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Galaxy question
by Fu, Yi-Ping 19 Nov '08

19 Nov '08

Hi, I just learned Galaxy in this ASHG meeting, but I wonder how I can use my own plink-format binary data. The tool side from http://main.g2.bx.psu.edu/ does not look like the one we had in class, and it keeps giving me error if I try to upload my *.bed data. Also, I would suggest Galaxy to provide a pdf manual to look things up, just like all the other genetic program/software. The screencasts takes too much time. Many thanks in advance! Regards, Yi-Ping ------------------------------------------------------------------------ ------ Yi-Ping Fu, MS, PhD candidate Human Genetics Center School of Public Health The University of Texas Health Science Center at Houston 1200 Hermann Pressler, Suite RAS-E427 Houston TX 77030 Office: 713-500-9898 Fax: 713-500-0900

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[hg] galaxy 1635: Always write keys in order when creating json ...
by Greg Von Kuster 19 Nov '08

19 Nov '08

details: http://www.bx.psu.edu/hg/galaxy/rev/2302d3914843 changeset: 1635:2302d3914843 user: James Taylor <james(a)jamestaylor.org> date: Tue Nov 18 15:47:13 2008 -0500 description: Always write keys in order when creating json strings. Also removed a bunch of unused stuff from JSONType -- if you don't need it... 1 file(s) affected in this change: lib/galaxy/model/custom_types.py diffs (89 lines): diff -r ad26fd305881 -r 2302d3914843 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py Tue Nov 18 11:23:09 2008 -0500 +++ b/lib/galaxy/model/custom_types.py Tue Nov 18 15:47:13 2008 -0500 @@ -6,6 +6,10 @@ from galaxy.util.bunch import Bunch from galaxy.util.aliaspickler import AliasPickleModule +# Default JSON encoder and decoder +json_encoder = simplejson.JSONEncoder( sort_keys=True ) +json_decoder = simplejson.JSONDecoder( ) + class JSONType( TypeDecorator ): """ Defines a JSONType for SQLAlchemy. Takes a primitive as input and @@ -13,63 +17,42 @@ """ impl = Binary - def __init__( self, jsonifyer=None, mutable=True ): - self.jsonifyer = jsonifyer or simplejson - self.mutable = mutable - super( JSONType, self).__init__() - def process_bind_param( self, value, dialect ): if value is None: return None - return self.jsonifyer.dumps( value ) + return json_encoder.encode( value ) def process_result_value( self, value, dialect ): if value is None: return None - return self.jsonifyer.loads( str( value ) ) + return json_decoder.decode( str( value ) ) def copy_value( self, value ): - if self.mutable: - return self.jsonifyer.loads( self.jsonifyer.dumps(value) ) - else: - return value + return json_decoder.decode( json_encoder.encode( value ) ) def compare_values( self, x, y ): - if self.mutable: - return self.jsonifyer.dumps( x ) == self.jsonifyer.dumps( y ) - else: - return x is y + return json_encoder.encode( x ) == json_encoder.encode( y ) - def is_mutable( self ): - return self.mutable - -MetadataPickler = AliasPickleModule( { +metadata_pickler = AliasPickleModule( { ( "cookbook.patterns", "Bunch" ) : ( "galaxy.util.bunch" , "Bunch" ) } ) class MetadataType( JSONType ): """ - Mixture between JSONType and PickleType...can read in either, and - writes JSON. + Backward compatible metadata type. Can read pickles or JSON, but always + writes in JSON. """ - - def __init__( self, pickler=MetadataPickler, jsonifyer=None, mutable=True ): - self.jsonifyer = jsonifyer or simplejson - self.pickler = pickler or pickle - self.mutable = mutable - super( MetadataType, self).__init__() - def process_result_value( self, value, dialect ): if value is None: return None - buf = value ret = None try: - ret = self.pickler.loads( str(buf) ) - if ret: ret = dict( ret.__dict__ ) + ret = metadata_pickler.loads( str( value ) ) + if ret: + ret = dict( ret.__dict__ ) except: try: - ret = self.jsonifyer.loads( str(buf) ) + ret = json_decoder.decode( str( value ) ) except: ret = None return ret

