November 2010 - galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 516a02525898: Move export_history.py script into lib/galaxy/tools/imp_exp so that it's simpler to execute.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1285793202 14400 # Node ID 516a02525898381be3a9af8f3ffec205133dbda1 # Parent a9694088cf69e31fbd3f940cca497e1d2e366f75 Move export_history.py script into lib/galaxy/tools/imp_exp so that it's simpler to execute. --- /dev/null +++ b/lib/galaxy/tools/imp_exp/export_history.py @@ -0,0 +1,71 @@ +#!/usr/bin/env python +""" +Export a history to an archive file using attribute files. + +usage: %prog history_attrs dataset_attrs job_attrs out_file + -G, --gzip: gzip archive file +""" + +from galaxy import eggs +from galaxy.util.json import * +import optparse, sys, os, tempfile, tarfile + +def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, out_file, gzip=False ): + """ Create archive from the given attribute/metadata files and save it to out_file. """ + tarfile_mode = "w" + if gzip: + tarfile_mode += ":gz" + try: + + history_archive = tarfile.open( out_file, tarfile_mode ) + + # Read datasets attributes from file. + datasets_attr_in = open( datasets_attrs_file, 'rb' ) + datasets_attr_str = '' + buffsize = 1048576 + try: + while True: + datasets_attr_str += datasets_attr_in.read( buffsize ) + if not datasets_attr_str or len( datasets_attr_str ) % buffsize != 0: + break + except OverflowError: + pass + datasets_attr_in.close() + datasets_attrs = from_json_string( datasets_attr_str ) + + # Add datasets to archive and update dataset attributes. + # TODO: security check to ensure that files added are in Galaxy dataset directory? + for dataset_attrs in datasets_attrs: + dataset_file_name = dataset_attrs[ 'file_name' ] # Full file name. + dataset_archive_name = os.path.join( "datasets", os.path.split( dataset_file_name )[-1] ) + history_archive.add( dataset_file_name, arcname=dataset_archive_name ) + # Update dataset filename to be archive name. + dataset_attrs[ 'file_name' ] = dataset_archive_name + + # Rewrite dataset attributes file. + datasets_attrs_out = open( datasets_attrs_file, 'w' ) + datasets_attrs_out.write( to_json_string( datasets_attrs ) ) + datasets_attrs_out.close() + + # Finish archive. + history_archive.add( history_attrs_file, arcname="history_attrs.txt" ) + history_archive.add( datasets_attrs_file, arcname="datasets_attrs.txt" ) + history_archive.add( jobs_attrs_file, arcname="jobs_attrs.txt" ) + history_archive.close() + + # Status. + return 'Created history archive.' + except Exception, e: + return 'Error creating history archive: %s' % str( e ), sys.stderr + +if __name__ == "__main__": + # Parse command line. + parser = optparse.OptionParser() + parser.add_option( '-G', '--gzip', dest='gzip', action="store_true", help='Compress archive using gzip.' ) + (options, args) = parser.parse_args() + gzip = bool( options.gzip ) + history_attrs, dataset_attrs, job_attrs, out_file = args + + # Create archive. + status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip ) + print status --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -199,9 +199,10 @@ class JobExportHistoryArchiveWrapper( ob options = "" if jeha.compressed: options = "-G" - return "%s %s %s %s %s %s" % ( os.path.join( os.path.abspath( os.getcwd() ), "export_history.sh" ), \ - options, history_attrs_filename, datasets_attrs_filename, \ - jobs_attrs_filename, jeha.dataset.file_name ) + return "python %s %s %s %s %s %s" % ( + os.path.join( os.path.abspath( os.getcwd() ), "lib/galaxy/tools/imp_exp/export_history.py" ), \ + options, history_attrs_filename, datasets_attrs_filename, jobs_attrs_filename, \ + jeha.dataset.file_name ) def cleanup_after_job( self, db_session ): """ Remove temporary directory and attribute files generated during setup for this job. """ --- a/scripts/export_history.py +++ /dev/null @@ -1,80 +0,0 @@ -#!/usr/bin/env python -""" -Export a history to an archive file using attribute files. - -NOTE: This should not be called directly. Use the set_metadata.sh script in Galaxy's -top level directly. - -usage: %prog history_attrs dataset_attrs job_attrs out_file - -G, --gzip: gzip archive file - -D, --delete_dir: delete attribute files' directory if operation completed successfully -""" -from galaxy import eggs -import os, pkg_resources, tempfile, tarfile -pkg_resources.require( "bx-python" ) -import sys, traceback, fileinput -from galaxy.util.json import * -from warnings import warn -from bx.cookbook import doc_optparse - -def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, out_file, gzip=False ): - """ Create archive from the given attribute/metadata files and save it to out_file. """ - tarfile_mode = "w" - if gzip: - tarfile_mode += ":gz" - try: - - history_archive = tarfile.open( out_file, tarfile_mode ) - - # Read datasets attributes from file. - datasets_attr_in = open( datasets_attrs_file, 'rb' ) - datasets_attr_str = '' - buffsize = 1048576 - try: - while True: - datasets_attr_str += datasets_attr_in.read( buffsize ) - if not datasets_attr_str or len( datasets_attr_str ) % buffsize != 0: - break - except OverflowError: - pass - datasets_attr_in.close() - datasets_attrs = from_json_string( datasets_attr_str ) - - # Add datasets to archive and update dataset attributes. - # TODO: security check to ensure that files added are in Galaxy dataset directory? - for dataset_attrs in datasets_attrs: - dataset_file_name = dataset_attrs[ 'file_name' ] # Full file name. - dataset_archive_name = os.path.join( "datasets", os.path.split( dataset_file_name )[-1] ) - history_archive.add( dataset_file_name, arcname=dataset_archive_name ) - # Update dataset filename to be archive name. - dataset_attrs[ 'file_name' ] = dataset_archive_name - - # Rewrite dataset attributes file. - datasets_attrs_out = open( datasets_attrs_file, 'w' ) - datasets_attrs_out.write( to_json_string( datasets_attrs ) ) - datasets_attrs_out.close() - - # Finish archive. - history_archive.add( history_attrs_file, arcname="history_attrs.txt" ) - history_archive.add( datasets_attrs_file, arcname="datasets_attrs.txt" ) - history_archive.add( jobs_attrs_file, arcname="jobs_attrs.txt" ) - history_archive.close() - - # Status. - return 'Created history archive.' - except Exception, e: - return 'Error creating history archive: %s' + str( e ), sys.stderr - -if __name__ == "__main__": - # Parse command line. - options, args = doc_optparse.parse( __doc__ ) - try: - gzip = bool( options.gzip ) - delete_dir = bool( options.delete_dir ) - history_attrs, dataset_attrs, job_attrs, out_file = args - except: - doc_optparse.exception() - - # Create archive. - status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip ) - print status --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -54,9 +54,6 @@ class ExportHistoryToolAction( ToolActio job_wrapper = JobExportHistoryArchiveWrapper( job ) cmd_line = job_wrapper.setup_job( trans, jeha, include_hidden=incoming[ 'include_hidden' ], \ include_deleted=incoming[ 'include_deleted' ] ) - - # Save jeha. - trans.sa_session.flush() # # Add parameters to job_parameter table. --- a/export_history.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0` -python ./scripts/export_history.py $@

