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commit/galaxy-central: inithello: Tool shed functional test enhancements. Functional tests for displaying images on a tool's page. Updated test string in tool migration stage test.
by commits-noreply＠bitbucket.org 03 Apr '13

03 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0dc6a4052711/ Changeset: 0dc6a4052711 User: inithello Date: 2013-04-03 17:56:58 Summary: Tool shed functional test enhancements. Functional tests for displaying images on a tool's page. Updated test string in tool migration stage test. Affected #: 5 files diff -r 1c7460ba03f9363c9d96e35dc53c3d3f95002346 -r 0dc6a4052711af50bbfaa438f3d591ff9bae4175 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -838,6 +838,11 @@ self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def load_page_for_installed_tool( self, tool_guid, strings_displayed=[], strings_not_displayed=[] ): + url = '/tool_runner?tool_id=%s' % tool_guid + self.visit_galaxy_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def load_workflow_image_in_tool_shed( self, repository, workflow_name, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ): if not changeset_revision: changeset_revision = self.get_repository_tip( repository ) diff -r 1c7460ba03f9363c9d96e35dc53c3d3f95002346 -r 0dc6a4052711af50bbfaa438f3d591ff9bae4175 test/tool_shed/functional/test_0140_tool_help_images.py --- /dev/null +++ b/test/tool_shed/functional/test_0140_tool_help_images.py @@ -0,0 +1,86 @@ +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__) + +repository_name = 'htseq_count_0140' +repository_description = "Converter: BED to GFF" +repository_long_description = "Convert bed to gff" + +category_name = 'Test 0140 Tool Help Images' +category_description = 'Test 0140 Tool Help Images' + +''' +1) Create and populate the htseq_count_0140 repository. +2) Visit the manage_repository page. +3) Simulate clicking the htseq_count tool button. +4) On the resulting display tool page, look for the image string similar to the following string where the encoded repository_id is previously determined: + +src="/repository/static/images/<id>/count_modes.png" + +''' + + +class TestToolHelpImages( ShedTwillTestCase ): + '''Test features related to tool help images.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + 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' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + 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' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_create_htseq_count_repository( self ): + '''Create and populate htseq_count_0140.''' + ''' + We are at step 1 - Create and populate the htseq_count_0140 repository. + Create the htseq_count_0140 repository and upload the tarball. + ''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + # Create a repository named htseq_count_0140 owned by user1. + repository = self.get_or_create_repository( name=repository_name, + description=repository_description, + long_description=repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + # Upload htseq_count.tar to the repository. + self.upload_file( repository, + filename='htseq_count/htseq_count.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded htseq_count.tar.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_load_tool_page( self ): + '''Load the tool page and check for the image.''' + ''' + We are at step 2 + Visit the manage_repository page and the tool page, and look for the image url + similar to the following string: + + src="/repository/static/images/<id>/count_modes.png" + ''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + # Get the repository tip. + changeset_revision = self.get_repository_tip( repository ) + self.display_manage_repository_page( repository ) + # Generate the image path. + image_path = 'src="/repository/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) + # The repository uploaded in this test should only have one metadata revision, with one tool defined, which + # should be the tool that contains a link to the image. + repository_metadata = repository.metadata_revisions[ 0 ].metadata + tool_path = repository_metadata[ 'tools' ][ 0 ][ 'tool_config' ] + self.load_display_tool_page( repository, tool_path, changeset_revision, strings_displayed=[ image_path ], strings_not_displayed=[] ) diff -r 1c7460ba03f9363c9d96e35dc53c3d3f95002346 -r 0dc6a4052711af50bbfaa438f3d591ff9bae4175 test/tool_shed/functional/test_0430_browse_utilities.py --- a/test/tool_shed/functional/test_0430_browse_utilities.py +++ b/test/tool_shed/functional/test_0430_browse_utilities.py @@ -1,7 +1,8 @@ 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__) + +log = logging.getLogger( __name__ ) datatypes_repository_name = 'emboss_datatypes_0430' datatypes_repository_description = 'Galaxy applicable datatypes for EMBOSS for test 0430' diff -r 1c7460ba03f9363c9d96e35dc53c3d3f95002346 -r 0dc6a4052711af50bbfaa438f3d591ff9bae4175 test/tool_shed/functional/test_1140_tool_help_images.py --- /dev/null +++ b/test/tool_shed/functional/test_1140_tool_help_images.py @@ -0,0 +1,119 @@ +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__) + +repository_name = 'htseq_count_0140' +repository_description = "Converter: BED to GFF" +repository_long_description = "Convert bed to gff" + +category_name = 'Test 0140 Tool Help Images' +category_description = 'Test 0140 Tool Help Images' + +''' +1) Create and populate the htseq_count_0140 repository. +2) Visit the manage_repository page, then the tool page, and look for the image string +similar to the following string where the encoded repository_id is previously determined: + +src="/repository/static/images/<id>/count_modes.png" + +Galaxy side: +1) Install the htseq_count repository from the tool shed into Galaxy. +2) In the center tool panel, look for the image string similar to the following string where the encoded_repository_id is previously determined as the installed ToolShedRepository id: + +src="/tool_runner/static/images/<id>/count_modes.png" +''' + + +class TestToolHelpImages( ShedTwillTestCase ): + '''Test features related to tool help images.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + 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' % test_user_1_email + test_user_1_private_role = test_db_util.get_private_role( test_user_1 ) + 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' % admin_email + admin_user_private_role = test_db_util.get_private_role( admin_user ) + + def test_0005_create_htseq_count_repository( self ): + '''Create and populate htseq_count_0140.''' + ''' + We are at step 1 - Create and populate the htseq_count_0140 repository. + Create the htseq_count_0140 repository and upload the tarball. + ''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + # Create a repository named htseq_count_0140 owned by user1. + repository = self.get_or_create_repository( name=repository_name, + description=repository_description, + long_description=repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + if self.repository_is_new( repository ): + # Upload htseq_count.tar to the repository if it hasn't already been populated. + self.upload_file( repository, + filename='htseq_count/htseq_count.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded htseq_count.tar.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_load_tool_page( self ): + '''Load the tool page and check for the image URL.''' + ''' + This is a duplicate of test method _0010 in test_0140_tool_help_images. + ''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + # Get the repository tip. + changeset_revision = self.get_repository_tip( repository ) + self.display_manage_repository_page( repository ) + # Generate the image path. + image_path = 'src="/repository/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) + # The repository uploaded in this test should only have one metadata revision, with one tool defined, which + # should be the tool that contains a link to the image. + repository_metadata = repository.metadata_revisions[ 0 ].metadata + tool_path = repository_metadata[ 'tools' ][ 0 ][ 'tool_config' ] + self.load_display_tool_page( repository, tool_path, changeset_revision, strings_displayed=[ image_path ], strings_not_displayed=[] ) + + def test_0015_install_htseq_count_repository( self ): + '''Install the htseq_count_0140 repository into Galaxy.''' + ''' + We are at step 1 - Install the htseq_count_0140 repository from the tool shed into Galaxy. + ''' + repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + self.install_repository( 'htseq_count_0140', + 'user1', + category_name, + strings_displayed=[], + install_tool_dependencies=False, + install_repository_dependencies=False ) + + def test_0020_verify_tool_image_link( self ): + '''Load the tool page and verify the image link.''' + ''' + We are at step 2 + + In the center tool panel, look for the image string similar to the following string where the + encoded_repository_id is previously determined as the installed ToolShedRepository id: + + src="/tool_runner/static/images/<id>/count_modes.png" + ''' + repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) + image_path = 'src="/tool_runner/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) + # The repository uploaded in this test should only define one tool, which should be the tool that contains a link to an image. + repository_metadata = repository.metadata + tool_id = repository_metadata[ 'tools' ][ 0 ][ 'guid' ] + self.load_page_for_installed_tool( tool_id, strings_displayed=[ image_path ] ) diff -r 1c7460ba03f9363c9d96e35dc53c3d3f95002346 -r 0dc6a4052711af50bbfaa438f3d591ff9bae4175 test/tool_shed/functional/test_1400_review_migration_stages.py --- a/test/tool_shed/functional/test_1400_review_migration_stages.py +++ b/test/tool_shed/functional/test_1400_review_migration_stages.py @@ -1,8 +1,10 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util + class TestToolMigrationStages( ShedTwillTestCase ): '''Verify that the migration stages display correctly.''' + def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" self.logout() @@ -15,11 +17,12 @@ 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 ) + def test_0005_load_migration_stages_page( self ): '''Load the migration page and check for the appropriate migration stages.''' stages = [ 'emboss_5', 'emboss_datatypes', 'emboss', '5.0.0', '0002_tools.sh', - 'freebayes', '0.9.4_a46483351fd0196637614121868fb5c386612b55', 'samtools', '0.1.18', 'FreeBayes requires g++', + 'freebayes', '0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8', 'samtools', '0.1.18', 'FreeBayes requires g++', 'ncurses', 'zlib', '0003_tools.sh', 'ncbi_blast_plus', 'blast_datatypes', 'blast+', '2.2.26+', 'blast.ncbi.nlm.nih.gov', 'NCBI BLAST+ tools', '0004_tools.sh', 'bwa_wrappers', '0.5.9', 'zlib and libpthread', 'Map with BWA for Illumina', '0005_tools.sh', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Allow anonymous access to list/show in api/histories.
by commits-noreply＠bitbucket.org 03 Apr '13

03 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1c7460ba03f9/ Changeset: 1c7460ba03f9 User: dannon Date: 2013-04-03 17:54:28 Summary: Allow anonymous access to list/show in api/histories. Affected #: 1 file diff -r c1faecf25f52a01cf55ba95df42791bf3399ed59 -r 1c7460ba03f9363c9d96e35dc53c3d3f95002346 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -11,7 +11,7 @@ class HistoriesController( BaseAPIController, UsesHistoryMixin ): - @web.expose_api + @web.expose_api_anonymous def index( self, trans, deleted='False', **kwd ): """ GET /api/histories @@ -42,7 +42,7 @@ trans.response.status = 500 return rval - @web.expose_api + @web.expose_api_anonymous def show( self, trans, id, deleted='False', **kwd ): """ GET /api/histories/{encoded_history_id} 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.

1 0

commit/galaxy-central: dannon: Move workflow linking styles to base, rebuild styles.
by commits-noreply＠bitbucket.org 03 Apr '13

03 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c1faecf25f52/ Changeset: c1faecf25f52 User: dannon Date: 2013-04-03 17:34:29 Summary: Move workflow linking styles to base, rebuild styles. Affected #: 3 files diff -r 80291f7ad4576c95f70eaed2f36cc5a95cf303fb -r c1faecf25f52a01cf55ba95df42791bf3399ed59 static/style/base.less --- a/static/style/base.less +++ b/static/style/base.less @@ -1515,10 +1515,29 @@ display:inline-block; margin-left:10px; } + .icon-button.multiinput.disabled{ background:url(../images/documents-stack-faded.png) no-repeat; - cursor:auto; + cursor:pointer; } + + +.icon-button.link{ + background:url(../images/silk/link.png) no-repeat; + cursor:pointer; + float:none; + display:inline-block; + margin-left:10px; +} + +.icon-button.link-broken{ + background:url(../images/silk/link_break.png) no-repeat; + cursor:pointer; + float:none; + display:inline-block; + margin-left:10px; +} + .workflow-invocation-complete{ border:solid 1px #6A6; border-left-width:5px; diff -r 80291f7ad4576c95f70eaed2f36cc5a95cf303fb -r c1faecf25f52a01cf55ba95df42791bf3399ed59 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2,7 +2,7 @@ audio,canvas,video{display:inline-block;*display:inline;*zoom:1;} audio:not([controls]){display:none;} html{font-size:100%;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%;} -a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} +a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} a:hover,a:active{outline:0;} sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline;} sup{top:-0.5em;} @@ -14,18 +14,18 @@ button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0;} button,html input[type="button"],input[type="reset"],input[type="submit"]{-webkit-appearance:button;cursor:pointer;} label,select,button,input[type="button"],input[type="reset"],input[type="submit"],input[type="radio"],input[type="checkbox"]{cursor:pointer;} -input[type="search"]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield;} +input[type="search"]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield;} input[type="search"]::-webkit-search-decoration,input[type="search"]::-webkit-search-cancel-button{-webkit-appearance:none;} textarea{overflow:auto;vertical-align:top;} @media print{*{text-shadow:none !important;color:#000 !important;background:transparent !important;box-shadow:none !important;} a,a:visited{text-decoration:underline;} a[href]:after{content:" (" attr(href) ")";} abbr[title]:after{content:" (" attr(title) ")";} .ir a:after,a[href^="javascript:"]:after,a[href^="#"]:after{content:"";} pre,blockquote{border:1px solid #999;page-break-inside:avoid;} thead{display:table-header-group;} tr,img{page-break-inside:avoid;} img{max-width:100% !important;} @page {margin:0.5cm;}p,h2,h3{orphans:3;widows:3;} h2,h3{page-break-after:avoid;}}.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";line-height:0;} .clearfix:after{clear:both;} .hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;} -.input-block-level{display:block;width:100%;min-height:26px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;} +.input-block-level{display:block;width:100%;min-height:26px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;} article,aside,details,figcaption,figure,footer,header,hgroup,nav,section{display:block;} audio,canvas,video{display:inline-block;*display:inline;*zoom:1;} audio:not([controls]){display:none;} html{font-size:100%;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%;} -a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} +a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} a:hover,a:active{outline:0;} sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline;} sup{top:-0.5em;} @@ -37,19 +37,19 @@ button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0;} button,html input[type="button"],input[type="reset"],input[type="submit"]{-webkit-appearance:button;cursor:pointer;} label,select,button,input[type="button"],input[type="reset"],input[type="submit"],input[type="radio"],input[type="checkbox"]{cursor:pointer;} -input[type="search"]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield;} +input[type="search"]{-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;-webkit-appearance:textfield;} input[type="search"]::-webkit-search-decoration,input[type="search"]::-webkit-search-cancel-button{-webkit-appearance:none;} textarea{overflow:auto;vertical-align:top;} @media print{*{text-shadow:none !important;color:#000 !important;background:transparent !important;box-shadow:none !important;} a,a:visited{text-decoration:underline;} a[href]:after{content:" (" attr(href) ")";} abbr[title]:after{content:" (" attr(title) ")";} .ir a:after,a[href^="javascript:"]:after,a[href^="#"]:after{content:"";} pre,blockquote{border:1px solid #999;page-break-inside:avoid;} thead{display:table-header-group;} tr,img{page-break-inside:avoid;} img{max-width:100% !important;} @page {margin:0.5cm;}p,h2,h3{orphans:3;widows:3;} h2,h3{page-break-after:avoid;}}.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";line-height:0;} .clearfix:after{clear:both;} .hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;} -.input-block-level{display:block;width:100%;min-height:26px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;} +.input-block-level{display:block;width:100%;min-height:26px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;} body{margin:0;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;color:#111111;background-color:#ffffff;} a{color:#303030;text-decoration:none;} a:hover{color:#0a0a0a;text-decoration:underline;} -.img-rounded{-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;} -.img-polaroid{padding:4px;background-color:#fff;border:1px solid #ccc;border:1px solid rgba(0, 0, 0, 0.2);-webkit-box-shadow:0 1px 3px rgba(0, 0, 0, 0.1);-moz-box-shadow:0 1px 3px rgba(0, 0, 0, 0.1);box-shadow:0 1px 3px rgba(0, 0, 0, 0.1);} -.img-circle{-webkit-border-radius:500px;-moz-border-radius:500px;border-radius:500px;} +.img-rounded{-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;} +.img-polaroid{padding:4px;background-color:#fff;border:1px solid #ccc;border:1px solid rgba(0, 0, 0, 0.2);-webkit-box-shadow:0 1px 3px rgba(0, 0, 0, 0.1);-moz-box-shadow:0 1px 3px rgba(0, 0, 0, 0.1);box-shadow:0 1px 3px rgba(0, 0, 0, 0.1);-webkit-box-shadow:0 1px 3px rgba(0, 0, 0, 0.1);-moz-box-shadow:0 1px 3px rgba(0, 0, 0, 0.1);box-shadow:0 1px 3px rgba(0, 0, 0, 0.1);} +.img-circle{-webkit-border-radius:500px;-moz-border-radius:500px;border-radius:500px;-webkit-border-radius:500px;-moz-border-radius:500px;border-radius:500px;-webkit-border-radius:500px;-moz-border-radius:500px;border-radius:500px;} p{margin:0 0 8px;} .lead{margin-bottom:16px;font-size:18px;font-weight:200;line-height:24px;} small{font-size:85%;} @@ -83,21 +83,21 @@ ul ul,ul ol,ol ol,ol ul{margin-bottom:0;} li{line-height:16px;} ul.unstyled,ol.unstyled{margin-left:0;list-style:none;} -ul.inline,ol.inline{margin-left:0;list-style:none;}ul.inline>li,ol.inline>li{display:inline-block;padding-left:5px;padding-right:5px;} +ul.inline,ol.inline{margin-left:0;list-style:none;}ul.inline >li,ol.inline >li{display:inline-block;padding-left:5px;padding-right:5px;} dl{margin-bottom:16px;} dt,dd{line-height:16px;} dt{font-weight:bold;} dd{margin-left:8px;} -.dl-horizontal{*zoom:1;}.dl-horizontal:before,.dl-horizontal:after{display:table;content:"";line-height:0;} +.dl-horizontal{*zoom:1;*zoom:1;}.dl-horizontal:before,.dl-horizontal:after{display:table;content:"";line-height:0;} .dl-horizontal:after{clear:both;} .dl-horizontal:before,.dl-horizontal:after{display:table;content:"";line-height:0;} .dl-horizontal:after{clear:both;} -.dl-horizontal dt{float:left;width:160px;clear:left;text-align:right;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;} +.dl-horizontal dt{float:left;width:160px;clear:left;text-align:right;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;} .dl-horizontal dd{margin-left:180px;} hr{margin:16px 0;border:0;border-top:1px solid #eeeeee;border-bottom:1px solid #ffffff;} abbr[title],abbr[data-original-title]{cursor:help;border-bottom:1px dotted #999999;} abbr.initialism{font-size:90%;text-transform:uppercase;} -blockquote{padding:0 0 0 15px;margin:0 0 16px;border-left:5px solid #eeeeee;}blockquote p{margin-bottom:0;font-size:16px;font-weight:300;line-height:20px;} +blockquote{padding:0 0 0 15px;margin:0 0 16px;border-left:5px solid #eeeeee;}blockquote p{margin-bottom:0;font-size:16px;font-weight:300;line-height:20px;font-size:16px;font-weight:300;line-height:20px;} blockquote small{display:block;line-height:16px;color:#999999;}blockquote small:before{content:'\2014 \00A0';} blockquote.pull-right{float:right;padding-right:15px;padding-left:0;border-right:5px solid #eeeeee;border-left:0;}blockquote.pull-right p,blockquote.pull-right small{text-align:right;} blockquote.pull-right small:before{content:'';} @@ -112,31 +112,31 @@ .table tbody+tbody{border-top:2px solid #dddddd;} .table .table{background-color:#ffffff;} .table-condensed th,.table-condensed td{padding:4px 5px;} -.table-bordered{border:1px solid #dddddd;border-collapse:separate;*border-collapse:collapse;border-left:0;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;}.table-bordered th,.table-bordered td{border-left:1px solid #dddddd;} +.table-bordered{border:1px solid #dddddd;border-collapse:separate;*border-collapse:collapse;border-left:0;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;}.table-bordered th,.table-bordered td{border-left:1px solid #dddddd;} .table-bordered caption+thead tr:first-child th,.table-bordered caption+tbody tr:first-child th,.table-bordered caption+tbody tr:first-child td,.table-bordered colgroup+thead tr:first-child th,.table-bordered colgroup+tbody tr:first-child th,.table-bordered colgroup+tbody tr:first-child td,.table-bordered thead:first-child tr:first-child th,.table-bordered tbody:first-child tr:first-child th,.table-bordered tbody:first-child tr:first-child td{border-top:0;} -.table-bordered thead:first-child tr:first-child>th:first-child,.table-bordered tbody:first-child tr:first-child>td:first-child{-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;} -.table-bordered thead:first-child tr:first-child>th:last-child,.table-bordered tbody:first-child tr:first-child>td:last-child{-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;} -.table-bordered thead:last-child tr:last-child>th:first-child,.table-bordered tbody:last-child tr:last-child>td:first-child,.table-bordered