galaxy-commits July 2013

galaxy-commits@lists.galaxyproject.org

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83 discussions

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 29 Jul '13

29 Jul '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f436b2313968/ Changeset: f436b2313968 User: jgoecks Date: 2013-07-26 01:45:29 Summary: Add --no-effective-length-correction parameter to Cufflinks wrapper Affected #: 2 files diff -r c55f7d1dc3a1e18b8f1b6e20157cc209caa647dd -r f436b23139681ae82b662a002e01b91ad87df21f tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py +++ b/tools/ngs_rna/cufflinks_wrapper.py @@ -28,6 +28,7 @@ # Normalization options. parser.add_option( "-N", "--quartile-normalization", dest="do_normalization", action="store_true" ) + parser.add_option( "--no-effective-length-correction", dest="no_effective_length_correction", action="store_true" ) # Wrapper / Galaxy options. parser.add_option( '-A', '--assembled-isoforms-output', dest='assembled_isoforms_output_file', help='Assembled isoforms output file; formate is GTF.' ) @@ -110,6 +111,8 @@ cmd += ( " -N" ) if options.do_bias_correction: cmd += ( " -b %s" % seq_path ) + if options.no_effective_length_correction: + cmd += ( " --no-effective-length-correction" ) # Debugging. print cmd diff -r c55f7d1dc3a1e18b8f1b6e20157cc209caa647dd -r f436b23139681ae82b662a002e01b91ad87df21f tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cufflinks" name="Cufflinks" version="0.0.6"> +<tool id="cufflinks" name="Cufflinks" version="0.0.7"><description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description><requirements> @@ -12,6 +12,7 @@ -I $max_intron_len -F $min_isoform_fraction -j $pre_mrna_fraction + $effective_length_correction ## Include reference annotation? #if $reference_annotation.use_ref == "Use reference annotation": @@ -101,6 +102,11 @@ <option value="Yes">Yes</option></param> + <param name="effective_length_correction" type="select" label="Use effective length correction" help="Cufflinks will not employ its 'effective' length normalization to transcript FPKM."> + <option value="" selected="true">Yes</option> + <option value="--no-effective-length-correction">No</option> + </param> + <param name="global_model" type="hidden_data" label="Global model (for use in Trackster)" optional="True"/></inputs> @@ -128,6 +134,7 @@ <param name="do_normalization" value="No" /><param name="do_bias_correction" value="No"/><param name="multiread_correct" value="No"/> + <param name="effective_length_correction" value="Yes"/><output name="genes_expression" format="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/><output name="transcripts_expression" format="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/><output name="assembled_isoforms" file="cufflinks_out1.gtf"/> https://bitbucket.org/galaxy/galaxy-central/commits/32a48938fe77/ Changeset: 32a48938fe77 User: jgoecks Date: 2013-07-29 23:36:39 Summary: Add and document welcome_url config option. Affected #: 1 file diff -r f436b23139681ae82b662a002e01b91ad87df21f -r 32a48938fe771147abb64524f57d2adb65787ac5 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -228,6 +228,10 @@ # -- Display sites +# The URL of the page to display in Galaxy's middle pane when loaded. This can be +# an absolute or relative URL. +#welcome_url = /static/welcome.html + # Galaxy can display data at various external browsers. These options specify # which browsers should be available. URLs and builds available at these # browsers are defined in the specifield files. https://bitbucket.org/galaxy/galaxy-central/commits/4d4faedba9b6/ Changeset: 4d4faedba9b6 User: jgoecks Date: 2013-07-29 23:37:14 Summary: Automated merge Affected #: 4 files diff -r 32a48938fe771147abb64524f57d2adb65787ac5 -r 4d4faedba9b6caa555e3825e0f86a34c483e51ff lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -24,7 +24,7 @@ import galaxy.webapps.tool_shed.config as tool_shed_config import galaxy.webapps.tool_shed.model.mapping import sqlalchemy as sa -from galaxy.model.orm import and_, not_ +from galaxy.model.orm import and_, not_, select from galaxy.util.json import from_json_string, to_json_string from galaxy.web import url_for from galaxy.tools import parameters @@ -200,6 +200,7 @@ } ''' start = time.time() + skip_metadata_ids = [] checked_repository_ids = [] tool_count = 0 has_tests = 0 @@ -208,13 +209,16 @@ valid_revisions = 0 invalid_revisions = 0 records_checked = 0 + # Do not check metadata records that have an entry in the skip_tool_tests table, since they won't be tested anyway. + skip_metadata_ids = select( [ app.model.SkipToolTest.table.c.repository_metadata_id ] ) # Get the list of metadata records to check for functional tests and test data. Limit this to records that have not been flagged do_not_test, # since there's no need to check them again if they won't be tested anyway. Also filter out changeset revisions that are not downloadable, # because it's redundant to test a revision that a user can't install. for metadata_record in app.sa_session.query( app.model.RepositoryMetadata ) \ .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, app.model.RepositoryMetadata.table.c.includes_tools == True, - app.model.RepositoryMetadata.table.c.do_not_test == False ) ): + app.model.RepositoryMetadata.table.c.do_not_test == False, + not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ): records_checked += 1 # Initialize the repository_status dict with the test environment, but leave the test_errors empty. repository_status = {} diff -r 32a48938fe771147abb64524f57d2adb65787ac5 -r 4d4faedba9b6caa555e3825e0f86a34c483e51ff lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -1,4 +1,5 @@ import cStringIO +import gzip import logging import os import pkg_resources diff -r 32a48938fe771147abb64524f57d2adb65787ac5 -r 4d4faedba9b6caa555e3825e0f86a34c483e51ff templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -445,18 +445,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #failed_test_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="failed_test_table"> + <table id="failed_test_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${failed_test.test_id | h}</td></tr> @@ -573,18 +563,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #missing_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="missing_table"> + <table id="missing_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${missing_test_component.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${missing_test_component.tool_version | h}</td></tr><tr><td><b>Tool guid:</b> ${missing_test_component.tool_guid | h}</td></tr> @@ -703,6 +683,19 @@ %></%def> +<%def name="render_tool_test_results_css()"> + <style type="text/css"> + table.tool_test_results{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } + </style> +</%def> + <%def name="render_tool_dependency_installation_error( installation_error, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( installation_error.id ) %><tr class="datasetRow" @@ -710,18 +703,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #td_install_error_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="td_install_error_table"> + <table id="td_install_error_table" class="tool_test_results"><tr bgcolor="#FFFFCC"><th>Type</th><th>Name</th><th>Version</th></tr> @@ -748,18 +731,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #rd_install_error_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="rd_install_error_table"> + <table id="rd_install_error_table" class="tool_test_results"> %if not is_current_repository: <tr bgcolor="#FFFFCC"><th>Tool shed</th><th>Name</th><th>Owner</th><th>Changeset revision</th> @@ -789,18 +762,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #not_tested_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="not_tested_table"> + <table id="not_tested_table" class="tool_test_results"><tr><td>${not_tested.reason | h}</td></tr></table></td> @@ -818,18 +781,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #passed_tests_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="passed_tests_table"> + <table id="passed_tests_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${passed_test.test_id | h}</td></tr> @@ -1206,6 +1159,7 @@ </div> %endif %if tool_test_results_root_folder: + ${render_tool_test_results_css()} <p/><div class="toolForm"><div class="toolFormTitle">Automated tool test results</div> diff -r 32a48938fe771147abb64524f57d2adb65787ac5 -r 4d4faedba9b6caa555e3825e0f86a34c483e51ff test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1191,13 +1191,7 @@ # This loop gets the filename/label for the selected values. item_labels = [ item.attrs[ 'label' ] for item in control.get_items() if item.selected ] for value in kwd[ control.name ]: - # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py. - # This (and other places where this is done) should be refactored to use the HDA id. - if len( value ) > 30 and control.is_of_kind( 'singlelist' ): - field_value = '%s..%s' % ( value[:17], value[-11:] ) - else: - field_value = value - if field_value not in control.value and True not in [ field_value in item_label for item_label in item_labels ]: + if value not in control.value and True not in [ value in item_label for item_label in item_labels ]: changed = True break if changed: @@ -1205,11 +1199,7 @@ control.clear() # kwd[control.name] should be a singlelist for elem in kwd[ control.name ]: - if len( elem ) > 30 and control.is_of_kind( 'singlelist' ): - elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) - else: - elem_name = elem - tc.fv( f.name, control.name, str( elem_name ) ) + tc.fv( f.name, control.name, str( elem ) ) # Create a new submit control, allows form to refresh, instead of going to next page control = ClientForm.SubmitControl( 'SubmitControl', '___refresh_grouping___', {'name':'refresh_grouping'} ) control.add_to_form( f ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Define a CSS class that applies to all tool test results subfolders.