1 0

galaxy-dist commit 940d77bec4d5: Remove unneeded grid initialization code.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1285797982 14400 # Node ID 940d77bec4d59a5418f9f731ca6ca114d748aa5d # Parent 2aee56b5875a201b09f736764390651a177702d8 Remove unneeded grid initialization code. --- a/templates/tracks/add_tracks.mako +++ b/templates/tracks/add_tracks.mako @@ -5,10 +5,3 @@ ${grid_javascripts()} ${render_grid_header( grid, False )} ${render_grid_table( grid, show_item_checkboxes=True )} - -## Initialize the grid. -## TODO: This may not be necessary -- check when adding tracks is working again. -<script type="text/javascript"> - init_grid_elements(); - init_grid_controls(); -</script>

1 0

galaxy-dist commit 2aee56b5875a: Updated test outputs for pdf/image output tools that differ slightly on updated dependencies.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1285795531 14400 # Node ID 2aee56b5875a201b09f736764390651a177702d8 # Parent 516a02525898381be3a9af8f3ffec205133dbda1 Updated test outputs for pdf/image output tools that differ slightly on updated dependencies. --- a/test-data/kpca_out2.pdf +++ b/test-data/kpca_out2.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100310152519) -/ModDate (D:20100310152519) +/CreationDate (D:20100929155208) +/ModDate (D:20100929155208) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 47.81 276.05 240.19 228.24 re W n Q q 0.000 0.000 0.000 RG @@ -1115,7 +1115,7 @@ Q endstream endobj 7 0 obj -22476 +22484 endobj 3 0 obj << @@ -1170,15 +1170,15 @@ 0 12 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000022843 00000 n -0000022926 00000 n +0000022851 00000 n +0000022934 00000 n 0000000213 00000 n 0000000293 00000 n -0000022822 00000 n -0000023030 00000 n -0000023287 00000 n -0000023370 00000 n -0000023467 00000 n +0000022830 00000 n +0000023038 00000 n +0000023295 00000 n +0000023378 00000 n +0000023475 00000 n trailer << /Size 12 @@ -1186,5 +1186,5 @@ trailer /Root 2 0 R >> startxref -23569 +23577 %%EOF --- a/test-data/cca_out2.pdf +++ b/test-data/cca_out2.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100310155029) -/ModDate (D:20100310155029) +/CreationDate (D:20100929152548) +/ModDate (D:20100929152548) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n 0.000 0.000 0.000 RG 0.75 w @@ -400,7 +400,7 @@ Q endstream endobj 7 0 obj -5992 +6000 endobj 8 0 obj << @@ -415,7 +415,7 @@ 9 0 obj /Length 10 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n Q q 59.04 73.44 486.72 443.52 re W n 0.000 0.000 0.000 RG @@ -788,7 +788,7 @@ Q endstream endobj 10 0 obj -6029 +6037 endobj 3 0 obj << @@ -805,7 +805,7 @@ 4 0 obj << /ProcSet [/PDF /Text] /Font <</F2 12 0 R /F3 13 0 R >> -/ExtGState << >> +/ExtGState << /GSais 14 0 R >> >> endobj 11 0 obj @@ -831,28 +831,35 @@ 13 0 obj << /BaseFont /Helvetica-Bold /Encoding 11 0 R >> endobj +14 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 14 +0 15 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000012542 00000 n -0000012631 00000 n +0000012558 00000 n +0000012647 00000 n 0000000213 00000 n 0000000293 00000 n -0000006338 00000 n -0000006358 00000 n -0000006438 00000 n -0000012521 00000 n -0000012724 00000 n -0000012982 00000 n -0000013080 00000 n +0000006346 00000 n +0000006366 00000 n +0000006446 00000 n +0000012537 00000 n +0000012754 00000 n +0000013012 00000 n +0000013110 00000 n +0000013213 00000 n trailer << -/Size 14 +/Size 15 /Info 1 0 R /Root 2 0 R >> startxref -13183 +13263 %%EOF --- a/test-data/q_values.tabular +++ b/test-data/q_values.tabular @@ -1,4 +1,4 @@ -pi0: 0.243863648325618 +pi0: 0.243863648325618 FDR level: 0.05 --- a/test-data/kpca_out4.pdf +++ b/test-data/kpca_out4.