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[hg] galaxy 1636: bugfix to last commit
by Greg Von Kuster 19 Nov '08

19 Nov '08

details: http://www.bx.psu.edu/hg/galaxy/rev/8412e0cbe7f0 changeset: 1636:8412e0cbe7f0 user: James Taylor <james(a)jamestaylor.org> date: Tue Nov 18 16:04:41 2008 -0500 description: bugfix to last commit 1 file(s) affected in this change: lib/galaxy/model/custom_types.py diffs (13 lines): diff -r 2302d3914843 -r 8412e0cbe7f0 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py Tue Nov 18 15:47:13 2008 -0500 +++ b/lib/galaxy/model/custom_types.py Tue Nov 18 16:04:41 2008 -0500 @@ -32,6 +32,9 @@ def compare_values( self, x, y ): return json_encoder.encode( x ) == json_encoder.encode( y ) + + def is_mutable( self ): + return True metadata_pickler = AliasPickleModule( { ( "cookbook.patterns", "Bunch" ) : ( "galaxy.util.bunch" , "Bunch" )

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[hg] galaxy 1634: (no commit message)
by Greg Von Kuster 19 Nov '08

19 Nov '08

details: http://www.bx.psu.edu/hg/galaxy/rev/ad26fd305881 changeset: 1634:ad26fd305881 user: wychung date: Tue Nov 18 11:23:09 2008 -0500 description: (no commit message) 3 file(s) affected in this change: lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py tools/fasta_tools/fasta_compute_length.py tools/fasta_tools/fasta_to_tabular.py diffs (36 lines): diff -r 950a71339420 -r ad26fd305881 lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py --- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py Fri Nov 14 13:21:02 2008 -0500 +++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py Tue Nov 18 11:23:09 2008 -0500 @@ -27,7 +27,7 @@ else: if line: sequence += line - if line.split()[0].isdigit(): + if line.split() and line.split()[0].isdigit(): sequence += ' ' if sequence: seq_hash[( sequence_count, title )] = sequence diff -r 950a71339420 -r ad26fd305881 tools/fasta_tools/fasta_compute_length.py --- a/tools/fasta_tools/fasta_compute_length.py Fri Nov 14 13:21:02 2008 -0500 +++ b/tools/fasta_tools/fasta_compute_length.py Tue Nov 18 11:23:09 2008 -0500 @@ -34,7 +34,7 @@ tmp_seq = '' else: tmp_seq = "%s%s" % ( tmp_seq, line ) - if line.split()[0].isdigit(): + if line.split() and line.split()[0].isdigit(): tmp_seq = "%s " % tmp_seq if len( tmp_seq ) > 0: seq_hash[ ( tmp_seq_count, tmp_title ) ] = tmp_seq diff -r 950a71339420 -r ad26fd305881 tools/fasta_tools/fasta_to_tabular.py --- a/tools/fasta_tools/fasta_to_tabular.py Fri Nov 14 13:21:02 2008 -0500 +++ b/tools/fasta_tools/fasta_to_tabular.py Tue Nov 18 11:23:09 2008 -0500 @@ -35,7 +35,7 @@ sequence = '' else: sequence = "%s%s" % ( sequence, line ) - if line.split()[0].isdigit(): + if line.split() and line.split()[0].isdigit(): sequence += ' ' if sequence: seq_hash[( sequence_count, title )] = sequence

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[hg] galaxy 1633: update poisson test tool for R warnings.
by Greg Von Kuster 17 Nov '08