by commits-noreply＠bitbucket.org 29 Jul '13

29 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/65a1a1a16552/ Changeset: 65a1a1a16552 User: Dave Bouvier Date: 2013-07-29 21:25:08 Summary: Define a CSS class that applies to all tool test results subfolders. Affected #: 1 file diff -r 5ad8db7ff74881f13420f9e0b6f171d4f2acfd99 -r 65a1a1a1655224d8bf1a8e32dde0e70f11f2d5ca templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -445,18 +445,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #failed_test_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="failed_test_table"> + <table id="failed_test_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${failed_test.test_id | h}</td></tr> @@ -573,18 +563,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #missing_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="missing_table"> + <table id="missing_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${missing_test_component.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${missing_test_component.tool_version | h}</td></tr><tr><td><b>Tool guid:</b> ${missing_test_component.tool_guid | h}</td></tr> @@ -703,6 +683,19 @@ %></%def> +<%def name="render_tool_test_results_css()"> + <style type="text/css"> + table.tool_test_results{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } + </style> +</%def> + <%def name="render_tool_dependency_installation_error( installation_error, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( installation_error.id ) %><tr class="datasetRow" @@ -710,18 +703,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #td_install_error_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="td_install_error_table"> + <table id="td_install_error_table" class="tool_test_results"><tr bgcolor="#FFFFCC"><th>Type</th><th>Name</th><th>Version</th></tr> @@ -748,18 +731,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #rd_install_error_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="rd_install_error_table"> + <table id="rd_install_error_table" class="tool_test_results"> %if not is_current_repository: <tr bgcolor="#FFFFCC"><th>Tool shed</th><th>Name</th><th>Owner</th><th>Changeset revision</th> @@ -789,18 +762,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #not_tested_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="not_tested_table"> + <table id="not_tested_table" class="tool_test_results"><tr><td>${not_tested.reason | h}</td></tr></table></td> @@ -818,18 +781,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #passed_tests_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="passed_tests_table"> + <table id="passed_tests_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${passed_test.test_id | h}</td></tr> @@ -1206,6 +1159,7 @@ </div> %endif %if tool_test_results_root_folder: + ${render_tool_test_results_css()} <p/><div class="toolForm"><div class="toolFormTitle">Automated tool test results</div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: When checking tool shed repositories for functional tests and test data, explicitly filter out metadata records that have been specified not to be tested by the repository owner.
by commits-noreply＠bitbucket.org 29 Jul '13

29 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5ad8db7ff748/ Changeset: 5ad8db7ff748 User: Dave Bouvier Date: 2013-07-29 19:50:55 Summary: When checking tool shed repositories for functional tests and test data, explicitly filter out metadata records that have been specified not to be tested by the repository owner. Affected #: 1 file diff -r fe04978dadac9974ab1954ab2091539e58caf3e4 -r 5ad8db7ff74881f13420f9e0b6f171d4f2acfd99 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -24,7 +24,7 @@ import galaxy.webapps.tool_shed.config as tool_shed_config import galaxy.webapps.tool_shed.model.mapping import sqlalchemy as sa -from galaxy.model.orm import and_, not_ +from galaxy.model.orm import and_, not_, select from galaxy.util.json import from_json_string, to_json_string from galaxy.web import url_for from galaxy.tools import parameters @@ -200,6 +200,7 @@ } ''' start = time.time() + skip_metadata_ids = [] checked_repository_ids = [] tool_count = 0 has_tests = 0 @@ -208,13 +209,16 @@ valid_revisions = 0 invalid_revisions = 0 records_checked = 0 + # Do not check metadata records that have an entry in the skip_tool_tests table, since they won't be tested anyway. + skip_metadata_ids = select( [ app.model.SkipToolTest.table.c.repository_metadata_id ] ) # Get the list of metadata records to check for functional tests and test data. Limit this to records that have not been flagged do_not_test, # since there's no need to check them again if they won't be tested anyway. Also filter out changeset revisions that are not downloadable, # because it's redundant to test a revision that a user can't install. for metadata_record in app.sa_session.query( app.model.RepositoryMetadata ) \ .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, app.model.RepositoryMetadata.table.c.includes_tools == True, - app.model.RepositoryMetadata.table.c.do_not_test == False ) ): + app.model.RepositoryMetadata.table.c.do_not_test == False, + not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ): records_checked += 1 # Initialize the repository_status dict with the test environment, but leave the test_errors empty. repository_status = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Do not truncate tool test input dataset names, as Galaxy no longer displays them truncated.
by commits-noreply＠bitbucket.org 29 Jul '13

29 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fe04978dadac/ Changeset: fe04978dadac User: Dave Bouvier Date: 2013-07-29 18:01:24 Summary: Do not truncate tool test input dataset names, as Galaxy no longer displays them truncated. Affected #: 1 file diff -r e19301cc51b90667ae829c6f9a61571f50906494 -r fe04978dadac9974ab1954ab2091539e58caf3e4 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1191,13 +1191,7 @@ # This loop gets the filename/label for the selected values. item_labels = [ item.attrs[ 'label' ] for item in control.get_items() if item.selected ] for value in kwd[ control.name ]: - # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py. - # This (and other places where this is done) should be refactored to use the HDA id. - if len( value ) > 30 and control.is_of_kind( 'singlelist' ): - field_value = '%s..%s' % ( value[:17], value[-11:] ) - else: - field_value = value - if field_value not in control.value and True not in [ field_value in item_label for item_label in item_labels ]: + if value not in control.value and True not in [ value in item_label for item_label in item_labels ]: changed = True break if changed: @@ -1205,11 +1199,7 @@ control.clear() # kwd[control.name] should be a singlelist for elem in kwd[ control.name ]: - if len( elem ) > 30 and control.is_of_kind( 'singlelist' ): - elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) - else: - elem_name = elem - tc.fv( f.name, control.name, str( elem_name ) ) + tc.fv( f.name, control.name, str( elem ) ) # Create a new submit control, allows form to refresh, instead of going to next page control = ClientForm.SubmitControl( 'SubmitControl', '___refresh_grouping___', {'name':'refresh_grouping'} ) control.add_to_form( f ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix import in the tool shed's commit_util.
