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Weird problem with importing datasets
by Chris Cole 09 Mar '10

09 Mar '10

Hi, I've enabled the 'library_import_dir' option in universe_wsgi.ini as: library_import_dir = /homes/www-galaxy/data_import It's contents is: www-galaxy@ge-004: data_import> ls -l total 96 lrwxrwxrwx 1 www-galaxy barton 40 Mar 4 14:40 Dd_inuc_1.txt -> /homes/pschofield/data/TOH/Dd_inuc_1.txt -rw-r--r-- 1 www-galaxy barton 142 Mar 5 13:50 README However, both files fail to import with this error: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 326, in __main__() File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 318, in __main__ add_file( dataset, error The strangeness comes in if I copy to the Dd_inuc_1.txt file a directory owned by the www-galaxy user and link to it there. Then, the imports works for both files. www-galaxy@ge-004: data_import> ls -l total 96 lrwxrwxrwx 1 www-galaxy barton 20 Mar 5 13:56 Dd_inuc_1.txt -> ../tmp/Dd_inuc_1.txt -rw-r--r-- 1 www-galaxy barton 142 Mar 5 13:50 README The permissions are correct for the file: www-galaxy@ge-004: data_import> ls -l /homes/pschofield/data/TOH/Dd_inuc_1.txt -rw-r--r-- 1 pschofield barton 966480362 Jan 18 16:39 /homes/pschofield/data/TOH/Dd_inuc_1.txt I've no idea why Galaxy cares about who owns the files as it should be able to see them, but something's screwy. Anyone have ideas as to what's going on here? Cheers, Chris -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris(a)compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096

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Problems with latest update
by Chris Cole 09 Mar '10

09 Mar '10

Hi, I just did an hg pull for the latest version and I've got errors trying to run the 'Fastq Groomer' and 'Fastq Summary Statistics' tools. It looks like they're related. The old Fastq Groomer as found in the 'Deprecated' tools section works fine. Groomer: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_groomer.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator, fastqWriter File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax Summary Stats: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_stats.py", line 3, in ? from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator File "/homes/www-galaxy/galaxy_devel/lib/galaxy_utils/sequence/fastq.py", line 267 class fastqAggregator(): ^ SyntaxError: invalid syntax Is this a problem at my end or in Galaxy itself? This is python 2.6, BTW. Cheers, Chris -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris(a)compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096

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how to specify sge options?
by Edward Kirton 08 Mar '10

08 Mar '10

Hello, Is there a way to pass SGE options to the runner? Specifically, i'd like to tell the scheduler the number of cores required by a tool (-pe). Thanks, Ed Kirton US DOE JGI