17 Nov '08

details: http://www.bx.psu.edu/hg/galaxy/rev/950a71339420 changeset: 1633:950a71339420 user: wychung date: Fri Nov 14 13:21:02 2008 -0500 description: update poisson test tool for R warnings. 2 file(s) affected in this change: tools/taxonomy/poisson2test.py tools/taxonomy/poisson2test.xml diffs (40 lines): diff -r a5ec5ab6144b -r 950a71339420 tools/taxonomy/poisson2test.py --- a/tools/taxonomy/poisson2test.py Thu Nov 13 19:19:03 2008 -0500 +++ b/tools/taxonomy/poisson2test.py Fri Nov 14 13:21:02 2008 -0500 @@ -5,7 +5,7 @@ from rpy import * -if ((len(sys.argv)-1) != 5): +if ((len(sys.argv)-1) != 6): print 'too few parameters' print 'usage: inputfile, col1, col2, d-value(not 0), p-val correction method(0 or 1)' sys.exit() @@ -21,6 +21,7 @@ j = int(sys.argv[3]) #second colum to compare d = float(sys.argv[4]) #correction factor k = int(sys.argv[5]) #p-val correction method + outfile = open(sys.argv[6],'w') # output data if (i>j): print 'column order not correct col1 < col2' @@ -114,7 +115,7 @@ #printing all columns for n in range(fsize): - print "%s\t%4.3f\t%4.3f\t%8.6f\t%8.6f\t%8.6f\t%8.6f" %(lines_arr[n].strip(),z1[n],z2[n],pz1[n],pz2[n],corrz1[n],corrz2[n]) + print >> outfile, "%s\t%4.3f\t%4.3f\t%8.6f\t%8.6f\t%8.6f\t%8.6f" %(lines_arr[n].strip(),z1[n],z2[n],pz1[n],pz2[n],corrz1[n],corrz2[n]) diff -r a5ec5ab6144b -r 950a71339420 tools/taxonomy/poisson2test.xml --- a/tools/taxonomy/poisson2test.xml Thu Nov 13 19:19:03 2008 -0500 +++ b/tools/taxonomy/poisson2test.xml Fri Nov 14 13:21:02 2008 -0500 @@ -1,6 +1,6 @@ <tool id="poisson2test" name="Poisson two-sample test" version="1.0.0"> <description></description> - <command interpreter="python">poisson2test.py $input1 $input2 $input3 $input4 $input5 > $output1 </command> + <command interpreter="python">poisson2test.py $input1 $input2 $input3 $input4 $input5 $output1 2>/dev/null </command> <inputs> <param name="input1" format="tabular" type="data" label="Input File"/> <param name="input2" type="integer" size="5" value="2" label="First Column"/>

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[hg] galaxy 1632: Some job runner fixes.
by Nate Coraor 14 Nov '08

14 Nov '08

details: http://www.bx.psu.edu/hg/galaxy/rev/a5ec5ab6144b changeset: 1632:a5ec5ab6144b user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Nov 13 19:19:03 2008 -0500 description: Some job runner fixes. 2 file(s) affected in this change: lib/galaxy/jobs/__init__.py lib/galaxy/jobs/runners/pbs.py diffs (37 lines): diff -r a39afe99b3bd -r a5ec5ab6144b lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Thu Nov 13 15:17:42 2008 -0500 +++ b/lib/galaxy/jobs/__init__.py Thu Nov 13 19:19:03 2008 -0500 @@ -64,7 +64,7 @@ """Start the job manager""" self.app = app # Should we use IPC to communicate (needed if forking) - self.track_jobs_in_database = app.config.get( 'track_jobs_in_database', False ) + self.track_jobs_in_database = app.config.get_bool( 'track_jobs_in_database', False ) # Check if any special scheduling policy should be used. If not, default is FIFO. sched_policy = app.config.get('job_scheduler_policy', 'FIFO') @@ -107,7 +107,8 @@ self.monitor_thread = threading.Thread( target=self.monitor ) self.monitor_thread.start() log.info( "job manager started" ) - self.check_jobs_at_startup() + if self.track_jobs_in_database: + self.check_jobs_at_startup() def check_jobs_at_startup( self ): """ diff -r a39afe99b3bd -r a5ec5ab6144b lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Thu Nov 13 15:17:42 2008 -0500 +++ b/lib/galaxy/jobs/runners/pbs.py Thu Nov 13 19:19:03 2008 -0500 @@ -267,7 +267,10 @@ except Empty: pass # Iterate over the list of watched jobs and check state - self.check_watched_items() + try: + self.check_watched_items() + except: + log.exception( "Uncaught exception checking jobs" ) # Sleep a bit before the next state check time.sleep( 1 )

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[hg] galaxy 1631: Missed translating the primaryTable data type ...
by Greg Von Kuster 13 Nov '08