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100310154313) -/ModDate (D:20100310154313) +/CreationDate (D:20100929160535) +/ModDate (D:20100929160535) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n 0.000 0.000 0.000 RG 0.75 w @@ -549,7 +549,7 @@ Q endstream endobj 7 0 obj -10735 +10743 endobj 3 0 obj << @@ -604,15 +604,15 @@ 0 12 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000011102 00000 n -0000011185 00000 n +0000011110 00000 n +0000011193 00000 n 0000000213 00000 n 0000000293 00000 n -0000011081 00000 n -0000011289 00000 n -0000011546 00000 n -0000011629 00000 n -0000011726 00000 n +0000011089 00000 n +0000011297 00000 n +0000011554 00000 n +0000011637 00000 n +0000011734 00000 n trailer << /Size 12 @@ -620,5 +620,5 @@ trailer /Root 2 0 R >> startxref -11828 +11836 %%EOF --- a/test-data/histogram_out1.pdf +++ b/test-data/histogram_out1.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20091214150037) -/ModDate (D:20091214150037) +/CreationDate (D:20100929153637) +/ModDate (D:20100929153637) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q BT 0.000 0.000 0.000 rg @@ -479,7 +479,7 @@ Q endstream endobj 7 0 obj -7417 +7425 endobj 3 0 obj << @@ -495,7 +495,7 @@ 4 0 obj << /ProcSet [/PDF /Text] /Font <</F2 9 0 R /F3 10 0 R >> -/ExtGState << >> +/ExtGState << /GSais 11 0 R >> >> endobj 8 0 obj @@ -521,25 +521,32 @@ 10 0 obj << /BaseFont /Helvetica-Bold /Encoding 8 0 R >> endobj +11 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 11 +0 12 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000007783 00000 n -0000007866 00000 n +0000007791 00000 n +0000007874 00000 n 0000000213 00000 n 0000000293 00000 n -0000007763 00000 n -0000007958 00000 n -0000008215 00000 n -0000008311 00000 n +0000007771 00000 n +0000007980 00000 n +0000008237 00000 n +0000008333 00000 n +0000008435 00000 n trailer << -/Size 11 +/Size 12 /Info 1 0 R /Root 2 0 R >> startxref -8413 +8485 %%EOF --- a/test-data/pca_out4.pdf +++ b/test-data/pca_out4.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100310155851) -/ModDate (D:20100310155851) +/CreationDate (D:20100929163248) +/ModDate (D:20100929163248) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 0.000 0.000 0.000 RG 0.75 w @@ -647,7 +647,7 @@ Q endstream endobj 7 0 obj -12853 +12861 endobj 3 0 obj << @@ -663,7 +663,7 @@ 4 0 obj << /ProcSet [/PDF /Text] /Font <</F2 9 0 R >> -/ExtGState << >> +/ExtGState << /GSais 10 0 R >> >> endobj 8 0 obj @@ -682,24 +682,31 @@ 9 0 obj << /BaseFont /Helvetica /Encoding 8 0 R >> endobj +10 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 10 +0 11 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000013220 00000 n -0000013303 00000 n +0000013228 00000 n +0000013311 00000 n 0000000213 00000 n 0000000293 00000 n -0000013199 00000 n -0000013384 00000 n -0000013641 00000 n +0000013207 00000 n +0000013406 00000 n +0000013663 00000 n +0000013759 00000 n trailer << -/Size 10 +/Size 11 /Info 1 0 R /Root 2 0 R >> startxref -13737 +13809 %%EOF --- a/test-data/pca_out6.pdf +++ b/test-data/pca_out6.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100914141739) -/ModDate (D:20100914141739) +/CreationDate (D:20100929164125) +/ModDate (D:20100929164125) /Title (R Graphics Output) -/Producer (R 2.11.1) +/Producer (R 2.11.0) /Creator (R) >> endobj Binary file test-data/454Score.png has changed --- a/test-data/regr_out.pdf +++ b/test-data/regr_out.