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[hg] galaxy 3489: Add the ability for tests to have a lines_diff...
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/3563fade2c86 changeset: 3489:3563fade2c86 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Mar 05 17:21:16 2010 -0500 description: Add the ability for tests to have a lines_diff attribute set for standard output datasets that will allow the specified number of lines to vary between test-data and tool run results; a 'change' to a line equates to a difference of 2 lines between files (i.e. 1 line added, 1 line removed). Add the ability for test comparisons to use single or multiline regular expressions, this is accessed by adding the attribute compare= "match_re" or "match_re_multiline" (respectively); the standard diff method can be explicitly declared as "diff", or is used at the default when not specified. diffstat: lib/galaxy/tools/__init__.py | 7 +- lib/galaxy/tools/test.py | 4 +- test/base/twilltestcase.py | 134 ++++++++++++++++++++++++++++----------- test/functional/test_toolbox.py | 4 +- 4 files changed, 106 insertions(+), 43 deletions(-) diffs (225 lines): diff -r 45cfcab6aed7 -r 3563fade2c86 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Fri Mar 05 12:55:51 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Fri Mar 05 17:21:16 2010 -0500 @@ -532,8 +532,11 @@ file = attrib.pop( 'file', None ) if file is None: raise Exception( "Test output does not have a 'file'") - sort = util.string_as_bool( attrib.pop( 'sort', False ) ) - test.add_output( name, file, sort ) + attributes = Bunch() + attributes.compare = attrib.pop( 'compare', 'diff' ).lower() #method of comparison + attributes.lines_diff = int( attrib.pop( 'lines_diff', '0' ) ) # allow a few lines (dates etc) to vary in logs + attributes.sort = util.string_as_bool( attrib.pop( 'sort', False ) ) + test.add_output( name, file, attributes ) except Exception, e: test.error = True test.exception = e diff -r 45cfcab6aed7 -r 3563fade2c86 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py Fri Mar 05 12:55:51 2010 -0500 +++ b/lib/galaxy/tools/test.py Fri Mar 05 17:21:16 2010 -0500 @@ -37,8 +37,8 @@ except Exception, e: log.debug( "Error in add_param for %s: %s" % ( name, e ) ) self.inputs.append( ( name, value, extra ) ) - def add_output( self, name, file, sort ): - self.outputs.append( ( name, file, sort ) ) + def add_output( self, name, file, extra ): + self.outputs.append( ( name, file, extra ) ) def __expand_grouping_for_data_input( self, name, value, extra, grouping_name, grouping_value ): # Currently handles grouping.Conditional and grouping.Repeat if isinstance( grouping_value, grouping.Conditional ): diff -r 45cfcab6aed7 -r 3563fade2c86 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Fri Mar 05 12:55:51 2010 -0500 +++ b/test/base/twilltestcase.py Fri Mar 05 17:21:16 2010 -0500 @@ -36,14 +36,21 @@ #self.set_history() # Functions associated with files - def files_diff( self, file1, file2, sort=False ): + def files_diff( self, file1, file2, attributes=None ): """Checks the contents of 2 files for differences""" + def get_lines_diff( diff ): + count = 0 + for line in diff: + if ( line.startswith( '+' ) and not line.startswith( '+++' ) ) or ( line.startswith( '-' ) and not line.startswith( '---' ) ): + count += 1 + return count if not filecmp.cmp( file1, file2 ): files_differ = False local_file = open( file1, 'U' ).readlines() history_data = open( file2, 'U' ).readlines() - if sort: + if attributes and attributes.sort: history_data.sort() + ##Why even bother with the check loop below, why not just use the diff output? This seems wasteful. if len( local_file ) == len( history_data ): for i in range( len( history_data ) ): if local_file[i].rstrip( '\r\n' ) != history_data[i].rstrip( '\r\n' ): @@ -52,37 +59,79 @@ else: files_differ = True if files_differ: - diff = difflib.unified_diff( local_file, history_data, "local_file", "history_data" ) - diff_slice = list( islice( diff, 40 ) ) - if file1.endswith( '.pdf' ) or file2.endswith( '.pdf' ): - # PDF files contain creation dates, modification dates, ids and descriptions that change with each - # new file, so we need to handle these differences. As long as the rest of the PDF file does - # not differ we're ok. - valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id' ] - valid_diff = False - for line in diff_slice: - # Make sure to lower case strings before checking. - line = line.lower() - # Diff lines will always start with a + or - character, but handle special cases: '--- local_file \n', '+++ history_data \n' - if ( line.startswith( '+' ) or line.startswith( '-' ) ) and line.find( 'local_file' ) < 0 and line.find( 'history_data' ) < 0: - for vdf in valid_diff_strs: - if line.find( vdf ) < 0: - valid_diff = False - else: - valid_diff = True - # Stop checking as soon as we know we have a valid difference - break - if not valid_diff: - # Print out diff_slice so we can see what failed - print "###### diff_slice ######" - raise AssertionError( "".join( diff_slice ) ) - break + if attributes and attributes.lines_diff: + allowed_diff_count = attributes.lines_diff else: - for line in diff_slice: - for char in line: - if ord( char ) > 128: - raise AssertionError( "Binary data detected, not displaying diff" ) - raise AssertionError( "".join( diff_slice ) ) + allowed_diff_count = 0 + diff = list( difflib.unified_diff( local_file, history_data, "local_file", "history_data" ) ) + diff_lines = get_lines_diff( diff ) + if diff_lines > allowed_diff_count: + diff_slice = diff[0:40] + #FIXME: This pdf stuff is rather special cased and has