bac445dcda93df7f1ca5010b0dddcc84 -r 8915d81958a3778fe538dd8cedd69dd209948189 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1322,7 +1322,6 @@ .ui-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none} .ui-select-multiple{height:100% !important;width:100% !important} .libraryRow{background-color:#ebd9b2} -tr{height:32px} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} div.libraryItemBody{padding:4px 4px 2px 4px} @@ -1334,7 +1333,7 @@ .library_table td{border-top:1px solid #5f6990 !important} .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} -.library_style_container{width:95%;margin:auto;margin-top:2em;overflow:auto !important} +.library_style_container{width:95%;margin:auto;margin-top:2em;overflow:auto !important}.library_style_container tr{height:32px} tr.light td{background-color:white;color:black} tr.light:hover td{background-color:#f5e8cc} tr.dark td{background-color:#d6b161;color:white} diff -r 49996549bac445dcda93df7f1ca5010b0dddcc84 -r 8915d81958a3778fe538dd8cedd69dd209948189 static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -1,7 +1,6 @@ a{text-decoration:underline} label{font-weight:normal} .libraryRow{background-color:#ebd9b2} -tr{height:32px} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} div.libraryItemBody{padding:4px 4px 2px 4px} @@ -13,7 +12,7 @@ .library_table td{border-top:1px solid #5f6990 !important} .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} -.library_style_container{width:95%;margin:auto;margin-top:2em;overflow:auto !important} +.library_style_container{width:95%;margin:auto;margin-top:2em;overflow:auto !important}.library_style_container tr{height:32px} tr.light td{background-color:white;color:black} tr.light:hover td{background-color:#f5e8cc} tr.dark td{background-color:#d6b161;color:white} diff -r 49996549bac445dcda93df7f1ca5010b0dddcc84 -r 8915d81958a3778fe538dd8cedd69dd209948189 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -5,9 +5,6 @@ background-color: @table-heading-bg; } -tr{ - height: 32px; -} .datasetHighlighted { background-color: @table-bg-accent; } @@ -58,11 +55,14 @@ } } } -.library_style_container{ +.library_style_container { width: 95%; margin: auto; margin-top:2em; overflow: auto !important; + tr { + height: 32px; + } } tr.light td 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: jmchilton: Merged in BjoernGruening/galaxy-central-6/BjoernGruening/add-u-user-argument-to-the-docker-call-1414094590823 (pull request #540)
by commits-noreply＠bitbucket.org 24 Oct '14

24 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/49996549bac4/ Changeset: 49996549bac4 User: jmchilton Date: 2014-10-24 16:25:18+00:00 Summary: Merged in BjoernGruening/galaxy-central-6/BjoernGruening/add-u-user-argument-to-the-docker-call-1414094590823 (pull request #540) Add `-u $USER` argument to the docker call. Affected #: 1 file diff -r ae33952d52dcf4f682b317aaf01dcaa4d79d79b9 -r 49996549bac445dcda93df7f1ca5010b0dddcc84 lib/galaxy/web/base/interactive_environments.py --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -159,6 +159,7 @@ """ Generate and return the docker command to execute """ - return '%s run -d --sig-proxy=true -p %s:%s -v "%s:/import/" %s' % \ - (self.attr.viz_config.get("docker", "command"), self.attr.PORT, self.attr.docker_port, - temp_dir, self.attr.viz_config.get("docker", "image")) + return '%s run -d -u %s --sig-proxy=true -p %s:%s -v "%s:/import/" %s' % \ + (self.attr.viz_config.get("docker", "command"), os.geteuid(), + self.attr.PORT, self.attr.docker_port, + temp_dir, self.attr.viz_config.get("docker", "image")) 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: 2 new changesets
by commits-noreply＠bitbucket.org 24 Oct '14