13 Nov '08

details: http://www.bx.psu.edu/hg/galaxy/rev/a39afe99b3bd changeset: 1631:a39afe99b3bd user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Nov 13 15:17:42 2008 -0500 description: Missed translating the primaryTable data type from UCSC in my last commit. 3 file(s) affected in this change: tools/data_source/ucsc_tablebrowser.xml tools/data_source/ucsc_tablebrowser_archaea.xml tools/data_source/ucsc_tablebrowser_test.xml diffs (33 lines): diff -r 311ee61dc989 -r a39afe99b3bd tools/data_source/ucsc_tablebrowser.xml --- a/tools/data_source/ucsc_tablebrowser.xml Thu Nov 13 14:56:33 2008 -0500 +++ b/tools/data_source/ucsc_tablebrowser.xml Thu Nov 13 15:17:42 2008 -0500 @@ -23,6 +23,7 @@ <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" > <data_type_translation> + <format galaxy_format="tabular" remote_format="primaryTable" /> <format galaxy_format="tabular" remote_format="selectedFields" /> </data_type_translation> </request_param> diff -r 311ee61dc989 -r a39afe99b3bd tools/data_source/ucsc_tablebrowser_archaea.xml --- a/tools/data_source/ucsc_tablebrowser_archaea.xml Thu Nov 13 14:56:33 2008 -0500 +++ b/tools/data_source/ucsc_tablebrowser_archaea.xml Thu Nov 13 15:17:42 2008 -0500 @@ -23,6 +23,7 @@ <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" /> <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" > <data_type_translation> + <format galaxy_format="tabular" remote_format="primaryTable" /> <format galaxy_format="tabular" remote_format="selectedFields" /> </data_type_translation> </request_param> diff -r 311ee61dc989 -r a39afe99b3bd tools/data_source/ucsc_tablebrowser_test.xml --- a/tools/data_source/ucsc_tablebrowser_test.xml Thu Nov 13 14:56:33 2008 -0500 +++ b/tools/data_source/ucsc_tablebrowser_test.xml Thu Nov 13 15:17:42 2008 -0500 @@ -23,6 +23,7 @@ <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" /> <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" > <data_type_translation> + <format galaxy_format="tabular" remote_format="primaryTable" /> <format galaxy_format="tabular" remote_format="selectedFields" /> </data_type_translation> </request_param>

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[hg] galaxy 1630: Add a new <data_type_translation> tag set to d...
by Greg Von Kuster 13 Nov '08