not been updated to consider lines_diff + #due to unknown desired behavior when used in conjunction with a non-zero lines_diff + #PDF forgiveness can probably be handled better by not special casing by __extension__ here + #and instead using lines_diff or a regular expression matching + #or by creating and using a specialized pdf comparison function + if file1.endswith( '.pdf' ) or file2.endswith( '.pdf' ): + # PDF files contain creation dates, modification dates, ids and descriptions that change with each + # new file, so we need to handle these differences. As long as the rest of the PDF file does + # not differ we're ok. + valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id' ] + valid_diff = False + for line in diff_slice: + # Make sure to lower case strings before checking. + line = line.lower() + # Diff lines will always start with a + or - character, but handle special cases: '--- local_file \n', '+++ history_data \n' + if ( line.startswith( '+' ) or line.startswith( '-' ) ) and line.find( 'local_file' ) < 0 and line.find( 'history_data' ) < 0: + for vdf in valid_diff_strs: + if line.find( vdf ) < 0: + valid_diff = False + else: + valid_diff = True + # Stop checking as soon as we know we have a valid difference + break + if not valid_diff: + # Print out diff_slice so we can see what failed + print "###### diff_slice ######" + raise AssertionError( "".join( diff_slice ) ) + else: + for line in diff_slice: + for char in line: + if ord( char ) > 128: + raise AssertionError( "Binary data detected, not displaying diff" ) + raise AssertionError( "".join( diff_slice ) ) + + def files_re_match( self, file1, file2, attributes=None ): + """Checks the contents of 2 files for differences using re.match""" + local_file = open( file1, 'U' ).readlines() #regex file + history_data = open( file2, 'U' ).readlines() + assert len( local_file ) == len( history_data ), 'Data File and Regular Expression File contain a different number of lines (%s != %s)' % ( len( local_file ), len( history_data ) ) + if attributes and attributes.sort: + history_data.sort() + if attributes and attributes.lines_diff: + lines_diff = attributes.lines_diff + else: + lines_diff = 0 + line_diff_count = 0 + diffs = [] + for i in range( len( history_data ) ): + if not re.match( local_file[i].rstrip( '\r\n' ), history_data[i].rstrip( '\r\n' ) ): + line_diff_count += 1 + diffs.append( 'Regular Expression: %s\nData file : %s' % ( local_file[i].rstrip( '\r\n' ), history_data[i].rstrip( '\r\n' ) ) ) + if line_diff_count > lines_diff: + raise AssertionError, "Regular expression did not match data file (allowed variants=%i):\n%s" % ( lines_diff, "".join( diffs ) ) + + def files_re_match_multiline( self, file1, file2, attributes=None ): + """Checks the contents of 2 files for differences using re.match in multiline mode""" + local_file = open( file1, 'U' ).read() #regex file + if attributes and attributes.sort: + history_data = open( file2, 'U' ).readlines() + history_data.sort() + history_data = ''.join( history_data ) + else: + history_data = open( file2, 'U' ).read() + #lines_diff not applicable to multiline matching + assert re.match( local_file, history_data, re.MULTILINE ), "Multiline Regular expression did not match data file" def get_filename( self, filename ): full = os.path.join( self.file_dir, filename) @@ -541,7 +590,7 @@ hid = elem.get('hid') hids.append(hid) return hids - def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, sort=False ): + def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, attributes=None ): """Verifies that the attributes and contents of a history item meet expectations""" if wait: self.wait( maxseconds=maxseconds ) #wait for job to finish @@ -576,13 +625,24 @@ data = self.last_page() file( temp_name, 'wb' ).write(data) try: - self.files_diff( local_name, temp_name, sort=sort ) + if attributes and 'compare' in attributes: + compare = attributes.compare + else: + compare = 'diff' + if compare == 'diff': + self.files_diff( local_name, temp_name, attributes=attributes ) + elif compare == 're_match': + self.files_re_match( local_name, temp_name, attributes=attributes ) + elif compare == 're_match_multiline': + self.files_re_match_multiline( local_name, temp_name, attributes=attributes ) + else: + raise Exception, 'Unimplemented Compare type: %s' % compare except AssertionError, err: - os.remove(temp_name) - errmsg = 'History item %s different than expected, difference:\n' % hid + errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare ) errmsg += str( err ) raise AssertionError( errmsg ) - os.remove(temp_name) + finally: + os.remove( temp_name ) def verify_composite_datatype_file_content( self, file_name, hda_id ): local_name = self.get_filename( file_name ) temp_name = self.get_filename( 'temp_%s' % file_name ) diff -r 45cfcab6aed7 -r 3563fade2c86 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Fri Mar 05 12:55:51 2010 -0500 +++ b/test/functional/test_toolbox.py Fri Mar 05 17:21:16 2010 -0500 @@ -66,13 +66,13 @@ self.assertTrue( data_list ) elem_index = 0 - len( testdef.outputs ) for output_tuple in testdef.outputs: - name, file, sort = output_tuple + name, outfile, attributes = output_tuple # Get the correct hid elem = data_list[ elem_index ] self.assertTrue( elem is not None ) elem_hid = elem.get( 'hid' ) elem_index += 1 - self.verify_dataset_correctness( file, hid=elem_hid, maxseconds=testdef.maxseconds, sort=sort ) + self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes ) self.delete_history( id=self.security.encode_id( latest_history.id ) ) def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ):