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100603105440) -/ModDate (D:20100603105440) +/CreationDate (D:20100929153009) +/ModDate (D:20100929153009) /Title (R Graphics Output) -/Producer (R 2.9.2) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 38.02 358.66 166.66 160.32 re W n Q q 0.000 0.000 0.000 RG @@ -524,7 +524,7 @@ Q endstream endobj 7 0 obj -9361 +9369 endobj 8 0 obj << @@ -539,7 +539,7 @@ 9 0 obj /Length 10 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n Q q 0.000 0.000 0.000 RG @@ -695,7 +695,7 @@ Q endstream endobj 10 0 obj -3090 +3098 endobj 11 0 obj << @@ -710,7 +710,7 @@ 12 0 obj /Length 13 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n Q q 59.04 73.44 486.72 443.52 re W n 0.000 0.000 0.000 RG @@ -850,7 +850,7 @@ Q endstream endobj 13 0 obj -2841 +2849 endobj 14 0 obj << @@ -865,7 +865,7 @@ 15 0 obj /Length 16 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n Q q 0.000 0.000 0.000 RG @@ -1090,7 +1090,7 @@ Q endstream endobj 16 0 obj -4322 +4330 endobj 17 0 obj << @@ -1105,7 +1105,7 @@ 18 0 obj /Length 19 0 R >> stream -q +1 J 1 j q Q q 59.04 73.44 486.72 443.52 re W n Q q 0.000 0.000 0.000 RG @@ -1499,7 +1499,7 @@ Q endstream endobj 19 0 obj -6882 +6890 endobj 3 0 obj << @@ -1519,7 +1519,7 @@ 4 0 obj << /ProcSet [/PDF /Text] /Font << /F1 21 0 R /F2 22 0 R /F3 23 0 R >> -/ExtGState << >> +/ExtGState << /GSais 24 0 R >> >> endobj 20 0 obj @@ -1553,38 +1553,45 @@ 23 0 obj << /BaseFont /Helvetica-Bold /Encoding 20 0 R >> endobj +24 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 24 +0 25 0000000000 65535 f 0000000021 00000 n -0000000163 00000 n -0000027490 00000 n -0000027600 00000 n -0000000212 00000 n -0000000292 00000 n -0000009706 00000 n -0000009726 00000 n -0000009806 00000 n -0000012950 00000 n -0000012971 00000 n -0000013053 00000 n -0000015949 00000 n -0000015970 00000 n -0000016052 00000 n -0000020429 00000 n -0000020450 00000 n -0000020532 00000 n -0000027469 00000 n -0000027705 00000 n -0000027963 00000 n -0000028047 00000 n -0000028145 00000 n +0000000164 00000 n +0000027531 00000 n +0000027641 00000 n +0000000213 00000 n +0000000293 00000 n +0000009715 00000 n +0000009735 00000 n +0000009815 00000 n +0000012967 00000 n +0000012988 00000 n +0000013070 00000 n +0000015974 00000 n +0000015995 00000 n +0000016077 00000 n +0000020462 00000 n +0000020483 00000 n +0000020565 00000 n +0000027510 00000 n +0000027760 00000 n +0000028018 00000 n +0000028102 00000 n +0000028200 00000 n +0000028303 00000 n trailer << -/Size 24 +/Size 25 /Info 1 0 R /Root 2 0 R >> startxref -28248 +28353 %%EOF --- a/test-data/pca_out2.pdf +++ b/test-data/pca_out2.pdf @@ -2,10 +2,10 @@ %��ρ�\r 1 0 obj << -/CreationDate (D:20100310155829) -/ModDate (D:20100310155829) +/CreationDate (D:20100929163120) +/ModDate (D:20100929163120) /Title (R Graphics Output) -/Producer (R 2.10.0) +/Producer (R 2.11.0) /Creator (R) >> endobj @@ -28,7 +28,7 @@ 6 0 obj /Length 7 0 R >> stream -q +1 J 1 j q Q q 0.000 0.000 0.000 RG 0.75 w @@ -647,7 +647,7 @@ Q endstream endobj 7 0 obj -12848 +12856 endobj 3 0 obj << @@ -663,7 +663,7 @@ 4 0 obj << /ProcSet [/PDF /Text] /Font <</F2 9 0 R >> -/ExtGState << >> +/ExtGState << /GSais 10 0 R >> >> endobj 8 0 obj @@ -682,24 +682,31 @@ 9 0 obj << /BaseFont /Helvetica /Encoding 8 0 R >> endobj +10 0 obj +<< +/Type /ExtGState +/AIS false +>> +endobj xref -0 10 +0 11 0000000000 65535 f 0000000021 00000 n 0000000164 00000 n -0000013215 00000 n -0000013298 00000 n +0000013223 00000 n +0000013306 00000 n 0000000213 00000 n 0000000293 00000 n -0000013194 00000 n -0000013379 00000 n -0000013636 00000 n +0000013202 00000 n +0000013401 00000 n +0000013658 00000 n +0000013754 00000 n trailer << -/Size 10 +/Size 11 /Info 1 0 R /Root 2 0 R >> startxref -13732 +13804 %%EOF Binary file test-data/boxplot_summary_statistics_out.png has changed Binary file test-data/solexaScore.png has changed