13 Nov '08

details: http://www.bx.psu.edu/hg/galaxy/rev/311ee61dc989 changeset: 1630:311ee61dc989 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Nov 13 14:56:33 2008 -0500 description: Add a new <data_type_translation> tag set to data_source tools that enable the translation of an unsupported data type to a supported one in Galaxy ( currently only used in UCSC ). Also some tweaks to the jobs reports. 9 file(s) affected in this change: lib/galaxy/tools/__init__.py lib/galaxy/util/__init__.py lib/galaxy/webapps/reports/controllers/jobs.py lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako tools/data_source/ucsc_tablebrowser.xml tools/data_source/ucsc_tablebrowser_archaea.xml tools/data_source/ucsc_tablebrowser_test.xml diffs (188 lines): diff -r df23879dec70 -r 311ee61dc989 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Nov 12 15:42:46 2008 -0500 +++ b/lib/galaxy/tools/__init__.py Thu Nov 13 14:56:33 2008 -0500 @@ -242,6 +242,19 @@ remote_name = req_param.get( "remote_name" ) trans_list.append( req_param.get( "galaxy_name" ) ) trans_list.append( req_param.get( "missing" ) ) + if req_param.get( "galaxy_name" ) == "data_type": + # The req_param tag for data_type is special in that it can contain another tag set like + # <data_type_translation> + # <format galaxy_format="tabular" remote_format="selectedFields" /> + # </data_type_translation> + format_trans = req_param.find( "data_type_translation" ) + if format_trans is not None: + format_trans_dict = {} + for format in format_trans.findall( "format" ): + remote_format = format.get( "remote_format" ) + galaxy_format = format.get( "galaxy_format" ) + format_trans_dict[ remote_format ] = galaxy_format + trans_list.append( format_trans_dict ) self.param_trans_dict[ remote_name ] = trans_list # Command line (template). Optional for tools that do not invoke a local program command = root.find("command") diff -r df23879dec70 -r 311ee61dc989 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Wed Nov 12 15:42:46 2008 -0500 +++ b/lib/galaxy/util/__init__.py Thu Nov 13 14:56:33 2008 -0500 @@ -155,7 +155,17 @@ if tool and tool.tool_type == 'data_source': if key in tool.param_trans_dict: new_key = tool.param_trans_dict[ key ][0] - if not value: + if new_key == 'data_type': + try: + # The Galaxy "data_type entry is special in that it can include the ability + # to translate the format to a Galaxy supported format. In the dict, this entry + # looks something like: {'hgta_outputType': ['data_type', 'bed', {'selectedFields': 'tabular'}] } + format_trans_dict = tool.param_trans_dict[ key ][2] + if value in format_trans_dict: + new_value = format_trans_dict[ value ] + except: + pass + if not value and not new_value: new_value = tool.param_trans_dict[ key ][1] if key not in self.NEVER_SANITIZE and sanitize: self.__dict__[ new_key ] = sanitize_param( new_value ) diff -r df23879dec70 -r 311ee61dc989 lib/galaxy/webapps/reports/controllers/jobs.py --- a/lib/galaxy/webapps/reports/controllers/jobs.py Wed Nov 12 15:42:46 2008 -0500 +++ b/lib/galaxy/webapps/reports/controllers/jobs.py Thu Nov 13 14:56:33 2008 -0500 @@ -91,8 +91,7 @@ year_label = start_date.strftime( "%Y" ) q = sa.select( ( sa.func.date( galaxy.model.Job.table.c.create_time ).label( 'date' ), sa.func.count( galaxy.model.Job.table.c.id ).label( 'total_jobs' ) ), - whereclause = sa.and_( sa.or_( galaxy.model.Job.table.c.state == 'error', - galaxy.model.Job.table.c.state == 'deleted' ), + whereclause = sa.and_( galaxy.model.Job.table.c.state == 'error', galaxy.model.Job.table.c.create_time >= start_date, galaxy.model.Job.table.c.create_time < end_date ), from_obj = [ sa.outerjoin( galaxy.model.Job.table, @@ -134,8 +133,7 @@ galaxy.model.Job.table.c.info, ( galaxy.model.User.table.c.email ).label( 'user_email' ), galaxy.model.GalaxySession.table.c.remote_addr ), - whereclause = sa.and_( sa.or_( galaxy.model.Job.table.c.state == 'error', - galaxy.model.Job.table.c.state == 'deleted' ), + whereclause = sa.and_( galaxy.model.Job.table.c.state == 'error', galaxy.model.Job.table.c.create_time >= start_date, galaxy.model.Job.table.c.create_time < end_date ), from_obj = [ sa.outerjoin( galaxy.model.Job.table, @@ -305,8 +303,7 @@ msg = '' q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( galaxy.model.Job.table.c.create_time ) ).label( 'date' ), sa.func.count( galaxy.model.Job.table.c.id ).label( 'total_jobs' ) ), - whereclause = sa.or_( galaxy.model.Job.table.c.state == 'error', - galaxy.model.Job.table.c.state == 'deleted' ), + whereclause = galaxy.model.Job.table.c.state == 'error', from_obj = [ galaxy.model.Job.table ], group_by = [ sa.func.date_trunc( 'month', sa.func.date( galaxy.model.Job.table.c.create_time ) ) ], order_by = [ sa.desc( 'date' ) ] ) diff -r df23879dec70 -r 311ee61dc989 lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako --- a/lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako Wed Nov 12 15:42:46 2008 -0500 +++ b/lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako Thu Nov 13 14:56:33 2008 -0500 @@ -2,7 +2,7 @@ <%def name="main_body()"> <div class="reportBody"> - <h3 align="center">Jobs In Error Per Month ( includes jobs deleted before finishing )</h3> + <h3 align="center">Jobs In Error Per Month</h3> <h4 align="center">Click Month to view the number of jobs in error for each day of that month</h4> %if msg: <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5"> @@ -11,7 +11,7 @@ %endif <table align="center" width="60%" class="colored"> %if len( jobs ) == 0: - <tr><td colspan="2">There are no jobs in the deleted or error state</td></tr> + <tr><td colspan="2">There are no jobs in the error state</td></tr> %else: <tr class="header"> <td>Month</td> diff -r df23879dec70 -r 311ee61dc989 lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako --- a/lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako Wed Nov 12 15:42:46 2008 -0500 +++ b/lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako Thu Nov 13 14:56:33 2008 -0500 @@ -10,15 +10,13 @@ %endif <table align="center" width="60%" class="colored"> %if len( jobs ) == 0: - <tr><td colspan="5">There are no jobs in the deleted or error state for ${day_label}, ${month_label} ${day_of_month}, ${year_label}</td></tr> + <tr><td colspan="5">There are no jobs in the error state for ${day_label}, ${month_label} ${day_of_month}, ${year_label}</td></tr> %else: %for job in jobs: <% state = job[0] if state == 'error': rowdef = '<tr class="headererror">' - elif state == 'deleted': - rowdef = '<tr class="headerdeleted">' else: rowdef = '<tr class="headerunknown">' %> diff -r df23879dec70 -r 311ee61dc989 lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako --- a/lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako Wed Nov 12 15:42:46 2008 -0500 +++ b/lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako Thu Nov 13 14:56:33 2008 -0500 @@ -2,7 +2,7 @@ <%def name="main_body()"> <div class="reportBody"> - <h3 align="center">Jobs in Error for ${month_label} ${year_label} ( includes jobs deleted before finishing )</h3> + <h3 align="center">Jobs in Error for ${month_label} ${year_label}</h3> <h4 align="center">Click Jobs in Error to view jobs in error for that day</h4> %if msg: <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5"> @@ -11,7 +11,7 @@ %endif <table align="center" width="60%" class="colored"> %if len( jobs ) == 0: - <tr><td colspan="3">There are no jobs in error for ${month_label} ${year_label}</td></tr> + <tr><td colspan="3">There are no jobs in the error state for ${month_label} ${year_label}</td></tr> %else: <tr class="header"> <td>Day</td> diff -r df23879dec70 -r 311ee61dc989 tools/data_source/ucsc_tablebrowser.xml --- a/tools/data_source/ucsc_tablebrowser.xml Wed Nov 12 15:42:46 2008 -0500 +++ b/tools/data_source/ucsc_tablebrowser.xml Thu Nov 13 14:56:33 2008 -0500 @@ -21,7 +21,11 @@ <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> <request_param galaxy_name="table" remote_name="hgta_track" missing="unknown table" /> <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" > + <data_type_translation> + <format galaxy_format="tabular" remote_format="selectedFields" /> + </data_type_translation> + </request_param> </request_param_translation> <uihints minwidth="800"/> <outputs> diff -r df23879dec70 -r 311ee61dc989 tools/data_source/ucsc_tablebrowser_archaea.xml --- a/tools/data_source/ucsc_tablebrowser_archaea.xml Wed Nov 12 15:42:46 2008 -0500 +++ b/tools/data_source/ucsc_tablebrowser_archaea.xml Thu Nov 13 14:56:33 2008 -0500 @@ -21,7 +21,11 @@ <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> <request_param galaxy_name="table" remote_name="hgta_track" missing="" /> <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" > + <data_type_translation> + <format galaxy_format="tabular" remote_format="selectedFields" /> + </data_type_translation> + </request_param> </request_param_translation> <uihints minwidth="800"/> <outputs> diff -r df23879dec70 -r 311ee61dc989 tools/data_source/ucsc_tablebrowser_test.xml --- a/tools/data_source/ucsc_tablebrowser_test.xml Wed Nov 12 15:42:46 2008 -0500 +++ b/tools/data_source/ucsc_tablebrowser_test.xml Thu Nov 13 14:56:33 2008 -0500 @@ -21,7 +21,11 @@ <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> <request_param galaxy_name="table" remote_name="hgta_track" missing="" /> <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" > + <data_type_translation> + <format galaxy_format="tabular" remote_format="selectedFields" /> + </data_type_translation> + </request_param> </request_param_translation> <uihints minwidth="800"/> <outputs>

