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commit/galaxy-central: jgoecks: Python 2.5 compatibility fix.
by Bitbucket 13 Feb '13

13 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b6241599d1d0/ changeset: b6241599d1d0 user: jgoecks date: 2013-02-13 19:19:55 summary: Python 2.5 compatibility fix. affected #: 1 file diff -r a6710d64e2d8081e07050696e377c5f864dd1f9f -r b6241599d1d0bbb4b9ba670bde9fbb421ef6c396 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -244,7 +244,7 @@ separator_char = (lambda c: '<TAB>' if c == '\t' else c)(self.separator) rval = [] - for i, line in enumerate( reader, start=1 ): + for i, line in enumerate( reader ): if line.lstrip().startswith( self.comment_char ): continue line = line.rstrip( "\n\r" ) @@ -255,7 +255,7 @@ else: log.warn( "Line %i in tool data table '%s' is invalid (HINT: " "'%s' characters must be used to separate fields):\n%s" - % ( i, self.name, separator_char, line ) ) + % ( ( i + 1 ), self.name, separator_char, line ) ) return rval def get_entry( self, query_attr, query_val, return_attr ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 13 Feb '13

13 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c8b7dfb1e76d/ changeset: c8b7dfb1e76d branch: bugfixes user: Bjoern Gruening date: 2013-02-09 16:48:20 summary: Display the toolshed tools in the workflow search. affected #: 1 file diff -r 506484344db3a370f8ae24096041d38557d1967e -r c8b7dfb1e76d45532a339592f72c57918fbe6ba6 templates/webapps/galaxy/workflow/editor.mako --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -93,12 +93,12 @@ $(".toolSectionWrapper").find(".toolTitle").hide(); if ( data.length != 0 ) { // Map tool ids to element ids and join them. - var s = $.map( data, function( n, i ) { return "#link-" + n; } ).join( ", " ); + var s = $.map( data, function( n, i ) { return "link-" + n; } ); // First pass to show matching tools and their parents. - $(s).each( function() { + $(s).each( function(index,id) { // Add class to denote match. - $(this).parent().addClass("search_match"); - $(this).parent().show().parent().parent().show().parent().show(); + $("[id='"+id+"']").parent().addClass("search_match"); + $("[id='"+id+"']").parent().show().parent().parent().show().parent().show(); }); // Hide labels that have no visible children. $(".toolPanelLabel").each( function() { https://bitbucket.org/galaxy/galaxy-central/commits/a6710d64e2d8/ changeset: a6710d64e2d8 user: dannon date: 2013-02-13 19:15:00 summary: Merged in BjoernGruening/galaxy-central-bgruening/bugfixes (pull request #120) Display the toolshed tools in the workflow search. affected #: 1 file diff -r 0ea9f5196fde94701cf2ec8404e9e33e53c51d0e -r a6710d64e2d8081e07050696e377c5f864dd1f9f templates/webapps/galaxy/workflow/editor.mako --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -93,12 +93,12 @@ $(".toolSectionWrapper").find(".toolTitle").hide(); if ( data.length != 0 ) { // Map tool ids to element ids and join them. - var s = $.map( data, function( n, i ) { return "#link-" + n; } ).join( ", " ); + var s = $.map( data, function( n, i ) { return "link-" + n; } ); // First pass to show matching tools and their parents. - $(s).each( function() { + $(s).each( function(index,id) { // Add class to denote match. - $(this).parent().addClass("search_match"); - $(this).parent().show().parent().parent().show().parent().show(); + $("[id='"+id+"']").parent().addClass("search_match"); + $("[id='"+id+"']").parent().show().parent().parent().show().parent().show(); }); // Hide labels that have no visible children. $(".toolPanelLabel").each( function() { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 13 Feb '13

13 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c8b7dfb1e76d/ changeset: c8b7dfb1e76d branch: bugfixes user: Bjoern Gruening date: 2013-02-09 16:48:20 summary: Display the toolshed tools in the workflow search. affected #: 1 file diff -r 506484344db3a370f8ae24096041d38557d1967e -r c8b7dfb1e76d45532a339592f72c57918fbe6ba6 templates/webapps/galaxy/workflow/editor.mako --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -93,12 +93,12 @@ $(".toolSectionWrapper").find(".toolTitle").hide(); if ( data.length != 0 ) { // Map tool ids to element ids and join them. - var s = $.map( data, function( n, i ) { return "#link-" + n; } ).join( ", " ); + var s = $.map( data, function( n, i ) { return "link-" + n; } ); // First pass to show matching tools and their parents. - $(s).each( function() { + $(s).each( function(index,id) { // Add class to denote match. - $(this).parent().addClass("search_match"); - $(this).parent().show().parent().parent().show().parent().show(); + $("[id='"+id+"']").parent().addClass("search_match"); + $("[id='"+id+"']").parent().show().parent().parent().show().parent().show(); }); // Hide labels that have no visible children. $(".toolPanelLabel").each( function() { https://bitbucket.org/galaxy/galaxy-central/commits/a6710d64e2d8/ changeset: a6710d64e2d8 user: dannon date: 2013-02-13 19:15:00 summary: Merged in BjoernGruening/galaxy-central-bgruening/bugfixes (pull request #120) Display the toolshed tools in the workflow search. affected #: 1 file diff -r 0ea9f5196fde94701cf2ec8404e9e33e53c51d0e -r a6710d64e2d8081e07050696e377c5f864dd1f9f templates/webapps/galaxy/workflow/editor.mako --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -93,12 +93,12 @@ $(".toolSectionWrapper").find(".toolTitle").hide(); if ( data.length != 0 ) { // Map tool ids to element ids and join them. - var s = $.map( data, function( n, i ) { return "#link-" + n; } ).join( ", " ); + var s = $.map( data, function( n, i ) { return "link-" + n; } ); // First pass to show matching tools and their parents. - $(s).each( function() { + $(s).each( function(index,id) { // Add class to denote match. - $(this).parent().addClass("search_match"); - $(this).parent().show().parent().parent().show().parent().show(); + $("[id='"+id+"']").parent().addClass("search_match"); + $("[id='"+id+"']").parent().show().parent().parent().show().parent().show(); }); // Hide labels that have no visible children. $(".toolPanelLabel").each( function() { 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: carlfeberhard: Patch base.less for select2-container, min-width; Fix .hgignore to handle new static/style path