1 0

galaxy-dist commit 546dc4845175: New hyphy nj tree test output for ps2pdf version standardized across all systems, and fix for the wig_to_bigwig test.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1285818943 14400 # Node ID 546dc4845175c92c91e181af61b6e1d2a108230e # Parent 940d77bec4d59a5418f9f731ca6ca114d748aa5d New hyphy nj tree test output for ps2pdf version standardized across all systems, and fix for the wig_to_bigwig test. --- /dev/null +++ b/test-data/wig_to_bigwig_hg17.len @@ -0,0 +1,46 @@ +chr10 135413628 +chr10_random 113275 +chr11 134452384 +chr12 132449811 +chr12_random 466818 +chr13 114142980 +chr13_random 186858 +chr14 106368585 +chr15 100338915 +chr15_random 784346 +chr16 88827254 +chr16_random 105485 +chr17 78774742 +chr17_random 2618010 +chr18 76117153 +chr18_random 4262 +chr19 63811651 +chr19_random 301858 +chr1 245522847 +chr1_random 3897131 +chr20 62435964 +chr21 46944323 +chr22 49554710 +chr22_random 257318 +chr2 243018229 +chr2_random 418158 +chr3 199505740 +chr3_random 970716 +chr4 191411218 +chr4_random 1030282 +chr5 180857866 +chr5_random 143687 +chr6 170975699 +chr6_random 1875562 +chr6_hla_hap1 139182 +chr6_hla_hap2 150447 +chr7 158628139 +chr7_random 778964 +chr8 146274826 +chr8_random 943810 +chr9 138429268 +chr9_random 1312665 +chrM 16571 +chrX 154824264 +chrX_random 1719168 +chrY 57701691 Binary file test-data/nj_tree_pdf_out.pdf has changed --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -108,4 +108,10 @@ for dir in $DIRS; do fi done +# for wig_to_bigWig +if [ ! -f "tool-data/shared/ucsc/chrom/hg17.len" -a -f "test-data/wig_to_bigwig_hg17.len" ]; then + mkdir -p tool-data/shared/ucsc/chrom + cp test-data/wig_to_bigwig_hg17.len tool-data/shared/ucsc/chrom/hg17.len +fi + python ./scripts/fetch_eggs.py all

1 0

galaxy-dist commit ddf70ed04c8b: sff_extractor tool
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1285855763 14400 # Node ID ddf70ed04c8b24f9095d4b16f6041907f7c6d428 # Parent 546dc4845175c92c91e181af61b6e1d2a108230e sff_extractor tool output is now explicitly set to fastqsanger when the fastq option is selected. patch by peter(a)maubp.freeserve.co.uk --- a/tools/filters/sff_extractor.xml +++ b/tools/filters/sff_extractor.xml @@ -14,7 +14,7 @@ <param name="fastq_output" type="boolean" truevalue="fastq_true" falsevalue="fastq_false" checked="False" label="Do you want FASTQ file instead of FASTA + FASTA quality file?" /></inputs><outputs> - <data format="fastq" name="out_file1" > + <data format="fastqsanger" name="out_file1" ><filter>fastq_output is True</filter></data><data format="xml" name="out_file2">

1 0

galaxy-dist commit 19b10fff1335: More bug fixes.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1290010215 18000 # Node ID 19b10fff133595cb5cd1851a7f24024c2637ad2b # Parent 918a25ed14f5427f70970b0c436159fc58fd111e More bug fixes. --- a/lib/galaxy/web/controllers/forms.py +++ b/lib/galaxy/web/controllers/forms.py @@ -602,7 +602,7 @@ class Forms( BaseController ): self.fieldtype.add_option( ft.__name__, ft.__name__ ) else: for ft in trans.model.FormDefinition.supported_field_types: - self.fieldtype.add_option( ft.__name__, ft__name__ ) + self.fieldtype.add_option( ft.__name__, ft.__name__ ) self.required = SelectField('field_required_'+str(index), display='radio') self.required.add_option('Required', 'required') self.required.add_option('Optional', 'optional', selected=True) @@ -713,7 +713,7 @@ class Forms( BaseController ): form_details=form_details, field_details=field_details, form_definition=form_definition, - field_types=BaseField.form_field_types(), + field_types=trans.model.FormDefinition.supported_field_types, message=message, status=status, current_form_type=current_form[ 'type' ],

1 0

galaxy-dist commit 39f41821aa4e: Adding data table configuration file for backwards compatibility with local installs: for people who don't want to update loc file style (changes made in rev 4550:535d276c92bc)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1290011565 18000 # Node ID 39f41821aa4eec15b04509d24715946552bb14a6 # Parent 19b10fff133595cb5cd1851a7f24024c2637ad2b Adding data table configuration file for backwards compatibility with local installs: for people who don't want to update loc file style (changes made in rev 4550:535d276c92bc) --- /dev/null +++ b/tool_data_table_conf.xml.oldlocstyle @@ -0,0 +1,73 @@ + +<tables> +  + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +  + <table name="bfast_indexes" comment_char="#"> + <columns>value, dbkey, formats, name, path</columns> + <file path="tool-data/bfast_indexes.loc" /> + </table> +  + <table name="blastdb" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/blastdb.loc" /> + </table> +  + <table name="blastdb_p" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/blastdb_p.loc" /> + </table> +  + <table name="bowtie_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> +  + <table name="bowtie_indexes_color" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/bowtie_indices_color.loc" /> + </table> +  + <table name="bwa_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/bwa_index.loc" /> + </table> +  + <table name="indexed_maf_files"> + <columns>name, value, dbkey, species</columns> + <file path="tool-data/maf_index.loc" /> + </table> +  + <table name="ngs_sim_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/ngs_sim_fasta.loc" /> + </table> +  + <table name="lastz_seqs" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/lastz_seqs.loc" /> + </table> +  + <table name="perm_base_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/perm_base_index.loc" /> + </table> +  + <table name="perm_color_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/perm_color_index.loc" /> + </table> +  + <table name="srma_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/srma_index.loc" /> + </table> +  + <table name="tophat_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> +</tables>

1 0

galaxy-dist commit 7d46c23bb276: Merge with 39f41821aa4eec15b04509d24715946552bb14a6
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1290011867 18000 # Node ID 7d46c23bb276790160fe05560aa87c3d41185a27 # Parent 8ce82d60b2ab55966d133db136fcb2f809201c4b # Parent 39f41821aa4eec15b04509d24715946552bb14a6 Merge with 39f41821aa4eec15b04509d24715946552bb14a6