24 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ba83dd543a46/ Changeset: ba83dd543a46 Branch: BjoernGruening/add-u-user-argument-to-the-docker-call-1414094590823 User: BjoernGruening Date: 2014-10-23 20:03:49+00:00 Summary: Add `-u $USER` argument to the docker call. Affected #: 1 file diff -r ae33952d52dcf4f682b317aaf01dcaa4d79d79b9 -r ba83dd543a46720653b8d585b09d866d740db1db lib/galaxy/web/base/interactive_environments.py --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -159,6 +159,7 @@ """ Generate and return the docker command to execute """ - return '%s run -d --sig-proxy=true -p %s:%s -v "%s:/import/" %s' % \ - (self.attr.viz_config.get("docker", "command"), self.attr.PORT, self.attr.docker_port, - temp_dir, self.attr.viz_config.get("docker", "image")) + return '%s run -d -u %s --sig-proxy=true -p %s:%s -v "%s:/import/" %s' % \ + (self.attr.viz_config.get("docker", "command"), os.geteuid(), + self.attr.PORT, self.attr.docker_port, + temp_dir, self.attr.viz_config.get("docker", "image")) https://bitbucket.org/galaxy/galaxy-central/commits/49996549bac4/ Changeset: 49996549bac4 User: jmchilton Date: 2014-10-24 16:25:18+00:00 Summary: Merged in BjoernGruening/galaxy-central-6/BjoernGruening/add-u-user-argument-to-the-docker-call-1414094590823 (pull request #540) Add `-u $USER` argument to the docker call. Affected #: 1 file diff -r ae33952d52dcf4f682b317aaf01dcaa4d79d79b9 -r 49996549bac445dcda93df7f1ca5010b0dddcc84 lib/galaxy/web/base/interactive_environments.py --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -159,6 +159,7 @@ """ Generate and return the docker command to execute """ - return '%s run -d --sig-proxy=true -p %s:%s -v "%s:/import/" %s' % \ - (self.attr.viz_config.get("docker", "command"), self.attr.PORT, self.attr.docker_port, - temp_dir, self.attr.viz_config.get("docker", "image")) + return '%s run -d -u %s --sig-proxy=true -p %s:%s -v "%s:/import/" %s' % \ + (self.attr.viz_config.get("docker", "command"), os.geteuid(), + self.attr.PORT, self.attr.docker_port, + temp_dir, self.attr.viz_config.get("docker", "image")) 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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[galaxyproject/usegalaxy-playbook] da2571: Stampede banner on Main.
by GitHub 23 Oct '14

23 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: da257112ada52ca8b75104fef523a51ba014c01f https://github.com/galaxyproject/usegalaxy-playbook/commit/da257112ada52ca8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-23 (Thu, 23 Oct 2014) Changed paths: M production/group_vars/galaxyservers.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Stampede banner on Main.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 23 Oct '14

23 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/21e3d69f6495/ Changeset: 21e3d69f6495 User: davebgx Date: 2014-10-23 14:34:17+00:00 Summary: Add optional display of stdout/stderr to the jobs API return value, defaulting to not displayed. Rework the test API interactor to wait for jobs instead of histories and get the stdout and stderr from the API. Affected #: 3 files diff -r 1f82617c06887e82e01175d24e45576da1e6ed92 -r 21e3d69f64953a848f5fcbfe4c4213c3a8d3c37b lib/galaxy/webapps/galaxy/api/jobs.py --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -93,7 +93,11 @@ :returns: dictionary containing full description of job data """ job = self.__get_job( trans, id ) - return self.encode_all_ids( trans, job.to_dict( 'element' ), True ) + job_dict = self.encode_all_ids( trans, job.to_dict( 'element' ), True ) + full_output = util.asbool( kwd.get( 'full', 'false' ) ) + if full_output: + job_dict.update( dict( stderr=job.stderr, stdout=job.stdout ) ) + return job_dict @expose_api def inputs( self, trans, id, **kwd ): diff -r 1f82617c06887e82e01175d24e45576da1e6ed92 -r 21e3d69f64953a848f5fcbfe4c4213c3a8d3c37b test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -54,11 +54,12 @@ self.api_key = self.__get_user_key( twill_test_case.user_api_key, twill_test_case.master_api_key, test_user=test_user ) self.uploads = {} - def verify_output( self, history_id, output_data, output_testdef, shed_tool_id, maxseconds ): + def verify_output( self, history_id, jobs, output_data, output_testdef, shed_tool_id, maxseconds ): outfile = output_testdef.outfile attributes = output_testdef.attributes name = output_testdef.name - self.wait_for_history( history_id, maxseconds ) + for job in jobs: + self.wait_for_job( job[ 'id' ], maxseconds ) hid = self.__output_id( output_data ) fetcher = self.