by Bitbucket 13 Feb '13

13 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0ea9f5196fde/ changeset: 0ea9f5196fde user: carlfeberhard date: 2013-02-13 19:12:33 summary: Patch base.less for select2-container, min-width; Fix .hgignore to handle new static/style path affected #: 3 files diff -r 06b9f3ddce047c8db70e892732441a35cc91b241 -r 0ea9f5196fde94701cf2ec8404e9e33e53c51d0e .hgignore --- a/.hgignore +++ b/.hgignore @@ -79,7 +79,7 @@ # CSS build artifacts. */variables.less -static/june_2007_style/blue/base_sprites.less +static/style/blue/base_sprites.less # Testing selenium-server.jar diff -r 06b9f3ddce047c8db70e892732441a35cc91b241 -r 0ea9f5196fde94701cf2ec8404e9e33e53c51d0e static/style/base.less --- a/static/style/base.less +++ b/static/style/base.less @@ -5,6 +5,10 @@ @import "fontawesome/font-awesome.less"; @import "select2.less"; +/* fix for zero width select2 - remove when fixed there */ +.select2-container { + min-width: 256px; +} // Mixins diff -r 06b9f3ddce047c8db70e892732441a35cc91b241 -r 0ea9f5196fde94701cf2ec8404e9e33e53c51d0e static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -886,7 +886,8 @@ .select2-result-selectable .select2-match,.select2-result-unselectable .select2-result-selectable .select2-match{text-decoration:underline;} .select2-result-unselectable .select2-match{text-decoration:none;} .select2-offscreen{position:absolute;left:-10000px;} -@media only screen and (-webkit-min-device-pixel-ratio:1.5){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice div b{background-image:url(select2x2.png) !important;background-repeat:no-repeat !important;background-size:60px 40px !important;} .select2-search input{background-position:100% -21px !important;}}.unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;} +@media only screen and (-webkit-min-device-pixel-ratio:1.5){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice div b{background-image:url(select2x2.png) !important;background-repeat:no-repeat !important;background-size:60px 40px !important;} .select2-search input{background-position:100% -21px !important;}}.select2-container{min-width:256px;} +.unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;} .parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%;} .clear{*zoom:1;}.clear:before,.clear:after{display:table;content:"";line-height:0;} .clear:after{clear:both;} @@ -1078,7 +1079,7 @@ .action-button [class^="fa-icon-"].fa-icon-spin.icon-large,.action-button [class*=" fa-icon-"].fa-icon-spin.icon-large{height:.75em;} a.action-button{text-decoration:none;} .action-button>img{vertical-align:middle;} -.action-button:active{background-image:none;outline:0;-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);color:inherit;} +.action-button:active{color:inherit;} .menubutton{*display:inline;*zoom:1;padding:4px 12px;margin-bottom:0;font-size:12px;line-height:16px;text-align:center;vertical-align:middle;color:#333333;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(to bottom, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe6e6e6', GradientType=0);border-color:#e6e6e6 #e6e6e6 #bfbfbf;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);*background-color:#e6e6e6;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);border:1px solid #999999;*border:0;border-bottom-color:#808080;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;*margin-left:.3em;-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);border-color:#c5c5c5;border-color:rgba(0, 0, 0, 0.15) rgba(0, 0, 0, 0.15) rgba(0, 0, 0, 0.25);padding:2px 10px 2px;border-color:#999999;border-color:rgba(0, 0, 0, 0.4) rgba(0, 0, 0, 0.4) rgba(0, 0, 0, 0.4);display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;}.menubutton:hover,.menubutton:active,.menubutton.active,.menubutton.disabled,.menubutton[disabled]{color:#333333;background-color:#e6e6e6;*background-color:#d9d9d9;} .menubutton:active,.menubutton.active{background-color:#cccccc \9;} .menubutton:hover,.menubutton:active,.menubutton.active,.menubutton.disabled,.menubutton[disabled]{color:#333333;background-color:#e6e6e6;*background-color:#d9d9d9;} @@ -1092,7 +1093,7 @@ .menubutton [class^="fa-icon-"],.menubutton [class*=" fa-icon-"]{display:inline;line-height:.6em;}.menubutton [class^="fa-icon-"].fa-icon-spin,.menubutton [class*=" fa-icon-"].fa-icon-spin{display:inline-block;} .menubutton [class^="fa-icon-"].pull-left.fa-icon-2x,.menubutton [class*=" fa-icon-"].pull-left.fa-icon-2x,.menubutton [class^="fa-icon-"].pull-right.fa-icon-2x,.menubutton [class*=" fa-icon-"].pull-right.fa-icon-2x{margin-top:.35em;} .menubutton [class^="fa-icon-"].fa-icon-spin.icon-large,.menubutton [class*=" fa-icon-"].fa-icon-spin.icon-large{height:.75em;} -.menubutton:active{background-image:none;outline:0;-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);color:inherit;} +.menubutton:active{color:inherit;} .menubutton:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} .menubutton a{text-decoration:none;} .menubutton .label,.menubutton>label{position:relative;display:inline-block;border-right:none;text-decoration:none;text-align:left;max-height:32px;line-height:16px;overflow:hidden;text-overflow:ellipsis;} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix tool shed functional test that uploaded a tar archive without properly setting the option to not remove files from the repository that are not included in the uploaded archive. This resulted in setting metadata on the repository after upload in such a way that functional tests were not properly testing behavior.