1 0

galaxy-dist commit d1baa724b393: Modified some test fastq files to make valid
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1290011865 18000 # Node ID d1baa724b393de6871df7249ebe35ecfe2054e31 # Parent 39f41821aa4eec15b04509d24715946552bb14a6 Modified some test fastq files to make valid --- a/test-data/bwa_wrapper_in2.fastq +++ b/test-data/bwa_wrapper_in2.fastq @@ -1,120 +1,120 @@ @seq1/1 GGACTCAGATAGTAATCC -+/1 ++ II#IIIIIII$5+.(9II @seq2/1 ATTCGACCTATCCTTGCG -+/1 ++ IIIIIIIIIIIIIIIIII @seq3/1 GTAACAAAGTTTGGATTG -+/1 ++ IIIIIIIIIIIIIIIIII @seq4/1 AGCCGCTCGTCTTTTATG -+/1 ++ IIIIIIIIIIIIIIIIII @seq5/1 CAGTTATATGGCTTTTGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq6/1 AGGCGCTCGTCTTGGTAT -+/1 ++ IIIIIIIIIIIIIIIIII @seq7/1 TGTAGGTGGTCAACCAAT -+/1 ++ IIIIIIIIIIIIIIIIII @seq8/1 ACACCCGTCCTTTACGTC -+/1 ++ IIIIIIIIIIIIIIIIII @seq9/1 GCCGCTATTCAGGTTGTT -+/1 ++ IIIIIIIIIIIIIIIIII @seq10/1 ATTCTTTCTTTTCGTATC -+/1 ++ IIIIIIIIIIIIIIIIII @seq11/1 GCATTTCTACTCCTTCTC -+/1 ++ II#IIIIIII$5+.(9II @seq12/1 CGCGCTTCGATAAAAATG -+/1 ++ IIIIIIIIIIIIIIIIII @seq13/1 ATTTCTACTCTTTCTCAT -+/1 ++ IIIIIIIIIIIIIIIIII @seq14/1 CCCTTTTGAATGTCACGC -+/1 ++ IIIIIIIIIIIIIIIIII @seq15/1 CCAACTTACCAAGGTGGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq16/1 TCAGGGTATTAAAAGAGA -+/1 ++ IIIIIIIIIIIIIIIIII @seq17/1 GTGATGTGCTTGCTACCG -+/1 ++ IIIIIIIIIIIIIIIIII @seq18/1 TCAATCCCCCATGCTTGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq19/1 TTCCTGCGCTTAATGCTT -+/1 ++ IIIIIIIIIIIIIIIIII @seq20/1 CTTATTACCATTTCAACT -+/1 ++ IIIIIIIIIIIIIIIIII @seq21/1 CTGATACCAATAAAACCC -+/1 ++ II#IIIIIII$5+.(9II @seq22/1 AATCAAACTTACCAAGGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq23/1 TGTGCTTCCCCAACTTGA -+/1 ++ IIIIIIIIIIIIIIIIII @seq24/1 TTTCTCAATCCCCAATGC -+/1 ++ IIIIIIIIIIIIIIIIII @seq25/1 TTGCTACTGACCGCTCTT -+/1 ++ IIIIIIIIIIIIIIIIII @seq26/1 CCGCGTGAAATTTCTATG -+/1 ++ IIIIIIIIIIIIIIIIII @seq27/1 CGCTAATCAAGTTGTTTC -+/1 ++ IIIIIIIIIIIIIIIIII @seq28/1 AAAGAGATTATTTGTCGG -+/1 ++ IIIIIIIIIIIIIIIIII @seq29/1 CAAATTAATGCGCGCTTC -+/1 ++ IIIIIIIIIIIIIIIIII @seq30/1 ATCCCCTATGCTTGGCTT -+/1 ++ IIIIIIIIIIIIIIIIII --- a/test-data/bwa_wrapper_in3.fastq +++ b/test-data/bwa_wrapper_in3.fastq @@ -1,74 +1,74 @@ @seq1/2 ACGCTCCTTTAAAATATC -+/2 ++ IIIII$%*$G$A31I&&B @seq2/2 CAGCTCGAGAAGCTCTTA -+/2 ++ IIIIIIIIIIIIIIIIII @seq3/2 CTACTGACCGCTCTCGTG -+/2 ++ IIIIIIIIIIIIIIIIII @seq4/2 TAGGTGGTCAACCATTTT -+/2 ++ IIIIIIIIIIIIIIIIII @seq5/2 TTTCTATGTGGCTTAATA -+/2 ++ IIIIIIIIIIIIIIIIII @seq6/2 GTAGGTGGTCAACAATTT -+/2 ++ IIIIIIIIIIIIIIIIII @seq7/2 TTTAATTGCAGGGGCTTC -+/2 ++ IIIIIIIIIIIIIIIIII @seq8/2 ATGCGCTCTATTCTCTGG -+/2 ++ IIIIIIIIIIIIIIIIII @seq9/2 TTCTGTTGGTGCTGATAT -+/2 ++ IIIIIIIIIIIIIIIIII @seq10/2 AGGGCGTTGAGTTCGATA -+/2 ++ IIIIIIIIIIIIIIIIII @seq11/2 ATCCCCAATGCTTGGCTT -+/2 ++ IIIII$%*$G$A31I&&B @seq12/2 GGATTGGCGTTTCCAACC -+/2 ++ IIIIIIIIIIIIIIIIII @seq13/2 CCCCAATCCTTGCCTTCC -+/2 ++ IIIAAIIIIIIIIIIIII @seq14/2 TGATATTTTGACTTTGAG -+/2 ++ IIIIIIIIIIIIIIIIII @seq15/2 TTACGAAACGCGACGCCG -+/2 ++ IIIIIIIIIIIIIIIIII @seq16/2 TTATTTTTCTCCAGCCAC -+/2 ++ IIIIIIIIIIIIIIIIII @seq17/2 AAACAATACTTTAGGCAT -+/2 ++ IIIIIIIIIIIIIIIIII @seq18/2 CCGTTCCATAAGCAGATG -+/2 ++ IIIIIIIIIIIIIIIIII @seq19/2 GAGCGTCCTGGTGCTGAT @@ -76,45 +76,45 @@ GAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIII @seq20/2 ACTCCGGTTATCGCTGGC -+/2 ++ IIIIIIIIIIIIIIIIII @seq21/2 TAAGCATTTGGTTCAGGG -+/2 ++ IIIII$%*$G$A31I&&B @seq22/2 GTTACGACGCGACGCCGT -+/2 ++ IIIIIIIIIIIIIIIIII @seq23/2 TTTAATAACCCTATAGAC -+/2 ++ IIIIIIIIIIIIIIIIII @seq24/2 CTTGGCTTCCCTAAGCAG -+/2 ++ IIIIIIIIIIIIIIIIII @seq25/2 CGTGCTCGTTGCTGCGTT -+/2 ++ IIIIIIIIIIIIIIIIII @seq26/2 AAGGATGTTTTCCGTTCT -+/2 ++ IIIIIIIIIIIIIIIIII @seq27/2 TGTTTGGTGCTGATATTG -+/2 ++ IIIIIIIIIIIIIIIIII @seq28/2 TCCAGCCACTAAAGTGAG -+/2 ++ IIIIIIIIIIIIIIIIII @seq29/2 GATAATGATTGGGGTATC -+/2 ++ IIIIIIIIIIIIIIIIII @seq30/2 ACCATAAGCAGATGGATA -+/2 ++ IIIIIIIIIIIIIIIIII --- a/test-data/bowtie_in2.fastqsanger +++ b/test-data/bowtie_in2.fastqsanger @@ -1,5 +1,5 @@ @HWI-EAS91_1_30788AAXX:1:1:1513:715/1 GTTTTTTNNGCATAGATGTTTAGTTGTGGTAGTCAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I