__dataset_fetcher( history_id ) ## TODO: Twill version verifys dataset is 'ok' in here. @@ -114,10 +115,17 @@ def wait_for_history( self, history_id, maxseconds ): self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) - def get_job_stream( self, history_id, output_data, stream ): - hid = self.__output_id( output_data ) - data = self._dataset_provenance( history_id, hid ) - return data.get( stream, '' ) + def wait_for_job( self, job_id, maxseconds ): + self.twill_test_case.wait_for( lambda: not self.__job_ready( job_id ), maxseconds=maxseconds) + + def get_job_stdio( self, job_id, stream ): + job_stdio = self.__get_job_stdio( job_id ).json() + + def __get_job( self, job_id ): + return self._get( 'jobs/%s' % job_id ) + + def __get_job_stdio( self, job_id ): + return self._get( 'jobs/%s?full=true' % job_id ) def new_history( self ): history_json = self._post( "histories", {"name": "test_history"} ).json() @@ -204,7 +212,7 @@ datasets = self.__submit_tool( history_id, tool_id=testdef.tool.id, tool_input=inputs_tree ) datasets_object = datasets.json() try: - return self.__dictify_outputs( datasets_object ) + return self.__dictify_outputs( datasets_object ), datasets_object[ 'jobs' ] except KeyError: raise Exception( datasets_object[ 'message' ] ) @@ -261,6 +269,22 @@ pass return wait + def __wait_for_job( self, job_id ): + def wait(): + while not self.__job_ready( job_id ): + pass + return wait + + def __job_ready( self, job_id ): + job_json = self._get( "jobs/%s" % job_id ).json() + state = job_json[ 'state' ] + try: + return self._state_ready( state, error_msg="Job in error state." ) + except Exception: + if VERBOSE_ERRORS: + self._summarize_job_errors( history_id ) + raise + def __history_ready( self, history_id ): history_json = self._get( "histories/%s" % history_id ).json() state = history_json[ 'state' ] diff -r 1f82617c06887e82e01175d24e45576da1e6ed92 -r 21e3d69f64953a848f5fcbfe4c4213c3a8d3c37b test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -29,10 +29,10 @@ stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) - data_list = galaxy_interactor.run_tool( testdef, test_history ) + data_list, jobs = galaxy_interactor.run_tool( testdef, test_history ) self.assertTrue( data_list ) - self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor ) + self._verify_outputs( testdef, test_history, jobs, shed_tool_id, data_list, galaxy_interactor ) galaxy_interactor.delete_history( test_history ) @@ -47,7 +47,7 @@ else: raise Exception( "Test parse failure" ) - def _verify_outputs( self, testdef, history, shed_tool_id, data_list, galaxy_interactor ): + def _verify_outputs( self, testdef, history, jobs, shed_tool_id, data_list, galaxy_interactor ): maxseconds = testdef.maxseconds if testdef.num_outputs is not None: expected = testdef.num_outputs @@ -72,11 +72,13 @@ output_data = data_list[ len(data_list) - len(testdef.outputs) + output_index ] self.assertTrue( output_data is not None ) try: - galaxy_interactor.verify_output( history, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) + galaxy_interactor.verify_output( history, jobs, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) except Exception: - for stream in ['stdout', 'stderr']: - stream_output = galaxy_interactor.get_job_stream( history, output_data, stream=stream ) - print >>sys.stderr, self._format_stream( stream_output, stream=stream, format=True ) + for job in jobs: + job_stdio = galaxy_interactor.get_job_stdio( job[ 'id' ] ) + for stream in ['stdout', 'stderr']: + if stream in job_stdio: + print >>sys.stderr, self._format_stream( job_stdio[ stream ], stream=stream, format=True ) raise https://bitbucket.org/galaxy/galaxy-central/commits/ae33952d52dc/ Changeset: ae33952d52dc User: davebgx Date: 2014-10-23 14:35:43+00:00 Summary: Merge stable into default. Affected #: 1 file diff -r 21e3d69f64953a848f5fcbfe4c4213c3a8d3c37b -r ae33952d52dcf4f682b317aaf01dcaa4d79d79b9 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -a7b2aabb27ffe5cc3216774ab01b18f13b4fc941 latest_2014.10.06 +9bc08bc7f393362ee7e6cf1d04bb9d8cee68f2d8 latest_2014.10.06 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: Update tag latest_2014.10.06 for changeset 9bc08bc7f393
by commits-noreply＠bitbucket.org 23 Oct '14