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[hg] galaxy 3488: Import some math functions in 'Compute express...
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/45cfcab6aed7 changeset: 3488:45cfcab6aed7 user: gua110 date: Fri Mar 05 12:55:51 2010 -0500 description: Import some math functions in 'Compute expression' tool. diffstat: tools/stats/column_maker.py | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r b4dc8ea68ac7 -r 45cfcab6aed7 tools/stats/column_maker.py --- a/tools/stats/column_maker.py Fri Mar 05 10:13:36 2010 -0500 +++ b/tools/stats/column_maker.py Fri Mar 05 12:55:51 2010 -0500 @@ -6,6 +6,7 @@ from galaxy import eggs from galaxy.tools import validation from galaxy.datatypes import metadata +from math import log,exp,sqrt,ceil,floor assert sys.version_info[:2] >= ( 2, 4 )

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[hg] galaxy 3487: Make fastqAggregator a new style class.
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b4dc8ea68ac7 changeset: 3487:b4dc8ea68ac7 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Mar 05 10:13:36 2010 -0500 description: Make fastqAggregator a new style class. diffstat: lib/galaxy_utils/sequence/fastq.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 1cd52787c0bb -r b4dc8ea68ac7 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py Fri Mar 05 09:09:26 2010 -0500 +++ b/lib/galaxy_utils/sequence/fastq.py Fri Mar 05 10:13:36 2010 -0500 @@ -264,7 +264,7 @@ FASTQ_FORMATS[ format.format ] = format -class fastqAggregator(): +class fastqAggregator( object ): VALID_FORMATS = FASTQ_FORMATS.keys() def __init__( self, ): self.ascii_values_used = [] #quick lookup of all ascii chars used