by Bitbucket 13 Feb '13

13 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/06b9f3ddce04/ changeset: 06b9f3ddce04 user: greg date: 2013-02-13 18:40:11 summary: Fix tool shed functional test that uploaded a tar archive without properly setting the option to not remove files from the repository that are not included in the uploaded archive. This resulted in setting metadata on the repository after upload in such a way that functional tests were not properly testing behavior. affected #: 1 file diff -r 6b10699dc0950691097400e83fa6b51e35501e6f -r 06b9f3ddce047c8db70e892732441a35cc91b241 test/tool_shed/functional/test_0400_repository_component_reviews.py --- a/test/tool_shed/functional/test_0400_repository_component_reviews.py +++ b/test/tool_shed/functional/test_0400_repository_component_reviews.py @@ -452,7 +452,10 @@ """ repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) user = test_db_util.get_user( common.test_user_2_email ) - self.upload_file( repository, 'filtering/filtering_test_data.tar', commit_message="Uploaded test data." ) + self.upload_file( repository, + 'filtering/filtering_test_data.tar', + commit_message="Uploaded test data.", + remove_repo_files_not_in_tar='No' ) def test_0110_review_new_changeset_functional_tests( self ): '''Update the filtering repository's readme component review to reflect the presence of the readme file.''' """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 13 Feb '13

13 Feb '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/91c6fa5712b5/ changeset: 91c6fa5712b5 user: jmchilton date: 2013-02-10 18:13:51 summary: Add optional "upload" attribute to tool definitions. When extracting workflows, such tools are treated as inputs. This eliminates the need for the hack of hardcoding 'upload1' in tools.py and allows multiple upload tools to exist and function properly when extracting workflows. affected #: 2 files diff -r 506484344db3a370f8ae24096041d38557d1967e -r 91c6fa5712b5eaac805b576418de699e216fa384 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1085,7 +1085,7 @@ if requirements_elem: self.parse_requirements( requirements_elem ) # Determine if this tool can be used in workflows - self.is_workflow_compatible = self.check_workflow_compatible() + self.is_workflow_compatible = self.check_workflow_compatible(root) # Trackster configuration. trackster_conf = root.find( "trackster_conf" ) if trackster_conf is not None: @@ -1653,7 +1653,7 @@ version = requirement_elem.get( "version", None ) requirement = ToolRequirement( name=name, type=type, version=version ) self.requirements.append( requirement ) - def check_workflow_compatible( self ): + def check_workflow_compatible( self, root ): """ Determine if a tool can be used in workflows. External tools and the upload tool are currently not supported by workflows. @@ -1666,9 +1666,7 @@ # right now if self.tool_type.startswith( 'data_source' ): return False - # HACK: upload is (as always) a special case becuase file parameters - # can't be persisted. - if self.id == "upload1": + if util.string_as_bool( root.get( "upload", "False" ) ): return False # TODO: Anyway to capture tools that dynamically change their own # outputs? diff -r 506484344db3a370f8ae24096041d38557d1967e -r 91c6fa5712b5eaac805b576418de699e216fa384 tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -1,6 +1,6 @@ <?xml version="1.0"?> -<tool name="Upload File" id="upload1" version="1.1.3"> +<tool name="Upload File" id="upload1" version="1.1.3" upload="true"><description> from your computer </description> https://bitbucket.org/galaxy/galaxy-central/commits/46b01a48a40d/ changeset: 46b01a48a40d user: jmchilton date: 2013-02-13 17:45:56 summary: Based on input from natefoo, replace root tool tag "upload" with inverse tag "workflow_compatible". Adjust logic in tools module accordingly. affected #: 2 files diff -r 91c6fa5712b5eaac805b576418de699e216fa384 -r 46b01a48a40d70ec5d5fa9c3a21a3e2dec4cee24 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1666,7 +1666,7 @@ # right now if self.tool_type.startswith( 'data_source' ): return False - if util.string_as_bool( root.get( "upload", "False" ) ): + if not util.string_as_bool( root.get( "workflow_compatible", "True" ) ): return False # TODO: Anyway to capture tools that dynamically change their own # outputs? diff -r 91c6fa5712b5eaac805b576418de699e216fa384 -r 46b01a48a40d70ec5d5fa9c3a21a3e2dec4cee24 tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -1,6 +1,6 @@ <?xml version="1.0"?> -<tool name="Upload File" id="upload1" version="1.1.3" upload="true"> +<tool name="Upload File" id="upload1" version="1.1.3" workflow_compatible="false"><description> from your computer </description> https://bitbucket.org/galaxy/galaxy-central/commits/6b10699dc095/ changeset: 6b10699dc095 user: natefoo date: 2013-02-13 17:51:56 summary: Merged in jmchilton/galaxy-central-allow-additional-upload-tools (pull request #122) Add optional "upload" attribute to tool definitions. affected #: 2 files diff -r c19fa5da36cc51fd5ee6005ed801a7e2c9aba229 -r 6b10699dc0950691097400e83fa6b51e35501e6f lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1097,7 +1097,7 @@ if requirements_elem: self.parse_requirements( requirements_elem ) # Determine if this tool can be used in workflows - self.is_workflow_compatible = self.check_workflow_compatible() + self.is_workflow_compatible = self.check_workflow_compatible(root) # Trackster configuration. trackster_conf = root.find( "trackster_conf" ) if trackster_conf is not None: @@ -1665,7 +1665,7 @@ version = requirement_elem.get( "version", None ) requirement = ToolRequirement( name=name, type=type, version=version ) self.requirements.append( requirement ) - def check_workflow_compatible( self ): + def check_workflow_compatible( self, root ): """ Determine if a tool can be used in workflows. External tools and the upload tool are currently not supported by workflows. @@ -1678,9 +1678,7 @@ # right now if self.tool_type.startswith( 'data_source' ): return False - # HACK: upload is (as always) a special case becuase file parameters - # can't be persisted. - if self.id == "upload1": + if not util.string_as_bool( root.get( "workflow_compatible", "True" ) ): return False # TODO: Anyway to capture tools that dynamically change their own # outputs? diff -r c19fa5da36cc51fd5ee6005ed801a7e2c9aba229 -r 6b10699dc0950691097400e83fa6b51e35501e6f tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -1,6 +1,6 @@ <?xml version="1.0"?> -<tool name="Upload File" id="upload1" version="1.1.3"> +<tool name="Upload File" id="upload1" version="1.1.3" workflow_compatible="false"><description> from your computer </description> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Improved documentation in bowtie2 loc file.