1 0

galaxy-dist commit 8ce82d60b2ab: - added the change data library sample operation functional test.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1290011634 18000 # Node ID 8ce82d60b2ab55966d133db136fcb2f809201c4b # Parent 19b10fff133595cb5cd1851a7f24024c2637ad2b - added the change data library sample operation functional test. - renaming dataset now checks for incorrect filename characters - fixed bugs --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -1079,7 +1079,7 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, action='update_request_state', request_id=trans.security.encode_id( request.id ) ) ) - elif sample_operation == trans.model.sample.bulk_operations.SELECT_LIBRARY: + elif sample_operation == trans.model.Sample.bulk_operations.SELECT_LIBRARY: # TODO: fix the code so that the sample_operation_select_field does not use # sample_0_library_id as it's name. it should use something like sample_operation_library_id # and sample_operation_folder_id because the name sample_0_library_id should belong to the --- a/templates/admin/requests/rename_datasets.mako +++ b/templates/admin/requests/rename_datasets.mako @@ -16,6 +16,7 @@ <div class="toolForm"><form name="rename_datasets" id="rename_datasets" action="${h.url_for( controller='requests_admin', action='rename_datasets', id_list=id_list, sample_id=trans.security.encode_id( sample.id ) )}" method="post" > + <table class="grid"><thead><tr> @@ -43,9 +44,16 @@ </tbody></table><br/> + <div class="form-row"> + <div class="toolParamHelp" style="clear: both;"> + A dataset name should only contain the alphanumeric characters or underscore(_). + If a dataset name contains any other character, it would be replaced by an underscore(_). + </div> + </div><div class="form-row"><input type="submit" name="rename_datasets_button" value="Save"/><input type="submit" name="cancel_rename_datasets_button" value="Close"/></div></form> + </div> --- a/scripts/galaxy_messaging/server/setup_rabbitmq.py +++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py @@ -24,7 +24,7 @@ def main( config_file ): cmd_list = [ 'add_user %s %s' % ( username, password ), - 'add_vhost %s' % config.get( 'galaxy_amqp', 'virtual_host' ), + 'add_vhost %s' % virtual_host, 'set_permissions -p %s %s ".*" ".*" ".*"' % ( virtual_host, username ) ] --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -430,8 +430,8 @@ class TestFormsAndRequests( TwillTestCas """Testing editing the sample information of new request1""" # logged in as regular_user1 # target data library - change it to library1 - target_library_info = dict(library=self.security.encode_id(library1.id), - folder=self.security.encode_id(library1_folder1.id) ) + target_library_info = dict(library=self.security.encode_id( library1.id ), + folder=self.security.encode_id( library1_folder1.id ) ) new_sample_value_tuples = \ [ ( 'Sample1_renamed', target_library_info, [ 'option2', 'sample1 field2 value edited', 'sample1 field3 value edited' ] ), ( 'Sample2_renamed', target_library_info, [ 'option1', 'sample2 field2 value edited', 'sample2 field3 value edited' ] ), @@ -494,6 +494,23 @@ class TestFormsAndRequests( TwillTestCas strings_displayed_count=strings_displayed_count, strings_not_displayed=[ request1.states.COMPLETE, request1.states.REJECTED ] ) + # change the target data library back to library2 using sample operation user interface + self.change_sample_target_data_library( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + sample_ids=[ sample.id for sample in request1.samples ], + new_library_id=self.security.encode_id( library2.id ), + new_folder_id=self.security.encode_id( library2_folder1.id ), + strings_displayed=[ 'Edit Current Samples of Sequencing Request "%s"' % request1.name ], + strings_displayed_after_submit=[ 'Changes made to the samples have been saved.' ] ) + # check the changed target data library & folder on the request page + strings_displayed_count = [] + strings_displayed_count.append( ( library2.name, len( request1.samples ) ) ) + strings_displayed_count.append( ( library2_folder1.name, len( request1.samples ) ) ) + self.view_request( cntrller='requests', + request_id=self.security.encode_id( request1.id ), + strings_displayed=[], + strings_displayed_count=strings_displayed_count ) + # # ====== Sequencing request test methods - Admin perspective ================ # @@ -537,7 +554,7 @@ class TestFormsAndRequests( TwillTestCas request1.type.states[4].desc ] # check history of each sample for sample in request1.samples: - strings_displayed = [ 'Events for Sample "%s"' % sample.name, + strings_displayed = [ 'History of sample "%s"' % sample.name, 'Sequencing request submitted and sample state set to %s' % request1.type.states[0].name, request1.type.states[0].name, request1.type.states[1].name ] --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -361,17 +361,29 @@ class RequestsAdmin( BaseController, Use sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) sample_datasets.append( sample_dataset ) if params.get( 'rename_datasets_button', False ): + incorrect_dataset_names = [] for sample_dataset in sample_datasets: encoded_id = trans.security.encode_id( sample_dataset.id ) selected_option = util.restore_text( params.get( 'rename_datasets_for_sample_%s' % encoded_id, '' ) ) new_name = util.restore_text( params.get( 'new_name_%s' % encoded_id, '' ) ) + if not new_name: + incorrect_dataset_names.append( sample_dataset.name ) + continue + new_name = util.sanitize_for_filename( new_name ) if selected_option == 'none': sample_dataset.name = new_name else: sample_dataset.name = '%s_%s' % ( selected_option, new_name ) trans.sa_session.add( sample_dataset ) trans.sa_session.flush() - message = 'Changes saved successfully.' + if len( sample_datasets ) == len( incorrect_dataset_names ): + status = 'error' + message = 'All datasets renamed incorrectly.' + elif len( incorrect_dataset_names ): + status = 'done' + message = 'Changes saved successfully. The following datasets were renamed incorrectly: %s.' % str( incorrect_dataset_names ) + else: + message = 'Changes saved successfully.' return trans.fill_template( '/admin/requests/rename_datasets.mako', sample=sample, id_list=id_list, --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1638,6 +1638,23 @@ class TwillTestCase( unittest.TestCase ) tc.submit( "save_samples_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) + def change_sample_target_data_library( self, cntrller, request_id, sample_ids, new_library_id, new_folder_id, comment='', strings_displayed=[], strings_displayed_after_submit=[] ): + url = "%s/requests_common/edit_samples?cntrller=%s&id=%s&editing_samples=True" % ( self.url, cntrller, request_id ) + self.visit_url( url ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) + for sample_id in sample_ids: + tc.fv( "1", "select_sample_%i" % sample_id, True ) + tc.fv( "1", "sample_operation", 'Select data library and folder' ) + self.refresh_form( "sample_operation", 'Select data library and folder' ) + self.check_page_for_string( "Select data library:" ) + tc.fv( "1", "sample_0_library_id", new_library_id ) + self.refresh_form( "sample_0_library_id", new_library_id ) + self.check_page_for_string( "Select folder:" ) + tc.fv( "1", "sample_0_folder_id", new_folder_id ) + tc.submit( "save_samples_button" ) + for check_str in strings_displayed_after_submit: + self.check_page_for_string( check_str ) def add_user_address( self, user_id, address_dict ): self.home() self.visit_url( "%s/user/new_address?admin_view=False&user_id=%i" % ( self.url, user_id ) ) --- a/lib/galaxy/web/controllers/forms.py +++ b/lib/galaxy/web/controllers/forms.py @@ -635,8 +635,8 @@ class Forms( BaseController ): if form_type == trans.model.FormDefinition.types.SAMPLE: for ft in trans.model.Sample.supported_field_types: if ft.__name__ == field[ 'type' ]: - self.fieldtype.add_option( ft.__name__, ft__name__, selected=True ) - if ft == 'SelectField': + self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True ) + if ft.__name__ == 'SelectField': self.selectbox_ui( field ) else: self.fieldtype.add_option( ft.__name__, ft.__name__ ) @@ -644,7 +644,7 @@ class Forms( BaseController ): for ft in trans.model.FormDefinition.supported_field_types: if ft.__name__ == field[ 'type' ]: self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True ) - if ft == 'SelectField': + if ft.__name__ == 'SelectField': self.selectbox_ui( field ) else: self.fieldtype.add_option( ft.__name__, ft.__name__ )

1 0