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[hg] galaxy 3486: Handle dialog box overflow gracefully by scrol...
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1cd52787c0bb changeset: 3486:1cd52787c0bb user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Mar 05 09:09:26 2010 -0500 description: Handle dialog box overflow gracefully by scrolling body; this fix makes it possible to place item selection grids in dialog boxes without poor overflow. Also fixed msg when displaying an empty history. diffstat: static/june_2007_style/blue/panel_layout.css | 3 ++- static/june_2007_style/panel_layout.css.tmpl | 8 +++++++- templates/base_panels.mako | 2 +- templates/history/display.mako | 2 +- 4 files changed, 11 insertions(+), 4 deletions(-) diffs (56 lines): diff -r ef90fbe0eda1 -r 1cd52787c0bb static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css Thu Mar 04 18:33:11 2010 -0500 +++ b/static/june_2007_style/blue/panel_layout.css Fri Mar 05 09:09:26 2010 -0500 @@ -27,7 +27,8 @@ .dialog-box-container{position:relative;margin-top:80px;margin-right:auto;margin-left:auto;} .dialog-box-wrapper{position:relative;padding:1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;} .dialog-box{border:solid #999 1px;background:white;z-index:80000;} -.dialog-box .body,.dialog-box .buttons{padding:5px;} +.dialog-box .body{padding:5px;overflow:auto;max-height:500px;} +.dialog-box .buttons{padding:5px;} .panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#FFCCCC;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} .panel-warning-message{background-image:url(warn_small.png);background-color:#FFFFCC;} .panel-done-message{background-image:url(done_small.png);background-color:#CCFFCC;} diff -r ef90fbe0eda1 -r 1cd52787c0bb static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Thu Mar 04 18:33:11 2010 -0500 +++ b/static/june_2007_style/panel_layout.css.tmpl Fri Mar 05 09:09:26 2010 -0500 @@ -190,7 +190,13 @@ z-index: 80000; } -.dialog-box .body, .dialog-box .buttons { +.dialog-box .body { + padding: 5px; + overflow: auto; + max-height: 500px; +} + +.dialog-box .buttons { padding: 5px; } diff -r ef90fbe0eda1 -r 1cd52787c0bb templates/base_panels.mako --- a/templates/base_panels.mako Thu Mar 04 18:33:11 2010 -0500 +++ b/templates/base_panels.mako Fri Mar 05 09:09:26 2010 -0500 @@ -314,7 +314,7 @@ <div class="unified-panel-header"> <div class="unified-panel-header-inner"><span class='title'>${title}</span></div> </div> - <div class="body" style="max-height: 600px;">${content}</div> + <div class="body">${content}</div> <div> <div class="buttons" style="display: none; float: right;"></div> <div class="extra_buttons" style="display: none; padding: 5px;"></div> diff -r ef90fbe0eda1 -r 1cd52787c0bb templates/history/display.mako --- a/templates/history/display.mako Thu Mar 04 18:33:11 2010 -0500 +++ b/templates/history/display.mako Fri Mar 05 09:09:26 2010 -0500 @@ -277,7 +277,7 @@ </table> <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> %endif - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} + ${_("This history is empty.")} </div> </%def> \ No newline at end of file

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[hg] galaxy 3485: Add boxplot tool to tool_conf.xml.main
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ef90fbe0eda1 changeset: 3485:ef90fbe0eda1 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Mar 04 18:33:11 2010 -0500 description: Add boxplot tool to tool_conf.xml.main diffstat: tool_conf.xml.main | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r d1900a25eb45 -r ef90fbe0eda1 tool_conf.xml.main --- a/tool_conf.xml.main Thu Mar 04 16:16:42 2010 -0500 +++ b/tool_conf.xml.main Thu Mar 04 18:33:11 2010 -0500 @@ -119,6 +119,7 @@ <tool file="plotting/histogram2.xml" /> <tool file="plotting/scatterplot.xml" /> <tool file="plotting/xy_plot.xml" /> + <tool file="plotting/boxplot.xml" /> <tool file="visualization/GMAJ.xml" /> <tool file="visualization/build_ucsc_custom_track.xml" /> </section>