23 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5123ed7f1603/ Changeset: 5123ed7f1603 Branch: stable User: natefoo Date: 2014-10-23 14:00:16+00:00 Summary: Update tag latest_2014.10.06 for changeset 9bc08bc7f393 Affected #: 1 file diff -r 9bc08bc7f393362ee7e6cf1d04bb9d8cee68f2d8 -r 5123ed7f16037c67a66f90ce63ef5a15faab21c9 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -a7b2aabb27ffe5cc3216774ab01b18f13b4fc941 latest_2014.10.06 +9bc08bc7f393362ee7e6cf1d04bb9d8cee68f2d8 latest_2014.10.06 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: guerler: ToolForm: Pack scripts
by commits-noreply＠bitbucket.org 23 Oct '14

23 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1f82617c0688/ Changeset: 1f82617c0688 User: guerler Date: 2014-10-23 13:54:05+00:00 Summary: ToolForm: Pack scripts Affected #: 2 files diff -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c -r 1f82617c06887e82e01175d24e45576da1e6ed92 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -283,6 +283,11 @@ console.debug('tools-form::_addRow() : Auto matched field type (' + field_type + ').'); } + // deactivate dynamic fields + if (input_def.is_dynamic) { + this.app.incompatible = true; + } + // set field value if (input_def.value !== undefined) { field.value(input_def.value); diff -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c -r 1f82617c06887e82e01175d24e45576da1e6ed92 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){if(i.app.is_dynamic){i.app.rebuild()}var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.is_dynamic=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.incompatible=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){if(i.app.is_dynamic){i.app.rebuild()}var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.is_dynamic=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ 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.

1 0

commit/galaxy-central: guerler: ToolForm: Add support for dynamic parameters, add tool version check
by commits-noreply＠bitbucket.org 23 Oct '14

23 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3b4784d5fc0d/ Changeset: 3b4784d5fc0d User: guerler Date: 2014-10-23 13:50:31+00:00 Summary: ToolForm: Add support for dynamic parameters, add tool version check Affected #: 14 files diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -42,24 +42,11 @@ // creates the job handler this.job_handler = new ToolJobs(this); - // reset field list, which contains the input field elements - this.field_list = {}; - - // reset sequential input definition list, which contains the input definitions as provided from the api - this.input_list = {}; - - // reset input element list, which contains the dom elements of each input element (includes also the input field) - this.element_list = {}; - - // for now the initial tool model is parsed through the mako - this.model = this.options; - this.inputs = this.options.inputs; - // request history content and build form this.content = new ToolContent({ history_id : self.options.history_id, success : function() { - self._buildForm(); + self._buildForm(self.options); } }); }, @@ -137,7 +124,7 @@ }, // refresh form data - _refreshForm: function() { + rebuild: function() { // link this var self = this; @@ -161,6 +148,10 @@ url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', data : current_state, success : function(response) { + // rebuild form + self._rebuildForm(response); + + // log success console.debug('tools-form::_refreshForm() - Refreshed inputs/states.'); console.debug(response); }, @@ -171,11 +162,55 @@ }); }, + // rebuild the form elements + _rebuildForm: function(new_model) { + var self = this; + this.tree.matchModel(new_model, function(input_id, node) { + var input = self.input_list[input_id]; + if (input && input.options) { + if (JSON.stringify(input.options) != JSON.stringify(node.options)) { + // backup new options + input.options = node.options; + + // get/update field (currently only done for select fields) + var field = self.field_list[input_id]; + if (field.update && input.type == 'select') { + var new_options = []; + for (var i in node.options) { + var opt = node.options[i]; + if (opt.length > 2) { + new_options.push({ + 'label': opt[0], + 