by commits-noreply＠bitbucket.org 26 Jul '13

26 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e19301cc51b9/ Changeset: e19301cc51b9 User: greg Date: 2013-07-26 15:10:23 Summary: Fix import in the tool shed's commit_util. Affected #: 1 file diff -r c55f7d1dc3a1e18b8f1b6e20157cc209caa647dd -r e19301cc51b90667ae829c6f9a61571f50906494 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -1,4 +1,5 @@ import cStringIO +import gzip import logging import os import pkg_resources Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Change ToolInput to ToolParameter in JavaScript tools implementation to match language used in model.
by commits-noreply＠bitbucket.org 25 Jul '13

25 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c55f7d1dc3a1/ Changeset: c55f7d1dc3a1 User: jgoecks Date: 2013-07-25 18:56:30 Summary: Change ToolInput to ToolParameter in JavaScript tools implementation to match language used in model. Affected #: 1 file diff -r a5a6c75e9af7098b4a4b35b917d49b8cc5abad43 -r c55f7d1dc3a1e18b8f1b6e20157cc209caa647dd static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -33,9 +33,9 @@ }); /** - * A tool input. + * A tool parameter. */ -var ToolInput = Backbone.RelationalModel.extend({ +var ToolParameter = Backbone.RelationalModel.extend({ defaults: { name: null, label: null, @@ -49,7 +49,7 @@ }, copy: function() { - return new ToolInput(this.toJSON()); + return new ToolParameter(this.toJSON()); }, /** @@ -88,7 +88,7 @@ { type: Backbone.HasMany, key: 'inputs', - relatedModel: ToolInput, + relatedModel: ToolParameter, reverseRelation: { key: 'tool', includeInJSON: false Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Fix for installing a repository with a complex tool dependency where the dependent repository's tool dependency definition does not define any set_environment actions.
by commits-noreply＠bitbucket.org 25 Jul '13

25 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a5a6c75e9af7/ Changeset: a5a6c75e9af7 User: Dave Bouvier Date: 2013-07-25 17:37:13 Summary: Fix for installing a repository with a complex tool dependency where the dependent repository's tool dependency definition does not define any set_environment actions. Affected #: 1 file diff -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 -r a5a6c75e9af7098b4a4b35b917d49b8cc5abad43 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -193,9 +193,9 @@ else: action_dict[ 'environment_variable' ] = env_var_dicts actions.append( ( 'set_environment', action_dict ) ) - return tool_dependency, actions else: raise NotImplementedError( 'Only install version 1.0 is currently supported (i.e., change your tag to be <install version="1.0">).' ) + return tool_dependency, actions return None, actions def install_and_build_package_via_fabric( app, tool_dependency, actions_dict ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: A bit of refactoring of the tool shed's repository controller.
by commits-noreply＠bitbucket.org 25 Jul '13

25 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8059779d2a6c/ Changeset: 8059779d2a6c User: greg Date: 2013-07-25 17:01:18 Summary: A bit of refactoring of the tool shed's repository controller. Affected #: 6 files diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1,7 +1,5 @@ -import ConfigParser import logging import os -import re import string import tempfile from time import gmtime @@ -11,22 +9,21 @@ from galaxy import util from galaxy import web from galaxy.util.odict import odict -from galaxy.util.expressions import ExpressionContext from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import CheckboxField -from galaxy.web.form_builder import build_select_field from galaxy.webapps.tool_shed import model from galaxy.webapps.tool_shed.model import directory_hash_id from galaxy.web.framework.helpers import grids from galaxy.util import json from galaxy.model.orm import and_ -from galaxy.model.orm import or_ import tool_shed.util.shed_util_common as suc from tool_shed.util import encoding_util from tool_shed.util import metadata_util from tool_shed.util import readme_util from tool_shed.util import repository_dependency_util +from tool_shed.util import repository_maintenance_util from tool_shed.util import review_util +from tool_shed.util import search_util from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import workflow_util @@ -48,7 +45,6 @@ log = logging.getLogger( __name__ ) -VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) malicious_error = " This changeset cannot be downloaded because it potentially produces malicious behavior or contains inappropriate content." malicious_error_can_push = " Correct this changeset as soon as possible, it potentially produces malicious behavior or contains inappropriate content." @@ -142,7 +138,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', **kwd ) ) - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -168,7 +164,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='deprecate', **kwd ) ) - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -390,7 +386,7 @@ kwd[ 'message' ] = 'You must be logged in to set email alerts.' kwd[ 'status' ] = 'error' del kwd[ 'operation' ] - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -421,7 +417,7 @@ kwd[ 'user_id' ] = trans.security.encode_id( repository.user.id ) else: # The user selected a repository revision which results in a refresh_on_change. - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', @@ -449,7 +445,7 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='deprecate', **kwd ) ) - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -478,7 +474,7 @@ self.repositories_by_user_grid.title = "Repositories owned by %s" % user.username kwd[ 'user_id' ] = user_id return self.repositories_by_user_grid( trans, **kwd ) - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: # The user selected a repository revision which results in a refresh_on_change. return trans.response.send_redirect( web.url_for( controller='repository', @@ -796,7 +792,7 @@ category_id = kwd.get( 'id', None ) category = suc.get_category( trans, category_id ) kwd[ 'f-Category.name' ] = category.name - selected_changeset_revision, repository = self.__get_repository_from_refresh_on_change( trans, **kwd ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) if repository: return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', @@ -811,28 +807,6 @@ async_compatible=False ) ] return self.valid_repository_grid( trans, **kwd ) - def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ): - options = [] - for user in trans.sa_session.query( trans.model.User ): - if user.username not in current_push_list: - options.append( user ) - return build_select_field( trans, - objs=options, - label_attr='username', - select_field_name='allow_push', - selected_value=selected_value, - refresh_on_change=False, - multiple=True ) - - def __change_repository_name_in_hgrc_file( self, hgrc_file, new_name ): - config = ConfigParser.ConfigParser() - config.read( hgrc_file ) - config.read( hgrc_file ) - config.set( 'web', 'name', new_name ) - new_file = open( hgrc_file, 'wb' ) - config.write( new_file ) - new_file.close() - @web.expose def check_for_updates( self, trans, **kwd ): """Handle a request from a local Galaxy instance.""" @@ -929,24 +903,6 @@ # Do all we can to eliminate spam. return trans.show_error_message( "You must be logged in to contact the owner of a repository." ) - def __create_hgrc_file( self, trans, repository ): - # At this point, an entry for the repository is required to be in the hgweb.config file so we can call repository.repo_path( trans.app ). - # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api. The hg - # purge extension purges all files and directories not being tracked by mercurial in the current repository. It'll remove unknown files - # and empty directories. This is not currently used because it is not supported in the mercurial API. - repo = hg.repository( suc.get_configured_ui(), path=repository.repo_path( trans.app ) ) - fp = repo.opener( 'hgrc', 'wb' ) - fp.write( '[paths]\n' ) - fp.write( 'default = .\n' ) - fp.write( 'default-push = .\n' ) - fp.write( '[web]\n' ) - fp.write( 'allow_push = %s\n' % repository.user.username ) - fp.write( 'name = %s\n' % repository.name ) - fp.write( 'push_ssl = false\n' ) - fp.write( '[extensions]\n' ) - fp.write( 'hgext.purge=' ) - fp.close() - @web.expose def create_repository( self, trans, **kwd ): message = kwd.get( 'message', '' ) @@ -968,7 +924,7 @@ repository_type = kwd.get( 'repository_type', rt_util.UNRESTRICTED ) if kwd.get( 'create_repository_button', False ): error = False - message = self.