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[hg] galaxy 3484: Better handling of workflow step annotations.
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d1900a25eb45 changeset: 3484:d1900a25eb45 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Mar 04 16:16:42 2010 -0500 description: Better handling of workflow step annotations. diffstat: static/scripts/galaxy.workflow_editor.canvas.js | 8 +++++++- templates/workflow/editor.mako | 7 +++---- 2 files changed, 10 insertions(+), 5 deletions(-) diffs (43 lines): diff -r c349f517ffb8 -r d1900a25eb45 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Thu Mar 04 13:55:21 2010 -0500 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Thu Mar 04 16:16:42 2010 -0500 @@ -308,6 +308,7 @@ this.tool_state = data.tool_state; this.form_html = data.form_html; this.tool_errors = data.tool_errors; + this.annotation = data['annotation']; if ( this.tool_errors ) { el.addClass( "tool-node-error" ); } else { @@ -447,7 +448,12 @@ // If active form has changed, save it if (this.active_form_has_changes) { this.has_changes = true; - $("#right-content").find("form").submit(); + // Get annotation and add to form. + var annotation = $("textarea[name=annotation]").val(); + var tool_form = $("#right-content").find("form"); + tool_form.append( "<input type='hidden' name='annotation' value='"+annotation+"' />" ); + // Submit form. + tool_form.submit(); this.active_form_has_changes = false; } }, diff -r c349f517ffb8 -r d1900a25eb45 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Thu Mar 04 13:55:21 2010 -0500 +++ b/templates/workflow/editor.mako Thu Mar 04 16:16:42 2010 -0500 @@ -367,11 +367,10 @@ </div> \ </div> \ </div>"); - // When metadata is changed, update node and set workflow changes flag. + // See above comment: this is necessary to handle autosaving. var textarea = $(metadata_div).find("textarea"); - textarea.change( function () { - node.annotation = $(this).val(); - workflow.has_changes = true; + textarea.focus( function () { + workflow.active_form_has_changes = true; }); $("#right-content").find(".toolForm").after( metadata_div ); }

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[hg] galaxy 3483: Fix for running workflows with steps that don'...
by Greg Von Kuster 08 Mar '10

08 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c349f517ffb8 changeset: 3483:c349f517ffb8 user: James Taylor <james(a)jamestaylor.org> date: Thu Mar 04 13:55:21 2010 -0500 description: Fix for running workflows with steps that don't have jobs diffstat: lib/galaxy/model/mapping.py | 2 +- lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py | 62 ++++++++++ 2 files changed, 63 insertions(+), 1 deletions(-) diffs (79 lines): diff -r 66fda01625f3 -r c349f517ffb8 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Thu Mar 04 13:49:09 2010 -0500 +++ b/lib/galaxy/model/mapping.py Thu Mar 04 13:55:21 2010 -0500 @@ -571,7 +571,7 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ), Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ), - Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False ) + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=True ) ) StoredWorkflowUserShareAssociation.table = Table( "stored_workflow_user_share_connection", metadata, diff -r 66fda01625f3 -r c349f517ffb8 lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py Thu Mar 04 13:55:21 2010 -0500 @@ -0,0 +1,62 @@ +""" +Drop and readd workflow invocation tables, allowing null jobs +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +logging.basicConfig( level=logging.DEBUG ) +log = logging.getLogger( __name__ ) + +import datetime +now = datetime.datetime.utcnow + +def upgrade(): + print __doc__ + + metadata = MetaData( migrate_engine ) + db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + metadata.reflect() + + # 1) Drop + + for table_name in [ "workflow_invocation_step", "workflow_invocation" ]: + try: + t = Table( table_name, metadata, autoload=True ).drop() + except: + log.exception( "Failed to drop table '%s', ignoring (might result in wrong schema)" % table_name ) + + # 2) Readd + + metadata = MetaData( migrate_engine ) + db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + metadata.reflect() + + WorkflowInvocation_table = Table( "workflow_invocation", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ), + ) + + WorkflowInvocationStep_table = Table( "workflow_invocation_step", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ), + Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=True ), + ) + + for table in [ WorkflowInvocation_table, WorkflowInvocationStep_table ]: + try: + table.create() + except: + log.exception( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name ) + +def downgrade(): + # No downgrade + pass \ No newline at end of file

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