by Bitbucket 13 Feb '13

13 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c19fa5da36cc/ changeset: c19fa5da36cc user: jgoecks date: 2013-02-13 17:04:54 summary: Improved documentation in bowtie2 loc file. affected #: 1 file diff -r 7bf8f6a1da9c7d6148712e574f16a34a2c6e1525 -r c19fa5da36cc51fd5ee6005ed801a7e2c9aba229 tool-data/bowtie2_indices.loc.sample --- a/tool-data/bowtie2_indices.loc.sample +++ b/tool-data/bowtie2_indices.loc.sample @@ -1,37 +1,37 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Bowtie2 indexed sequences data files. You will -#need to create these data files and then create a bowtie_indices.loc -#file similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bowtie2_indices.loc -#file has this format (longer white space characters are TAB characters): +# bowtie2_indices.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a bowtie_indices.loc file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. # -#<unique_build_id><dbkey><display_name><file_base_path> +# <unique_build_id><dbkey><display_name><file_base_path> # -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/bowtie2/hg18/, -#then the bowtie2_indices.loc entry would look like this: +# So, for example, if you had hg18 indexes stored in: # -#hg18 hg18 hg18 /depot/data2/galaxy/bowtie2/hg18/hg18 +# /depot/data2/galaxy/hg19/bowtie2/ # -#and your /depot/data2/galaxy/bowtie2/hg18/ directory -#would contain hg18.*.ebwt files: +# containing hg19 genome and hg19.*.bt2 files, such as: +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 +# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 +# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 # -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt -#...etc... +# then the bowtie2_indices.loc entry could look like this: # -#Your bowtie2_indices.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: +#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon # -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie2/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie2/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 -#...etc... +#More examples: # -#Note that for backwards compatibility with workflows, the unique ID of -#an entry must be the path that was in the original loc file, because that -#is the value stored in the workflow for that parameter. That is why the -#hg19 entry above looks odd. New genomes can be better-looking. +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 # +# 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: inithello: Tool shed functional test enhancements and documentation.
by Bitbucket 13 Feb '13

13 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7bf8f6a1da9c/ changeset: 7bf8f6a1da9c user: inithello date: 2013-02-13 16:58:10 summary: Tool shed functional test enhancements and documentation. affected #: 3 files diff -r 3eff396a81d833a2dcabce2fd34b53badf707984 -r 7bf8f6a1da9c7d6148712e574f16a34a2c6e1525 test/tool_shed/base/test_db_util.py --- a/test/tool_shed/base/test_db_util.py +++ b/test/tool_shed/base/test_db_util.py @@ -1,9 +1,11 @@ -import galaxy.model +import galaxy.model, logging import galaxy.webapps.community.model as model from galaxy.model.orm import * from galaxy.webapps.community.model.mapping import context as sa_session from galaxy.model.mapping import context as ga_session +log = logging.getLogger( 'test.tool_shed.test_db_util' ) + def delete_obj( obj ): sa_session.delete( obj ) sa_session.flush() @@ -57,10 +59,44 @@ if role.name == user.email and role.description == 'Private Role for %s' % user.email: return role raise AssertionError( "Private role not found for user '%s'" % user.email ) +def get_repository_reviews( repository_id, reviewer_user_id=None, changeset_revision=None ): + if reviewer_user_id and changeset_revision: + reviews = sa_session.query( model.RepositoryReview ) \ + .filter( and_( model.RepositoryReview.table.c.repository_id == repository_id, + model.RepositoryReview.table.c.deleted == False, + model.RepositoryReview.table.c.changeset_revision == changeset_revision, + model.RepositoryReview.table.c.user_id == reviewer_user_id ) ) \ + .all() + elif reviewer_user_id: + reviews = sa_session.query( model.RepositoryReview ) \ + .filter( and_( model.RepositoryReview.table.c.repository_id == repository_id, + model.RepositoryReview.table.c.deleted == False, + model.RepositoryReview.table.c.user_id == reviewer_user_id ) ) \ + .all() + else: + reviews = sa_session.query( model.RepositoryReview ) \ + .filter( and_( model.RepositoryReview.table.c.repository_id == repository_id, + model.RepositoryReview.table.c.deleted == False ) ) \ + .all() + return reviews +def get_reviews_ordered_by_changeset_revision( repository_id, changelog_tuples, reviewer_user_id=None ): + reviews = get_repository_reviews( repository_id, reviewer_user_id=reviewer_user_id ) + ordered_reviews = [] + for ctx_rev, changeset_hash in changelog_tuples: + for review in reviews: + if str( review.changeset_revision ) == str( changeset_hash ): + ordered_reviews.append( review ) + return ordered_reviews def get_repository_by_id( repository_id ): return sa_session.query( model.Repository ) \ .filter( model.Repository.table.c.id == repository_id ) \ .first() +def get_repository_downloadable_revisions( repository_id ): + revisions = sa_session.query( model.RepositoryMetadata ) \ + .filter( and_( model.RepositoryMetadata.table.c.repository_id == repository_id, + model.RepositoryMetadata.table.c.downloadable == True ) ) \ + .all() + return revisions def get_repository_review_by_user_id_changeset_revision( user_id, repository_id, changeset_revision ): review = sa_session.query( model.RepositoryReview ) \ .filter( and_( model.RepositoryReview.table.c.user_id == user_id, diff -r 3eff396a81d833a2dcabce2fd34b53badf707984 -r 7bf8f6a1da9c7d6148712e574f16a34a2c6e1525 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -493,6 +493,14 @@ return os.path.abspath( os.path.join( filepath, filename ) ) else: return os.path.abspath( os.path.join( self.file_dir, filename ) ) + def get_last_reviewed_revision_by_user( self, user, repository ): + changelog_tuples = self.get_repository_changelog_tuples( repository ) + reviews = test_db_util.get_reviews_ordered_by_changeset_revision( repository.id, changelog_tuples, reviewer_user_id = user.id ) + if reviews: + last_review = reviews[ -1 ] + else: + last_review = None + return last_review def get_or_create_repository( self, owner=None, strings_displayed=[], strings_not_displayed=[], **kwd ): repository = test_db_util.get_repository_by_name_and_owner( kwd[ 'name' ], owner ) if repository is None: @@ -508,9 +516,13 @@ return self.hgweb_config_manager.get_entry( lhs ) except: raise Exception( "Entry for repository %s missing in hgweb config file %s." % ( lhs, self.hgweb_config_manager.hgweb_config ) ) - def get_repository_changelog( self, repository ): + def get_repository_changelog_tuples( self, repository ): repo = hg.repository( ui.ui(), self.get_repo_path( repository ) ) - return [ ( repo.changectx( changeset ), changeset ) for changeset in