tfoot:last-child tr:last-child>td:first-child{-webkit-border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;border-bottom-left-radius:4px;} -.table-bordered thead:last-child tr:last-child>th:last-child,.table-bordered tbody:last-child tr:last-child>td:last-child,.table-bordered tfoot:last-child tr:last-child>td:last-child{-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px;} -.table-bordered tfoot+tbody:last-child tr:last-child td:first-child{-webkit-border-bottom-left-radius:0;-moz-border-radius-bottomleft:0;border-bottom-left-radius:0;} -.table-bordered tfoot+tbody:last-child tr:last-child td:last-child{-webkit-border-bottom-right-radius:0;-moz-border-radius-bottomright:0;border-bottom-right-radius:0;} -.table-bordered caption+thead tr:first-child th:first-child,.table-bordered caption+tbody tr:first-child td:first-child,.table-bordered colgroup+thead tr:first-child th:first-child,.table-bordered colgroup+tbody tr:first-child td:first-child{-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;} -.table-bordered caption+thead tr:first-child th:last-child,.table-bordered caption+tbody tr:first-child td:last-child,.table-bordered colgroup+thead tr:first-child th:last-child,.table-bordered colgroup+tbody tr:first-child td:last-child{-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;} +.table-bordered thead:first-child tr:first-child>th:first-child,.table-bordered tbody:first-child tr:first-child>td:first-child{-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;} +.table-bordered thead:first-child tr:first-child>th:last-child,.table-bordered tbody:first-child tr:first-child>td:last-child{-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;} +.table-bordered thead:last-child tr:last-child>th:first-child,.table-bordered tbody:last-child tr:last-child>td:first-child,.table-bordered tfoot:last-child tr:last-child>td:first-child{-webkit-border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;border-bottom-left-radius:4px;-webkit-border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;border-bottom-left-radius:4px;} +.table-bordered thead:last-child tr:last-child>th:last-child,.table-bordered tbody:last-child tr:last-child>td:last-child,.table-bordered tfoot:last-child tr:last-child>td:last-child{-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px;-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px;} +.table-bordered tfoot+tbody:last-child tr:last-child td:first-child{-webkit-border-bottom-left-radius:0;-moz-border-radius-bottomleft:0;border-bottom-left-radius:0;-webkit-border-bottom-left-radius:0;-moz-border-radius-bottomleft:0;border-bottom-left-radius:0;} +.table-bordered tfoot+tbody:last-child tr:last-child td:last-child{-webkit-border-bottom-right-radius:0;-moz-border-radius-bottomright:0;border-bottom-right-radius:0;-webkit-border-bottom-right-radius:0;-moz-border-radius-bottomright:0;border-bottom-right-radius:0;} +.table-bordered caption+thead tr:first-child th:first-child,.table-bordered caption+tbody tr:first-child td:first-child,.table-bordered colgroup+thead tr:first-child th:first-child,.table-bordered colgroup+tbody tr:first-child td:first-child{-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;} +.table-bordered caption+thead tr:first-child th:last-child,.table-bordered caption+tbody tr:first-child td:last-child,.table-bordered colgroup+thead tr:first-child th:last-child,.table-bordered colgroup+tbody tr:first-child td:last-child{-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;} .table-striped tbody>tr:nth-child(odd)>td,.table-striped tbody>tr:nth-child(odd)>th{background-color:#f9f9f9;} .table-hover tbody tr:hover td,.table-hover tbody tr:hover th{background-color:#f5f5f5;} table td[class*="span"],table th[class*="span"],.row-fluid table td[class*="span"],.row-fluid table th[class*="span"]{display:table-cell;float:none;margin-left:0;} -.table td.span1,.table th.span1{float:none;width:44px;margin-left:0;} -.table td.span2,.table th.span2{float:none;width:124px;margin-left:0;} -.table td.span3,.table th.span3{float:none;width:204px;margin-left:0;} -.table td.span4,.table th.span4{float:none;width:284px;margin-left:0;} -.table td.span5,.table th.span5{float:none;width:364px;margin-left:0;} -.table td.span6,.table th.span6{float:none;width:444px;margin-left:0;} -.table td.span7,.table th.span7{float:none;width:524px;margin-left:0;} -.table td.span8,.table th.span8{float:none;width:604px;margin-left:0;} -.table td.span9,.table th.span9{float:none;width:684px;margin-left:0;} -.table td.span10,.table th.span10{float:none;width:764px;margin-left:0;} -.table td.span11,.table th.span11{float:none;width:844px;margin-left:0;} -.table td.span12,.table th.span12{float:none;width:924px;margin-left:0;} +.table td.span1,.table th.span1{float:none;width:44px;margin-left:0;float:none;width:44px;margin-left:0;} +.table td.span2,.table th.span2{float:none;width:124px;margin-left:0;float:none;width:124px;margin-left:0;} +.table td.span3,.table th.span3{float:none;width:204px;margin-left:0;float:none;width:204px;margin-left:0;} +.table td.span4,.table th.span4{float:none;width:284px;margin-left:0;float:none;width:284px;margin-left:0;} +.table td.span5,.table th.span5{float:none;width:364px;margin-left:0;float:none;width:364px;margin-left:0;} +.table td.span6,.table th.span6{float:none;width:444px;margin-left:0;float:none;width:444px;margin-left:0;} +.table td.span7,.table th.span7{float:none;width:524px;margin-left:0;float:none;width:524px;margin-left:0;} +.table td.span8,.table th.span8{float:none;width:604px;margin-left:0;float:none;width:604px;margin-left:0;} +.table td.span9,.table th.span9{float:none;width:684px;margin-left:0;float:none;width:684px;margin-left:0;} +.table td.span10,.table th.span10{float:none;width:764px;margin-left:0;float:none;width:764px;margin-left:0;} +.table td.span11,.table th.span11{float:none;width:844px;margin-left:0;float:none;width:844px;margin-left:0;} +.table td.span12,.table th.span12{float:none;width:924px;margin-left:0;float:none;width:924px;margin-left:0;} .table tbody tr.success td{background-color:#ccffcc;} .table tbody tr.error td{background-color:#ffcccc;} .table tbody tr.warning td{background-color:#ffffcc;} @@ -150,75 +150,75 @@ .dropdown-toggle:active,.open .dropdown-toggle{outline:0;} .caret{display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";} .dropdown .caret{margin-top:8px;margin-left:2px;} -.dropdown-menu{position:absolute;top:100%;left:0;z-index:1000;display:none;float:left;min-width:160px;padding:5px 0;margin:2px 0 0;list-style:none;background-color:#ffffff;border:1px solid #ccc;border:1px solid rgba(0, 0, 0, 0.2);*border-right-width:2px;*border-bottom-width:2px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-moz-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-webkit-background-clip:padding-box;-moz-background-clip:padding;background-clip:padding-box;}.dropdown-menu.pull-right{right:0;left:auto;} -.dropdown-menu .divider{*width:100%;height:1px;margin:7px 1px;*margin:-5px 0 5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;} +.dropdown-menu{position:absolute;top:100%;left:0;z-index:1000;display:none;float:left;min-width:160px;padding:5px 0;margin:2px 0 0;list-style:none;background-color:#ffffff;border:1px solid #ccc;border:1px solid rgba(0, 0, 0, 0.2);*border-right-width:2px;*border-bottom-width:2px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-moz-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-webkit-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-moz-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-webkit-background-clip:padding-box;-moz-background-clip:padding;background-clip:padding-box;}.dropdown-menu.pull-right{right:0;left:auto;} +.dropdown-menu .divider{*width:100%;height:1px;margin:7px 1px;*margin:-5px 0 5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;*width:100%;height:1px;margin:7px 1px;*margin:-5px 0 5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;} .dropdown-menu li>a{display:block;padding:3px 20px;clear:both;font-weight:normal;line-height:16px;color:#333333;white-space:nowrap;} -.dropdown-menu li>a:hover,.dropdown-menu li>a:focus,.dropdown-submenu:hover>a{text-decoration:none;color:#ffffff;background-color:#2b2b2b;background-image:-moz-linear-gradient(top, #303030, #232323);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#303030), to(#232323));background-image:-webkit-linear-gradient(top, #303030, #232323);background-image:-o-linear-gradient(top, #303030, #232323);background-image:linear-gradient(to bottom, #303030, #232323);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff303030', endColorstr='#ff232323', GradientType=0);} -.dropdown-menu .active>a,.dropdown-menu .active>a:hover{color:#ffffff;text-decoration:none;outline:0;background-color:#2b2b2b;background-image:-moz-linear-gradient(top, #303030, #232323);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#303030), to(#232323));background-image:-webkit-linear-gradient(top, #303030, #232323);background-image:-o-linear-gradient(top, #303030, #232323);background-image:linear-gradient(to bottom, #303030, #232323);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff303030', endColorstr='#ff232323', GradientType=0);} +.dropdown-menu li>a:hover,.dropdown-menu li>a:focus,.dropdown-submenu:hover>a{text-decoration:none;color:#ffffff;background-color:#2b2b2b;background-image:-moz-linear-gradient(top, #303030, #232323);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#303030), to(#232323));background-image:-webkit-linear-gradient(top, #303030, #232323);background-image:-o-linear-gradient(top, #303030, #232323);background-image:linear-gradient(to bottom, #303030, #232323);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff303030', endColorstr='#ff232323', GradientType=0);background-color:#2b2b2b;background-image:-moz-linear-gradient(top, #303030, #232323);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#303030), to(#232323));background-image:-webkit-linear-gradient(top, #303030, #232323);background-image:-o-linear-gradient(top, #303030, #232323);background-image:linear-gradient(to bottom, #303030, #232323);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff303030', endColorstr='#ff232323', GradientType=0);} +.dropdown-menu .active>a,.dropdown-menu .active>a:hover{color:#ffffff;text-decoration:none;outline:0;background-color:#2b2b2b;background-image:-moz-linear-gradient(top, #303030, #232323);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#303030), to(#232323));background-image:-webkit-linear-gradient(top, #303030, #232323);background-image:-o-linear-gradient(top, #303030, #232323);background-image:linear-gradient(to bottom, #303030, #232323);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff303030', endColorstr='#ff232323', GradientType=0);background-color:#2b2b2b;background-image:-moz-linear-gradient(top, #303030, #232323);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#303030), to(#232323));background-image:-webkit-linear-gradient(top, #303030, #232323);background-image:-o-linear-gradient(top, #303030, #232323);background-image:linear-gradient(to bottom, #303030, #232323);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff303030', endColorstr='#ff232323', GradientType=0);} .dropdown-menu .disabled>a,.dropdown-menu .disabled>a:hover{color:#999999;} -.dropdown-menu .disabled>a:hover{text-decoration:none;background-color:transparent;background-image:none;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);cursor:default;} -.open{*z-index:1000;}.open>.dropdown-menu{display:block;} +.dropdown-menu .disabled>a:hover{text-decoration:none;background-color:transparent;background-image:none;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);cursor:default;} +.open{*z-index:1000;}.open >.dropdown-menu{display:block;} .pull-right>.dropdown-menu{right:0;left:auto;} .dropup .caret,.navbar-fixed-bottom .dropdown .caret{border-top:0;border-bottom:4px solid #000000;content:"";} .dropup .dropdown-menu,.navbar-fixed-bottom .dropdown .dropdown-menu{top:auto;bottom:100%;margin-bottom:1px;} .dropdown-submenu{position:relative;} -.dropdown-submenu>.dropdown-menu{top:0;left:100%;margin-top:-6px;margin-left:-1px;-webkit-border-radius:0 6px 6px 6px;-moz-border-radius:0 6px 6px 6px;border-radius:0 6px 6px 6px;} +.dropdown-submenu>.dropdown-menu{top:0;left:100%;margin-top:-6px;margin-left:-1px;-webkit-border-radius:0 6px 6px 6px;-moz-border-radius:0 6px 6px 6px;border-radius:0 6px 6px 6px;-webkit-border-radius:0 6px 6px 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+.btn-group>.btn:last-child,.btn-group>.dropdown-toggle{-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px;-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px;} +.btn-group>.btn.large:first-child{margin-left:0;-webkit-border-top-left-radius:6px;-moz-border-radius-topleft:6px;border-top-left-radius:6px;-webkit-border-top-left-radius:6px;-moz-border-radius-topleft:6px;border-top-left-radius:6px;-webkit-border-bottom-left-radius:6px;-moz-border-radius-bottomleft:6px;border-bottom-left-radius:6px;-webkit-border-bottom-left-radius:6px;-moz-border-radius-bottomleft:6px;border-bottom-left-radius:6px;} +.btn-group>.btn.large:last-child,.btn-group>.large.dropdown-toggle{-webkit-border-top-right-radius:6px;-moz-border-radius-topright:6px;border-top-right-radius:6px;-webkit-border-top-right-radius:6px;-moz-border-radius-topright:6px;border-top-right-radius:6px;-webkit-border-bottom-right-radius:6px;-moz-border-radius-bottomright:6px;border-bottom-right-radius:6px;-webkit-border-bottom-right-radius:6px;-moz-border-radius-bottomright:6px;border-bottom-right-radius:6px;} .btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active{z-index:2;} .btn-group .dropdown-toggle:active,.btn-group.open .dropdown-toggle{outline:0;} -.btn-group>.btn+.dropdown-toggle{padding-left:8px;padding-right:8px;-webkit-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);*padding-top:5px;*padding-bottom:5px;} +.btn-group>.btn+.dropdown-toggle{padding-left:8px;padding-right:8px;-webkit-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-webkit-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);*padding-top:5px;*padding-bottom:5px;} .btn-group>.btn-mini+.dropdown-toggle{padding-left:5px;padding-right:5px;*padding-top:2px;*padding-bottom:2px;} .btn-group>.btn-small+.dropdown-toggle{*padding-top:5px;*padding-bottom:4px;} .btn-group>.btn-large+.dropdown-toggle{padding-left:12px;padding-right:12px;*padding-top:7px;*padding-bottom:7px;} -.btn-group.open .dropdown-toggle{background-image:none;-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);} +.btn-group.open .dropdown-toggle{background-image:none;-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);-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);} .btn-group.open .btn.dropdown-toggle{background-color:#e6e6e6;} .btn-group.open .btn-primary.dropdown-toggle{background-color:#0031cd;} .btn-group.open .btn-warning.dropdown-toggle{background-color:#f89406;} @@ -263,14 +263,14 @@ .btn-large .caret{border-left-width:5px;border-right-width:5px;border-top-width:5px;} .dropup .btn-large .caret{border-bottom-width:5px;} .btn-primary .caret,.btn-warning .caret,.btn-danger .caret,.btn-info .caret,.btn-success .caret,.btn-inverse .caret{border-top-color:#ffffff;border-bottom-color:#ffffff;} -.btn-group-vertical{display:inline-block;*display:inline;*zoom:1;} -.btn-group-vertical>.btn{display:block;float:none;max-width:100%;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} +.btn-group-vertical{display:inline-block;*display:inline;*zoom:1;*display:inline;*zoom:1;} +.btn-group-vertical>.btn{display:block;float:none;max-width:100%;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} .btn-group-vertical>.btn+.btn{margin-left:0;margin-top:-1px;} -.btn-group-vertical>.btn:first-child{-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;} -.btn-group-vertical>.btn:last-child{-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;} -.btn-group-vertical>.btn-large:first-child{-webkit-border-radius:6px 6px 0 0;-moz-border-radius:6px 6px 0 0;border-radius:6px 6px 0 0;} -.btn-group-vertical>.btn-large:last-child{-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;} -.alert{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.btn-group-vertical>.btn:first-child{-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;} +.btn-group-vertical>.btn:last-child{-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;} +.btn-group-vertical>.btn-large:first-child{-webkit-border-radius:6px 6px 0 0;-moz-border-radius:6px 6px 0 0;border-radius:6px 6px 0 0;-webkit-border-radius:6px 6px 0 0;-moz-border-radius:6px 6px 0 0;border-radius:6px 6px 0 0;-webkit-border-radius:6px 6px 0 0;-moz-border-radius:6px 6px 0 0;border-radius:6px 6px 0 0;} +.btn-group-vertical>.btn-large:last-child{-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;} +.alert{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} .alert,.alert h4{color:#666600;} .alert h4{margin:0;} .alert .close{position:relative;top:-2px;right:-21px;line-height:16px;} @@ -295,8 +295,8 @@ .nav-list>li>a{padding:3px 15px;} .nav-list>.active>a,.nav-list>.active>a:hover{color:#ffffff;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.2);background-color:#303030;} .nav-list [class^="icon-"],.nav-list [class*=" icon-"]{margin-right:2px;} -.nav-list .divider{*width:100%;height:1px;margin:7px 1px;*margin:-5px 0 5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;} -.nav-tabs,.nav-pills{*zoom:1;}.nav-tabs:before,.nav-pills:before,.nav-tabs:after,.nav-pills:after{display:table;content:"";line-height:0;} +.nav-list .divider{*width:100%;height:1px;margin:7px 1px;*margin:-5px 0 5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;*width:100%;height:1px;margin:7px 1px;*margin:-5px 0 5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;} +.nav-tabs,.nav-pills{*zoom:1;*zoom:1;}.nav-tabs:before,.nav-pills:before,.nav-tabs:after,.nav-pills:after{display:table;content:"";line-height:0;} .nav-tabs:after,.nav-pills:after{clear:both;} .nav-tabs:before,.nav-pills:before,.nav-tabs:after,.nav-pills:after{display:table;content:"";line-height:0;} .nav-tabs:after,.nav-pills:after{clear:both;} @@ -304,21 +304,21 @@ .nav-tabs>li>a,.nav-pills>li>a{padding-right:12px;padding-left:12px;margin-right:2px;line-height:14px;} .nav-tabs{border-bottom:1px solid #ddd;} .nav-tabs>li{margin-bottom:-1px;} -.nav-tabs>li>a{padding-top:8px;padding-bottom:8px;line-height:16px;border:1px solid transparent;-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;}.nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #dddddd;} +.nav-tabs>li>a{padding-top:8px;padding-bottom:8px;line-height:16px;border:1px solid transparent;-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;}.nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #dddddd;} .nav-tabs>.active>a,.nav-tabs>.active>a:hover{color:#555555;background-color:#ffffff;border:1px solid #ddd;border-bottom-color:transparent;cursor:default;} -.nav-pills>li>a{padding-top:8px;padding-bottom:8px;margin-top:2px;margin-bottom:2px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;} +.nav-pills>li>a{padding-top:8px;padding-bottom:8px;margin-top:2px;margin-bottom:2px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;} .nav-pills>.active>a,.nav-pills>.active>a:hover{color:#ffffff;background-color:#303030;} .nav-stacked>li{float:none;} .nav-stacked>li>a{margin-right:0;} .nav-tabs.nav-stacked{border-bottom:0;} -.nav-tabs.nav-stacked>li>a{border:1px solid #ddd;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} -.nav-tabs.nav-stacked>li:first-child>a{-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;} -.nav-tabs.nav-stacked>li:last-child>a{-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px;-webkit-border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;border-bottom-left-radius:4px;} +.nav-tabs.nav-stacked>li>a{border:1px solid #ddd;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} +.nav-tabs.nav-stacked>li:first-child>a{-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;} +.nav-tabs.nav-stacked>li:last-child>a{-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px;-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px;-webkit-border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;border-bottom-left-radius:4px;-webkit-border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;border-bottom-left-radius:4px;-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px;-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px;-webkit-border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;border-bottom-left-radius:4px;-webkit-border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;border-bottom-left-radius:4px;} .nav-tabs.nav-stacked>li>a:hover{border-color:#ddd;z-index:2;} .nav-pills.nav-stacked>li>a{margin-bottom:3px;} .nav-pills.nav-stacked>li:last-child>a{margin-bottom:1px;} -.nav-tabs .dropdown-menu{-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;} -.nav-pills .dropdown-menu{-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;} +.nav-tabs .dropdown-menu{-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;} +.nav-pills .dropdown-menu{-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;} .nav .dropdown-toggle .caret{border-top-color:#303030;border-bottom-color:#303030;margin-top:6px;} .nav .dropdown-toggle:hover .caret{border-top-color:#0a0a0a;border-bottom-color:#0a0a0a;} .nav-tabs .dropdown-toggle .caret{margin-top:8px;} @@ -326,9 +326,9 @@ .nav-tabs .active .dropdown-toggle .caret{border-top-color:#555555;border-bottom-color:#555555;} .nav>.dropdown.active>a:hover{cursor:pointer;} .nav-tabs .open .dropdown-toggle,.nav-pills .open .dropdown-toggle,.nav>li.dropdown.open.active>a:hover{color:#ffffff;background-color:#999999;border-color:#999999;} -.nav li.dropdown.open .caret,.nav li.dropdown.open.active .caret,.nav li.dropdown.open a:hover .caret{border-top-color:#ffffff;border-bottom-color:#ffffff;opacity:1;filter:alpha(opacity=100);} +.nav li.dropdown.open .caret,.nav li.dropdown.open.active .caret,.nav li.dropdown.open a:hover .caret{border-top-color:#ffffff;border-bottom-color:#ffffff;opacity:1;filter:alpha(opacity=100);opacity:1;filter:alpha(opacity=100);} .tabs-stacked .open>a:hover{border-color:#999999;} -.tabbable{*zoom:1;}.tabbable:before,.tabbable:after{display:table;content:"";line-height:0;} +.tabbable{*zoom:1;*zoom:1;}.tabbable:before,.tabbable:after{display:table;content:"";line-height:0;} .tabbable:after{clear:both;} .tabbable:before,.tabbable:after{display:table;content:"";line-height:0;} .tabbable:after{clear:both;} @@ -338,22 +338,22 @@ .tab-content>.active,.pill-content>.active{display:block;} .tabs-below>.nav-tabs{border-top:1px solid #ddd;} .tabs-below>.nav-tabs>li{margin-top:-1px;margin-bottom:0;} -.tabs-below>.nav-tabs>li>a{-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;}.tabs-below>.nav-tabs>li>a:hover{border-bottom-color:transparent;border-top-color:#ddd;} +.tabs-below>.nav-tabs>li>a{-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;}.tabs-below>.nav-tabs>li>a:hover{border-bottom-color:transparent;border-top-color:#ddd;} .tabs-below>.nav-tabs>.active>a,.tabs-below>.nav-tabs>.active>a:hover{border-color:transparent #ddd #ddd #ddd;} .tabs-left>.nav-tabs>li,.tabs-right>.nav-tabs>li{float:none;} .tabs-left>.nav-tabs>li>a,.tabs-right>.nav-tabs>li>a{min-width:74px;margin-right:0;margin-bottom:3px;} .tabs-left>.nav-tabs{float:left;margin-right:19px;border-right:1px solid #ddd;} -.tabs-left>.nav-tabs>li>a{margin-right:-1px;-webkit-border-radius:4px 0 0 4px;-moz-border-radius:4px 0 0 4px;border-radius:4px 0 0 4px;} +.tabs-left>.nav-tabs>li>a{margin-right:-1px;-webkit-border-radius:4px 0 0 4px;-moz-border-radius:4px 0 0 4px;border-radius:4px 0 0 4px;-webkit-border-radius:4px 0 0 4px;-moz-border-radius:4px 0 0 4px;border-radius:4px 0 0 4px;-webkit-border-radius:4px 0 0 4px;-moz-border-radius:4px 0 0 4px;border-radius:4px 0 0 4px;} .tabs-left>.nav-tabs>li>a:hover{border-color:#eeeeee #dddddd #eeeeee #eeeeee;} .tabs-left>.nav-tabs .active>a,.tabs-left>.nav-tabs .active>a:hover{border-color:#ddd transparent #ddd #ddd;*border-right-color:#ffffff;} .tabs-right>.nav-tabs{float:right;margin-left:19px;border-left:1px solid #ddd;} -.tabs-right>.nav-tabs>li>a{margin-left:-1px;-webkit-border-radius:0 4px 4px 0;-moz-border-radius:0 4px 4px 0;border-radius:0 4px 4px 0;} +.tabs-right>.nav-tabs>li>a{margin-left:-1px;-webkit-border-radius:0 4px 4px 0;-moz-border-radius:0 4px 4px 0;border-radius:0 4px 4px 0;-webkit-border-radius:0 4px 4px 0;-moz-border-radius:0 4px 4px 0;border-radius:0 4px 4px 0;-webkit-border-radius:0 4px 4px 0;-moz-border-radius:0 4px 4px 0;border-radius:0 4px 4px 0;} .tabs-right>.nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #eeeeee #dddddd;} .tabs-right>.nav-tabs .active>a,.tabs-right>.nav-tabs .active>a:hover{border-color:#ddd #ddd #ddd transparent;*border-left-color:#ffffff;} .nav>.disabled>a{color:#999999;} .nav>.disabled>a:hover{text-decoration:none;background-color:transparent;cursor:default;} .navbar{overflow:visible;margin-bottom:16px;*position:relative;*z-index:2;} -.navbar-inner{min-height:32px;padding-left:20px;padding-right:20px;background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(to bottom, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff333333', endColorstr='#ff2c3143', GradientType=0);border:1px solid #14161e;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);-moz-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);*zoom:1;}.navbar-inner:before,.navbar-inner:after{display:table;content:"";line-height:0;} +.navbar-inner{min-height:32px;padding-left:20px;padding-right:20px;background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(to bottom, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff333333', endColorstr='#ff2c3143', GradientType=0);background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(to bottom, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff333333', endColorstr='#ff2c3143', GradientType=0);border:1px solid #14161e;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);-moz-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);-webkit-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);-moz-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);*zoom:1;*zoom:1;}.navbar-inner:before,.navbar-inner:after{display:table;content:"";line-height:0;} .navbar-inner:after{clear:both;} .navbar-inner:before,.navbar-inner:after{display:table;content:"";line-height:0;} .navbar-inner:after{clear:both;} @@ -363,38 +363,38 @@ .navbar-text{margin-bottom:0;line-height:32px;color:#999999;} .navbar-link{color:#999999;}.navbar-link:hover{color:#ffffff;} .navbar .divider-vertical{height:32px;margin:0 9px;border-left:1px solid #2c3143;border-right:1px solid #333333;} -.navbar .btn,.navbar .btn-group{margin-top:1px;} +.navbar .btn,.navbar .btn-group{margin-top:1px;margin-top:1px;} .navbar .btn-group .btn,.navbar .input-prepend .btn,.navbar .input-append .btn{margin-top:0;} -.navbar-form{margin-bottom:0;*zoom:1;}.navbar-form:before,.navbar-form:after{display:table;content:"";line-height:0;} +.navbar-form{margin-bottom:0;*zoom:1;*zoom:1;}.navbar-form:before,.navbar-form:after{display:table;content:"";line-height:0;} .navbar-form:after{clear:both;} .navbar-form:before,.navbar-form:after{display:table;content:"";line-height:0;} .navbar-form:after{clear:both;} -.navbar-form input,.navbar-form select,.navbar-form .radio,.navbar-form .checkbox{margin-top:1px;} +.navbar-form input,.navbar-form select,.navbar-form .radio,.navbar-form .checkbox{margin-top:1px;margin-top:1px;} .navbar-form input,.navbar-form select,.navbar-form .btn{display:inline-block;margin-bottom:0;} .navbar-form input[type="image"],.navbar-form input[type="checkbox"],.navbar-form input[type="radio"]{margin-top:3px;} .navbar-form .input-append,.navbar-form .input-prepend{margin-top:5px;white-space:nowrap;}.navbar-form .input-append input,.navbar-form .input-prepend input{margin-top:0;} -.navbar-search{position:relative;float:left;margin-top:1px;margin-bottom:0;}.navbar-search .search-query{margin-bottom:0;padding:4px 14px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:13px;font-weight:normal;line-height:1;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;} -.navbar-static-top{position:static;margin-bottom:0;}.navbar-static-top .navbar-inner{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} +.navbar-search{position:relative;float:left;margin-top:1px;margin-top:1px;margin-bottom:0;}.navbar-search .search-query{margin-bottom:0;padding:4px 14px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:13px;font-weight:normal;line-height:1;font-size:13px;font-weight:normal;line-height:1;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:13px;font-weight:normal;line-height:1;font-size:13px;font-weight:normal;line-height:1;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;} +.navbar-static-top{position:static;margin-bottom:0;}.navbar-static-top .navbar-inner{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} .navbar-fixed-top,.navbar-fixed-bottom{position:fixed;right:0;left:0;z-index:1030;margin-bottom:0;} .navbar-fixed-top .navbar-inner,.navbar-static-top .navbar-inner{border-width:0 0 1px;} .navbar-fixed-bottom .navbar-inner{border-width:1px 0 0;} -.navbar-fixed-top .navbar-inner,.navbar-fixed-bottom .navbar-inner{padding-left:0;padding-right:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} -.navbar-static-top .container,.navbar-fixed-top .container,.navbar-fixed-bottom .container{width:940px;} +.navbar-fixed-top .navbar-inner,.navbar-fixed-bottom .navbar-inner{padding-left:0;padding-right:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} +.navbar-static-top .container,.navbar-fixed-top .container,.navbar-fixed-bottom .container{width:940px;width:940px;} .navbar-fixed-top{top:0;} -.navbar-fixed-top .navbar-inner,.navbar-static-top .navbar-inner{-webkit-box-shadow:0 1px 10px rgba(0,0,0,.1);-moz-box-shadow:0 1px 10px rgba(0,0,0,.1);box-shadow:0 1px 10px rgba(0,0,0,.1);} -.navbar-fixed-bottom{bottom:0;}.navbar-fixed-bottom .navbar-inner{-webkit-box-shadow:0 -1px 10px rgba(0,0,0,.1);-moz-box-shadow:0 -1px 10px rgba(0,0,0,.1);box-shadow:0 -1px 10px rgba(0,0,0,.1);} +.navbar-fixed-top .navbar-inner,.navbar-static-top .navbar-inner{-webkit-box-shadow:0 1px 10px rgba(0,0,0,.1);-moz-box-shadow:0 1px 10px rgba(0,0,0,.1);box-shadow:0 1px 10px rgba(0,0,0,.1);-webkit-box-shadow:0 1px 10px rgba(0,0,0,.1);-moz-box-shadow:0 1px 10px rgba(0,0,0,.1);box-shadow:0 1px 10px rgba(0,0,0,.1);} +.navbar-fixed-bottom{bottom:0;}.navbar-fixed-bottom .navbar-inner{-webkit-box-shadow:0 -1px 10px rgba(0,0,0,.1);-moz-box-shadow:0 -1px 10px rgba(0,0,0,.1);box-shadow:0 -1px 10px rgba(0,0,0,.1);-webkit-box-shadow:0 -1px 10px rgba(0,0,0,.1);-moz-box-shadow:0 -1px 10px rgba(0,0,0,.1);box-shadow:0 -1px 10px rgba(0,0,0,.1);} .navbar .nav{position:relative;left:0;display:block;float:left;margin:0 10px 0 0;} .navbar .nav.pull-right{float:right;margin-right:0;} .navbar .nav>li{float:left;} .navbar .nav>li>a{float:none;padding:8px 15px 8px;color:#999999;text-decoration:none;text-shadow:0 1px 0 #333333;} .navbar .nav .dropdown-toggle .caret{margin-top:8px;} .navbar .nav>li>a:focus,.navbar .nav>li>a:hover{background-color:transparent;color:#ffffff;text-decoration:none;} -.navbar .nav>.active>a,.navbar .nav>.active>a:hover,.navbar .nav>.active>a:focus{color:#ffffff;text-decoration:none;background-color:rgba(0, 0, 0, 0.5);-webkit-box-shadow:inset 0 3px 8px rgba(0, 0, 0, 0.125);-moz-box-shadow:inset 0 3px 8px rgba(0, 0, 0, 0.125);box-shadow:inset 0 3px 8px rgba(0, 0, 0, 0.125);} -.navbar .btn-navbar{display:none;float:right;padding:7px 10px;margin-left:5px;margin-right:5px;color:#ffffff;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);background-color:#25262c;background-image:-moz-linear-gradient(top, #262626, #222634);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#262626), to(#222634));background-image:-webkit-linear-gradient(top, #262626, #222634);background-image:-o-linear-gradient(top, #262626, #222634);background-image:linear-gradient(to bottom, #262626, #222634);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff262626', endColorstr='#ff222634', GradientType=0);border-color:#222634 #222634 #040405;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);*background-color:#222634;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);}.navbar .btn-navbar:hover,.navbar .btn-navbar:active,.navbar .btn-navbar.active,.navbar .btn-navbar.disabled,.navbar .btn-navbar[disabled]{color:#ffffff;background-color:#222634;*background-color:#181a24;} +.navbar .nav>.active>a,.navbar .nav>.active>a:hover,.navbar .nav>.active>a:focus{color:#ffffff;text-decoration:none;background-color:rgba(0, 0, 0, 0.5);-webkit-box-shadow:inset 0 3px 8px rgba(0, 0, 0, 0.125);-moz-box-shadow:inset 0 3px 8px rgba(0, 0, 0, 0.125);box-shadow:inset 0 3px 8px rgba(0, 0, 0, 0.125);-webkit-box-shadow:inset 0 3px 8px rgba(0, 0, 0, 0.125);-moz-box-shadow:inset 0 3px 8px rgba(0, 0, 0, 0.125);box-shadow:inset 0 3px 8px rgba(0, 0, 0, 0.125);} +.navbar .btn-navbar{display:none;float:right;padding:7px 10px;margin-left:5px;margin-right:5px;color:#ffffff;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);background-color:#25262c;background-image:-moz-linear-gradient(top, #262626, #222634);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#262626), to(#222634));background-image:-webkit-linear-gradient(top, #262626, #222634);background-image:-o-linear-gradient(top, #262626, #222634);background-image:linear-gradient(to bottom, #262626, #222634);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff262626', endColorstr='#ff222634', GradientType=0);background-color:#25262c;background-image:-moz-linear-gradient(top, #262626, #222634);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#262626), to(#222634));background-image:-webkit-linear-gradient(top, #262626, #222634);background-image:-o-linear-gradient(top, #262626, #222634);background-image:linear-gradient(to bottom, #262626, #222634);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff262626', endColorstr='#ff222634', GradientType=0);border-color:#222634 #222634 #040405;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);color:#ffffff;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);background-color:#25262c;background-image:-moz-linear-gradient(top, #262626, #222634);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#262626), to(#222634));background-image:-webkit-linear-gradient(top, #262626, #222634);background-image:-o-linear-gradient(top, #262626, #222634);background-image:linear-gradient(to bottom, #262626, #222634);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff262626', endColorstr='#ff222634', GradientType=0);background-color:#25262c;background-image:-moz-linear-gradient(top, #262626, #222634);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#262626), to(#222634));background-image:-webkit-linear-gradient(top, #262626, #222634);background-image:-o-linear-gradient(top, #262626, #222634);background-image:linear-gradient(to bottom, #262626, #222634);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff262626', endColorstr='#ff222634', GradientType=0);border-color:#222634 #222634 #040405;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);*background-color:#222634;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);color:#ffffff;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);background-color:#25262c;background-image:-moz-linear-gradient(top, #262626, #222634);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#262626), to(#222634));background-image:-webkit-linear-gradient(top, #262626, #222634);background-image:-o-linear-gradient(top, #262626, #222634);background-image:linear-gradient(to bottom, #262626, #222634);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff262626', endColorstr='#ff222634', GradientType=0);background-color:#25262c;background-image:-moz-linear-gradient(top, #262626, #222634);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#262626), to(#222634));background-image:-webkit-linear-gradient(top, #262626, #222634);background-image:-o-linear-gradient(top, #262626, #222634);background-image:linear-gradient(to bottom, #262626, #222634);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff262626', endColorstr='#ff222634', GradientType=0);border-color:#222634 #222634 #040405;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);color:#ffffff;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);background-color:#25262c;background-image:-moz-linear-gradient(top, #262626, #222634);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#262626), to(#222634));background-image:-webkit-linear-gradient(top, #262626, #222634);background-image:-o-linear-gradient(top, #262626, #222634);background-image:linear-gradient(to bottom, #262626, #222634);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff262626', endColorstr='#ff222634', GradientType=0);background-color:#25262c;background-image:-moz-linear-gradient(top, #262626, #222634);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#262626), to(#222634));background-image:-webkit-linear-gradient(top, #262626, #222634);background-image:-o-linear-gradient(top, #262626, #222634);background-image:linear-gradient(to bottom, #262626, #222634);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff262626', endColorstr='#ff222634', GradientType=0);border-color:#222634 #222634 #040405;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);*background-color:#222634;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);}.navbar .btn-navbar:hover,.navbar .btn-navbar:active,.navbar .btn-navbar.active,.navbar .btn-navbar.disabled,.navbar .btn-navbar[disabled]{color:#ffffff;background-color:#222634;*background-color:#181a24;} .navbar .btn-navbar:active,.navbar .btn-navbar.active{background-color:#0e0f15 \9;} .navbar .btn-navbar:hover,.navbar .btn-navbar:active,.navbar .btn-navbar.active,.navbar .btn-navbar.disabled,.navbar .btn-navbar[disabled]{color:#ffffff;background-color:#222634;*background-color:#181a24;} .navbar .btn-navbar:active,.navbar .btn-navbar.active{background-color:#0e0f15 \9;} -.navbar .btn-navbar .icon-bar{display:block;width:18px;height:2px;background-color:#f5f5f5;-webkit-border-radius:1px;-moz-border-radius:1px;border-radius:1px;-webkit-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);-moz-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);} +.navbar .btn-navbar .icon-bar{display:block;width:18px;height:2px;background-color:#f5f5f5;-webkit-border-radius:1px;-moz-border-radius:1px;border-radius:1px;-webkit-border-radius:1px;-moz-border-radius:1px;border-radius:1px;-webkit-border-radius:1px;-moz-border-radius:1px;border-radius:1px;-webkit-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);-moz-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);-webkit-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);-moz-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);} .btn-navbar .icon-bar+.icon-bar{margin-top:3px;} .navbar .nav>li>.dropdown-menu:before{content:'';display:inline-block;border-left:7px solid transparent;border-right:7px solid transparent;border-bottom:7px solid #ccc;border-bottom-color:rgba(0, 0, 0, 0.2);position:absolute;top:-7px;left:9px;} .navbar .nav>li>.dropdown-menu:after{content:'';display:inline-block;border-left:6px solid transparent;border-right:6px solid transparent;border-bottom:6px solid #ffffff;position:absolute;top:-6px;left:10px;} @@ -406,8 +406,8 @@ .navbar .nav li.dropdown.open>.dropdown-toggle .caret,.navbar .nav li.dropdown.active>.dropdown-toggle .caret,.navbar .nav li.dropdown.open.active>.dropdown-toggle .caret{border-top-color:#ffffff;border-bottom-color:#ffffff;} .navbar .pull-right>li>.dropdown-menu,.navbar .nav>li>.dropdown-menu.pull-right{left:auto;right:0;}.navbar .pull-right>li>.dropdown-menu:before,.navbar .nav>li>.dropdown-menu.pull-right:before{left:auto;right:12px;} .navbar .pull-right>li>.dropdown-menu:after,.navbar .nav>li>.dropdown-menu.pull-right:after{left:auto;right:13px;} -.navbar .pull-right>li>.dropdown-menu .dropdown-menu,.navbar .nav>li>.dropdown-menu.pull-right .dropdown-menu{left:auto;right:100%;margin-left:0;margin-right:-1px;-webkit-border-radius:6px 0 6px 6px;-moz-border-radius:6px 0 6px 6px;border-radius:6px 0 6px 6px;} -.navbar-inverse .navbar-inner{background-color:#1b1b1b;background-image:-moz-linear-gradient(top, #222222, #111111);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#222222), to(#111111));background-image:-webkit-linear-gradient(top, #222222, #111111);background-image:-o-linear-gradient(top, #222222, #111111);background-image:linear-gradient(to bottom, #222222, #111111);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff222222', endColorstr='#ff111111', GradientType=0);border-color:#252525;} +.navbar .pull-right>li>.dropdown-menu .dropdown-menu,.navbar .nav>li>.dropdown-menu.pull-right .dropdown-menu{left:auto;right:100%;margin-left:0;margin-right:-1px;-webkit-border-radius:6px 0 6px 6px;-moz-border-radius:6px 0 6px 6px;border-radius:6px 0 6px 6px;-webkit-border-radius:6px 0 6px 6px;-moz-border-radius:6px 0 6px 6px;border-radius:6px 0 6px 6px;-webkit-border-radius:6px 0 6px 6px;-moz-border-radius:6px 0 6px 6px;border-radius:6px 0 6px 6px;} +.navbar-inverse .navbar-inner{background-color:#1b1b1b;background-image:-moz-linear-gradient(top, #222222, #111111);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#222222), to(#111111));background-image:-webkit-linear-gradient(top, #222222, #111111);background-image:-o-linear-gradient(top, #222222, #111111);background-image:linear-gradient(to bottom, #222222, #111111);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff222222', endColorstr='#ff111111', GradientType=0);background-color:#1b1b1b;background-image:-moz-linear-gradient(top, #222222, #111111);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#222222), to(#111111));background-image:-webkit-linear-gradient(top, #222222, 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6px;font-size:9px;} -.pager{margin:16px 0;list-style:none;text-align:center;*zoom:1;}.pager:before,.pager:after{display:table;content:"";line-height:0;} +.pager{margin:16px 0;list-style:none;text-align:center;*zoom:1;*zoom:1;}.pager:before,.pager:after{display:table;content:"";line-height:0;} .pager:after{clear:both;} .pager:before,.pager:after{display:table;content:"";line-height:0;} .pager:after{clear:both;} .pager li{display:inline;} -.pager li>a,.pager li>span{display:inline-block;padding:5px 14px;background-color:#fff;border:1px solid #ddd;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;} +.pager li>a,.pager li>span{display:inline-block;padding:5px 14px;background-color:#fff;border:1px solid #ddd;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;} .pager li>a:hover{text-decoration:none;background-color:#f5f5f5;} .pager .next>a,.pager .next>span{float:right;} .pager .previous>a,.pager .previous>span{float:left;} .pager .disabled>a,.pager .disabled>a:hover,.pager .disabled>span{color:#999999;background-color:#fff;cursor:default;} .modal-backdrop{position:fixed;top:0;right:0;bottom:0;left:0;z-index:1040;background-color:#000000;}.modal-backdrop.fade{opacity:0;} -.modal-backdrop,.modal-backdrop.fade.in{opacity:0.8;filter:alpha(opacity=80);} -.modal{position:fixed;top:10%;left:50%;z-index:1050;width:560px;margin-left:-280px;background-color:#ffffff;border:1px solid #999;border:1px solid rgba(0, 0, 0, 0.3);*border:1px solid #999;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;outline:none;}.modal.fade{-webkit-transition:opacity .3s linear, top .3s ease-out;-moz-transition:opacity .3s linear, top .3s ease-out;-o-transition:opacity .3s linear, top .3s ease-out;transition:opacity .3s linear, top .3s ease-out;top:-25%;} +.modal-backdrop,.modal-backdrop.fade.in{opacity:0.8;filter:alpha(opacity=80);opacity:0.8;filter:alpha(opacity=80);} +.modal{position:fixed;top:10%;left:50%;z-index:1050;width:560px;margin-left:-280px;background-color:#ffffff;border:1px solid #999;border:1px solid rgba(0, 0, 0, 0.3);*border:1px solid #999;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;outline:none;}.modal.fade{-webkit-transition:opacity .3s linear, top .3s ease-out;-moz-transition:opacity .3s linear, top .3s ease-out;-o-transition:opacity .3s linear, top .3s ease-out;transition:opacity .3s linear, top .3s ease-out;-webkit-transition:opacity .3s linear, top .3s ease-out;-moz-transition:opacity .3s linear, top .3s ease-out;-o-transition:opacity .3s linear, top .3s ease-out;transition:opacity .3s linear, top .3s ease-out;top:-25%;} .modal.fade.in{top:10%;} .modal-header{padding:9px 15px;border-bottom:1px solid #eee;}.modal-header .close{margin-top:2px;} .modal-header h3{margin:0;line-height:30px;} .modal-body{position:relative;overflow-y:auto;max-height:400px;padding:15px;} .modal-form{margin-bottom:0;} -.modal-footer{padding:14px 