__validate_repository_name( name, trans.user ) + message = repository_maintenance_util.validate_repository_name( name, trans.user ) if message: error = True if not description: @@ -1002,7 +958,7 @@ lhs = "repos/%s/%s" % ( repository.user.username, repository.name ) trans.app.hgweb_config_manager.add_entry( lhs, repository_path ) # Create a .hg/hgrc file for the local repository - self.__create_hgrc_file( trans, repository ) + repository_maintenance_util.create_hgrc_file( trans, repository ) flush_needed = False if category_ids: # Create category associations @@ -1061,7 +1017,7 @@ repository, tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) if message: status = 'error' - tool_state = self.__new_state( trans, tool, invalid=False ) + tool_state = tool_util.new_state( trans, tool, invalid=False ) metadata = self.get_metadata( trans, repository_id, changeset_revision ) try: return trans.fill_template( "/webapps/tool_shed/repository/tool_form.mako", @@ -1176,7 +1132,11 @@ match_tuples = [] ok = True if tool_ids or tool_names or tool_versions: - ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, tool_versions=tool_versions ) + ok, match_tuples = search_util.search_repository_metadata( trans, + exact_matches_checked, + tool_ids=tool_ids, + tool_names=tool_names, + tool_versions=tool_versions ) if ok: kwd[ 'match_tuples' ] = match_tuples # Render the list view @@ -1195,7 +1155,7 @@ return self.install_matched_repository_grid( trans, **kwd ) else: kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ - ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) ) + ( common_util.stringify( tool_ids ), common_util.stringify( tool_names ), common_util.stringify( tool_versions ), str( exact_matches_checked ) ) self.matched_repository_grid.title = "Repositories with matching tools" return self.matched_repository_grid( trans, **kwd ) else: @@ -1203,9 +1163,9 @@ status = "error" exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/tool_shed/repository/find_tools.mako', - tool_id=self.__stringify( tool_ids ), - tool_name=self.__stringify( tool_names ), - tool_version=self.__stringify( tool_versions ), + tool_id=common_util.stringify( tool_ids ), + tool_name=common_util.stringify( tool_names ), + tool_version=common_util.stringify( tool_versions ), exact_matches_check_box=exact_matches_check_box, message=message, status=status ) @@ -1259,9 +1219,9 @@ match_tuples = [] ok = True if workflow_names: - ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names ) + ok, match_tuples = search_util.search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names ) else: - ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=[], all_workflows=True ) + ok, match_tuples = search_util.search_repository_metadata( trans, exact_matches_checked, workflow_names=[], all_workflows=True ) if ok: kwd[ 'match_tuples' ] = match_tuples if trans.webapp.name == 'galaxy': @@ -1279,7 +1239,7 @@ return self.install_matched_repository_grid( trans, **kwd ) else: kwd[ 'message' ] = "workflow name: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ - ( self.__stringify( workflow_names ), str( exact_matches_checked ) ) + ( common_util.stringify( workflow_names ), str( exact_matches_checked ) ) self.matched_repository_grid.title = "Repositories with matching workflows" return self.matched_repository_grid( trans, **kwd ) else: @@ -1290,7 +1250,7 @@ workflow_names = [] exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/tool_shed/repository/find_workflows.mako', - workflow_name=self.__stringify( workflow_names ), + workflow_name=common_util.stringify( workflow_names ), exact_matches_check_box=exact_matches_check_box, message=message, status=status ) @@ -1559,23 +1519,6 @@ return encoding_util.tool_shed_encode( repository_dependencies ) return '' - def __get_repository_from_refresh_on_change( self, trans, **kwd ): - # The changeset_revision_select_field in several grids performs a refresh_on_change which sends in request parameters like - # changeset_revison_1, changeset_revision_2, etc. One of the many select fields on the grid performed the refresh_on_change, - # so we loop through all of the received values to see which value is not the repository tip. If we find it, we know the - # refresh_on_change occurred and we have the necessary repository id and change set revision to pass on. - repository_id = None - v = None - for k, v in kwd.items(): - changeset_revision_str = 'changeset_revision_' - if k.startswith( changeset_revision_str ): - repository_id = trans.security.encode_id( int( k.lstrip( changeset_revision_str ) ) ) - repository = suc.get_repository_in_tool_shed( trans, repository_id ) - if repository.tip( trans.app ) != v: - return v, repository - # This should never be reached - raise an exception? - return v, None - @web.json def get_repository_information( self, trans, repository_ids, changeset_revisions, **kwd ): """ @@ -1792,53 +1735,6 @@ status = kwd.get( 'status', 'done' ) return trans.fill_template( '/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd ) - def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): - found = False - if tool_id and not tool_name and not tool_version: - tool_dict_tool_id = tool_dict[ 'id' ].lower() - found = ( tool_id == tool_dict_tool_id ) or \ - ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 ) - elif tool_name and not tool_id and not tool_version: - tool_dict_tool_name = tool_dict[ 'name' ].lower() - found = ( tool_name == tool_dict_tool_name ) or \ - ( not exact_matches_checked and tool_dict_tool_name.find( tool_name ) >= 0 ) - elif tool_version and not tool_id and not tool_name: - tool_dict_tool_version = tool_dict[ 'version' ].lower() - found = ( tool_version == tool_dict_tool_version ) or \ - ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 ) - elif tool_id and tool_name and not tool_version: - tool_dict_tool_id = tool_dict[ 'id' ].lower() - tool_dict_tool_name = tool_dict[ 'name' ].lower() - found = ( tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name ) or \ - ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) - elif tool_id and tool_version and not tool_name: - tool_dict_tool_id = tool_dict[ 'id' ].lower() - tool_dict_tool_version = tool_dict[ 'version' ].lower() - found = ( tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version ) or \ - ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_version.find( tool_version ) >= 0 ) - elif tool_version and tool_name and not tool_id: - tool_dict_tool_version = tool_dict[ 'version' ].lower() - tool_dict_tool_name = tool_dict[ 'name' ].lower() - found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ - ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) - elif tool_version and tool_name and tool_id: - tool_dict_tool_version = tool_dict[ 'version' ].lower() - tool_dict_tool_name = tool_dict[ 'name' ].lower() - tool_dict_tool_id = tool_dict[ 'id' ].lower() - found = ( tool_version == tool_dict_tool_version and \ - tool_name == tool_dict_tool_name and \ - tool_id == tool_dict_tool_id ) or \ - ( not exact_matches_checked and \ - tool_dict_tool_version.find( tool_version ) >= 0 and \ - tool_dict_tool_name.find( tool_name ) >= 0 and \ - tool_dict_tool_id.find( tool_id ) >= 0 ) - return found - - def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ): - workflow_dict_workflow_name = workflow_dict[ 'name' ].lower() - return ( workflow_name == workflow_dict_workflow_name ) or \ - ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 ) - @web.expose def index( self, trans, **kwd ): message = kwd.get( 'message', '' ) @@ -1908,7 +1804,7 @@ status = kwd.get( 'status', 'error' ) render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) repository, tool, error_message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) - tool_state = self.__new_state( trans, tool, invalid=True ) + tool_state = tool_util.new_state( trans, tool, invalid=True ) invalid_file_tups = [] if tool: invalid_file_tups = tool_util.check_tool_input_params( trans.app, @@ -1946,16 +1842,6 @@ message=message, status='error' ) ) - def __make_same_length( self, list1, list2 ): - # If either list is 1 item, we'll append to it until its length is the same as the other. - if len( list1 ) == 1: - for i in range( 1, len( list2 ) ): - list1.append( list1[ 0 ] ) - elif len( list2 ) == 1: - for i in range( 1, len( list1 ) ): - list2.append( list2[ 0 ] ) - return list1, list2 - @web.expose @web.require_login( "manage email alerts" ) def manage_email_alerts( self, trans, **kwd ): @@ -2035,7 +1921,7 @@ repository.long_description = long_description flush_needed = True if repository.times_downloaded == 0 and repo_name != repository.name: - message = self.