repo.changelog ] + changelog_tuples = [] + for changeset in repo.changelog: + ctx = repo.changectx( changeset ) + changelog_tuples.append( ( ctx.rev(), repo.changectx( changeset ) ) ) + return changelog_tuples def get_repository_datatypes_count( self, repository ): metadata = self.get_repository_metadata( repository )[0].metadata if 'datatypes' not in metadata: diff -r 3eff396a81d833a2dcabce2fd34b53badf707984 -r 7bf8f6a1da9c7d6148712e574f16a34a2c6e1525 test/tool_shed/functional/test_0400_repository_component_reviews.py --- a/test/tool_shed/functional/test_0400_repository_component_reviews.py +++ b/test/tool_shed/functional/test_0400_repository_component_reviews.py @@ -5,10 +5,45 @@ repository_description = 'Galaxy filtering tool for test 0400' repository_long_description = 'Long description of Galaxy filtering tool for test 0400' +''' +1. Create users. +2. Grant reviewer role to test_user_2. +3. Check that the review components that are to be tested are defined in this tool shed instance. +4. Create a repository, owned by test_user_1, to be reviewed by test_user_2. +5. Review the datatypes component on the repository. +6. Check that no other components besides datatypes display as reviewed. +7. Review the functional tests component on the repository. +8. Check that only functional tests and datatypes display as reviewed. +9. Review the readme component on the repository. +10. Check that only functional tests, datatypes, and readme display as reviewed. +11. Review the repository dependencies component. +12. Check that only repository dependencies, functional tests, datatypes, and readme display as reviewed. +13. Review the tool dependencies component. +14. Check that only tool dependencies, repository dependencies, functional tests, datatypes, and readme display as reviewed. +15. Review the tools component. +16. Check that only tools, tool dependencies, repository dependencies, functional tests, datatypes, and readme display as reviewed. +17. Review the workflows component. +18. Check that all components display as reviewed. +19. Upload readme.txt to the repository. +20. Copy the previous review, and update the readme component review to reflect the existence of a readme file. +21. Check that the readme component review has been updated, and the other component reviews are present. +22. Upload test data to the repository. This will also create a new changeset revision. +23. Review the functional tests component on the repository, copying the other components from the previous review. +24. Verify that the functional tests component review has been updated, and as in step 21, the other reviews are unchanged. +25. Upload a new version of the tool. +26. Review the new revision's functional tests component. +27. Verify that the functional tests component review displays correctly. +''' + class TestRepositoryComponentReviews( ShedTwillTestCase ): '''Test repository component review features.''' def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" + """ + We are at step 1. + Create all the user accounts that are needed for this test script to run independently of other test. + Previously created accounts will not be re-created. + """ 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 ) @@ -26,11 +61,21 @@ admin_user_private_role = test_db_util.get_private_role( admin_user ) def test_0005_grant_reviewer_role( self ): '''Grant the repository reviewer role to test_user_2.''' + """ + We are at step 2. + We now have an admin user (admin_user) and two non-admin users (test_user_1 and test_user_2). Grant the repository + reviewer role to test_user_2, who will not be the owner of the reviewed repositories. + """ reviewer_role = test_db_util.get_role_by_name( 'Repository Reviewer' ) test_user_2 = test_db_util.get_user( common.test_user_2_email ) self.grant_role_to_user( test_user_2, reviewer_role ) def test_0010_verify_repository_review_components( self ): '''Ensure that the required review components exist.''' + """ + We are at step 3. + We now have an admin user (admin_user) and two non-admin users (test_user_1 and test_user_2). Grant the repository + reviewer role to test_user_2, who will not be the owner of the reviewed repositories. + """ strings_not_displayed=[ 'Repository dependencies' ] self.manage_review_components( strings_not_displayed=strings_not_displayed ) self.add_repository_review_component( name='Repository dependencies', @@ -39,6 +84,11 @@ self.manage_review_components( strings_displayed=strings_displayed ) def test_0015_create_repository( self ): """Create and populate the filtering repository""" + """ + We are at step 4. + Log in as test_user_1 and create the filtering repository, then upload a basic set of + components to be reviewed in subsequent tests. + """ category = self.create_category( name='Test 0400 Repository Component Reviews', description='Test 0400 Repository Component Reviews' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) @@ -53,21 +103,32 @@ self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" ) def test_0020_review_initial_revision_data_types( self ): '''Review the datatypes component for the current tip revision.''' + """ + We are at step 5. + Log in as test_user_2 and review the data types component of the filtering repository owned by test_user_1. # Review this revision: # Data types (N/A) - # Functional tests (One star, comment 'functional tests missing') - # README (N/A) - # Repository dependencies (N/A) - # Tool dependencies (N/A) - # Tools (5 stars, good review) - # Workflows (N/A) + """ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + # The create_repository_review method takes a dict( component label=review contents ). + # If review_contents is empty, it marks that component as not applicable. The review + # contents dict should have the structure: + # { + # rating: 1-5, + # comment: <text> + # approved: yes/no + # private: yes/no + # } review_contents_dict = { 'Data types': dict() } self.create_repository_review( repository, review_contents_dict ) def test_0025_verify_datatype_review( self ): '''Verify that the datatypes component review displays correctly.''' + """ + We are at step 6. + Log in as test_user_1 and check that the filtering repository only has a review for the data types component. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -76,11 +137,28 @@ strings_not_displayed = [ 'Functional tests', 'README', 'Repository dependencies', 'Tool dependencies', 'Tools', 'Workflows' ] self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) def test_0030_review_initial_revision_functional_tests( self ): - '''Review the datatypes component for the current tip revision.''' + '''Review the functional tests component for the current tip revision.''' + """ + We are at step 7. + Log in as test_user_2 and review the functional tests component for this repository. Since the repository + has not been altered, this will update the existing review to add a component. + # Review this revision: + # Data types (N/A) + # Functional tests (One star, comment 'functional tests missing') + """ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) user = test_db_util.get_user( common.test_user_2_email ) + # The create_repository_review method takes a dict( component label=review contents ). + # If review_contents is empty, it marks that component as not applicable. The review + # contents dict should have the structure: + # { + # rating: 1-5, + # comment: <text> + # approved: yes/no + # private: yes/no + # } review_contents_dict = { 'Functional tests': dict( rating=1, comment='Functional tests missing', approved='no', private='yes' ) } self.review_repository( repository, review_contents_dict, user ) # def test_0030_verify_review_display( self ): @@ -89,7 +167,13 @@ # self.logout() # self.login( email=common.test_user_3_email, username=common.test_user_3_name ) def test_0035_verify_functional_test_review( self ): - '''Verify that the datatypes component review displays correctly.''' + '''Verify that the functional tests component review displays correctly.''' + """ + We are at step 8. + Log in as test_user_1 and check that the filtering repository now has reviews + for the data types and functional tests components. Since the functional tests component was not marked as 'Not applicable', + also check for the review comment. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -99,14 +183,35 @@ self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) def test_0040_review_readme( self ): '''Review the readme component for the current tip revision.''' + """ + We are at step 9. + Log in as test_user_2 and update the review with the readme component marked as 'Not applicable'. + # Review this revision: + # Data types (N/A) + # Functional tests (One star, comment 'functional tests missing') + # README (N/A) + """ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) user = test_db_util.get_user( common.test_user_2_email ) + # The create_repository_review method takes a dict( component label=review contents ). + # If review_contents is empty, it marks that component as not applicable. The review + # contents dict should have the structure: + # { + # rating: 1-5, + # comment: <text> + # approved: yes/no + # private: yes/no + # } review_contents_dict = { 'README': dict() } self.review_repository( repository, review_contents_dict, user ) def test_0045_verify_readme_review( self ): - '''Verify that the datatypes component review displays correctly.''' + '''Verify that the readme component review displays correctly.''' + """ + We are at step 10. + Log in as test_user_1 and verify that the repository component reviews now include a review for the readme component. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -116,14 +221,37 @@ self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) def test_0050_review_repository_dependencies( self ): '''Review the repository dependencies component for the current tip revision.''' + """ + We are at step 11. + Log in as test_user_2 and update the review with the repository dependencies component marked as 'Not applicable'. + # Review this revision: + # Data types (N/A) + # Functional tests (One star, comment 'functional tests missing') + # README (N/A) + # Repository dependencies (N/A) + """ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) user = test_db_util.get_user( common.test_user_2_email ) + # The create_repository_review method takes a dict( component label=review contents ). + # If review_contents is empty, it marks that component as not applicable. The review + # contents dict should have the structure: + # { + # rating: 1-5, + # comment: <text> + # approved: yes/no + # private: yes/no + # } review_contents_dict = { 'Repository dependencies': dict() } self.review_repository( repository, review_contents_dict, user ) def test_0055_verify_repository_dependency_review( self ): - '''Verify that the datatypes component review displays correctly.''' + '''Verify that the repository dependencies component review displays correctly.''' + """ + We are at step 12. + Log in as test_user_1 and verify that the repository component reviews now include a review + for the repository dependencies component. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -133,14 +261,38 @@ self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) def test_0060_review_tool_dependencies( self ): '''Review the tool dependencies component for the current tip revision.''' + """ + We are at step 13. + Log in as test_user_2 and update the review with the tool dependencies component marked as 'Not applicable'. + # Review this revision: + # Data types (N/A) + # Functional tests (One star, comment 'functional tests missing') + # README (N/A) + # Repository dependencies (N/A) + # Tool dependencies (N/A) + """ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) user = test_db_util.get_user( common.test_user_2_email ) + # The create_repository_review method takes a dict( component label=review contents ). + # If review_contents is empty, it marks that component as not applicable. The review + # contents dict should have the structure: + # { + # rating: 1-5, + # comment: <text> + # approved: yes/no + # private: yes/no + # } review_contents_dict = { 'Tool dependencies': dict() } self.review_repository( repository, review_contents_dict, user ) def test_0065_verify_tool_dependency_review( self ): - '''Verify that the datatypes component review displays correctly.''' + '''Verify that the tool dependencies component review displays correctly.''' + """ + We are at step 14. + Log in as test_user_1 and verify that the repository component reviews now include a review + for the tool dependencies component. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -150,14 +302,40 @@ self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) def test_0070_review_tools( self ): '''Review the tools component for the current tip revision.''' + """ + We are at step 15. + Log in as test_user_2 and update the review with the tools component given + a favorable review, with 5 stars, and approved status. + # Review this revision: + # Data types (N/A) + # Functional tests (One star, comment 'functional tests missing') + # README (N/A) + # Repository dependencies (N/A) + # Tool dependencies (N/A) + # Tools (5 stars, good review) + """ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) user = test_db_util.get_user( common.test_user_2_email ) + # The create_repository_review method takes a dict( component label=review contents ). + # If review_contents is empty, it marks that component as not applicable. The review + # contents dict should have the structure: + # { + # rating: 1-5, + # comment: <text> + # approved: yes/no + # private: yes/no + # } review_contents_dict = { 'Tools': dict( rating=5, comment='Excellent tool, easy to use.', approved='yes', private='no' ) } self.review_repository( repository, review_contents_dict, test_db_util.get_user( common.test_user_2_email ) ) def test_0075_verify_tools_review( self ): - '''Verify that the datatypes component review displays correctly.''' + '''Verify that the tools component review displays correctly.''' + """ + We are at step 16. + Log in as test_user_1 and verify that the repository component reviews now include a review + for the tools component. As before, check for the presence of the comment on this review. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -167,14 +345,40 @@ self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) def test_0080_review_workflows( self ): '''Review the workflows component for the current tip revision.''' + """ + We are at step 17. + Log in as test_user_2 and update the review with the workflows component marked as 'Not applicable'. + # Review this revision: + # Data types (N/A) + # Functional tests (One star, comment 'functional tests missing') + # README (N/A) + # Repository dependencies (N/A) + # Tool dependencies (N/A) + # Tools (5 stars, good review) + # Workflows (N/A) + """ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) user = test_db_util.get_user( common.test_user_2_email ) + # The create_repository_review method takes a dict( component label=review contents ). + # If review_contents is empty, it marks that component as not applicable. The review + # contents dict should have the structure: + # { + # rating: 1-5, + # comment: <text> + # approved: yes/no + # private: yes/no + # } review_contents_dict = { 'Workflows': dict() } self.review_repository( repository, review_contents_dict, user ) def test_0085_verify_workflows_review( self ): - '''Verify that the datatypes component review displays correctly.''' + '''Verify that the workflows component review displays correctly.''' + """ + We are at step 18. + Log in as test_user_1 and verify that the repository component reviews now include a review + for the workflows component. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -183,6 +387,11 @@ self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) def test_0090_upload_readme_file( self ): '''Upload a readme file to the filtering repository.''' + """ + We are at step 19. + Log in as test_user_1, the repository owner, and upload readme.txt to the repository. This will create + a new changeset revision for this repository, which will need to be reviewed. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -190,21 +399,42 @@ self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme.txt" ) def test_0095_review_new_changeset_readme_component( self ): '''Update the filtering repository's readme component review to reflect the presence of the readme file.''' + """ + We are at step 20. + There is now a new changeset revision in the repository's changelog, but it has no review associated with it. + Get the previously reviewed changeset hash, and pass that and the review id to the create_repository_review + method, in order to copy the previous review's contents. Then update the new review to reflect the presence of + a readme file. + """ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) user = test_db_util.get_user( common.test_user_2_email ) - # Get the changeset immediately prior to the tip, and pass it to the create review method. - changelog = self.get_repository_changelog( repository ) - changeset_revision, ctx_revision = changelog[-2] - previous_review = test_db_util.get_repository_review_by_user_id_changeset_revision( user.id, repository.id, str( changeset_revision ) ) + # Get the last changeset revision that has a review associated with it. + last_review = self.get_last_reviewed_revision_by_user( user, repository ) + if last_review is None: + raise AssertionError( 'Previous review expected, none found.' ) + # The create_repository_review method takes a dict( component label=review contents ). + # If review_contents is empty, it marks that component as not applicable. The review + # contents dict should have the structure: + # { + # rating: 1-5, + # comment: <text> + # approved: yes/no + # private: yes/no + # } review_contents_dict = { 'README': dict( rating=5, comment='Clear and concise readme file, a true pleasure to read.', approved='yes', private='no' ) } self.create_repository_review( repository, review_contents_dict, changeset_revision=self.get_repository_tip( repository ), - copy_from=( str( changeset_revision ), previous_review.id ) ) + copy_from=( str( last_review.changeset_revision ), last_review.id ) ) def test_0100_verify_readme_review( self ): '''Verify that the readme component review displays correctly.''' + """ + We are at step 21. + Log in as the repository owner (test_user_1) and check the repository component reviews to + verify that the readme component is now reviewed and approved. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -213,28 +443,51 @@ self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) def test_0105_upload_test_data( self ): '''Upload the missing test data to the filtering repository.''' - self.logout() - self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + """ + We are at step 22. + Remain logged in as test_user_1 and upload test data to the repository. This will also create a + new changeset revision that needs to be reviewed. This will replace the changeset hash associated with + the last dowloadable revision, but the last repository review will still be associated with the + last dowloadable revision hash. + """ repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) user = test_db_util.get_user( common.test_user_2_email ) self.upload_file( repository, 'filtering/filtering_test_data.tar', commit_message="Uploaded test data." ) def test_0110_review_new_changeset_functional_tests( self ): '''Update the filtering repository's readme component review to reflect the presence of the readme file.''' + """ + We are at step 23. + Log in as test_user_2 and get the last reviewed changeset hash, and pass that and the review id to + the create_repository_review method, then update the copied review to approve the functional tests + component. + """ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) user = test_db_util.get_user( common.test_user_2_email ) # Get the changeset immediately prior to the tip, and pass it to the create review method. - changelog = self.get_repository_changelog( repository ) - changeset_revision, ctx_revision = changelog[-2] - previous_review = test_db_util.get_repository_review_by_user_id_changeset_revision( user.id, repository.id, str( changeset_revision ) ) + last_review = self.get_last_reviewed_revision_by_user( user, repository ) + # The create_repository_review method takes a dict( component label=review contents ). + # If review_contents is empty, it marks that component as not applicable. The review + # contents dict should have the structure: + # { + # rating: 1-5, + # comment: <text> + # approved: yes/no + # private: yes/no + # } review_contents_dict = { 'Functional tests': dict( rating=5, comment='A good set of functional tests.', approved='yes', private='no' ) } self.create_repository_review( repository, review_contents_dict, changeset_revision=self.get_repository_tip( repository ), - copy_from=( str( changeset_revision ), previous_review.id ) ) + copy_from=( str( last_review.changeset_revision ), last_review.id ) ) def test_0115_verify_functional_tests_review( self ): '''Verify that the functional tests component review displays correctly.''' + """ + We are at step 24. + Log in as the repository owner, test_user_1, and verify that the new revision's functional tests component + review has been updated with an approved status and favorable comment. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -243,6 +496,11 @@ self.verify_repository_reviews( repository, reviewer=user, strings_displayed=strings_displayed ) def test_0120_upload_new_tool_version( self ): '''Upload filtering 2.2.0 to the filtering repository.''' + """ + We are at step 25. + Log in as test_user_1 and upload a new version of the tool to the filtering repository. This will create + a new downloadable revision, with no associated repository component reviews. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -253,22 +511,38 @@ remove_repo_files_not_in_tar='No' ) def test_0125_review_new_changeset_functional_tests( self ): '''Update the filtering repository's review to apply to the new changeset with filtering 2.2.0.''' + """ + We are at step 26. + Log in as test_user_2 and copy the last review for this repository to the new changeset. Then + update the tools component review to refer to the new tool version. + """ self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) user = test_db_util.get_user( common.test_user_2_email ) - # Get the changeset immediately prior to the tip, and pass it to the create review method. - changelog = self.get_repository_changelog( repository ) - changeset_revision, ctx_revision = changelog[-2] - previous_review = test_db_util.get_repository_review_by_user_id_changeset_revision( user.id, repository.id, str( changeset_revision ) ) + last_review = self.get_last_reviewed_revision_by_user( user, repository ) # Something needs to change so that the review will save. + # The create_repository_review method takes a dict( component label=review contents ). + # If review_contents is empty, it marks that component as not applicable. The review + # contents dict should have the structure: + # { + # rating: 1-5, + # comment: <text> + # approved: yes/no + # private: yes/no + # } review_contents_dict = { 'Tools': dict( rating=5, comment='Version 2.2.0 does the impossible and improves this tool.', approved='yes', private='yes' ) } self.create_repository_review( repository, review_contents_dict, changeset_revision=self.get_repository_tip( repository ), - copy_from=( str( changeset_revision ), previous_review.id ) ) + copy_from=( str( last_review.changeset_revision ), last_review.id ) ) def test_0135_verify_review_for_new_version( self ): '''Verify that the reviews display correctly for this changeset revision.''' + """ + We are at step 27. + Log in as test_user_1 and check that the tools component review is for filtering 2.2.0, but that the other component + reviews had their contents copied from the last reviewed changeset. + """ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 13 Feb '13

13 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4b1a5865d413/ changeset: 4b1a5865d413 user: Kyle Ellrott date: 2013-02-08 01:54:06 summary: Adding variable 'host_url' to provide qualified URL of host to tool help section. affected #: 1 file diff -r ce9789a35356da2b2ee4ae723506d5af57a0ce69 -r 4b1a5865d413005668b4a3c2c590c7dddb09205d templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -345,7 +345,7 @@ tool_help = tool.help # Help is Mako template, so render using current static path. - tool_help = tool_help.render( static_path=h.url_for( '/static' ) ) + tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) ) # Convert to unicode to display non-ascii characters. if type( tool_help ) is not unicode: https://bitbucket.org/galaxy/galaxy-central/commits/3eff396a81d8/ changeset: 3eff396a81d8 user: dannon date: 2013-02-13 15:47:21 summary: Merged in kellrott/galaxy-central (pull request #119) Adding variable 'host_url' to provide qualified URL of host to tool help section. affected #: 1 file diff -r 2f8989a1a16001e5dfcded4e0526ef3e2d6f55f9 -r 3eff396a81d833a2dcabce2fd34b53badf707984 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -345,7 +345,7 @@ tool_help = tool.help # Help is Mako template, so render using current static path. - tool_help = tool_help.render( static_path=h.url_for( '/static' ) ) + tool_help = tool_help.render( static_path=h.url_for( '/static' ), host_url=h.url_for('/', qualified=True) ) # Convert to unicode to display non-ascii characters. if type( tool_help ) is not unicode: 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: Tool data tables: (a) add spaces between function per PEP8 and (b) add warning when an invalid line is found in tool data table.
by Bitbucket 12 Feb '13

12 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f8989a1a160/ changeset: 2f8989a1a160 user: jgoecks date: 2013-02-13 00:44:06 summary: Tool data tables: (a) add spaces between function per PEP8 and (b) add warning when an invalid line is found in tool data table. affected #: 1 file diff -r 04b8060562f865fa5b3ec6dac4ecfe590bd3ec07 -r 2f8989a1a16001e5dfcded4e0526ef3e2d6f55f9 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -158,6 +158,7 @@ def __init__( self, config_element, tool_data_path ): super( TabularToolDataTable, self ).__init__( config_element, tool_data_path ) self.configure_and_load( config_element, tool_data_path ) + def configure_and_load( self, config_element, tool_data_path ): """ Configure and load table from an XML element. @@ -196,11 +197,14 @@ self.missing_index_file = filename log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) ) self.data = all_rows + def handle_found_index_file( self, filename ): self.missing_index_file = None self.data.extend( self.parse_file_fields( open( filename ) ) ) + def get_fields( self ): return self.data + def parse_column_spec( self, config_element ): """ Parse column definitions, which can either be a set of 'column' elements @@ -230,14 +234,17 @@ assert 'value' in self.columns, "Required 'value' column missing from column def" if 'name' not in self.columns: self.columns['name'] = self.columns['value'] + def parse_file_fields( self, reader ): """ Parse separated lines from file and return a list of tuples. TODO: Allow named access to fields using the column names. """ + separator_char = (lambda c: '<TAB>' if c == '\t' else c)(self.separator) + rval = [] - for line in reader: + for i, line in enumerate( reader, start=1 ): if line.lstrip().startswith( self.comment_char ): continue line = line.rstrip( "\n\r" ) @@ -245,6 +252,10 @@ fields = line.split( self.separator ) if self.largest_index < len( fields ): rval.append( fields ) + else: + log.warn( "Line %i in tool data table '%s' is invalid (HINT: " + "'%s' characters must be used to separate fields):\n%s" + % ( i, self.name, separator_char, line ) ) return rval def get_entry( self, query_attr, query_val, return_attr ): 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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