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[hg] galaxy 1629: Fix a bug I missed in my last commit.
by Greg Von Kuster 12 Nov '08

12 Nov '08

details: http://www.bx.psu.edu/hg/galaxy/rev/df23879dec70 changeset: 1629:df23879dec70 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Nov 12 15:42:46 2008 -0500 description: Fix a bug I missed in my last commit. 1 file(s) affected in this change: scripts/others/incorrect_gops_jobs.py diffs (19 lines): diff -r 54f12bb6cb29 -r df23879dec70 scripts/others/incorrect_gops_jobs.py --- a/scripts/others/incorrect_gops_jobs.py Wed Nov 12 15:19:27 2008 -0500 +++ b/scripts/others/incorrect_gops_jobs.py Wed Nov 12 15:42:46 2008 -0500 @@ -77,11 +77,12 @@ print "\n\n# Number of incorrect Jobs: %d\n\n" % ( len( jobs ) ) print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email" for jid in jobs: - print "%s\t%s\t%s\t%s\t%s\t%s\t%s" % \ - ( jid, jobs[ jid ][ 'hda_id' ], + print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % \ + ( str( jid ), + str( jobs[ jid ][ 'hda_id' ] ), jobs[ jid ][ 'hda_name' ], jobs[ jid ][ 'hda_info' ], - jobs[ jid ][ 'history_id' ], + str( jobs[ jid ][ 'history_id' ] ), jobs[ jid ][ 'history_name' ], jobs[ jid ][ 'history_update_time' ], jobs[ jid ][ 'user_email' ]

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[hg] galaxy 1628: Fixes for the incorrect_gops_jobs script.
by Greg Von Kuster 12 Nov '08