15px 15px;margin-bottom:0;text-align:right;background-color:#f5f5f5;border-top:1px solid #ddd;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;*zoom:1;}.modal-footer:before,.modal-footer:after{display:table;content:"";line-height:0;} +.modal-footer{padding:14px 15px 15px;margin-bottom:0;text-align:right;background-color:#f5f5f5;border-top:1px solid #ddd;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;*zoom:1;*zoom:1;}.modal-footer:before,.modal-footer:after{display:table;content:"";line-height:0;} .modal-footer:after{clear:both;} .modal-footer:before,.modal-footer:after{display:table;content:"";line-height:0;} .modal-footer:after{clear:both;} .modal-footer .btn+.btn{margin-left:5px;margin-bottom:0;} .modal-footer .btn-group .btn+.btn{margin-left:-1px;} .modal-footer .btn-block+.btn-block{margin-left:0;} -.popover{position:absolute;top:0;left:0;z-index:1010;display:none;width:236px;padding:1px;text-align:left;background-color:#ffffff;-webkit-background-clip:padding-box;-moz-background-clip:padding;background-clip:padding-box;border:1px solid #ccc;border:1px solid rgba(0, 0, 0, 0.2);-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-moz-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);white-space:normal;}.popover.top{margin-top:-10px;} +.popover{position:absolute;top:0;left:0;z-index:1010;display:none;width:236px;padding:1px;text-align:left;background-color:#ffffff;-webkit-background-clip:padding-box;-moz-background-clip:padding;background-clip:padding-box;border:1px solid #ccc;border:1px solid rgba(0, 0, 0, 0.2);-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-moz-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-webkit-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-moz-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);white-space:normal;}.popover.top{margin-top:-10px;} .popover.right{margin-left:10px;} .popover.bottom{margin-top:10px;} .popover.left{margin-left:-10px;} -.popover-title{margin:0;padding:8px 14px;font-size:14px;font-weight:normal;line-height:18px;background-color:#f7f7f7;border-bottom:1px solid #ebebeb;-webkit-border-radius:5px 5px 0 0;-moz-border-radius:5px 5px 0 0;border-radius:5px 5px 0 0;} +.popover-title{margin:0;padding:8px 14px;font-size:14px;font-weight:normal;line-height:18px;background-color:#f7f7f7;border-bottom:1px solid #ebebeb;-webkit-border-radius:5px 5px 0 0;-moz-border-radius:5px 5px 0 0;border-radius:5px 5px 0 0;-webkit-border-radius:5px 5px 0 0;-moz-border-radius:5px 5px 0 0;border-radius:5px 5px 0 0;-webkit-border-radius:5px 5px 0 0;-moz-border-radius:5px 5px 0 0;border-radius:5px 5px 0 0;} .popover-content{padding:9px 14px;} .popover .arrow,.popover .arrow:after{position:absolute;display:block;width:0;height:0;border-color:transparent;border-style:solid;} .popover .arrow{border-width:11px;} @@ -488,28 +488,28 @@ .popover.right .arrow{top:50%;left:-11px;margin-top:-11px;border-left-width:0;border-right-color:#999;border-right-color:rgba(0, 0, 0, 0.25);}.popover.right .arrow:after{left:1px;bottom:-10px;border-left-width:0;border-right-color:#ffffff;} .popover.bottom .arrow{left:50%;margin-left:-11px;border-top-width:0;border-bottom-color:#999;border-bottom-color:rgba(0, 0, 0, 0.25);top:-11px;}.popover.bottom .arrow:after{top:1px;margin-left:-10px;border-top-width:0;border-bottom-color:#ffffff;} .popover.left .arrow{top:50%;right:-11px;margin-top:-11px;border-right-width:0;border-left-color:#999;border-left-color:rgba(0, 0, 0, 0.25);}.popover.left .arrow:after{right:1px;border-right-width:0;border-left-color:#ffffff;bottom:-10px;} -@-webkit-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-ms-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-o-keyframes progress-bar-stripes{from{background-position:0 0;} to{background-position:40px 0;}}@keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}.progress{overflow:hidden;height:16px;margin-bottom:16px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(to bottom, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#fff9f9f9', GradientType=0);-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} -.progress .bar{width:0%;height:100%;color:#ffffff;float:left;font-size:12px;text-align:center;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);background-color:#0e90d2;background-image:-moz-linear-gradient(top, #149bdf, #0480be);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#149bdf), to(#0480be));background-image:-webkit-linear-gradient(top, #149bdf, #0480be);background-image:-o-linear-gradient(top, #149bdf, #0480be);background-image:linear-gradient(to bottom, #149bdf, #0480be);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff149bdf', endColorstr='#ff0480be', GradientType=0);-webkit-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-moz-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;-webkit-transition:width 0.6s ease;-moz-transition:width 0.6s ease;-o-transition:width 0.6s ease;transition:width 0.6s ease;} -.progress .bar+.bar{-webkit-box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);-moz-box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);} -.progress-striped .bar{background-color:#149bdf;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px;} +@-webkit-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-ms-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-o-keyframes progress-bar-stripes{from{background-position:0 0;} to{background-position:40px 0;}}@keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}.progress{overflow:hidden;height:16px;margin-bottom:16px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(to bottom, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#fff9f9f9', GradientType=0);background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(to bottom, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#fff9f9f9', GradientType=0);-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.progress .bar{width:0%;height:100%;color:#ffffff;float:left;font-size:12px;text-align:center;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);background-color:#0e90d2;background-image:-moz-linear-gradient(top, #149bdf, #0480be);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#149bdf), to(#0480be));background-image:-webkit-linear-gradient(top, #149bdf, #0480be);background-image:-o-linear-gradient(top, #149bdf, #0480be);background-image:linear-gradient(to bottom, #149bdf, #0480be);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff149bdf', endColorstr='#ff0480be', GradientType=0);background-color:#0e90d2;background-image:-moz-linear-gradient(top, #149bdf, #0480be);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#149bdf), to(#0480be));background-image:-webkit-linear-gradient(top, #149bdf, #0480be);background-image:-o-linear-gradient(top, #149bdf, #0480be);background-image:linear-gradient(to bottom, #149bdf, #0480be);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff149bdf', endColorstr='#ff0480be', GradientType=0);-webkit-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-moz-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-webkit-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-moz-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;-webkit-transition:width 0.6s ease;-moz-transition:width 0.6s ease;-o-transition:width 0.6s ease;transition:width 0.6s ease;-webkit-transition:width 0.6s ease;-moz-transition:width 0.6s ease;-o-transition:width 0.6s ease;transition:width 0.6s ease;} +.progress .bar+.bar{-webkit-box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);-moz-box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);-webkit-box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);-moz-box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);box-shadow:inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15);} +.progress-striped .bar{background-color:#149bdf;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, 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.bar,.progress .bar-danger{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(to bottom, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffee5f5b', endColorstr='#ffc43c35', GradientType=0);background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(to bottom, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffee5f5b', endColorstr='#ffc43c35', GradientType=0);} +.progress-danger.progress-striped .bar,.progress-striped .bar-danger{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, 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transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-info .bar,.progress .bar-info{background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(to bottom, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff339bb9', GradientType=0);background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(to bottom, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff339bb9', GradientType=0);} +.progress-info.progress-striped .bar,.progress-striped 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255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-warning .bar,.progress .bar-warning{background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(to bottom, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffbb450', endColorstr='#fff89406', GradientType=0);background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(to bottom, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffbb450', endColorstr='#fff89406', GradientType=0);} +.progress-warning.progress-striped .bar,.progress-striped .bar-warning{background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} .accordion{margin-bottom:16px;} -.accordion-group{margin-bottom:2px;border:1px solid #e5e5e5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.accordion-group{margin-bottom:2px;border:1px solid #e5e5e5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} .accordion-heading{border-bottom:0;} .accordion-heading .accordion-toggle{display:block;padding:8px 15px;} .accordion-toggle{cursor:pointer;} .accordion-inner{padding:9px 15px;border-top:1px solid #e5e5e5;} .carousel{position:relative;margin-bottom:16px;line-height:1;} .carousel-inner{overflow:hidden;width:100%;position:relative;} -.carousel-inner>.item{display:none;position:relative;-webkit-transition:0.6s ease-in-out left;-moz-transition:0.6s ease-in-out left;-o-transition:0.6s ease-in-out left;transition:0.6s ease-in-out left;} +.carousel-inner>.item{display:none;position:relative;-webkit-transition:0.6s ease-in-out left;-moz-transition:0.6s ease-in-out left;-o-transition:0.6s ease-in-out left;transition:0.6s ease-in-out left;-webkit-transition:0.6s ease-in-out left;-moz-transition:0.6s ease-in-out left;-o-transition:0.6s ease-in-out left;transition:0.6s ease-in-out left;} .carousel-inner>.item>img{display:block;line-height:1;} .carousel-inner>.active,.carousel-inner>.next,.carousel-inner>.prev{display:block;} .carousel-inner>.active{left:0;} @@ -519,13 +519,13 @@ .carousel-inner>.next.left,.carousel-inner>.prev.right{left:0;} .carousel-inner>.active.left{left:-100%;} .carousel-inner>.active.right{left:100%;} -.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#ffffff;text-align:center;background:#222222;border:3px solid #ffffff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:0.5;filter:alpha(opacity=50);}.carousel-control.right{left:auto;right:15px;} -.carousel-control:hover{color:#ffffff;text-decoration:none;opacity:0.9;filter:alpha(opacity=90);} +.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#ffffff;text-align:center;background:#222222;border:3px solid #ffffff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:0.5;filter:alpha(opacity=50);opacity:0.5;filter:alpha(opacity=50);}.carousel-control.right{left:auto;right:15px;} +.carousel-control:hover{color:#ffffff;text-decoration:none;opacity:0.9;filter:alpha(opacity=90);opacity:0.9;filter:alpha(opacity=90);} .carousel-caption{position:absolute;left:0;right:0;bottom:0;padding:15px;background:#333333;background:rgba(0, 0, 0, 0.75);} .carousel-caption h4,.carousel-caption p{color:#ffffff;line-height:16px;} .carousel-caption h4{margin:0 0 5px;} .carousel-caption p{margin-bottom:0;} -.hero-unit{padding:60px;margin-bottom:30px;font-size:18px;font-weight:200;line-height:24px;color:inherit;background-color:#eeeeee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;color:inherit;letter-spacing:-1px;} +.hero-unit{padding:60px;margin-bottom:30px;font-size:18px;font-weight:200;line-height:24px;color:inherit;background-color:#eeeeee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;color:inherit;letter-spacing:-1px;} .hero-unit li{line-height:24px;} .pull-right{float:right;} .pull-left{float:left;} @@ -543,7 +543,7 @@ .nav-tabs{border-bottom:1px solid #999999;} .nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #999999;} .nav-tabs>.active>a,.nav-tabs>.active>a:hover{border:1px solid #999999;border-bottom-color:transparent;} -.bs-tooltip{position:absolute;z-index:1020;display:block;visibility:visible;padding:5px;font-size:11px;opacity:0;filter:alpha(opacity=0);}.bs-tooltip.in{opacity:0.8;filter:alpha(opacity=80);} +.bs-tooltip{position:absolute;z-index:1020;display:block;visibility:visible;padding:5px;font-size:11px;opacity:0;filter:alpha(opacity=0);opacity:0;filter:alpha(opacity=0);}.bs-tooltip.in{opacity:0.8;filter:alpha(opacity=80);opacity:0.8;filter:alpha(opacity=80);} .bs-tooltip.top{margin-top:-3px;} .bs-tooltip.right{margin-left:3px;} .bs-tooltip.bottom{margin-top:3px;} @@ -562,10 +562,10 @@ li [class^="fa-icon-"],li [class*=" fa-icon-"]{display:inline-block;width:1.25em;text-align:center;}li [class^="fa-icon-"].fa-icon-large,li [class*=" fa-icon-"].fa-icon-large{width:1.5625em;} ul.icons{list-style-type:none;text-indent:-0.75em;}ul.icons li [class^="fa-icon-"],ul.icons li [class*=" fa-icon-"]{width:.75em;} .fa-icon-muted{color:#eeeeee;} -.fa-icon-border{border:solid 1px #eeeeee;padding:.2em .25em .15em;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;} -.fa-icon-2x{font-size:2em;}.fa-icon-2x.fa-icon-border{border-width:2px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} -.fa-icon-3x{font-size:3em;}.fa-icon-3x.fa-icon-border{border-width:3px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;} -.fa-icon-4x{font-size:4em;}.fa-icon-4x.icon-border{border-width:4px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;} +.fa-icon-border{border:solid 1px #eeeeee;padding:.2em .25em .15em;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;} +.fa-icon-2x{font-size:2em;}.fa-icon-2x.fa-icon-border{border-width:2px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.fa-icon-3x{font-size:3em;}.fa-icon-3x.fa-icon-border{border-width:3px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;} +.fa-icon-4x{font-size:4em;}.fa-icon-4x.icon-border{border-width:4px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;} .pull-right{float:right;} .pull-left{float:left;} [class^="fa-icon-"].pull-left,[class*=" fa-icon-"].pull-left{margin-right:.35em;} @@ -826,14 +826,14 @@ .fa-icon-folder-open-alt:before{content:"\f115";} .select2-container{position:relative;display:inline-block;zoom:1;*display:inline;vertical-align:top;} .select2-container,.select2-drop,.select2-search,.select2-search input{-moz-box-sizing:border-box;-ms-box-sizing:border-box;-webkit-box-sizing:border-box;-khtml-box-sizing:border-box;box-sizing:border-box;} -.select2-container .select2-choice{background-color:#fff;background-image:-webkit-gradient(linear, left bottom, left top, color-stop(0, #eeeeee), color-stop(0.5, #ffffff));background-image:-webkit-linear-gradient(center bottom, #eeeeee 0%, #ffffff 50%);background-image:-moz-linear-gradient(center bottom, #eeeeee 0%, #ffffff 50%);background-image:-o-linear-gradient(bottom, #eeeeee 0%, #ffffff 50%);background-image:-ms-linear-gradient(top, #eeeeee 0%, #ffffff 50%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#eeeeee', endColorstr='#ffffff', GradientType=0);background-image:linear-gradient(top, #eeeeee 0%, #ffffff 50%);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-moz-background-clip:padding;-webkit-background-clip:padding-box;background-clip:padding-box;border:1px solid #aaa;display:block;overflow:hidden;white-space:nowrap;position:relative;height:26px;line-height:26px;padding:0 0 0 8px;color:#444;text-decoration:none;} -.select2-container.select2-drop-above .select2-choice{border-bottom-color:#aaa;-webkit-border-radius:0px 0px 4px 4px;-moz-border-radius:0px 0px 4px 4px;border-radius:0px 0px 4px 4px;background-image:-webkit-gradient(linear, left bottom, left top, color-stop(0, #eeeeee), color-stop(0.9, #ffffff));background-image:-webkit-linear-gradient(center bottom, #eeeeee 0%, #ffffff 90%);background-image:-moz-linear-gradient(center bottom, #eeeeee 0%, #ffffff 90%);background-image:-o-linear-gradient(bottom, #eeeeee 0%, #ffffff 90%);background-image:-ms-linear-gradient(top, #eeeeee 0%, #ffffff 90%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#eeeeee', endColorstr='#ffffff', GradientType=0);background-image:linear-gradient(top, #eeeeee 0%, #ffffff 90%);} +.select2-container .select2-choice{background-color:#fff;background-image:-webkit-gradient(linear, left bottom, left top, color-stop(0, #eeeeee), color-stop(0.5, #ffffff));background-image:-webkit-linear-gradient(center bottom, #eeeeee 0%, #ffffff 50%);background-image:-moz-linear-gradient(center bottom, #eeeeee 0%, #ffffff 50%);background-image:-o-linear-gradient(bottom, #eeeeee 0%, #ffffff 50%);background-image:-ms-linear-gradient(top, #eeeeee 0%, #ffffff 50%);filter:progid:dximagetransform.microsoft.gradient(startColorstr='#eeeeee', endColorstr='#ffffff', GradientType=0);background-image:linear-gradient(top, #eeeeee 0%, #ffffff 50%);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-moz-background-clip:padding;-webkit-background-clip:padding-box;background-clip:padding-box;border:1px solid #aaa;display:block;overflow:hidden;white-space:nowrap;position:relative;height:26px;line-height:26px;padding:0 0 0 8px;color:#444;text-decoration:none;} +.select2-container.select2-drop-above .select2-choice{border-bottom-color:#aaa;-webkit-border-radius:0px 0px 4px 4px;-moz-border-radius:0px 0px 4px 4px;border-radius:0px 0px 4px 4px;background-image:-webkit-gradient(linear, left bottom, left top, color-stop(0, #eeeeee), color-stop(0.9, #ffffff));background-image:-webkit-linear-gradient(center bottom, #eeeeee 0%, #ffffff 90%);background-image:-moz-linear-gradient(center bottom, #eeeeee 0%, #ffffff 90%);background-image:-o-linear-gradient(bottom, #eeeeee 0%, #ffffff 90%);background-image:-ms-linear-gradient(top, #eeeeee 0%, #ffffff 90%);filter:progid:dximagetransform.microsoft.gradient(startColorstr='#eeeeee', endColorstr='#ffffff', GradientType=0);background-image:linear-gradient(top, #eeeeee 0%, #ffffff 90%);} .select2-container .select2-choice span{margin-right:26px;display:block;overflow:hidden;white-space:nowrap;-o-text-overflow:ellipsis;-ms-text-overflow:ellipsis;text-overflow:ellipsis;} .select2-container .select2-choice abbr{display:block;position:absolute;right:26px;top:8px;width:12px;height:12px;font-size:1px;background:url('../images/select2.png') right top no-repeat;cursor:pointer;text-decoration:none;border:0;outline:0;} .select2-container .select2-choice abbr:hover{background-position:right -11px;cursor:pointer;} .select2-drop{background:#fff;color:#000;border:1px solid #aaa;border-top:0;position:absolute;top:100%;-webkit-box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);-moz-box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);-o-box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);z-index:9999;width:100%;margin-top:-1px;-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;} .select2-drop.select2-drop-above{-webkit-border-radius:4px 4px 0px 0px;-moz-border-radius:4px 4px 0px 0px;border-radius:4px 4px 0px 0px;margin-top:1px;border-top:1px solid #aaa;border-bottom:0;-webkit-box-shadow:0 -4px 5px rgba(0, 0, 0, 0.15);-moz-box-shadow:0 -4px 5px rgba(0, 0, 0, 0.15);-o-box-shadow:0 -4px 5px rgba(0, 0, 0, 0.15);box-shadow:0 -4px 5px rgba(0, 0, 0, 0.15);} -.select2-container .select2-choice div{-webkit-border-radius:0 4px 4px 0;-moz-border-radius:0 4px 4px 0;border-radius:0 4px 4px 0;-moz-background-clip:padding;-webkit-background-clip:padding-box;background-clip:padding-box;background:#ccc;background-image:-webkit-gradient(linear, left bottom, left top, color-stop(0, #cccccc), color-stop(0.6, #eeeeee));background-image:-webkit-linear-gradient(center bottom, #cccccc 0%, #eeeeee 60%);background-image:-moz-linear-gradient(center bottom, #cccccc 0%, #eeeeee 60%);background-image:-o-linear-gradient(bottom, #cccccc 0%, #eeeeee 60%);background-image:-ms-linear-gradient(top, #cccccc 0%, #eeeeee 60%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#cccccc', endColorstr='#eeeeee', GradientType=0);background-image:linear-gradient(top, #cccccc 0%, #eeeeee 60%);border-left:1px solid #aaa;position:absolute;right:0;top:0;display:block;height:100%;width:18px;} +.select2-container .select2-choice div{-webkit-border-radius:0 4px 4px 0;-moz-border-radius:0 4px 4px 0;border-radius:0 4px 4px 0;-moz-background-clip:padding;-webkit-background-clip:padding-box;background-clip:padding-box;background:#ccc;background-image:-webkit-gradient(linear, left bottom, left top, color-stop(0, #cccccc), color-stop(0.6, #eeeeee));background-image:-webkit-linear-gradient(center bottom, #cccccc 0%, #eeeeee 60%);background-image:-moz-linear-gradient(center bottom, #cccccc 0%, #eeeeee 60%);background-image:-o-linear-gradient(bottom, #cccccc 0%, #eeeeee 60%);background-image:-ms-linear-gradient(top, #cccccc 0%, #eeeeee 60%);filter:progid:dximagetransform.microsoft.gradient(startColorstr='#cccccc', endColorstr='#eeeeee', GradientType=0);background-image:linear-gradient(top, #cccccc 0%, #eeeeee 60%);border-left:1px solid #aaa;position:absolute;right:0;top:0;display:block;height:100%;width:18px;} .select2-container .select2-choice div b{background:url('../images/select2.png') no-repeat 0 1px;display:block;width:100%;height:100%;} .select2-search{display:inline-block;white-space:nowrap;z-index:10000;min-height:26px;width:100%;margin:0;padding-left:4px;padding-right:4px;} .select2-search-hidden{display:block;position:absolute;left:-10000px;} @@ -841,7 +841,7 @@ .select2-drop.select2-drop-above .select2-search input{margin-top:4px;} .select2-search