'value': opt[1] + }); + } + } + field.update(new_options); + console.debug('Updating options for ' + input_id); + } + } + } + }); + }, + // builds the tool form - _buildForm: function() { + _buildForm: function(options) { // link this var self = this; + // reset field list, which contains the input field elements + this.field_list = {}; + + // reset sequential input definition list, which contains the input definitions as provided from the api + this.input_list = {}; + + // reset input element list, which contains the dom elements of each input element (includes also the input field) + this.element_list = {}; + + // for now the initial tool model is parsed through the mako + this.model = options; + this.inputs = options.inputs; + // button menu var menu = new Ui.ButtonMenu({ icon : 'fa-gear', @@ -183,7 +218,7 @@ }); // configure button selection - if(this.options.biostar_url) { + if(options.biostar_url) { // add question option menu.addMenu({ icon : 'fa-question-circle', @@ -256,29 +291,30 @@ cls : 'btn btn-primary', floating : 'clear', onclick : function() { - //self._refreshForm(); + //self.rebuild(); self.job_handler.submit(); } }) } }); - // append form + // start form + this.$el.empty(); this.$el.append(this.portlet.$el); // append help - if (this.options.help != '') { - this.$el.append(ToolTemplate.help(this.options.help)); + if (options.help != '') { + this.$el.append(ToolTemplate.help(options.help)); } // append citations - if (this.options.citations) { + if (options.citations) { // append html this.$el.append(ToolTemplate.citations()); // fetch citations var citations = new CitationModel.ToolCitationCollection(); - citations.tool_id = this.options.id; + citations.tool_id = options.id; var citation_list_view = new CitationView.CitationListView({ collection: citations } ); citation_list_view.render(); citations.fetch(); diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -50,7 +50,7 @@ var input_def = jQuery.extend(true, {}, input); // create unique id - input_def.id = Utils.uuid(); + input_def.id = input.id = Utils.uuid(); // add to sequential list of inputs this.app.input_list[input_def.id] = input_def; @@ -208,7 +208,7 @@ _addRow: function(field_type, input_def) { // get id var id = input_def.id; - + // field wrapper var field = null; @@ -283,6 +283,11 @@ console.debug('tools-form::_addRow() : Auto matched field type (' + field_type + ').'); } + // deactivate dynamic fields + if (input_def.is_dynamic) { + this.app.incompatible = true; + } + // set field value if (input_def.value !== undefined) { field.value(input_def.value); @@ -380,6 +385,11 @@ extensions : input_def.extensions, multiple : input_def.multiple, onchange : function(dict) { + // rebuild the form + if (self.app.is_dynamic) { + self.app.rebuild(); + } + // pick the first content only (todo: maybe collect multiple meta information) var content_def = dict.values[0]; var content_id = content_def.id; @@ -485,7 +495,7 @@ _fieldSelect : function (input_def) { // check compatibility if (input_def.is_dynamic) { - this.app.incompatible = true; + this.app.is_dynamic = true; } // configure options fields diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -30,7 +30,7 @@ if (njobs == 1) { njobs_text = '1 job has'; } else { - njobs_text = njobs + ' jobs have been'; + njobs_text = njobs + ' jobs have'; } // create template string diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -146,7 +146,48 @@ return this.job_ids && this.job_ids[job_input_id]; }, - /** Matches identifier from api response to input element + /** Matches identifier from api model to input elements + */ + matchModel: function(model, callback) { + // final result dictionary + var result = {}; + + // link this + var self = this; + + // search throughout response + function search (id, head) { + for (var i in head) { + var node = head[i]; + var index = node.name; + if (id != '') { + index = id + '|' + index; + } + if (node.type == 'repeat') { + for (var j in node.cache) { + search (index + '_' + j, node.cache[j]); + } + } else { + if (node.type == 'conditional') { + search (index, node.inputs); + } else { + var input_id = self.app.tree.job_ids[index]; + if (input_id) { + callback(input_id, node); + } + } + } + } + } + + // match all ids and return messages + search('', model.inputs); + + // return matched results + return result; + }, + + /** Matches identifier from api response to input elements */ matchResponse: function(response) { // final result dictionary diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -131,6 +131,7 @@ """ api_type = "file" encoded_id = trans.security.encode_id( hda.id ) + # TODO: handle failed_metadata here as well return { 'id' : encoded_id, diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -510,16 +510,18 @@ trans.response.status = 500 return { 'error': 'Failed to get job information.' } - # check if job was identified + # load job parameters into incoming + tool_message = '' if job: try: job_params = job.get_param_values( trans.app, ignore_errors = True ) job_messages = tool.check_and_update_param_values( job_params, trans, update_values=False ) + tool_message = self._compare_tool_version(trans, tool, job) params_to_incoming( kwd, tool.inputs, job_params, trans.app ) except Exception, exception: trans.response.status = 500 return { 'error': str( exception ) } - + # create parameter object params = galaxy.util.Params( kwd, sanitize = False ) @@ -644,8 +646,52 @@ tool_model.update({ 'help' : tool_help, 'citations' : tool_citations, - 'biostar_url' : trans.app.config.biostar_url + 'biostar_url' : trans.app.config.biostar_url, + 'message' : tool_message }) # return enriched tool model return tool_model + + def _get_tool_components( self, trans, tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False ): + return self.get_toolbox().get_tool_components( tool_id, tool_version, get_loaded_tools_by_lineage, set_selected ) + + def _compare_tool_version( self, trans, tool, job ): + """ + Compares a tool version with the tool version from a job (from ToolRunne. + """ + id = job.tool_id + version = job.tool_version + message = '' + try: + select_field, tools, tool = self._get_tool_components( trans, id, tool_version=version, get_loaded_tools_by_lineage=False, set_selected=True ) + if tool is None: + trans.response.status = 500 + return { 'error': 'This dataset was created by an obsolete tool (%s). Can\'t re-run.' % id } + if ( tool.id != id and tool.old_id != id ) or tool.version != version: + if tool.id == id: + if version == None: + # for some reason jobs don't always keep track of the tool version. + message = '' + else: + message = 'This job was initially run with tool version "%s", which is currently not available. ' % version + if len( tools ) > 1: + message += 'You can re-run the job with the selected tool or choose another derivation of the tool.' + else: + message += 'You can re-run the job with this tool version, which is a derivation of the original tool.' + else: + if len( tools ) > 1: + message = 'This job was initially run with tool version "%s", which is currently not available. ' % version + message += 'You can re-run the job with the selected tool or choose another derivation of the tool.' + else: + message = 'This job was initially run with tool id "%s", version "%s", which is ' % ( id, version ) + message += 'currently not available. You can re-run the job with this tool, which is a derivation of the original tool.' + except Exception, error: + trans.response.status = 500 + return { 'error': str (error) } + + # can't rerun upload, external data sources, et cetera. workflow compatible will proxy this for now + if not tool.is_workflow_compatible: + trans.response.status = 500 + return { 'error': 'The \'%s\' tool does currently not support re-running.' % tool.name } + return message diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -42,24 +42,11 @@ // creates the job handler this.job_handler = new ToolJobs(this); - // reset field list, which contains the input field elements - this.field_list = {}; - - // reset sequential input definition list, which contains the input definitions as provided from the api - this.input_list = {}; - - // reset input element list, which contains the dom elements of each input element (includes also the input field) - this.element_list = {}; - - // for now the initial tool model