12 Nov '08

details: http://www.bx.psu.edu/hg/galaxy/rev/54f12bb6cb29 changeset: 1628:54f12bb6cb29 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Nov 12 15:19:27 2008 -0500 description: Fixes for the incorrect_gops_jobs script. 2 file(s) affected in this change: scripts/others/incorrect_gops_jobs.py scripts/others/incorrect_gops_jobs.sh diffs (106 lines): diff -r 2cf304a0c1c6 -r 54f12bb6cb29 scripts/others/incorrect_gops_jobs.py --- a/scripts/others/incorrect_gops_jobs.py Wed Nov 12 10:16:04 2008 -0500 +++ b/scripts/others/incorrect_gops_jobs.py Wed Nov 12 15:19:27 2008 -0500 @@ -1,6 +1,7 @@ #!/usr/bin/env python """ -Fetch jobs using gops_intersect, gops_merge, gops_subtract, gops_complement, gops_coverage wherein the second dataset doesn't have chr, start and end in standard columns 1,2 and 3. +Fetch jobs using gops_intersect, gops_merge, gops_subtract, gops_complement, gops_coverage +wherein the second dataset doesn't have chr, start and end in standard columns 1, 2 and 3. """ from galaxy import eggs @@ -38,39 +39,53 @@ file_path = configuration['file_path'] app = TestApplication( database_connection=database_connection, file_path=file_path ) jobs = {} - for job in app.model.Job.filter( - sa.and_( - app.model.Job.table.c.create_time.between('2008-05-23','2008-11-29'), - app.model.Job.table.c.state == 'ok', - sa.or_(app.model.Job.table.c.tool_id == 'gops_intersect_1', - app.model.Job.table.c.tool_id == 'gops_subtract_1', - app.model.Job.table.c.tool_id == 'gops_merge_1', - app.model.Job.table.c.tool_id == 'gops_coverage_1', - app.model.Job.table.c.tool_id == 'gops_complement_1', - ), - sa.not_(app.model.Job.table.c.command_line.like('%-2 1,2,3%')) - )).all(): - for od in job.output_datasets: - ds = app.model.Dataset.get(od.dataset_id) - if not ds.deleted: - for hda in ds.history_associations: - hist = app.model.History.get(hda.history_id) - if hist.user_id: - user = app.model.User.get(hist.user_id) - jobs[job.id] = {} - jobs[job.id]['dataset_id'] = ds.id - jobs[job.id]['dataset_create_time'] = ds.create_time - jobs[job.id]['dataset_name'] = hda.name - jobs[job.id]['hda_id'] = hda.id - jobs[job.id]['hist_id'] = hist.id - jobs[job.id]['hist_name'] = hist.name - jobs[job.id]['hist_modified_time'] = hist.update_time - jobs[job.id]['user_email'] = user.email + try: + for job in app.model.Job.filter( sa.and_( app.model.Job.table.c.create_time.between( '2008-05-23', '2008-11-29' ), + app.model.Job.table.c.state == 'ok', + sa.or_( app.model.Job.table.c.tool_id == 'gops_intersect_1', + app.model.Job.table.c.tool_id == 'gops_subtract_1', + app.model.Job.table.c.tool_id == 'gops_merge_1', + app.model.Job.table.c.tool_id == 'gops_coverage_1', + app.model.Job.table.c.tool_id == 'gops_complement_1', + ), + sa.not_( app.model.Job.table.c.command_line.like( '%-2 1,2,3%' ) ) + ) + ).all(): + print "# processing job id %s" % str( job.id ) + for jtoda in job.output_datasets: + print "# --> processing JobToOutputDatasetAssociation id %s" % str( jtoda.id ) + hda = app.model.HistoryDatasetAssociation.get( jtoda.dataset_id ) + print "# ----> processing HistoryDatasetAssociation id %s" % str( hda.id ) + if not hda.deleted: + # Probably don't need this check, since the job state should suffice, but... + if hda.dataset.state == 'ok': + history = app.model.History.get( hda.history_id ) + print "# ------> processing history id %s" % str( history.id ) + if history.user_id: + user = app.model.User.get( history.user_id ) + jobs[ job.id ] = {} + jobs[ job.id ][ 'hda_id' ] = hda.id + jobs[ job.id ][ 'hda_name' ] = hda.name + jobs[ job.id ][ 'hda_info' ] = hda.info + jobs[ job.id ][ 'history_id' ] = history.id + jobs[ job.id ][ 'history_name' ] = history.name + jobs[ job.id ][ 'history_update_time' ] = history.update_time + jobs[ job.id ][ 'user_email' ] = user.email + except Exception, e: + print "# caught exception: %s" % str( e ) - print "Number of Incorrect Jobs: %d\n"%(len(jobs)) - print "#job_id\tdataset_id\tdataset_create_time\thda_id\thistory_id\thistory_name\thistory_modified_time\tuser_email" + print "\n\n# Number of incorrect Jobs: %d\n\n" % ( len( jobs ) ) + print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email" for jid in jobs: - print "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" %(jid,jobs[jid]['dataset_id'],jobs[jid]['dataset_create_time'],jobs[jid]['dataset_name'],jobs[jid]['hda_id'],jobs[jid]['hist_id'],jobs[jid]['hist_name'],jobs[jid]['hist_modified_time'],jobs[jid]['user_email'] ) + print "%s\t%s\t%s\t%s\t%s\t%s\t%s" % \ + ( jid, jobs[ jid ][ 'hda_id' ], + jobs[ jid ][ 'hda_name' ], + jobs[ jid ][ 'hda_info' ], + jobs[ jid ][ 'history_id' ], + jobs[ jid ][ 'history_name' ], + jobs[ jid ][ 'history_update_time' ], + jobs[ jid ][ 'user_email' ] + ) sys.exit(0) if __name__ == "__main__": diff -r 2cf304a0c1c6 -r 54f12bb6cb29 scripts/others/incorrect_gops_jobs.sh --- a/scripts/others/incorrect_gops_jobs.sh Wed Nov 12 10:16:04 2008 -0500 +++ b/scripts/others/incorrect_gops_jobs.sh Wed Nov 12 15:19:27 2008 -0500 @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -python ./scripts/others/incorrect_gops_jobs.py ./universe_wsgi.ini +python ./scripts/others/incorrect_gops_jobs.py ./universe_wsgi.ini >> ./scripts/others/incorrect_gops_jobs.log

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