input.select2-active{background:#ffffff url('../images/select2-spinner.gif') no-repeat 100%;background:url('../images/select2-spinner.gif') no-repeat 100%,-webkit-gradient(linear, left bottom, left top, color-stop(0.85, #ffffff), color-stop(0.99, #eeeeee));background:url('../images/select2-spinner.gif') no-repeat 100%,-webkit-linear-gradient(center bottom, #ffffff 85%, #eeeeee 99%);background:url('../images/select2-spinner.gif') no-repeat 100%,-moz-linear-gradient(center bottom, #ffffff 85%, #eeeeee 99%);background:url('../images/select2-spinner.gif') no-repeat 100%,-o-linear-gradient(bottom, #ffffff 85%, #eeeeee 99%);background:url('../images/select2-spinner.gif') no-repeat 100%,-ms-linear-gradient(top, #ffffff 85%, #eeeeee 99%);background:url('../images/select2-spinner.gif') no-repeat 100%,linear-gradient(top, #ffffff 85%, #eeeeee 99%);} .select2-container-active .select2-choice,.select2-container-active .select2-choices{-webkit-box-shadow:0 0 5px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 0 5px rgba(0, 0, 0, 0.3);-o-box-shadow:0 0 5px rgba(0, 0, 0, 0.3);box-shadow:0 0 5px rgba(0, 0, 0, 0.3);border:1px solid #5897fb;outline:none;} -.select2-dropdown-open .select2-choice{border:1px solid #aaa;border-bottom-color:transparent;-webkit-box-shadow:0 1px 0 #fff inset;-moz-box-shadow:0 1px 0 #fff inset;-o-box-shadow:0 1px 0 #fff inset;box-shadow:0 1px 0 #fff inset;background-color:#eee;background-image:-webkit-gradient(linear, left bottom, left top, color-stop(0, #ffffff), color-stop(0.5, #eeeeee));background-image:-webkit-linear-gradient(center bottom, #ffffff 0%, #eeeeee 50%);background-image:-moz-linear-gradient(center bottom, #ffffff 0%, #eeeeee 50%);background-image:-o-linear-gradient(bottom, #ffffff 0%, #eeeeee 50%);background-image:-ms-linear-gradient(top, #ffffff 0%, #eeeeee 50%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#eeeeee', GradientType=0);background-image:linear-gradient(top, #ffffff 0%, #eeeeee 50%);-webkit-border-bottom-left-radius:0;-webkit-border-bottom-right-radius:0;-moz-border-radius-bottomleft:0;-moz-border-radius-bottomright:0;border-bottom-left-radius:0;border-bottom-right-radius:0;} +.select2-dropdown-open .select2-choice{border:1px solid #aaa;border-bottom-color:transparent;-webkit-box-shadow:0 1px 0 #fff inset;-moz-box-shadow:0 1px 0 #fff inset;-o-box-shadow:0 1px 0 #fff inset;box-shadow:0 1px 0 #fff inset;background-color:#eee;background-image:-webkit-gradient(linear, left bottom, left top, color-stop(0, #ffffff), color-stop(0.5, #eeeeee));background-image:-webkit-linear-gradient(center bottom, #ffffff 0%, #eeeeee 50%);background-image:-moz-linear-gradient(center bottom, #ffffff 0%, #eeeeee 50%);background-image:-o-linear-gradient(bottom, #ffffff 0%, #eeeeee 50%);background-image:-ms-linear-gradient(top, #ffffff 0%, #eeeeee 50%);filter:progid:dximagetransform.microsoft.gradient(startColorstr='#ffffff', endColorstr='#eeeeee', GradientType=0);background-image:linear-gradient(top, #ffffff 0%, #eeeeee 50%);-webkit-border-bottom-left-radius:0;-webkit-border-bottom-right-radius:0;-moz-border-radius-bottomleft:0;-moz-border-radius-bottomright:0;border-bottom-left-radius:0;border-bottom-right-radius:0;} .select2-dropdown-open .select2-choice div{background:transparent;border-left:none;} .select2-dropdown-open .select2-choice div b{background-position:-18px 1px;} .select2-results{margin:4px 4px 4px 0;padding:0 0 0 4px;position:relative;overflow-x:hidden;overflow-y:auto;max-height:200px;} @@ -873,7 +873,7 @@ .select2-container-multi .select2-choices .select2-search-field input{color:#666;background:transparent !important;font-family:sans-serif;font-size:100%;height:15px;padding:5px;margin:1px 0;outline:0;border:0;-webkit-box-shadow:none;-moz-box-shadow:none;-o-box-shadow:none;box-shadow:none;} .select2-container-multi .select2-choices .select2-search-field input.select2-active{background:#ffffff url('spinner.gif') no-repeat 100% !important;} .select2-default{color:#999 !important;} -.select2-container-multi .select2-choices .select2-search-choice{-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;-moz-background-clip:padding;-webkit-background-clip:padding-box;background-clip:padding-box;background-color:#e4e4e4;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f4f4f4', endColorstr='#eeeeee', GradientType=0);background-image:-webkit-gradient(linear, 0% 0%, 0% 100%, color-stop(20%, #f4f4f4), color-stop(50%, #f0f0f0), color-stop(52%, #e8e8e8), color-stop(100%, #eeeeee));background-image:-webkit-linear-gradient(top, #f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%);background-image:-moz-linear-gradient(top, #f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%);background-image:-o-linear-gradient(top, #f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%);background-image:-ms-linear-gradient(top, #f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%);background-image:linear-gradient(top, #f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%);-webkit-box-shadow:0 0 2px #ffffff inset,0 1px 0 rgba(0, 0, 0, 0.05);-moz-box-shadow:0 0 2px #ffffff inset,0 1px 0 rgba(0, 0, 0, 0.05);box-shadow:0 0 2px #ffffff inset,0 1px 0 rgba(0, 0, 0, 0.05);color:#333;border:1px solid #aaaaaa;line-height:13px;padding:3px 5px 3px 18px;margin:3px 0 3px 5px;position:relative;cursor:default;} +.select2-container-multi .select2-choices .select2-search-choice{-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;-moz-background-clip:padding;-webkit-background-clip:padding-box;background-clip:padding-box;background-color:#e4e4e4;filter:progid:dximagetransform.microsoft.gradient(startColorstr='#f4f4f4', endColorstr='#eeeeee', GradientType=0);background-image:-webkit-gradient(linear, 0% 0%, 0% 100%, color-stop(20%, #f4f4f4), color-stop(50%, #f0f0f0), color-stop(52%, #e8e8e8), color-stop(100%, #eeeeee));background-image:-webkit-linear-gradient(top, #f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%);background-image:-moz-linear-gradient(top, #f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%);background-image:-o-linear-gradient(top, #f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%);background-image:-ms-linear-gradient(top, #f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%);background-image:linear-gradient(top, #f4f4f4 20%, #f0f0f0 50%, #e8e8e8 52%, #eeeeee 100%);-webkit-box-shadow:0 0 2px #ffffff inset,0 1px 0 rgba(0, 0, 0, 0.05);-moz-box-shadow:0 0 2px #ffffff inset,0 1px 0 rgba(0, 0, 0, 0.05);box-shadow:0 0 2px #ffffff inset,0 1px 0 rgba(0, 0, 0, 0.05);color:#333;border:1px solid #aaaaaa;line-height:13px;padding:3px 5px 3px 18px;margin:3px 0 3px 5px;position:relative;cursor:default;} .select2-container-multi .select2-choices .select2-search-choice span{cursor:default;} .select2-container-multi .select2-choices .select2-search-choice-focus{background:#d4d4d4;} .select2-search-choice-close{display:block;position:absolute;right:3px;top:4px;width:12px;height:13px;font-size:1px;background:url('../images/select2.png') right top no-repeat;outline:none;} @@ -887,9 +887,9 @@ .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;}}.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;} +.unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;-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;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%;} +.clear{*zoom:1;*zoom:1;}.clear:before,.clear:after{display:table;content:"";line-height:0;} .clear:after{clear:both;} .clear:before,.clear:after{display:table;content:"";line-height:0;} .clear:after{clear:both;} @@ -913,13 +913,13 @@ #center{left:250px;right:250px;overflow:hidden;z-index:1;} #right-border{right:250px;} #right{width:250px;right:0px;z-index:200;border-left:solid #999999 1px;} -.subnavbar{background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe6e6e6', GradientType=0);border-bottom:solid #999999 1px;border-top:solid #999999 1px;padding:5px;color:#555;} -.unified-panel-header{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;height:30px;z-index:1000;text-shadow:rgba(255, 255, 255, 0.8) 0 1px 0;background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe6e6e6', GradientType=0);border-bottom:solid #999999 1px;margin:0;padding:0;padding-right:10px;padding-left:10px;font-weight:bold;color:#555;}.unified-panel-header a{color:#555;} +.subnavbar{background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe6e6e6', GradientType=0);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe6e6e6', GradientType=0);border-bottom:solid #999999 1px;border-top:solid #999999 1px;padding:5px;color:#555;} +.unified-panel-header{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;height:30px;z-index:1000;text-shadow:rgba(255, 255, 255, 0.8) 0 1px 0;background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe6e6e6', GradientType=0);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe6e6e6', GradientType=0);border-bottom:solid #999999 1px;margin:0;padding:0;padding-right:10px;padding-left:10px;font-weight:bold;color:#555;}.unified-panel-header a{color:#555;} .unified-panel-header-inner{padding-top:8px;} -.unified-panel-footer{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2f2f2', endColorstr='#ffe6e6e6', GradientType=0);color:#555;}.unified-panel-footer a{color:#555;} +.unified-panel-footer{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2f2f2', endColorstr='#ffe6e6e6', GradientType=0);background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2f2f2', endColorstr='#ffe6e6e6', GradientType=0);color:#555;}.unified-panel-footer a{color:#555;} .unified-panel-footer .drag{position:absolute;top:0;right:0;padding:0 5px;text-align:center;height:25px;width:20px;background-image:url(../images/visualization/draggable_horizontal.png);background-repeat:no-repeat;background-position:50% 50%;cursor:w-resize;} #right>.unified-panel-footer .drag{left:0;} -.panel-collapse{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;position:absolute;width:100%;z-index:1000;color:#555;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat;font-size:1.3333333333333333em;z-index:10000;display:block;position:fixed;left:0;top:inherit;bottom:0;padding:0 5px;text-align:center;height:25px;line-height:25px;width:20px;background:none;border-right:solid #999999 1px;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2f2f2', endColorstr='#ffe6e6e6', GradientType=0);}.panel-collapse a{color:#555;} +.panel-collapse{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2f2f2', endColorstr='#ffe6e6e6', GradientType=0);background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2f2f2', endColorstr='#ffe6e6e6', GradientType=0);color:#555;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat;font-size:1.3333333333333333em;z-index:10000;display:block;position:fixed;left:0;top:inherit;bottom:0;padding:0 5px;text-align:center;height:25px;line-height:25px;width:20px;background:none;border-right:solid #999999 1px;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2f2f2', endColorstr='#ffe6e6e6', GradientType=0);background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2f2f2', endColorstr='#ffe6e6e6', GradientType=0);}.panel-collapse a{color:#555;} .panel-collapse .drag{position:absolute;top:0;right:0;padding:0 5px;text-align:center;height:25px;width:20px;background-image:url(../images/visualization/draggable_horizontal.png);background-repeat:no-repeat;background-position:50% 50%;cursor:w-resize;} .panel-collapse:before{content:'\f053';} .panel-collapse.hidden:before{content:'\f054';} @@ -928,7 +928,7 @@ .menu-bg{background:whiteSmoke top repeat-x;} div.unified-panel-body{position:absolute;top:30px;bottom:0;width:100%;margin-top:1px;} #left>div.unified-panel-body,#right>div.unified-panel-body{bottom:25px;} -.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;padding-right:0.5em;padding-left:0.5em;}.panel-header-button:hover{color:maroon;-webkit-transition:color 0.25s linear;-moz-transition:color 0.25s linear;-o-transition:color 0.25s linear;transition:color 0.25s linear;} +.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;padding-right:0.5em;padding-left:0.5em;}.panel-header-button:hover{color:maroon;-webkit-transition:color 0.25s linear;-moz-transition:color 0.25s linear;-o-transition:color 0.25s linear;transition:color 0.25s linear;-webkit-transition:color 0.25s linear;-moz-transition:color 0.25s linear;-o-transition:color 0.25s linear;transition:color 0.25s linear;} .panel-header-button .caret{margin-top:7px;} .panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px;} #overlay{position:absolute;top:0;left:0;width:100%;height:100%;z-index:20000;overflow-y:auto;} @@ -937,14 +937,14 @@ .panel-warning-message{background-image:url(warn_small.png);background-color:#ffffcc;} .panel-done-message{background-image:url(ok_small.png);background-color:#ccffcc;} .panel-info-message{background-image:url(info_small.png);background-color:#d9edf7;} -#masthead{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;overflow:visible;margin-bottom:16px;*position:relative;*z-index:2;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;background:#2c3143;border-bottom:solid #444444 1px;z-index:15000;padding:0;}#masthead .nav{z-index:10000;background-color:#2c3143;} +#masthead{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;overflow:visible;margin-bottom:16px;*position:relative;*z-index:2;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;background:#2c3143;border-bottom:solid #444444 1px;z-index:15000;padding:0;}#masthead .nav{z-index:10000;background-color:#2c3143;} #masthead .nav>li>a{padding:8px 10px 8px;cursor:pointer;}#masthead .nav>li>a:hover{color:gold;} #masthead .dropdown-menu a,#masthead .dropdown-menu a:hover{text-decoration:none;} #masthead .dropdown-toggle .caret{margin-top:7px;} #masthead li.dropdown>a:hover .caret{border-top-color:gold;border-bottom-color:gold;} #masthead .title{position:absolute;left:0;top:0;font-family:verdana;font-weight:bold;font-size:20px;line-height:1;color:white;padding:5px 20px 12px;margin-left:-15px;z-index:2000;}#masthead .title img{display:inline;width:26px;vertical-align:top;} #masthead .title a{color:white;text-decoration:none;} -#masthead .masthead-inner{min-height:32px;padding-left:20px;padding-right:20px;background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(to bottom, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff333333', endColorstr='#ff2c3143', GradientType=0);border:1px solid #14161e;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);-moz-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);*zoom:1;border-width:0 0 1px;padding-left:0;padding-right:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-box-shadow:0 1px 10px rgba(0,0,0,.1);-moz-box-shadow:0 1px 10px rgba(0,0,0,.1);box-shadow:0 1px 10px rgba(0,0,0,.1);border:none;border-width:0px;height:32px;}#masthead .masthead-inner:before,#masthead .masthead-inner:after{display:table;content:"";line-height:0;} +#masthead .masthead-inner{min-height:32px;padding-left:20px;padding-right:20px;background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(to bottom, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff333333', endColorstr='#ff2c3143', GradientType=0);background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(to bottom, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff333333', endColorstr='#ff2c3143', GradientType=0);border:1px solid #14161e;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);-moz-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);-webkit-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);-moz-box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);box-shadow:0 1px 4px rgba(0, 0, 0, 0.065);*zoom:1;*zoom:1;border-width:0 0 1px;padding-left:0;padding-right:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-box-shadow:0 1px 10px rgba(0,0,0,.1);-moz-box-shadow:0 1px 10px rgba(0,0,0,.1);box-shadow:0 1px 10px rgba(0,0,0,.1);-webkit-box-shadow:0 1px 10px rgba(0,0,0,.1);-moz-box-shadow:0 1px 10px rgba(0,0,0,.1);box-shadow:0 1px 10px rgba(0,0,0,.1);border:none;border-width:0px;height:32px;}#masthead .masthead-inner:before,#masthead .masthead-inner:after{display:table;content:"";line-height:0;} #masthead .masthead-inner:after{clear:both;} #masthead .masthead-inner:before,#masthead .masthead-inner:after{display:table;content:"";line-height:0;} #masthead .masthead-inner:after{clear:both;} @@ -987,17 +987,17 @@ select,input,textarea{font:inherit;} .form-row select,.form-row textarea,.form-row input[type="text"],.form-row input[type="file"],.form-row input[type="password"]{max-width:90%;} textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:16px;border:1px solid #999999;padding:3px;} -.search-query{display:inline-block;padding:4px;font-size:12px;line-height:16px;color:#555555;border:1px solid #999999;padding-left:14px !important;padding-right:14px !important;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto;} -.search-query:focus{border-color:rgba(24, 132, 218, 0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);outline:0;outline:thin dotted \9;} +.search-query{display:inline-block;padding:4px;font-size:12px;line-height:16px;color:#555555;border:1px solid #999999;padding-left:14px !important;padding-right:14px !important;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto;} +.search-query:focus{border-color:rgba(24, 132, 218, 0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);outline:0;outline:thin dotted \9;} .search-spinner{position:absolute;display:none;right:5px;top:9px;} #search-clear-btn{position:absolute;right:5px;top:9px;display:block;font-size:1.4em;text-decoration:none;color:#888;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat;}#search-clear-btn:before{content:"\f057";} -.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:36px;padding-left:52px;background-image:url(error_large.png);background-repeat:no-repeat;background-position:10px 10px;} +.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:36px;padding-left:52px;background-image:url(error_large.png);background-repeat:no-repeat;background-position:10px 10px;} .errormessagelarge{background-color:#ffcccc;border-color:#ff3355;color:#660000;padding-left:52px;} .warningmessagelarge{background-image:url(warn_large.png);border-color:#aaaa66;background-color:#ffffcc;} .donemessagelarge{background-color:#ccffcc;border-color:#1a9900;color:#006600;padding-left:52px;background-image:url(ok_large.png);} -.infomessagelarge{border-color:#1b7183;color:#134158;background-image:url(info_large.png);border-color:#6666aa;background-color:#d9edf7;} +.infomessagelarge{background-color:#d9edf7;border-color:#1b7183;color:#134158;background-image:url(info_large.png);border-color:#6666aa;background-color:#d9edf7;} .screencastBox{padding-left:10px;border-color:#AAAA66;background-color:#FFFFCC;background-image:none;} -.errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;padding:5px;padding-left:25px;min-height:15px;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} +.errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;padding:5px;padding-left:25px;min-height:15px;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} .errormessage{background-color:#ffcccc;border-color:#ff3355;color:#660000;} .warningmessage,.warningmessagesmall{background-image:url(warn_small.png);} .donemessage,.donemessagesmall{background-color:#ccffcc;border-color:#1a9900;color:#006600;background-image:url(ok_small.png);} @@ -1064,37 +1064,37 @@ .state-fg-ok{color:#66AA66;} .state-fg-error{color:#AA6666;} .state-fg-deleted{color:#3399FF;} -.action-button{display:inline-block;*display:inline;*zoom:1;padding:4px 12px;margin-bottom:0;font-size:12px;line-height:16px;text-align:center;vertical-align:middle;cursor:pointer;color:#333333;text-shadow:0 1px 1px rgba(255, 255, 255, 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.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;} .menubutton.popup .label{border-right:solid #999999 1px;padding-right:6px;} @@ -1116,7 +1116,9 @@ .editable-text{cursor:pointer;} .editable-text:hover{cursor:text;border:dotted #999999 1px;} .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} -.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} +.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:pointer;} +.icon-button.link{background:url(../images/silk/link.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} +.icon-button.link-broken{background:url(../images/silk/link_break.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} .workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} body.historyPage{background:#dfe5f9;color:#303030;margin:5px;border:0;padding:0;} div.historyLinks{margin:5px 5px;} @@ -1192,6 +1194,6 @@ div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px 0px;} div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} -.text-and-autocomplete-select{background:none;position:relative;padding-right:18px;}.text-and-autocomplete-select:after{margin-top:6px;position:absolute;top:2px;right:6px;width:10px;height:10px;display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.8;filter:alpha(opacity=80);} +.text-and-autocomplete-select{background:none;position:relative;padding-right:18px;}.text-and-autocomplete-select:after{margin-top:6px;position:absolute;top:2px;right:6px;width:10px;height:10px;display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.8;filter:alpha(opacity=80);opacity:0.8;filter:alpha(opacity=80);} .icon-button.general-question{background:url(question-octagon-frame.png) no-repeat;float:right;margin-top:3px;margin-right:4px;} .icon-button.tag-question{background:url(question-balloon.png) no-repeat;float:right;margin-top:3px;margin-right:4px;} diff -r 80291f7ad4576c95f70eaed2f36cc5a95cf303fb -r c1faecf25f52a01cf55ba95df42791bf3399ed59 templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -1,11 +1,5 @@ <%inherit file="/base.mako"/> -<style> -/* TODO: Move this block into base.less? base.css? Someone more familiar with GUI should move this. */ -.icon-button.link {background:url(../images/silk/link.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} -.icon-button.link-broken {background:url(../images/silk/link_break.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} -</style> - <%def name="javascripts()"> ${parent.javascripts()} ${h.js( "libs/jquery/select2" )} 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: dannon: Merge GalaxyUI/API transactions -- now just GalaxyWebTransaction since we allow session-based access to the API.