__validate_repository_name( repo_name, user ) + message = repository_maintenance_util.validate_repository_name( repo_name, user ) if message: error = True else: @@ -2045,7 +1931,7 @@ trans.app.hgweb_config_manager.change_entry( old_lhs, new_lhs, repo_dir ) # Change the entry in the repository's hgrc file. hgrc_file = os.path.join( repo_dir, '.hg', 'hgrc' ) - self.__change_repository_name_in_hgrc_file( hgrc_file, repo_name ) + repository_maintenance_util.change_repository_name_in_hgrc_file( hgrc_file, repo_name ) repository.name = repo_name flush_needed = True elif repository.times_downloaded != 0 and repo_name != repository.name: @@ -2130,7 +2016,7 @@ current_allow_push_list = current_allow_push.split( ',' ) else: current_allow_push_list = [] - allow_push_select_field = self.__build_allow_push_select_field( trans, current_allow_push_list ) + allow_push_select_field = repository_maintenance_util.build_allow_push_select_field( trans, current_allow_push_list ) checked = alerts_checked or user.email in email_alerts alerts_check_box = CheckboxField( 'alerts', checked=checked ) changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, @@ -2248,28 +2134,6 @@ self.email_alerts_repository_grid.title = "Set email alerts for repository changes" return self.email_alerts_repository_grid( trans, **kwd ) - def __new_state( self, trans, tool, invalid=False ): - """ - Create a new `DefaultToolState` for this tool. It will not be initialized - with default values for inputs. - - Only inputs on the first page will be initialized unless `all_pages` is - True, in which case all inputs regardless of page are initialized. - """ - state = galaxy.tools.DefaultToolState() - state.inputs = {} - if invalid: - # We're attempting to display a tool in the tool shed that has been determined to have errors of some kind. - return state - inputs = tool.inputs_by_page[ 0 ] - context = ExpressionContext( state.inputs, parent=None ) - for input in inputs.itervalues(): - try: - state.inputs[ input.name ] = input.get_initial_value( trans, context ) - except: - state.inputs[ input.name ] = [] - return state - @web.json def open_folder( self, trans, folder_path ): # Avoid caching @@ -2420,106 +2284,6 @@ message=message, status=status ) - def __search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ): - for i, tool_id in enumerate( tool_ids ): - tool_name = tool_names[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - return match_tuples - - def __search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ): - for i, tool_id in enumerate( tool_ids ): - tool_version = tool_versions[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - return match_tuples - - def __search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ): - for i, tool_name in enumerate( tool_names ): - tool_version = tool_versions[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - return match_tuples - - def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ): - match_tuples = [] - ok = True - if tool_ids or tool_names or tool_versions: - for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.includes_tools == True ) \ - .join( trans.model.Repository ) \ - .filter( and_( trans.model.Repository.table.c.deleted == False, - trans.model.Repository.table.c.deprecated == False ) ): - metadata = repository_metadata.metadata - if metadata: - tools = metadata.get( 'tools', [] ) - for tool_dict in tools: - if tool_ids and not tool_names and not tool_versions: - for tool_id in tool_ids: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_names and not tool_ids and not tool_versions: - for tool_name in tool_names: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_versions and not tool_ids and not tool_names: - for tool_version in tool_versions: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_ids and tool_names and not tool_versions: - if len( tool_ids ) == len( tool_names ): - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - elif len( tool_ids ) == 1 or len( tool_names ) == 1: - tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - else: - ok = False - elif tool_ids and tool_versions and not tool_names: - if len( tool_ids ) == len( tool_versions ): - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - elif len( tool_ids ) == 1 or len( tool_versions ) == 1: - tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and not tool_ids: - if len( tool_versions ) == len( tool_names ): - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - elif len( tool_versions ) == 1 or len( tool_names ) == 1: - tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and tool_ids: - if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): - for i, tool_version in enumerate( tool_versions ): - tool_name = tool_names[ i ] - tool_id = tool_ids[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - else: - ok = False - elif workflow_names or all_workflows: - for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.includes_workflows == True ) \ - .join( trans.model.Repository ) \ - .filter( and_( trans.model.Repository.table.c.deleted == False, - trans.model.Repository.table.c.deprecated == False ) ): - metadata = repository_metadata.metadata - if metadata: - # metadata[ 'workflows' ] is a list of tuples where each contained tuple is - # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - if workflow_names: - workflow_tups = metadata.get( 'workflows', [] ) - workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ] - for workflow_dict in workflows: - for workflow_name in workflow_names: - if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif all_workflows: - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - return ok, match_tuples - @web.expose def select_files_to_delete( self, trans, id, **kwd ): message = kwd.get( 'message', '' ) @@ -2772,11 +2536,6 @@ action='sharable_owner', owner=owner ) ) - def __stringify( self, list ): - if list: - return ','.join( list ) - return '' - @web.expose def updated_changeset_revisions( self, trans, **kwd ): """ @@ -2806,24 +2565,6 @@ return changeset_hashes_str return '' - def __validate_repository_name( self, name, user ): - # Repository names must be unique for each user, must be at least four characters - # in length and must contain only lower-case letters, numbers, and the '_' character. - if name in [ 'None', None, '' ]: - return 'Enter the required repository name.' - if name in [ 'repos' ]: - return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name - for repository in user.active_repositories: - if repository.name == name: - return "You already have a repository named <b>%s</b>, so choose a different name." % name - if len( name ) < 4: - return "Repository names must be at least 4 characters in length." - if len( name ) > 80: - return "Repository names cannot be more than 80 characters in length." - if not( VALID_REPOSITORYNAME_RE.match( name ) ): - return "Repository names must contain only lower-case letters, numbers and underscore <b>_</b>." - return '' - @web.expose def view_changelog( self, trans, id, **kwd ): message = kwd.get( 'message', '' ) diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 lib/galaxy/webapps/tool_shed/util/common_util.py --- a/lib/galaxy/webapps/tool_shed/util/common_util.py +++ b/lib/galaxy/webapps/tool_shed/util/common_util.py @@ -25,3 +25,8 @@ trans.sa_session.add( item_rating ) trans.sa_session.flush() return item_rating + +def stringify( list ): + if list: + return ','.join( list ) + return '' diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 lib/tool_shed/util/repository_maintenance_util.py --- /dev/null +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -0,0 +1,75 @@ +import ConfigParser +import logging +import re +import tool_shed.util.shed_util_common as suc +from galaxy.web.form_builder import build_select_field + +from galaxy import eggs +eggs.require('mercurial') + +from mercurial import commands +from mercurial import hg +from mercurial import patch +from mercurial import ui + +log = logging.getLogger( __name__ ) + +VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) + +def build_allow_push_select_field( trans, current_push_list, selected_value='none' ): + options = [] + for user in trans.sa_session.query( trans.model.User ): + if user.username not in current_push_list: + options.append( user ) + return build_select_field( trans, + objs=options, + label_attr='username', + select_field_name='allow_push', + selected_value=selected_value, + refresh_on_change=False, + multiple=True ) + +def change_repository_name_in_hgrc_file( hgrc_file, new_name ): + config = ConfigParser.ConfigParser() + config.read( hgrc_file ) + config.read( hgrc_file ) + config.set( 'web', 'name', new_name ) + new_file = open( hgrc_file, 'wb' ) + config.write( new_file ) + new_file.close() + +def create_hgrc_file( trans, repository ): + # At this point, an entry for the repository is required to be in the hgweb.config file so we can call repository.repo_path( trans.app ). + # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api. The hg + # purge extension purges all files and directories not being tracked by mercurial in the current repository. It'll remove unknown files + # and empty directories. This is not currently used because it is not supported in the mercurial API. + repo = hg.repository( suc.get_configured_ui(), path=repository.repo_path( trans.app ) ) + fp = repo.opener( 'hgrc', 'wb' ) + fp.write( '[paths]\n' ) + fp.write( 'default = .