is parsed through the mako - this.model = this.options; - this.inputs = this.options.inputs; - // request history content and build form this.content = new ToolContent({ history_id : self.options.history_id, success : function() { - self._buildForm(); + self._buildForm(self.options); } }); }, @@ -137,7 +124,7 @@ }, // refresh form data - _refreshForm: function() { + rebuild: function() { // link this var self = this; @@ -161,6 +148,10 @@ url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', data : current_state, success : function(response) { + // rebuild form + self._rebuildForm(response); + + // log success console.debug('tools-form::_refreshForm() - Refreshed inputs/states.'); console.debug(response); }, @@ -171,11 +162,55 @@ }); }, + // rebuild the form elements + _rebuildForm: function(new_model) { + var self = this; + this.tree.matchModel(new_model, function(input_id, node) { + var input = self.input_list[input_id]; + if (input && input.options) { + if (JSON.stringify(input.options) != JSON.stringify(node.options)) { + // backup new options + input.options = node.options; + + // get/update field (currently only done for select fields) + var field = self.field_list[input_id]; + if (field.update && input.type == 'select') { + var new_options = []; + for (var i in node.options) { + var opt = node.options[i]; + if (opt.length > 2) { + new_options.push({ + 'label': opt[0], + 'value': opt[1] + }); + } + } + field.update(new_options); + console.debug('Updating options for ' + input_id); + } + } + } + }); + }, + // builds the tool form - _buildForm: function() { + _buildForm: function(options) { // link this var self = this; + // reset field list, which contains the input field elements + this.field_list = {}; + + // reset sequential input definition list, which contains the input definitions as provided from the api + this.input_list = {}; + + // reset input element list, which contains the dom elements of each input element (includes also the input field) + this.element_list = {}; + + // for now the initial tool model is parsed through the mako + this.model = options; + this.inputs = options.inputs; + // button menu var menu = new Ui.ButtonMenu({ icon : 'fa-gear', @@ -183,7 +218,7 @@ }); // configure button selection - if(this.options.biostar_url) { + if(options.biostar_url) { // add question option menu.addMenu({ icon : 'fa-question-circle', @@ -256,29 +291,30 @@ cls : 'btn btn-primary', floating : 'clear', onclick : function() { - //self._refreshForm(); + //self.rebuild(); self.job_handler.submit(); } }) } }); - // append form + // start form + this.$el.empty(); this.$el.append(this.portlet.$el); // append help - if (this.options.help != '') { - this.$el.append(ToolTemplate.help(this.options.help)); + if (options.help != '') { + this.$el.append(ToolTemplate.help(options.help)); } // append citations - if (this.options.citations) { + if (options.citations) { // append html this.$el.append(ToolTemplate.citations()); // fetch citations var citations = new CitationModel.ToolCitationCollection(); - citations.tool_id = this.options.id; + citations.tool_id = options.id; var citation_list_view = new CitationView.CitationListView({ collection: citations } ); citation_list_view.render(); citations.fetch(); diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -50,7 +50,7 @@ var input_def = jQuery.extend(true, {}, input); // create unique id - input_def.id = Utils.uuid(); + input_def.id = input.id = Utils.uuid(); // add to sequential list of inputs this.app.input_list[input_def.id] = input_def; @@ -208,7 +208,7 @@ _addRow: function(field_type, input_def) { // get id var id = input_def.id; - + // field wrapper var field = null; @@ -380,6 +380,11 @@ extensions : input_def.extensions, multiple : input_def.multiple, onchange : function(dict) { + // rebuild the form + if (self.app.is_dynamic) { + self.app.rebuild(); + } + // pick the first content only (todo: maybe collect multiple meta information) var content_def = dict.values[0]; var content_id = content_def.id; @@ -485,7 +490,7 @@ _fieldSelect : function (input_def) { // check compatibility if (input_def.is_dynamic) { - this.app.incompatible = true; + this.app.is_dynamic = true; } // configure options fields diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -30,7 +30,7 @@ if (njobs == 1) { njobs_text = '1 job has'; } else { - njobs_text = njobs + ' jobs have been'; + njobs_text = njobs + ' jobs have'; } // create template string diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -146,7 +146,48 @@ return this.job_ids && this.job_ids[job_input_id]; }, - /** Matches identifier from api response to input element + /** Matches identifier from api model to input elements + */ + matchModel: function(model, callback) { + // final result dictionary + var result = {}; + + // link this + var self = this; + + // search throughout response + function search (id, head) { + for (var i in head) { + var node = head[i]; + var index = node.name; + if (id != '') { + index = id + '|' + index; + } + if (node.type == 'repeat') { + for (var j in node.cache) { + search (index + '_' + j, node.cache[j]); + } + } else { + if (node.type == 'conditional') { + search (index, node.inputs); + } else { + var input_id = self.app.tree.job_ids[index]; + if (input_id) { + callback(input_id, node); + } + } + } + } + } + + // match all ids and return messages + search('', model.inputs); + + // return matched results + return result; + }, + + /** Matches identifier from api response to input elements */ matchResponse: function(response) { // final result dictionary diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.model=this.options;this.inputs=this.options.inputs;this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},_refreshForm:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildForm:function(){var n=this;var p=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(this.options.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:p},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=this.options.id;var o=new a.CitationListView({collection:m});o.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},rebuild:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){m._rebuildForm(o);console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type=="select"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.incompatible=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){if(i.app.is_dynamic){i.app.rebuild()}var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.is_dynamic=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(k,n){for(var h in n){var f=n[h];if(f.input){var p=f.input;var j=k;if(k!=""){j+="|"}j+=p.name;switch(p.type){case"repeat":var e="section-";var s=[];var m=null;for(var r in f){var l=r.indexOf(e);if(l!=-1){l+=e.length;s.push(parseInt(r.substr(l)));if(!m){m=r.substr(0,l)}}}s.sort(function(t,i){return t-i});var h=0;for(var g in s){b(j+"_"+h++,f[m+s[g]])}break;case"conditional":var q=a.app.field_list[p.id].value();c(j+"|"+p.test_param.name,p.id,q);for(var g in p.cases){if(p.cases[g].value==q){b(j,n[p.id+"-section-"+g]);break}}break;default:var o=a.app.field_list[p.id];var q=o.value();if(d[p.type]){q=d[p.type](q)}if(!o.skip){c(j,p.id,q)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(k,n){for(var h in n){var f=n[h];if(f.input){var p=f.input;var j=k;if(k!=""){j+="|"}j+=p.name;switch(p.type){case"repeat":var e="section-";var s=[];var m=null;for(var r in f){var l=r.indexOf(e);if(l!=-1){l+=e.length;s.push(parseInt(r.substr(l)));if(!m){m=r.substr(0,l)}}}s.sort(function(t,i){return t-i});var h=0;for(var g in s){b(j+"_"+h++,f[m+s[g]])}break;case"conditional":var q=a.app.field_list[p.id].value();c(j+"|"+p.test_param.name,p.id,q);for(var g in p.cases){if(p.cases[g].value==q){b(j,n[p.id+"-section-"+g]);break}}break;default:var o=a.app.field_list[p.id];var q=o.value();if(d[p.type]){q=d[p.type](q)}if(!o.skip){c(j,p.id,q)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchModel:function(c,e){var a={};var b=this;function d(n,l){for(var k in l){var m=l[k];var h=m.name;if(n!=""){h=n+"|"+h}if(m.type=="repeat"){for(var g in m.cache){d(h+"_"+g,m.cache[g])}}else{if(m.type=="conditional"){d(h,m.inputs)}else{var f=b.app.tree.job_ids[h];if(f){e(f,m)}}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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