\n' ) + fp.write( 'default-push = .\n' ) + fp.write( '[web]\n' ) + fp.write( 'allow_push = %s\n' % repository.user.username ) + fp.write( 'name = %s\n' % repository.name ) + fp.write( 'push_ssl = false\n' ) + fp.write( '[extensions]\n' ) + fp.write( 'hgext.purge=' ) + fp.close() + +def validate_repository_name( name, user ): + # Repository names must be unique for each user, must be at least four characters + # in length and must contain only lower-case letters, numbers, and the '_' character. + if name in [ 'None', None, '' ]: + return 'Enter the required repository name.' + if name in [ 'repos' ]: + return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name + for repository in user.active_repositories: + if repository.name == name: + return "You already have a repository named <b>%s</b>, so choose a different name." % name + if len( name ) < 4: + return "Repository names must be at least 4 characters in length." + if len( name ) > 80: + return "Repository names cannot be more than 80 characters in length." + if not( VALID_REPOSITORYNAME_RE.match( name ) ): + return "Repository names must contain only lower-case letters, numbers and underscore <b>_</b>." + return '' diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 lib/tool_shed/util/search_util.py --- /dev/null +++ b/lib/tool_shed/util/search_util.py @@ -0,0 +1,161 @@ +import logging +from galaxy.model.orm import and_ + +log = logging.getLogger( __name__ ) + +def in_tool_dict( tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): + found = False + if tool_id and not tool_name and not tool_version: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + found = ( tool_id == tool_dict_tool_id ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 ) + elif tool_name and not tool_id and not tool_version: + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_version and not tool_id and not tool_name: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + found = ( tool_version == tool_dict_tool_version ) or \ + ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 ) + elif tool_id and tool_name and not tool_version: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_id and tool_version and not tool_name: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + tool_dict_tool_version = tool_dict[ 'version' ].lower() + found = ( tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_version.find( tool_version ) >= 0 ) + elif tool_version and tool_name and not tool_id: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_version and tool_name and tool_id: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + tool_dict_tool_id = tool_dict[ 'id' ].lower() + found = ( tool_version == tool_dict_tool_version and \ + tool_name == tool_dict_tool_name and \ + tool_id == tool_dict_tool_id ) or \ + ( not exact_matches_checked and \ + tool_dict_tool_version.find( tool_version ) >= 0 and \ + tool_dict_tool_name.find( tool_name ) >= 0 and \ + tool_dict_tool_id.find( tool_id ) >= 0 ) + return found + +def in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): + workflow_dict_workflow_name = workflow_dict[ 'name' ].lower() + return ( workflow_name == workflow_dict_workflow_name ) or \ + ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 ) + +def make_same_length( list1, list2 ): + # If either list is 1 item, we'll append to it until its length is the same as the other. + if len( list1 ) == 1: + for i in range( 1, len( list2 ) ): + list1.append( list1[ 0 ] ) + elif len( list2 ) == 1: + for i in range( 1, len( list1 ) ): + list2.append( list2[ 0 ] ) + return list1, list2 + +def search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ): + for i, tool_id in enumerate( tool_ids ): + tool_name = tool_names[ i ] + if in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples + +def search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ): + for i, tool_id in enumerate( tool_ids ): + tool_version = tool_versions[ i ] + if in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples + +def search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ): + for i, tool_name in enumerate( tool_names ): + tool_version = tool_versions[ i ] + if in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples + +def search_repository_metadata( trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ): + match_tuples = [] + ok = True + if tool_ids or tool_names or tool_versions: + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.includes_tools == True ) \ + .join( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ): + metadata = repository_metadata.metadata + if metadata: + tools = metadata.get( 'tools', [] ) + for tool_dict in tools: + if tool_ids and not tool_names and not tool_versions: + for tool_id in tool_ids: + if in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_names and not tool_ids and not tool_versions: + for tool_name in tool_names: + if in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_versions and not tool_ids and not tool_names: + for tool_version in tool_versions: + if in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_ids and tool_names and not tool_versions: + if len( tool_ids ) == len( tool_names ): + match_tuples = search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + elif len( tool_ids ) == 1 or len( tool_names ) == 1: + tool_ids, tool_names = make_same_length( tool_ids, tool_names ) + match_tuples = search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + else: + ok = False + elif tool_ids and tool_versions and not tool_names: + if len( tool_ids ) == len( tool_versions ): + match_tuples = search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + elif len( tool_ids ) == 1 or len( tool_versions ) == 1: + tool_ids, tool_versions = make_same_length( tool_ids, tool_versions ) + match_tuples = search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and not tool_ids: + if len( tool_versions ) == len( tool_names ): + match_tuples = search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + elif len( tool_versions ) == 1 or len( tool_names ) == 1: + tool_versions, tool_names = make_same_length( tool_versions, tool_names ) + match_tuples = search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and tool_ids: + if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): + for i, tool_version in enumerate( tool_versions ): + tool_name = tool_names[ i ] + tool_id = tool_ids[ i ] + if in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + ok = False + elif workflow_names or all_workflows: + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.includes_workflows == True ) \ + .join( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ): + metadata = repository_metadata.metadata + if metadata: + # metadata[ 'workflows' ] is a list of tuples where each contained tuple is + # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + if workflow_names: + workflow_tups = metadata.get( 'workflows', [] ) + workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ] + for workflow_dict in workflows: + for workflow_name in workflow_names: + if in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif all_workflows: + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return ok, match_tuples diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -804,6 +804,23 @@ contents.sort() return contents +def get_repository_from_refresh_on_change( trans, **kwd ): + # The changeset_revision_select_field in several grids performs a refresh_on_change which sends in request parameters like + # changeset_revison_1, changeset_revision_2, etc. One of the many select fields on the grid performed the refresh_on_change, + # so we loop through all of the received values to see which value is not the repository tip. If we find it, we know the + # refresh_on_change occurred and we have the necessary repository id and change set revision to pass on. + repository_id = None + v = None + for k, v in kwd.items(): + changeset_revision_str = 'changeset_revision_' + if k.startswith( changeset_revision_str ): + repository_id = trans.security.encode_id( int( k.lstrip( changeset_revision_str ) ) ) + repository = suc.get_repository_in_tool_shed( trans, repository_id ) + if repository.tip( trans.app ) != v: + return v, repository + # This should never be reached - raise an exception? + return v, None + def get_repository_in_tool_shed( trans, id ): """Get a repository on the tool shed side from the database via id.""" return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 8059779d2a6ca853d43c5831fc7cfb70b65d6e55 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -11,6 +11,7 @@ from galaxy.tools import parameters from galaxy.tools.parameters import dynamic_options from galaxy.tools.search import ToolBoxSearch +from galaxy.util.expressions import ExpressionContext from galaxy.web.form_builder import SelectField from tool_shed.util import xml_util from galaxy.tools.actions.upload import UploadToolAction @@ -890,6 +891,22 @@ pass return tool, message +def new_state( trans, tool, invalid=False ): + """Create a new `DefaultToolState` for the received tool. Only inputs on the first page will be initialized.""" + state = galaxy.tools.DefaultToolState() + state.inputs = {} + if invalid: + # We're attempting to display a tool in the tool shed that has been determined to have errors, so is invalid. + return state + inputs = tool.inputs_by_page[ 0 ] + context = ExpressionContext( state.inputs, parent=None ) + for input in inputs.itervalues(): + try: + state.inputs[ input.name ] = input.get_initial_value( trans, context ) + except: + state.inputs[ input.name ] = [] + return state + def panel_entry_per_tool( tool_section_dict ): # Return True if tool_section_dict looks like this. # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the ability to display tool form components that are inside conditionals for tools contained in repositories in the tool shed. Also fix tool shed functional tests I recently broke sue to messing with rendering readme files in tool shed repositories.
by commits-noreply＠bitbucket.org 24 Jul '13

24 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2abd0819d354/ Changeset: 2abd0819d354 User: greg Date: 2013-07-24 22:36:52 Summary: Add the ability to display tool form components that are inside conditionals for tools contained in repositories in the tool shed. Also fix tool shed functional tests I recently broke sue to messing with rendering readme files in tool shed repositories. Affected #: 3 files diff -r ab4582614f70e35bb1023f73d4d2dc409225bc21 -r 2abd0819d354d3d11182297c7206408d299f0d16 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -11,6 +11,7 @@ from galaxy import util from galaxy import web from galaxy.util.odict import odict +from galaxy.util.expressions import ExpressionContext from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import CheckboxField from galaxy.web.form_builder import build_select_field @@ -1060,7 +1061,7 @@ repository, tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) if message: status = 'error' - tool_state = self.__new_state( trans ) + tool_state = self.__new_state( trans, tool, invalid=False ) metadata = self.get_metadata( trans, repository_id, changeset_revision ) try: return trans.fill_template( "/webapps/tool_shed/repository/tool_form.mako", @@ -1907,7 +1908,7 @@ status = kwd.get( 'status', 'error' ) render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) repository, tool, error_message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) - tool_state = self.__new_state( trans ) + tool_state = self.__new_state( trans, tool, invalid=True ) invalid_file_tups = [] if tool: invalid_file_tups = tool_util.check_tool_input_params( trans.app, @@ -2247,7 +2248,7 @@ self.email_alerts_repository_grid.title = "Set email alerts for repository changes" return self.email_alerts_repository_grid( trans, **kwd ) - def __new_state( self, trans, all_pages=False ): + def __new_state( self, trans, tool, invalid=False ): """ Create a new `DefaultToolState` for this tool. It will not be initialized with default values for inputs. @@ -2257,6 +2258,16 @@ """ state = galaxy.tools.DefaultToolState() state.inputs = {} + if invalid: + # We're attempting to display a tool in the tool shed that has been determined to have errors of some kind. + return state + inputs = tool.inputs_by_page[ 0 ] + context = ExpressionContext( state.inputs, parent=None ) + for input in inputs.itervalues(): + try: + state.inputs[ input.name ] = input.get_initial_value( trans, context ) + except: + state.inputs[ input.name ] = [] return state @web.json diff -r ab4582614f70e35bb1023f73d4d2dc409225bc21 -r 2abd0819d354d3d11182297c7206408d299f0d16 templates/webapps/tool_shed/repository/tool_form.mako --- a/templates/webapps/tool_shed/repository/tool_form.mako +++ b/templates/webapps/tool_shed/repository/tool_form.mako @@ -35,8 +35,11 @@ %elif input.type == "conditional": %if tool_state.items(): <% - group_state = tool_state[input.name][0] - current_case = group_state['__current_case__'] + try: + group_state = tool_state[ input.name ][ 0 ] + except Exception, e: + group_state = tool_state[ input.name ] + current_case = group_state[ '__current_case__' ] group_prefix = prefix + input.name + "|" %> %if input.value_ref_in_group: @@ -120,7 +123,7 @@ <div class="toolFormBody"><form id="tool_form" name="tool_form" action="" method="get"><input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> - ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, "" )} + ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, "" )} </form></div></div> diff -r ab4582614f70e35bb1023f73d4d2dc409225bc21 -r 2abd0819d354d3d11182297c7206408d299f0d16 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -151,7 +151,7 @@ commit_message="Uploaded filtering.txt", strings_displayed=[], strings_not_displayed=[] ) - self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) def test_0055_upload_filtering_test_data( self ): '''Upload filtering test data.''' @@ -219,19 +219,19 @@ commit_message="Uploaded readme.txt", strings_displayed=[], strings_not_displayed=[] ) - self.display_manage_repository_page( repository, strings_displayed=[ 'This is a readme file.' ] ) + self.display_manage_repository_page( repository, strings_displayed=[ 'This is a readme file.' ] ) # Verify that there is a different readme file for each metadata revision. metadata_revisions = self.get_repository_metadata_revisions( repository ) self.display_manage_repository_page( repository, - strings_displayed=[ 'Readme file for filtering 1.1.0', - 'This is a readme file.' ] ) + strings_displayed=[ 'Readme file for filtering 1.1.0', + 'This is a readme file.' ] ) def test_0075_delete_readme_txt_file( self ): '''Delete the readme.txt file.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.delete_files_from_repository( repository, filenames=[ 'readme.txt' ] ) self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=2 ) - self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) def test_0080_search_for_valid_filter_tool( self ): '''Search for the filtering tool by tool ID, name, and version.''' @@ -335,7 +335,7 @@ commit_message="Uploaded new readme.txt with invalid ascii characters.", strings_displayed=[], strings_not_displayed=[] ) - self.display_manage_repository_page( repository, strings_displayed=[ 'These characters should not' ] ) + self.display_manage_repository_page( repository, strings_displayed=[ 'These characters should not' ] ) def test_0130_verify_handling_of_invalid_characters( self ): '''Load the above changeset in the change log and confirm that there is no server error displayed.''' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Tool shed functional tests for repairing an installed repository.
by commits-noreply＠bitbucket.org 24 Jul '13

24 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ab4582614f70/ Changeset: ab4582614f70 User: Dave Bouvier Date: 2013-07-24 21:19:38 Summary: Tool shed functional tests for repairing an installed repository. Affected #: 2 files diff -r b42dfe74e237ea7f9c77059e427db92d9859bc67 -r ab4582614f70e35bb1023f73d4d2dc409225bc21 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -984,6 +984,12 @@ self.visit_url( url ) self.check_for_strings( [ 'All repository metadata has been reset.' ] ) + def repair_installed_repository( self, repository ): + repository_id = self.security.encode_id( repository.id ) + url = '/admin_toolshed/repair_repository?id=%s' % repository_id + self.visit_galaxy_url( url ) + self.submit_form( 'repair_repository', 'repair_repository_button' ) + def review_repository( self, repository, review_contents_dict, user=None, changeset_revision=None ): strings_displayed = [] strings_not_displayed = [] diff -r b42dfe74e237ea7f9c77059e427db92d9859bc67 -r ab4582614f70e35bb1023f73d4d2dc409225bc21 test/tool_shed/functional/test_1430_repair_installed_repository.py --- /dev/null +++ b/test/tool_shed/functional/test_1430_repair_installed_repository.py @@ -0,0 +1,180 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import tool_shed.base.test_db_util as test_db_util + +import logging +log = logging.getLogger( __name__ ) + +category_name = 'Test 1430 Repair installed repository' +category_description = 'Test script 1430 for repairing an installed repository.' +filter_repository_name = 'filter_1430' +column_repository_name = 'column_1430' +filter_repository_description = "Galaxy's filter tool for test 1430" +column_repository_description = 'Add a value as a new column' +filter_repository_long_description = '%s: %s' % ( filter_repository_name, filter_repository_description ) +column_repository_long_description = '%s: %s' % ( column_repository_name, column_repository_description ) + +''' +In the Tool Shed: + +1) Create and populate the filter_1430 repository + +2) Create and populate the column_1430 repository + +3) Upload a repository_dependencies.xml file to the column_1430 repository that creates a repository dependency on the filter_1430 repository. + +In Galaxy: + +1) Install the column_1430 repository, making sure to check the checkbox to Handle repository dependencies so that the filter + repository is also installed. Make sure to install the repositories in a specified section of the tool panel. + +2) Uninstall the filter_1430 repository. + +3) Repair the column_1430 repository. + +4) Make sure the filter_1430 repository is reinstalled and the tool is loaded into the tool panel in the same section specified in step 1. +''' + +class TestRepairRepository( ShedTwillTestCase ): + '''Test repairing an installed repository.''' + + def test_0000_initiate_users_and_category( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + test_user_2 = test_db_util.get_user( common.test_user_2_email ) + assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email + test_user_2_private_role = test_db_util.get_private_role( test_user_2 ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + + def test_0005_create_filter_repository( self ): + '''Create and populate the filter_1430 repository.''' + ''' + This is step 1 - Create and populate the filter_1430 repository. + + This repository will be depended on by the column_1430 repository. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=filter_repository_name, + description=filter_repository_description, + long_description=filter_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='filtering/filtering_1.1.0.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Populate filter_1430 with version 1.1.0.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_create_column_repository( self ): + '''Create and populate the column_1430 repository.''' + ''' + This is step 2 - Create and populate the column_1430 repository. + + This repository will depend on the filter_1430 repository. + ''' + category = test_db_util.get_category_by_name( category_name ) + repository = self.get_or_create_repository( name=column_repository_name, + description=column_repository_description, + long_description=column_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='column_maker/column_maker.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Populate column_1430 with tool definitions.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0015_create_repository_dependency( self ): + '''Create a dependency on filter_1430.''' + ''' + This is step 3 - Upload a repository_dependencies.xml file to the column_1430 repository that creates a repository + dependency on the filter_1430 repository. + ''' + column_repository = test_db_util.get_repository_by_name_and_owner( 'column_1430', common.test_user_1_name ) + filter_repository = test_db_util.get_repository_by_name_and_owner( 'filter_1430', common.test_user_1_name ) + tool_shed_url = self.url + name = filter_repository.name + owner = filter_repository.user.username + changeset_revision = self.get_repository_tip( filter_repository ) + repository_dependency_tuple = ( tool_shed_url, name, owner, changeset_revision ) + filepath = self.generate_temp_path( '1430_repository_dependency' ) + self.create_repository_dependency( column_repository, [ repository_dependency_tuple ], filepath=filepath ) + + def test_0020_install_column_repository( self ): + '''Install the column_1430 repository into Galaxy.''' + ''' + This is step 1 (galaxy side) - Install the column_1430 repository, making sure to check the checkbox to + handle repository dependencies so that the filter_1430 repository is also installed. Make sure to install + the repositories in a specified section of the tool panel. + ''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + post_submit_strings_displayed = [ 'column_1430', 'filter_1430' ] + self.install_repository( 'column_1430', + common.test_user_1_name, + category_name, + new_tool_panel_section='repair', + post_submit_strings_displayed=post_submit_strings_displayed, + install_tool_dependencies=False, + install_repository_dependencies=True ) + + def test_0025_uninstall_filter_repository( self ): + '''Uninstall the filter_1430 repository from Galaxy.''' + ''' + This is step 2 - Uninstall the filter_1430 repository. + ''' + installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filter_1430', common.test_user_1_name ) + self.uninstall_repository( installed_repository, remove_from_disk=True ) + strings_not_displayed = [ 'filter_1430', + "Galaxy's filter tool for test 1430", + installed_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) + + def test_0030_repair_column_repository( self ): + '''Repair the column_1430 repository.''' + ''' + This is step 3 - Repair the column_1430 repository. + ''' + column_repository = test_db_util.get_installed_repository_by_name_owner( 'column_1430', common.test_user_1_name ) + self.repair_installed_repository( column_repository ) + + def test_0035_verify_tool_panel_section( self ): + '''Check the tool panel section after repairing.''' + ''' + This is step 4 - Make sure the filter_1430 repository is reinstalled and the tool is loaded into the tool panel + in the same section specified in step 1. + ''' + filter_repository = test_db_util.get_installed_repository_by_name_owner( 'filter_1430', common.test_user_1_name ) + strings_displayed = [ 'filter_1430', + "Galaxy's filter tool for test 1430", + filter_repository.installed_changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + # Uninstall the filter repository again, so that the tool panel section metadata gets populated. + self.uninstall_repository( filter_repository, remove_from_disk=True ) + test_db_util.ga_refresh( filter_repository ) + tool_panel_section_metadata = filter_repository.metadata[ 'tool_panel_section' ] + for tool_id in tool_panel_section_metadata: + for panel_section in tool_panel_section_metadata[ tool_id ]: + assert panel_section[ 'name' ] == 'repair', 'Tool %s in tool panel section %s after repair, expected %s.' % \ + ( tool_id, panel_section[ 'name' ], 'repair' ) + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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