by commits-noreply＠bitbucket.org 03 Apr '13

03 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/80291f7ad457/ Changeset: 80291f7ad457 User: dannon Date: 2013-04-03 16:13:37 Summary: Merge GalaxyUI/API transactions -- now just GalaxyWebTransaction since we allow session-based access to the API. Merge UI/API mappers -- url_for invocations will now respond with the correct path regardless of controller origin. **IMPORTANT**: mapper.explicit is no longer set to false -- this means fully specifying the components of the url to be generated as there won't be any 'magic' guessing anymore. Affected #: 7 files diff -r ca242dca4762b4c299f1bffae13c59e2ffd1e03c -r 80291f7ad4576c95f70eaed2f36cc5a95cf303fb lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -2,11 +2,15 @@ Galaxy web application framework """ +import inspect +import os import pkg_resources +import random +import socket +import string +import time +from Cookie import CookieError -import os, time, socket, random, string -import inspect -from Cookie import CookieError pkg_resources.require( "Cheetah" ) from Cheetah.Template import Template @@ -119,15 +123,8 @@ start_response( error_status, [('Content-type', 'text/plain')] ) return error_message error_status = '403 Forbidden' - ## If there is a user, we've authenticated a session. - if key_required and not trans.user and isinstance( trans.galaxy_session, Bunch ): - # If trans.user is already set, don't check for a key. - # This happens when we're authenticating using session instead of an API key. - # The Bunch clause is used to prevent the case where there's no user, but there is a real session. - # DBTODO: This needs to be fixed when merging transaction types. - if 'key' not in kwargs: - error_message = 'No API key provided with request, please consult the API documentation.' - return error + #If no key supplied, we use the existing session which may be an anonymous user. + if key_required and not trans.user: try: provided_key = trans.sa_session.query( trans.app.model.APIKeys ).filter( trans.app.model.APIKeys.table.c.key == kwargs['key'] ).one() except NoResultFound: @@ -275,10 +272,7 @@ return base.WebApplication.make_body_iterable( self, trans, body ) def transaction_chooser( self, environ, galaxy_app, session_cookie ): - if 'is_api_request' in environ: - return GalaxyWebAPITransaction( environ, galaxy_app, self, session_cookie ) - else: - return GalaxyWebUITransaction( environ, galaxy_app, self, session_cookie ) + return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) def add_ui_controllers( self, package_name, app ): """ @@ -335,7 +329,7 @@ Encapsulates web transaction specific state for the Galaxy application (specifically the user's "cookie" session and history) """ - def __init__( self, environ, app, webapp ): + def __init__( self, environ, app, webapp, session_cookie = None): self.app = app self.webapp = webapp self.security = webapp.security @@ -349,6 +343,15 @@ self.workflow_building_mode = False # Flag indicating whether this is an API call and the API key user is an administrator self.api_inherit_admin = False + self.__user = None + # Always have a valid galaxy session + self._ensure_valid_session( session_cookie ) + # Prevent deleted users from accessing Galaxy + if self.app.config.use_remote_user and self.galaxy_session.user.deleted: + self.response.send_redirect( url_for( '/static/user_disabled.html' ) ) + if self.app.config.require_login: + self._ensure_logged_in_user( environ, session_cookie ) + def setup_i18n( self ): locales = [] if 'HTTP_ACCEPT_LANGUAGE' in self.environ: @@ -364,6 +367,7 @@ locales = 'en' t = Translations.load( dirname='locale', locales=locales, domain='ginga' ) self.template_context.update ( dict( _=t.ugettext, n_=t.ugettext, N_=t.ungettext ) ) + @property def sa_session( self ): """ @@ -372,6 +376,24 @@ to allow migration toward a more SQLAlchemy 0.4 style of use. """ return self.app.model.context.current + + + def get_user( self ): + """Return the current user if logged in or None.""" + if self.__user: + return self.__user + else: + return self.galaxy_session.user + + def set_user( self, user ): + """Set the current user.""" + self.galaxy_session.user = user + self.sa_session.add( self.galaxy_session ) + self.sa_session.flush() + self.__user = user + + user = property( get_user, set_user ) + def log_action( self, user=None, action=None, context=None, params=None): """ Application-level logging of user actions. @@ -391,6 +413,7 @@ action.session_id = None self.sa_session.add( action ) self.sa_session.flush() + def log_event( self, message, tool_id=None, **kwargs ): """ Application level logging. Still needs fleshing out (log levels and such) @@ -421,6 +444,7 @@ event.session_id = None self.sa_session.add( event ) self.sa_session.flush() + def get_cookie( self, name='galaxysession' ): """Convenience method for getting a session cookie""" try: @@ -431,6 +455,7 @@ return self.request.cookies[name].value except: return None + def set_cookie( self, value, name='galaxysession', path='/', age=90, version='1' ): """Convenience method for setting a session cookie""" # The galaxysession cookie value must be a high entropy 128 bit random number encrypted @@ -445,6 +470,7 @@ self.response.cookies[name]['httponly'] = True except CookieError, e: log.warning( "Error setting httponly attribute in cookie '%s': %s" % ( name, e ) ) + def _ensure_valid_session( self, session_cookie, create=True): """ Ensure that a valid Galaxy session exists and is available as @@ -531,6 +557,7 @@ # If the old session was invalid, get a new history with our new session if invalidate_existing_session: self.new_history() + def _ensure_logged_in_user( self, environ, session_cookie ): # The value of session_cookie can be one of # 'galaxysession' or 'galaxycommunitysession' @@ -909,16 +936,13 @@ dbnames = list() datasets = self.sa_session.query( self.app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=self.history.id, extension="len" ) - for dataset in datasets: dbnames.append( (dataset.dbkey, dataset.name) ) - user = self.get_user() if user and 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) for key, chrom_dict in user_keys.iteritems(): dbnames.append((key, "%s (%s) [Custom]" % (chrom_dict['name'], key) )) - dbnames.extend( util.dbnames ) return dbnames @@ -992,139 +1016,6 @@ self.help = help self.use_label = use_label -class GalaxyWebAPITransaction( GalaxyWebTransaction ): - """ - TODO: Unify this with WebUITransaction, since we allow session auth now. - Enable functionality of 'create' parameter in parent _ensure_valid_session - """ - def __init__( self, environ, app, webapp, session_cookie): - GalaxyWebTransaction.__init__( self, environ, app, webapp ) - self.__user = None - self._ensure_valid_session( session_cookie ) - def _ensure_valid_session( self, session_cookie ): - #Check to see if there is an existing session. Never create a new one. - # Try to load an existing session - secure_id = self.get_cookie( name=session_cookie ) - galaxy_session = None - prev_galaxy_session = None - user_for_new_session = None - invalidate_existing_session = False - # Track whether the session has changed so we can avoid calling flush - # in the most common case (session exists and is valid). - galaxy_session_requires_flush = False - if secure_id: - # Decode the cookie value to get the session_key - session_key = self.security.decode_guid( secure_id ) - try: - # Make sure we have a valid UTF-8 string - session_key = session_key.encode( 'utf8' ) - except UnicodeDecodeError: - # We'll end up creating a new galaxy_session - session_key = None - if session_key: - # Retrieve the galaxy_session id via the unique session_key - galaxy_session = self.sa_session.query( self.app.model.GalaxySession ) \ - .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, - self.app.model.GalaxySession.table.c.is_valid==True ) ) \ - .first() - if galaxy_session: - # If remote user is in use it can invalidate the session, so we need to to check some things now. - if self.app.config.use_remote_user: - assert "HTTP_REMOTE_USER" in self.environ, \ - "use_remote_user is set but no HTTP_REMOTE_USER variable" - remote_user_email = self.environ[ 'HTTP_REMOTE_USER' ] - # An existing session, make sure correct association exists - if galaxy_session.user is None: - # No user, associate - galaxy_session.user = self.get_or_create_remote_user( remote_user_email ) - galaxy_session_requires_flush = True - elif galaxy_session.user.email != remote_user_email: - # Session exists but is not associated with the correct remote user - log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", - remote_user_email, galaxy_session.user.email ) - galaxy_session = None - else: - if galaxy_session.user and galaxy_session.user.external: - # Remote user support is not enabled, but there is an existing - # session with an external user, invalidate - invalidate_existing_session = True - log.warning( "User '%s' is an external user with an existing session, invalidating session since external auth is disabled", - galaxy_session.user.email ) - galaxy_session = None - elif galaxy_session.user is not None and galaxy_session.user.deleted: - invalidate_existing_session = True - log.warning( "User '%s' is marked deleted, invalidating session" % galaxy_session.user.email ) - galaxy_session = None - # No relevant cookies, or couldn't find, or invalid, so create a new session - if galaxy_session: - self.galaxy_session = galaxy_session - self.user = galaxy_session.user - # Do we need to flush the session? - if galaxy_session_requires_flush: - self.sa_session.add( galaxy_session ) - # FIXME: If prev_session is a proper relation this would not - # be needed. - if prev_galaxy_session: - self.sa_session.add( prev_galaxy_session ) - self.sa_session.flush() - # If the old session was invalid, get a new history with our new session - if not galaxy_session: - #Failed to find a session. Set up fake stuff for API transaction - self.user = None - self.galaxy_session = Bunch() - self.galaxy_session.history = self.galaxy_session.current_history = Bunch() - self.galaxy_session.history.genome_build = None - self.galaxy_session.is_api = True - - def get_user( self ): - """Return the current user (the expose_api decorator ensures that it is set).""" - return self.__user - def set_user( self, user ): - """Compatibility method""" - self.__user = user - user = property( get_user, set_user ) - @property - def db_builds( self ): - dbnames = [] - if 'dbkeys' in self.user.preferences: - user_keys = from_json_string( self.user.preferences['dbkeys'] ) - for key, chrom_dict in user_keys.iteritems(): - dbnames.append((key, "%s (%s) [Custom]" % (chrom_dict['name'], key) )) - dbnames.extend( util.dbnames ) - return dbnames - - @property - def ucsc_builds( self ): - return util.dlnames['ucsc'] - - @property - def ensembl_builds( self ): - return util.dlnames['ensembl'] - - @property - def ncbi_builds( self ): - return util.dlnames['ncbi'] - -class GalaxyWebUITransaction( GalaxyWebTransaction ): - def __init__( self, environ, app, webapp, session_cookie ): - GalaxyWebTransaction.__init__( self, environ, app, webapp ) - # Always have a valid galaxy session - self._ensure_valid_session( session_cookie ) - # Prevent deleted users from accessing Galaxy - if self.app.config.use_remote_user and self.galaxy_session.user.deleted: - self.response.send_redirect( url_for( '/static/user_disabled.html' ) ) - if self.app.config.require_login: - self._ensure_logged_in_user( environ, session_cookie ) - def get_user( self ): - """Return the current user if logged in or None.""" - return self.galaxy_session.user - def set_user( self, user ): - """Set the current user.""" - self.galaxy_session.user = user - self.sa_session.add( self.galaxy_session ) - self.sa_session.flush() - user = property( get_user, set_user ) - class SelectInput( FormInput ): """ A select form input. """ def __init__( self, name, label, value=None, options=[], error=None, help=None, use_label=True ): diff -r ca242dca4762b4c299f1bffae13c59e2ffd1e03c -r 80291f7ad4576c95f70eaed2f36cc5a95cf303fb lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py +++ b/lib/galaxy/web/framework/base.py @@ -2,34 +2,33 @@ A simple WSGI application/framework. """ -import socket -import types +import cgi # For FieldStorage import logging import os.path -import sys +import socket import tarfile -import threading +import types -from Cookie import SimpleCookie +import pkg_resources -import pkg_resources; -pkg_resources.require( "Paste" ) -pkg_resources.require( "Routes" ) -pkg_resources.require( "WebOb" ) +pkg_resources.require("Paste") +pkg_resources.require("Routes") +pkg_resources.require("WebOb") import routes import webob +from Cookie import SimpleCookie + # We will use some very basic HTTP/wsgi utilities from the paste library -from paste.request import parse_headers, get_cookies, parse_formvars +from paste.request import get_cookies from paste import httpexceptions from paste.response import HeaderDict -# For FieldStorage -import cgi log = logging.getLogger( __name__ ) + def __resource_with_deleted( self, member_name, collection_name, **kwargs ): """ Method to monkeypatch on to routes.mapper.Mapper which does the same thing @@ -62,12 +61,11 @@ """ self.controllers = dict() self.api_controllers = dict() - self.mapper = routes.Mapper() + self.mapper = routes.Mapper() # FIXME: The following two options are deprecated and should be # removed. Consult the Routes documentation. self.mapper.minimization = True - self.mapper.explicit = False - self.api_mapper = routes.Mapper() + #self.mapper.explicit = False self.transaction_factory = DefaultWebTransaction # Set if trace logging is enabled self.trace_logger = None @@ -108,7 +106,6 @@ """ # Create/compile the regular expressions for route mapping self.mapper.create_regs( self.controllers.keys() ) - self.api_mapper.create_regs( self.api_controllers.keys() ) def trace( self, **fields ): if self.trace_logger: self.trace_logger.log( "WebApplication", **fields ) @@ -137,20 +134,17 @@ # Map url using routes path_info = environ.get( 'PATH_INFO', '' ) map = self.mapper.match( path_info, environ ) - if map is None: + if path_info.startswith('/api'): environ[ 'is_api_request' ] = True - map = self.api_mapper.match( path_info, environ ) - mapper = self.api_mapper controllers = self.api_controllers else: - mapper = self.mapper controllers = self.controllers if map == None: raise httpexceptions.HTTPNotFound( "No route for " + path_info ) self.trace( path_info=path_info, map=map ) # Setup routes rc = routes.request_config() - rc.mapper = mapper + rc.mapper = self.mapper rc.mapper_dict = map rc.environ = environ # Setup the transaction @@ -164,6 +158,10 @@ raise httpexceptions.HTTPNotFound( "No controller for " + path_info ) # Resolve action method on controller action = map.pop( 'action', 'index' ) + # This is the easiest way to make the controller/action accessible for + # url_for invocations. Specifically, grids. + trans.controller = controller_name + trans.action = action method = getattr( controller, action, None ) if method is None: method = getattr( controller, 'default', None ) @@ -280,7 +278,7 @@ # tempfiles. Necessary for externalizing the upload tool. It's a little hacky # but for performance reasons it's way better to use Paste's tempfile than to # create a new one and copy. -import cgi, tempfile +import tempfile class FieldStorage( cgi.FieldStorage ): def make_file(self, binary=None): return tempfile.NamedTemporaryFile() diff -r ca242dca4762b4c299f1bffae13c59e2ffd1e03c -r 80291f7ad4576c95f70eaed2f36cc5a95cf303fb lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -1,14 +1,15 @@ -from galaxy.model.orm import * -from galaxy.web.base.controller import * -from galaxy.web.framework.helpers import iff -from galaxy.web import url_for +import logging +import math + +from galaxy.model.item_attrs import RuntimeException, UsesAnnotations, UsesItemRatings from galaxy.util import sanitize_text from galaxy.util.json import from_json_string, to_json_string from galaxy.util.odict import odict -from galaxy.web.framework.helpers import to_unicode -from galaxy.model.item_attrs import * +from galaxy.web.framework import error, url_for +from galaxy.web.framework.helpers import iff -import sys, logging, math +from sqlalchemy.sql.expression import and_, func, or_ + log = logging.getLogger( __name__ ) @@ -193,7 +194,6 @@ page_num = int( kwargs['page'] ) else: page_num = 1 - if page_num == 0: # Show all rows in page. total_num_rows = query.count() @@ -209,11 +209,9 @@ # Defaults. page_num = 1 num_pages = 1 - # There are some places in grid templates where it's useful for a grid # to have its current filter. self.cur_filter_dict = cur_filter_dict - # Preserve grid state: save current filter and sort key. if self.preserve_state: pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name ) @@ -228,6 +226,7 @@ params['sort'] = sort_key params['async'] = ( 'async' in kwargs ) trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params ) + # Render grid. def url( *args, **kwargs ): # Only include sort/filter arguments if not linking to another @@ -247,7 +246,13 @@ new_kwargs[ 'id' ] = [ trans.security.encode_id( i ) for i in id ] else: new_kwargs[ 'id' ] = trans.security.encode_id( id ) - return url_for( **new_kwargs ) + #The url_for invocation *must* include a controller and action. + if 'controller' not in new_kwargs: + new_kwargs['controller'] = trans.controller + if 'action' not in new_kwargs: + new_kwargs['action'] = trans.action + return url_for( **new_kwargs) + self.use_panels = ( kwargs.get( 'use_panels', False ) in [ True, 'True', 'true' ] ) async_request = ( ( self.use_async ) and ( kwargs.get( 'async', False ) in [ True, 'True', 'true'] ) ) # Currently, filling the template returns a str object; this requires decoding the string into a diff -r ca242dca4762b4c299f1bffae13c59e2ffd1e03c -r 80291f7ad4576c95f70eaed2f36cc5a95cf303fb lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -8,14 +8,12 @@ from galaxy.util import asbool -from paste.request import parse_formvars -from paste.util import import_string from paste import httpexceptions import pkg_resources log = logging.getLogger( __name__ ) -from galaxy import config, jobs, util, tools +from galaxy import util import galaxy.model import galaxy.model.mapping import galaxy.datatypes.registry @@ -36,7 +34,7 @@ from galaxy.app import UniverseApplication app = UniverseApplication( global_conf = global_conf, **kwargs ) except: - import traceback, sys + import traceback traceback.print_exc() sys.exit( 1 ) # Call app's shutdown method when the interpeter exits, this cleanly stops @@ -67,91 +65,91 @@ webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app ) # The /folders section is experimental at this point: log.debug( "app.config.api_folders: %s" % app.config.api_folders ) - webapp.api_mapper.resource( 'folder', 'folders', path_prefix='/api' ) - webapp.api_mapper.resource( 'content', 'contents', + webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) + webapp.mapper.resource( 'content', 'contents', controller='folder_contents', name_prefix='folder_', path_prefix='/api/folders/:folder_id', parent_resources=dict( member_name='folder', collection_name='folders' ) ) - webapp.api_mapper.resource( 'content', + webapp.mapper.resource( 'content', 'contents', controller='library_contents', name_prefix='library_', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) - webapp.api_mapper.resource( 'content', + webapp.mapper.resource( 'content', 'contents', controller='history_contents', name_prefix='history_', path_prefix='/api/histories/:history_id', parent_resources=dict( member_name='history', collection_name='histories' ) ) - webapp.api_mapper.connect("history_contents_display", + webapp.mapper.connect("history_contents_display", "/api/histories/:history_id/contents/:history_content_id/display", controller="datasets", action="display", conditions=dict(method=["GET"])) - webapp.api_mapper.resource( 'permission', + webapp.mapper.resource( 'permission', 'permissions', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) - webapp.api_mapper.resource( 'user', + webapp.mapper.resource( 'user', 'users', controller='group_users', name_prefix='group_', path_prefix='/api/groups/:group_id', parent_resources=dict( member_name='group', collection_name='groups' ) ) - webapp.api_mapper.resource( 'role', + webapp.mapper.resource( 'role', 'roles', controller='group_roles', name_prefix='group_', path_prefix='/api/groups/:group_id', parent_resources=dict( member_name='group', collection_name='groups' ) ) - _add_item_tags_controller( webapp, + _add_item_tags_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) - _add_item_tags_controller( webapp, + _add_item_tags_controller( webapp, name_prefix="history_", path_prefix='/api/histories/:history_id' ) - _add_item_tags_controller( webapp, + _add_item_tags_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - _add_item_annotation_controller( webapp, + _add_item_annotation_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) - _add_item_annotation_controller( webapp, + _add_item_annotation_controller( webapp, name_prefix="history_", path_prefix='/api/histories/:history_id' ) - _add_item_annotation_controller( webapp, + _add_item_annotation_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - webapp.api_mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) - webapp.api_mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) - webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) - webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) - webapp.api_mapper.resource( 'form', 'forms', path_prefix='/api' ) - webapp.api_mapper.resource( 'request_type', 'request_types', path_prefix='/api' ) - webapp.api_mapper.resource( 'role', 'roles', path_prefix='/api' ) - webapp.api_mapper.resource( 'group', 'groups', path_prefix='/api' ) - webapp.api_mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) - webapp.api_mapper.resource( 'tool', 'tools', path_prefix='/api' ) - webapp.api_mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) - webapp.api_mapper.resource( 'genome', 'genomes', path_prefix='/api' ) - webapp.api_mapper.resource( 'visualization', 'visualizations', path_prefix='/api' ) - webapp.api_mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) - webapp.api_mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) - webapp.api_mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) - #webapp.api_mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) + webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) + webapp.mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) + webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) + webapp.mapper.resource( 'request', 'requests', path_prefix='/api' ) + webapp.mapper.resource( 'form', 'forms', path_prefix='/api' ) + webapp.mapper.resource( 'request_type', 'request_types', path_prefix='/api' ) + webapp.mapper.resource( 'role', 'roles', path_prefix='/api' ) + webapp.mapper.resource( 'group', 'groups', path_prefix='/api' ) + webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) + webapp.mapper.resource( 'tool', 'tools', path_prefix='/api' ) + webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) + webapp.mapper.resource( 'genome', 'genomes', path_prefix='/api' ) + webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' ) + webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) + webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) + webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) + #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) # "POST /api/workflows/import" => ``workflows.import_workflow()``. # Defines a named route "import_workflow". - webapp.api_mapper.connect("import_workflow", "/api/workflows/upload", controller="workflows", action="import_new_workflow", conditions=dict(method=["POST"])) - webapp.api_mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + webapp.mapper.connect("import_workflow", "/api/workflows/upload", controller="workflows", action="import_new_workflow", conditions=dict(method=["POST"])) + webapp.mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Preserve the following download route for now for dependent applications -- deprecate at some point - webapp.api_mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Galaxy API for tool shed features. - webapp.api_mapper.resource( 'tool_shed_repository', + webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', controller='tool_shed_repositories', name_prefix='tool_shed_repository_', @@ -198,7 +196,7 @@ controller = "%stags" % name_prefix name = "%stag" % name_prefix path = "%s/tags" % path_prefix - map = webapp.api_mapper + map = webapp.mapper # Allow view items' tags. map.connect(name, path, controller=controller, action="index", @@ -225,7 +223,7 @@ def _add_item_annotation_controller( webapp, name_prefix, path_prefix, **kwd ): controller = "%sannotations" % name_prefix name = "%sannotation" % name_prefix - webapp.api_mapper.resource(name, "annotation", path_prefix=path_prefix, controller=controller) + webapp.mapper.resource(name, "annotation", path_prefix=path_prefix, controller=controller) def wrap_in_middleware( app, global_conf, **local_conf ): """ diff -r ca242dca4762b4c299f1bffae13c59e2ffd1e03c -r 80291f7ad4576c95f70eaed2f36cc5a95cf303fb lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -76,14 +76,14 @@ webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) # Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app ) - webapp.api_mapper.resource( 'repository', + webapp.mapper.resource( 'repository', 'repositories', controller='repositories', collection={ 'get_repository_revision_install_info' : 'GET' }, name_prefix='repository_', path_prefix='/api', parent_resources=dict( member_name='repository', collection_name='repositories' ) ) - webapp.api_mapper.resource( 'repository_revision', + webapp.mapper.resource( 'repository_revision', 'repository_revisions', controller='repository_revisions', name_prefix='repository_revision_', diff -r ca242dca4762b4c299f1bffae13c59e2ffd1e03c -r 80291f7ad4576c95f70eaed2f36cc5a95cf303fb templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -56,7 +56,7 @@ <script type="text/javascript"> ## TODO: Can this be moved into base.mako? Also, this is history-specific grid code. %if refresh_frames: - %if 'masthead' in refresh_frames: + %if 'masthead' in refresh_frames: ## Refresh masthead == user changes (backward compatibility) if ( parent.user_changed ) { %if trans.user: @@ -68,7 +68,7 @@ %endif %if 'history' in refresh_frames: if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; + parent.frames.galaxy_history.location.href="${url( controller='root', action='history')}"; if ( parent.force_right_panel ) { parent.force_right_panel( 'show' ); } @@ -76,14 +76,13 @@ else { // TODO: redirecting to root should be done on the server side so that page // does not have to load. - // No history frame, so refresh to root to see history. - window.top.location.href = "${h.url_for( controller='root' )}"; + window.top.location.href = "${url( controller='root' )}"; } %endif %if 'tools' in refresh_frames: if ( parent.frames && parent.frames.galaxy_tools ) { - parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; + parent.frames.galaxy_tools.location.href="${url( controller='root', action='tool_menu')}"; if ( parent.force_left_panel ) { parent.force_left_panel( 'show' ); } @@ -92,8 +91,8 @@ %endif // Needed URLs for grid history searching. - var history_tag_autocomplete_url = "${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='History' )}", - history_name_autocomplete_url = "${h.url_for( controller='history', action='name_autocomplete_data' )}"; + var history_tag_autocomplete_url = "${url( controller='tag', action='tag_autocomplete_data', item_class='History' )}", + history_name_autocomplete_url = "${url( controller='history', action='name_autocomplete_data' )}"; // // Create grid object. @@ -117,9 +116,10 @@ /** Returns true if string denotes true. */ var is_true = function(s) { return _.indexOf(['True', 'true', 't'], s) !== -1; }; + // Create grid. var grid = new Grid({ - url_base: '${h.url_for()}', + url_base: '${trans.request.path_url}', async: is_true('${grid.use_async}'), async_ops: async_ops, categorical_filters: categorical_filters, @@ -135,7 +135,6 @@ $(document).ready(function() { init_grid_elements(); init_grid_controls(); - // Initialize text filters to select text on click and use normal font when user is typing. $('input[type=text]').each(function() { $(this).click(function() { $(this).select(); } ) @@ -197,13 +196,13 @@ <ul class="manage-table-actions"> %if len( grid.global_actions ) < 3: %for action in grid.global_actions: - <li><a class="action-button" href="${h.url_for( **action.url_args )}">${action.label}</a></li> + <li><a class="action-button" href="${url( **action.url_args )}">${action.label}</a></li> %endfor %else: <li><a class="action-button" id="action-8675309-popup" class="menubutton">Actions</a></li><div popupmenu="action-8675309-popup"> %for action in grid.global_actions: - <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label}</a> + <a class="action-button" href="${url( **action.url_args )}">${action.label}</a> %endfor </div> %endif diff -r ca242dca4762b4c299f1bffae13c59e2ffd1e03c -r 80291f7ad4576c95f70eaed2f36cc5a95cf303fb templates/grid_common.mako --- a/templates/grid_common.mako +++ b/templates/grid_common.mako @@ -1,5 +1,5 @@ -<%! - from galaxy.web.framework.helpers.grids import TextColumn, StateColumn, GridColumnFilter +<%! + from galaxy.web.framework.helpers.grids import TextColumn, StateColumn, GridColumnFilter from galaxy.web.framework.helpers import iff %> @@ -16,7 +16,7 @@ %endif <td style="padding: 0;"> %if isinstance(column, TextColumn): - <form class="text-filter-form" column_key="${column.key}" action="${url( dict() )}" method="get" > + <form class="text-filter-form" column_key="${column.key}" action="${url(dict())}" method="get" > ## Carry forward filtering criteria with hidden inputs. %for temp_column in grid.columns: %if temp_column.key in cur_filter_dict: @@ -30,7 +30,6 @@ %endif %endif %endfor - ## Print current filtering criteria and links to delete. <span id="${column.key}-filtering-criteria"> %if column.key in cur_filter_dict: @@ -40,7 +39,7 @@ <span class='text-filter-val'> ${cur_filter_dict[column.key]} <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - <a href="${url( filter_all.get_url_args() )}"><span class="delete-search-icon" /></a> + <a href="${url(filter_all.get_url_args())}"><span class="delete-search-icon" /></a></span> %endif %elif isinstance( column_filter, list ): @@ -54,7 +53,7 @@ del new_filter[ i ] new_column_filter = GridColumnFilter( "", { column.key : h.to_json_string( new_filter ) } ) %> - <a href="${url( new_column_filter.get_url_args() )}"><span class="delete-search-icon" /></a> + <a href="${url(new_column_filter.get_url_args())}"><span class="delete-search-icon" /></a></span> %endfor %endif @@ -91,7 +90,7 @@ <span class="categorical-filter ${column.key}-filter current-filter">${filter.label}</span> %else: <span class="categorical-filter ${column.key}-filter"> - <a href="${url( filter.get_url_args() )}" filter_key="${filter_key}" filter_val="${filter_arg}">${filter.label}</a> + <a href="${url(filter.get_url_args())}" filter_key="${filter_key}" filter_val="${filter_arg}">${filter.label}</a></span> %endif %endfor @@ -119,7 +118,7 @@ ## Clear the standard search. ##| ##<% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - ##<a href="${url( filter_all.get_url_args() )}">Clear All</a> + ##<a href="${url(filter_all.get_url_args())}">Clear All</a> ## Only show advanced search if there are filterable columns. <% @@ -133,7 +132,7 @@ %> %if show_advanced_search_link: <% args = { "advanced-search" : True } %> - <a href="${url( args )}" class="advanced-search-toggle">Advanced Search</a> + <a href="${url(args)}" class="advanced-search-toggle">Advanced Search</a> %endif </td></tr></table> @@ -157,13 +156,13 @@ <table><tr><td style="text-align: left" colspan="100"><% args = { "advanced-search" : False } %> - <a href="${url( args )}" class="advanced-search-toggle">Close Advanced Search</a> + <a href="${url(args)}" class="advanced-search-toggle">Close Advanced Search</a> ## Link to clear all filters. ##| ##<% ## no_filter = GridColumnFilter("Clear All", default_filter_dict) ##%> - ##<a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a> + ##<a href="${url(no_filter.get_url_args())}">${no_filter.label}</a></td></tr> %for column in grid.columns: %if column.filterable == "advanced": @@ -180,4 +179,4 @@ %endfor </table></div> -</%def> \ No newline at end of file +</%def> 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 commits-noreply＠bitbucket.org 03 Apr '13

03 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a85ae05b837c/ Changeset: a85ae05b837c User: dannon Date: 2013-04-03 15:59:33 Summary: User API: requesting current user allows anonymous access. Affected #: 1 file diff -r da459ec80aae65dcb918c9601f091be1f4a74ee8 -r a85ae05b837cbad8abb059e0fa6898c4c0634317 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -44,7 +44,7 @@ rval.append( item ) return rval - @web.expose_api + @web.expose_api_anonymous def show( self, trans, id, deleted='False', **kwd ): """ GET /api/users/{encoded_user_id} https://bitbucket.org/galaxy/galaxy-central/commits/ca242dca4762/ Changeset: ca242dca4762 User: dannon Date: 2013-04-03 16:01:39 Summary: api/users - Format spacing, trim trailing spaces. Affected #: 1 file diff -r a85ae05b837cbad8abb059e0fa6898c4c0634317 -r ca242dca4762b4c299f1bffae13c59e2ffd1e03c lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -8,7 +8,9 @@ log = logging.getLogger( __name__ ) + class UserAPIController( BaseAPIController ): + @web.expose_api def index( self, trans, deleted='False', **kwd ): """ @@ -66,26 +68,22 @@ user = trans.user else: user = self.get_user( trans, id, deleted=deleted ) - # check that the user is requesting themselves (and they aren't del'd) unless admin if not trans.user_is_admin(): assert trans.user == user assert not user.deleted - except: if trans.user_is_admin(): raise else: raise HTTPBadRequest( detail='Invalid user id ( %s ) specified' % id ) - item = user.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id, - 'total_disk_usage': float } ) + 'total_disk_usage': float } ) #TODO: move into api_values (needs trans, tho - can we do that with api_keys/@property??) #TODO: works with other users (from admin)?? item['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans ) + return item - return item - @web.expose_api def create( self, trans, payload, **kwd ): """ @@ -97,7 +95,7 @@ if trans.app.config.use_remote_user and trans.user_is_admin(): user = trans.get_or_create_remote_user(remote_user_email=payload['remote_user_email']) item = user.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id, - 'total_disk_usage': float } ) + 'total_disk_usage': float } ) else: raise HTTPNotImplemented() return item 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 commits-noreply＠bitbucket.org 03 Apr '13

03 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/da2d6ee29f30/ Changeset: da2d6ee29f30 Branch: stable User: inithello Date: 2013-04-03 15:27:44 Summary: Fix for errors encountered during installation of complex repository dependencies, courtesy of Björn Grüning. Affected #: 1 file diff -r 1c92aed71881e3a15648e3be9478a69f76c50498 -r da2d6ee29f309454f35d9f8cf9d6eb837c87a7dd 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 @@ -256,7 +256,7 @@ install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) else: message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ - ( str( name ), str( owner ), str( changeset_revision ) ) + ( str( required_repository_name ), str( required_repository_owner ), str( required_repository_changeset_revision ) ) raise Exception( message ) elif package_elem.tag == 'install': # <install version="1.0"> https://bitbucket.org/galaxy/galaxy-central/commits/da459ec80aae/ Changeset: da459ec80aae User: inithello Date: 2013-04-03 15:29:13 Summary: Merge in bugfix from stable branch. Affected #: 1 file diff -r 65d18f3829a0771910af5b65b5e4c9ed59774b2b -r da459ec80aae65dcb918c9601f091be1f4a74ee8 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 @@ -256,7 +256,7 @@ install_and_build_package_via_fabric( app, tool_dependency, actions_dict ) else: message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \ - ( str( name ), str( owner ), str( changeset_revision ) ) + ( str( required_repository_name ), str( required_repository_owner ), str( required_repository_changeset_revision ) ) raise Exception( message ) elif package_elem.tag == 'install': # <install version="1.0"> 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: dannon: Swap history_contents to use expose_api_anonymous.
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/65d18f3829a0/ Changeset: 65d18f3829a0 User: dannon Date: 2013-04-02 23:20:18 Summary: Swap history_contents to use expose_api_anonymous. Affected #: 1 file diff -r 4ed80ec3f309f5c8e1c9e735666a2b9b682ff388 -r 65d18f3829a0771910af5b65b5e4c9ed59774b2b lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -12,7 +12,7 @@ class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, UsesLibraryMixinItems ): - @web.expose_api + @web.expose_api_anonymous def index( self, trans, history_id, ids=None, **kwd ): """ GET /api/histories/{encoded_history_id}/contents @@ -35,7 +35,7 @@ try: # get the history, if anon user and requesting current history - allow it if( ( trans.user == None ) - and ( history_id == trans.security.encode_id( trans.history.id ) ) ): + and ( history_id == trans.security.encode_id( trans.history.id ) ) ): #TODO:?? is secure? history = trans.history @@ -117,7 +117,7 @@ 'error' : str( exception ) } - @web.expose_api + @web.expose_api_anonymous def show( self, trans, id, history_id, **kwd ): """ GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} 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: guerler: grep/select tool: fixed tab-delimiter matching for GNU version of grep
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ed80ec3f309/ Changeset: 4ed80ec3f309 User: guerler Date: 2013-04-02 21:18:22 Summary: grep/select tool: fixed tab-delimiter matching for GNU version of grep Affected #: 1 file diff -r 715dc4f4c8e218f50d08eb81dc1b3ef0453860a5 -r 4ed80ec3f309f5c8e1c9e735666a2b9b682ff388 tools/filters/grep.py --- a/tools/filters/grep.py +++ b/tools/filters/grep.py @@ -17,6 +17,7 @@ import re import string import commands +from subprocess import Popen, PIPE from tempfile import NamedTemporaryFile # This function is exceedingly useful, perhaps package for reuse? @@ -34,89 +35,100 @@ args = sys.argv[1:] try: - opts = getopts(args) + opts = getopts(args) except IndexError: - print "Usage:" - print " -i Input file" - print " -o Output file" - print " -pattern RegEx pattern" - print " -v true or false (Invert match)" - return 0 + print "Usage:" + print " -i Input file" + print " -o Output file" + print " -pattern RegEx pattern" + print " -v true or false (Invert match)" + return 0 outputfile = opts.get("-o") if outputfile == None: - print "No output file specified." - return -1 + print "No output file specified." + return -1 inputfile = opts.get("-i") if inputfile == None: - print "No input file specified." - return -2 + print "No input file specified." + return -2 invert = opts.get("-v") if invert == None: - print "Match style (Invert or normal) not specified." - return -3 + print "Match style (Invert or normal) not specified." + return -3 pattern = opts.get("-pattern") if pattern == None: - print "RegEx pattern not specified." - return -4 + print "RegEx pattern not specified." + return -4 # All inputs have been specified at this point, now validate. # replace if input has been escaped, remove sq # characters that are allowed but need to be escaped - mapped_chars = { '>' :'__gt__', - '<' :'__lt__', - '\'' :'__sq__', - '"' :'__dq__', - '[' :'__ob__', - ']' :'__cb__', - '{' :'__oc__', - '}' :'__cc__' - } + mapped_chars = { '>' :'__gt__', + '<' :'__lt__', + '\'':'__sq__', + '"' :'__dq__', + '[' :'__ob__', + ']' :'__cb__', + '{' :'__oc__', + '}' :'__cc__' + } - #with new sanitizing we only need to replace for single quote, but this needs to remain for backwards compatibility + # with new sanitizing we only need to replace for single quote, + # but this needs to remain for backwards compatibility for key, value in mapped_chars.items(): pattern = pattern.replace(value, key) - - fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$") #why? - invertRegEx = re.compile("(true)|(false)") #why? + # match filename and invert flag + fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$") + invertRegEx = re.compile("(true)|(false)") + + # verify that filename and inversion flag are in the correct format if not fileRegEx.match(outputfile): - print "Illegal output filename." - return -5 + print "Illegal output filename." + return -5 if not fileRegEx.match(inputfile): - print "Illegal input filename." - return -6 + print "Illegal input filename." + return -6 if not invertRegEx.match(invert): - print "Illegal invert option." - return -7 + print "Illegal invert option." + return -7 # invert grep search? if invert == "true": - invertflag = " -v" + invertflag = "-v" print "Not matching pattern: %s" % pattern else: invertflag = "" print "Matching pattern: %s" % pattern + + # set version flag + versionflag = "-P" - #Create temp file holding pattern - #By using a file to hold the pattern, we don't have worry about sanitizing grep commandline and can include single quotes in pattern + # MacOS 10.8.2 does not support -P option for perl-regex anymore + versionmatch = Popen("grep -V | grep 'BSD'", shell=True, stdout=PIPE).communicate()[0]; + if versionmatch: + versionflag = "-E" + + # create temp file holding pattern + # by using a file to hold the pattern, we don't have worry about sanitizing grep commandline and can include single quotes in pattern pattern_file_name = NamedTemporaryFile().name open( pattern_file_name, 'w' ).write( pattern ) - #generate grep command - commandline = "grep -E %s -f %s %s > %s" % ( invertflag, pattern_file_name, inputfile, outputfile ) + # generate grep command + commandline = "grep %s %s -f %s %s > %s" % ( versionflag, invertflag, pattern_file_name, inputfile, outputfile ) - #run grep + # run grep errorcode, stdout = commands.getstatusoutput(commandline) - #remove temp pattern file + # remove temp pattern file os.unlink( pattern_file_name ) - #return error code + # return error code return errorcode if __name__ == "__main__": 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 baseline support for ordering the installation of repository dependencies by supporting an attribute named prior_installation_required in repository dependency definitions. If this attribute is set to True in the repository dependency definition for a certain repository, then attempts will be made to ensure the repository dependency is installed prior to the repository being installed into Galaxy. The Galaxy installation process has not yet been enhanced to
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/715dc4f4c8e2/ Changeset: 715dc4f4c8e2 User: greg Date: 2013-04-02 21:03:00 Summary: Add baseline support for ordering the installation of repository dependencies by supporting an attribute named prior_installation_required in repository dependency definitions. If this attribute is set to True in the repository dependency definition for a certain repository, then attempts will be made to ensure the repository dependency is installed prior to the repository being installed into Galaxy. The Galaxy installation process has not yet been enhanced to leverage this feature, but the repsitory dependency framework in the tool shed itself is now using it. Affected #: 9 files diff -r d62c5edf1ef265000740cac2949f90c9b175db6c -r 715dc4f4c8e218f50d08eb81dc1b3ef0453860a5 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3210,6 +3210,31 @@ return 'repository_dependencies' in self.metadata return False @property + def requires_prior_installation_of( self ): + """ + Return a list of repository dependency tuples like (tool_shed, name, owner, changeset_revision, prior_installation_required) for this + repository's repository dependencies where prior_installation_required is True. By definition, repository dependencies are required to + be installed in order for this repository to function correctly. However, those repository dependencies that are defined for this + repository with prior_installation_required set to True place them in a special category in that the required repositories must be + installed before this repository is installed. Among other things, this enables these "special" repository dependencies to include + information that enables the successful intallation of this repository. + """ + required_rd_tups_that_must_be_installed = [] + if self.has_repository_dependencies: + rd_tups = self.metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] + for rd_tup in rd_tups: + if len( rd_tup ) == 4: + # Metadata should have been reset on this installed tool_shed_repository, but it wasn't. + tool_shed, name, owner, changeset_revision = rd_tup + # Default prior_installation_required to False. + prior_installation_required = False + elif len( rd_tup ) == 5: + tool_shed, name, owner, changeset_revision, prior_installation_required = rd_tup + prior_installation_required = util.asbool( str( prior_installation_required ) ) + if prior_installation_required: + required_rd_tups_that_must_be_installed.append( ( tool_shed, name, owner, changeset_revision, prior_installation_required ) ) + return required_rd_tups_that_must_be_installed + @property def includes_data_managers( self ): if self.metadata: return bool( len( self.metadata.get( 'data_manager', {} ).get( 'data_managers', {} ) ) ) diff -r d62c5edf1ef265000740cac2949f90c9b175db6c -r 715dc4f4c8e218f50d08eb81dc1b3ef0453860a5 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 @@ -242,7 +242,8 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', **kwd ) ) - if 'user_id' not in kwd: + user_id = kwd.get( 'user_id', None ) + if user_id is None: # The received id is the repository id, so we need to get the id of the user that uploaded the repository. repository_id = kwd.get( 'id', None ) if repository_id: @@ -256,8 +257,9 @@ action='view_or_manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=selected_changeset_revision ) ) - user = suc.get_user( trans, kwd[ 'user_id' ] ) - self.repositories_by_user_grid.title = "Repositories owned by %s" % user.username + if user_id: + user = suc.get_user( trans, user_id ) + self.repositories_by_user_grid.title = "Repositories owned by %s" % user.username return self.repositories_by_user_grid( trans, **kwd ) @web.expose @@ -1192,7 +1194,7 @@ encoded_repository_ids = [] changeset_revisions = [] for required_repository_tup in decoded_required_repository_tups: - tool_shed, name, owner, changeset_revision = required_repository_tup + tool_shed, name, owner, changeset_revision, prior_installation_required = suc.parse_repository_dependency_tuple( required_repository_tup ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) encoded_repository_ids.append( trans.security.encode_id( repository.id ) ) changeset_revisions.append( changeset_revision ) diff -r d62c5edf1ef265000740cac2949f90c9b175db6c -r 715dc4f4c8e218f50d08eb81dc1b3ef0453860a5 lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -1,13 +1,19 @@ -import os, logging, threading +import logging +import os +import threading +from galaxy.util import asbool from tool_shed.util import readme_util +import tool_shed.util.shed_util_common as suc log = logging.getLogger( __name__ ) # String separator STRSEP = '__ESEP__' + class Folder( object ): """Container object.""" + def __init__( self, id=None, key=None, label=None, parent=None ): self.id = id self.key = key @@ -26,40 +32,49 @@ self.repository_dependencies = [] self.readme_files = [] self.workflows = [] + def contains_folder( self, folder ): for index, contained_folder in enumerate( self.folders ): if folder == contained_folder: return index, contained_folder return 0, None + def contains_repository_dependency( self, repository_dependency ): listified_repository_dependency = repository_dependency.listify for contained_repository_dependency in self.repository_dependencies: if contained_repository_dependency.listify == listified_repository_dependency: return True return False + def remove_repository_dependency( self, repository_dependency ): listified_repository_dependency = repository_dependency.listify for contained_repository_dependency in self.repository_dependencies: if contained_repository_dependency.listify == listified_repository_dependency: self.repository_dependencies.remove( contained_repository_dependency ) + def to_repository_dependency( self, repository_dependency_id ): - toolshed, name, owner, changeset_revision = self.key.split( STRSEP ) + toolshed, name, owner, changeset_revision, prior_installation_required = suc.parse_repository_dependency_tuple( self.key.split( STRSEP ) ) return RepositoryDependency( id=repository_dependency_id, toolshed=toolshed, repository_name=name, repository_owner=owner, - changeset_revision=changeset_revision ) + changeset_revision=changeset_revision, + prior_installation_required=prior_installation_required ) + class DataManager( object ): """Data Manager object""" + def __init__( self, id=None, name=None, version=None, data_tables=None ): self.id = id self.name = name self.version = version self.data_tables = data_tables + class Datatype( object ): """Datatype object""" + def __init__( self, id=None, extension=None, type=None, mimetype=None, subclass=None, converters=None, display_app_containers=None ): self.id = id self.extension = extension @@ -69,25 +84,32 @@ self.converters = converters self.display_app_containers = display_app_containers + class InvalidDataManager( object ): - """Data Manager object""" + """Invalid data Manager object""" + def __init__( self, id=None, index=None, error=None ): self.id = id self.index = index self.error = error + class InvalidRepositoryDependency( object ): """Invalid repository dependency definition object""" - def __init__( self, id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None, error=None ): + + def __init__( self, id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None, prior_installation_required=False, error=None ): self.id = id self.toolshed = toolshed self.repository_name = repository_name self.repository_owner = repository_owner self.changeset_revision = changeset_revision + self.prior_installation_required = prior_installation_required self.error = error + class InvalidTool( object ): """Invalid tool object""" + def __init__( self, id=None, tool_config=None, repository_id=None, changeset_revision=None, repository_installation_status=None ): self.id = id self.tool_config = tool_config @@ -95,8 +117,10 @@ self.changeset_revision = changeset_revision self.repository_installation_status = repository_installation_status + class InvalidToolDependency( object ): """Invalid tool dependency definition object""" + def __init__( self, id=None, name=None, version=None, type=None, error=None ): self.id = id self.name = name @@ -104,29 +128,38 @@ self.type = type self.error = error + class ReadMe( object ): """Readme text object""" + def __init__( self, id=None, name=None, text=None ): self.id = id self.name = name self.text = text + class RepositoryDependency( object ): """Repository dependency object""" - def __init__( self, id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None, installation_status=None, tool_shed_repository_id=None ): + + def __init__( self, id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None, prior_installation_required=False, + installation_status=None, tool_shed_repository_id=None ): self.id = id self.toolshed = toolshed self.repository_name = repository_name self.repository_owner = repository_owner self.changeset_revision = changeset_revision + self.prior_installation_required = prior_installation_required self.installation_status = installation_status self.tool_shed_repository_id = tool_shed_repository_id + @property def listify( self ): - return [ self.toolshed, self.repository_name, self.repository_owner, self.changeset_revision ] + return [ self.toolshed, self.repository_name, self.repository_owner, self.changeset_revision, asbool( str( self.prior_installation_required ) ) ] + class Tool( object ): """Tool object""" + def __init__( self, id=None, tool_config=None, tool_id=None, name=None, description=None, version=None, requirements=None, repository_id=None, changeset_revision=None, repository_installation_status=None ): self.id = id @@ -140,8 +173,10 @@ self.changeset_revision = changeset_revision self.repository_installation_status = repository_installation_status + class ToolDependency( object ): """Tool dependency object""" + def __init__( self, id=None, name=None, version=None, type=None, install_dir=None, readme=None, installation_status=None, repository_id=None, tool_dependency_id=None, is_orphan=None ): self.id = id @@ -154,12 +189,15 @@ self.repository_id = repository_id self.tool_dependency_id = tool_dependency_id self.is_orphan = is_orphan + @property def listify( self ): return [ self.name, self.version, self.type ] + class Workflow( object ): """Workflow object.""" + def __init__( self, id=None, workflow_name=None, steps=None, format_version=None, annotation=None, repository_metadata_id=None, repository_id=None ): # When rendered in the tool shed, repository_metadata_id will have a value and repository_id will be None. When rendered in Galaxy, repository_id # will have a value and repository_metadata_id will be None. @@ -334,8 +372,9 @@ for invalid_repository_dependency in invalid_repository_dependencies: folder_id += 1 invalid_repository_dependency_id += 1 - toolshed, name, owner, changeset_revision, error = invalid_repository_dependency - key = generate_repository_dependencies_key_for_repository( toolshed, name, owner, changeset_revision ) + toolshed, name, owner, changeset_revision, prior_installation_required, error = \ + suc.parse_repository_dependency_tuple( invalid_repository_dependency, contains_error=True ) + key = generate_repository_dependencies_key_for_repository( toolshed, name, owner, changeset_revision, prior_installation_required ) label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % ( name, changeset_revision, owner ) folder = Folder( id=folder_id, key=key, @@ -346,6 +385,7 @@ repository_name=name, repository_owner=owner, changeset_revision=changeset_revision, + prior_installation_required=prior_installation_required, error=error ) folder.invalid_repository_dependencies.append( ird ) invalid_repository_dependencies_folder.folders.append( folder ) @@ -691,7 +731,6 @@ data_managers = metadata['data_manager'].get( 'invalid_data_managers', None ) folder_id, data_managers_root_folder = build_invalid_data_managers_folder( trans, folder_id, data_managers, error_messages, label="Invalid Data Managers" ) containers_dict[ 'invalid_data_managers' ] = data_managers_root_folder - except Exception, e: log.debug( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) ) finally: @@ -948,23 +987,30 @@ return cast_empty_repository_dependency_folders( sub_folder, repository_dependency_id ) return folder, repository_dependency_id -def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, key ): +def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, prior_installation_required, key ): """Return a repository dependency label based on the repository dependency key.""" - if key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, key ): + if key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, prior_installation_required, key ): label = 'Repository dependencies' else: - label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % ( repository_name, changeset_revision, repository_owner ) + if prior_installation_required: + prior_installation_required_str = " <i>(prior install required)</i>" + else: + prior_installation_required_str = "" + label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>%s" % \ + ( repository_name, changeset_revision, repository_owner, prior_installation_required_str ) return label -def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision ): +def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required ): # FIXME: assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported. - return '%s%s%s%s%s%s%s' % ( str( toolshed_base_url ).rstrip( '/' ), - STRSEP, - str( repository_name ), - STRSEP, - str( repository_owner ), - STRSEP, - str( changeset_revision ) ) + return '%s%s%s%s%s%s%s%s%s' % ( str( toolshed_base_url ).rstrip( '/' ), + STRSEP, + str( repository_name ), + STRSEP, + str( repository_owner ), + STRSEP, + str( changeset_revision ), + STRSEP, + str( prior_installation_required ) ) def generate_tool_dependencies_key( name, version, type ): return '%s%s%s%s%s' % ( str( name ), STRSEP, str( version ), STRSEP, str( type ) ) @@ -983,12 +1029,22 @@ repository_name = items[ 1 ] repository_owner = items[ 2 ] changeset_revision = items[ 3 ] - return toolshed_base_url, repository_name, repository_owner, changeset_revision + if len( items ) == 5: + prior_installation_required = asbool( str( items[ 4 ] ) ) + else: + # Metadata should have been reset on the repository that contains the definition for this repository_dependency. In the meantime we'll + # default the prior_installation_required to False. + prior_installation_required = False + return toolshed_base_url, repository_name, repository_owner, changeset_revision, prior_installation_required def handle_repository_dependencies_container_entry( trans, repository_dependencies_folder, rd_key, rd_value, folder_id, repository_dependency_id, folder_keys ): - toolshed, repository_name, repository_owner, changeset_revision = get_components_from_key( rd_key ) + toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required = get_components_from_key( rd_key ) folder = get_folder( repository_dependencies_folder, rd_key ) - label = generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, repository_dependencies_folder.key ) + label = generate_repository_dependencies_folder_label_from_key( repository_name, + repository_owner, + changeset_revision, + prior_installation_required, + repository_dependencies_folder.key ) if folder: if rd_key not in folder_keys: folder_id += 1 @@ -1013,10 +1069,18 @@ for repository_dependency in rd_value: if trans.webapp.name == 'galaxy': if len( repository_dependency ) == 6: - # We have two extra items in the tuple, repository.id and repository.status. + # Metadata should have been reset on this installed repository, but it wasn't. tool_shed_repository_id = repository_dependency[ 4 ] installation_status = repository_dependency[ 5 ] - repository_dependency = repository_dependency[ 0:4 ] + tool_shed, name, owner, changeset_revision = repository_dependency[ 0:4 ] + # Default prior_installation_required to False. + prior_installation_required = False + repository_dependency = [ tool_shed, name, owner, changeset_revision, prior_installation_required ] + elif len( repository_dependency ) == 7: + # We have a repository dependency tuple that includes a prior_installation_required value. + tool_shed_repository_id = repository_dependency[ 5 ] + installation_status = repository_dependency[ 6 ] + repository_dependency = repository_dependency[ 0:5 ] else: tool_shed_repository_id = None installation_status = 'unknown' @@ -1025,13 +1089,15 @@ installation_status = None can_create_dependency = not is_subfolder_of( sub_folder, repository_dependency ) if can_create_dependency: - toolshed, repository_name, repository_owner, changeset_revision = repository_dependency + toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required = \ + suc.parse_repository_dependency_tuple( repository_dependency ) repository_dependency_id += 1 repository_dependency = RepositoryDependency( id=repository_dependency_id, toolshed=toolshed, repository_name=repository_name, repository_owner=repository_owner, changeset_revision=changeset_revision, + prior_installation_required=prior_installation_required, installation_status=installation_status, tool_shed_repository_id=tool_shed_repository_id ) # Insert the repository_dependency into the folder. @@ -1039,16 +1105,20 @@ return repository_dependencies_folder, folder_id, repository_dependency_id def is_subfolder_of( folder, repository_dependency ): - toolshed, repository_name, repository_owner, changeset_revision = repository_dependency - key = generate_repository_dependencies_key_for_repository( toolshed, repository_name, repository_owner, changeset_revision ) + toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required = \ + suc.parse_repository_dependency_tuple( repository_dependency ) + key = generate_repository_dependencies_key_for_repository( toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required ) for sub_folder in folder.folders: if key == sub_folder.key: return True return False -def key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, key ): - toolshed_base_url, key_name, key_owner, key_changeset_revision = get_components_from_key( key ) - return repository_name == key_name and repository_owner == key_owner and changeset_revision == key_changeset_revision +def key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, prior_installation_required, key ): + toolshed_base_url, key_name, key_owner, key_changeset_revision, key_prior_installation_required = get_components_from_key( key ) + return repository_name == key_name and \ + repository_owner == key_owner and \ + changeset_revision == key_changeset_revision and \ + prior_installation_required == key_prior_installation_required def populate_repository_dependencies_container( trans, repository_dependencies_folder, repository_dependencies, folder_id, repository_dependency_id ): folder_keys = repository_dependencies.keys() diff -r d62c5edf1ef265000740cac2949f90c9b175db6c -r 715dc4f4c8e218f50d08eb81dc1b3ef0453860a5 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -478,7 +478,8 @@ old_container_repository_dependencies_folder.id = folder_id folder_id += 1 # Generate the label by retrieving the repository name. - toolshed, name, owner, changeset_revision = container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) + toolshed, name, owner, changeset_revision, prior_installation_required = \ + container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) old_container_repository_dependencies_folder.label = str( name ) repository_dependencies_folder.folders.append( old_container_repository_dependencies_folder ) # Merge tool_dependencies. diff -r d62c5edf1ef265000740cac2949f90c9b175db6c -r 715dc4f4c8e218f50d08eb81dc1b3ef0453860a5 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -138,14 +138,15 @@ installed_repository_dependencies = {} has_repository_dependencies = repository.has_repository_dependencies if has_repository_dependencies: + # The repository dependencies container will include only the immediate repository dependencies of this repository, so the container + # will be only a single level in depth. metadata = repository.metadata installed_rd_tups = [] missing_rd_tups = [] - # The repository dependencies container will include only the immediate repository dependencies of this repository, so - # the container will be only a single level in depth. - for rd in repository.repository_dependencies: - rd_tup = [ rd.tool_shed, rd.name, rd.owner, rd.changeset_revision, rd.id, rd.status ] - if rd.status == trans.model.ToolShedRepository.installation_status.INSTALLED: + for tsr in repository.repository_dependencies: + prior_installation_required = suc.set_prior_installation_required( repository, tsr ) + rd_tup = [ tsr.tool_shed, tsr.name, tsr.owner, tsr.changeset_revision, prior_installation_required, tsr.id, tsr.status ] + if tsr.status == trans.model.ToolShedRepository.installation_status.INSTALLED: installed_rd_tups.append( rd_tup ) else: missing_rd_tups.append( rd_tup ) @@ -153,12 +154,13 @@ # Get the description from the metadata in case it has a value. repository_dependencies = metadata.get( 'repository_dependencies', {} ) description = repository_dependencies.get( 'description', None ) - # We need to add a root_key entry to one or both of installed_repository_dependencies dictionary and the - # missing_repository_dependencies dictionary for proper display parsing. + # We need to add a root_key entry to one or both of installed_repository_dependencies dictionary and the missing_repository_dependencies + # dictionary for proper display parsing. root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed, repository.name, repository.owner, - repository.installed_changeset_revision ) + repository.installed_changeset_revision, + prior_installation_required ) if installed_rd_tups: installed_repository_dependencies[ 'root_key' ] = root_key installed_repository_dependencies[ root_key ] = installed_rd_tups @@ -189,7 +191,7 @@ if key in [ 'description', 'root_key' ]: continue for rd_tup in rd_tups: - tool_shed, name, owner, changeset_revision = rd_tup + tool_shed, name, owner, changeset_revision, prior_installation_required = suc.parse_repository_dependency_tuple( rd_tup ) # Updates to installed repository revisions may have occurred, so make sure to locate the appropriate repository revision if one exists. # We need to create a temporary repo_info_tuple that includes the correct repository owner which we get from the current rd_tup. The current # tuple looks like: ( description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td ) @@ -197,7 +199,7 @@ tmp_repo_info_tuple = ( None, tmp_clone_url, changeset_revision, None, owner, None, None ) repository, current_changeset_revision = suc.repository_was_previously_installed( trans, tool_shed, name, tmp_repo_info_tuple ) if repository: - new_rd_tup = [ tool_shed, name, owner, changeset_revision, repository.id, repository.status ] + new_rd_tup = [ tool_shed, name, owner, changeset_revision, prior_installation_required, repository.id, repository.status ] if repository.status == trans.model.ToolShedRepository.installation_status.INSTALLED: if new_rd_tup not in installed_rd_tups: installed_rd_tups.append( new_rd_tup ) @@ -205,7 +207,7 @@ if new_rd_tup not in missing_rd_tups: missing_rd_tups.append( new_rd_tup ) else: - new_rd_tup = [ tool_shed, name, owner, changeset_revision, None, 'Never installed' ] + new_rd_tup = [ tool_shed, name, owner, changeset_revision, prior_installation_required, None, 'Never installed' ] if new_rd_tup not in missing_rd_tups: missing_rd_tups.append( new_rd_tup ) if installed_rd_tups: @@ -261,8 +263,8 @@ for key, val in repository_dependencies.items(): if key in [ 'root_key', 'description' ]: continue - toolshed, name, owner, changeset_revision = container_util.get_components_from_key( key ) - components_list = [ toolshed, name, owner, changeset_revision ] + toolshed, name, owner, changeset_revision, prior_installation_required = container_util.get_components_from_key( key ) + components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required ] if components_list not in required_repository_tups: required_repository_tups.append( components_list ) for components_list in val: @@ -272,6 +274,8 @@ # The value of required_repository_tups is a list of tuples, so we need to encode it. encoded_required_repository_tups = [] for required_repository_tup in required_repository_tups: + # Convert every item in required_repository_tup to a string. + required_repository_tup = [ str( item ) for item in required_repository_tup ] encoded_required_repository_tups.append( encoding_util.encoding_sep.join( required_repository_tup ) ) encoded_required_repository_str = encoding_util.encoding_sep2.join( encoded_required_repository_tups ) encoded_required_repository_str = encoding_util.tool_shed_encode( encoded_required_repository_str ) diff -r d62c5edf1ef265000740cac2949f90c9b175db6c -r 715dc4f4c8e218f50d08eb81dc1b3ef0453860a5 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -169,18 +169,19 @@ def compare_repository_dependencies( ancestor_repository_dependencies, current_repository_dependencies ): """Determine if ancestor_repository_dependencies is the same as or a subset of current_repository_dependencies.""" - # The list of repository_dependencies looks something like: [["http://localhost:9009", "emboss_datatypes", "test", "ab03a2a5f407"]]. + # The list of repository_dependencies looks something like: [["http://localhost:9009", "emboss_datatypes", "test", "ab03a2a5f407", False]]. # Create a string from each tuple in the list for easier comparison. if len( ancestor_repository_dependencies ) <= len( current_repository_dependencies ): for ancestor_tup in ancestor_repository_dependencies: - ancestor_tool_shed, ancestor_repository_name, ancestor_repository_owner, ancestor_changeset_revision = ancestor_tup + ancestor_tool_shed, ancestor_repository_name, ancestor_repository_owner, ancestor_changeset_revision, ancestor_prior_installation_required = ancestor_tup found_in_current = False for current_tup in current_repository_dependencies: - current_tool_shed, current_repository_name, current_repository_owner, current_changeset_revision = current_tup + current_tool_shed, current_repository_name, current_repository_owner, current_changeset_revision, current_prior_installation_required = current_tup if current_tool_shed == ancestor_tool_shed and \ current_repository_name == ancestor_repository_name and \ current_repository_owner == ancestor_repository_owner and \ - current_changeset_revision == ancestor_changeset_revision: + current_changeset_revision == ancestor_changeset_revision and \ + current_prior_installation_required == ancestor_prior_installation_required: found_in_current = True break if not found_in_current: @@ -704,23 +705,23 @@ xml_is_valid = False if xml_is_valid: invalid_repository_dependencies_dict = dict( description=root.get( 'description' ) ) - invalid_repository_dependencies_tups = [] + invalid_repository_dependency_tups = [] valid_repository_dependencies_dict = dict( description=root.get( 'description' ) ) - valid_repository_dependencies_tups = [] + valid_repository_dependency_tups = [] for repository_elem in root.findall( 'repository' ): - repository_dependencies_tup, repository_dependency_is_valid, error_message = handle_repository_elem( app, repository_elem ) + repository_dependency_tup, repository_dependency_is_valid, error_message = handle_repository_elem( app, repository_elem ) if repository_dependency_is_valid: - valid_repository_dependencies_tups.append( repository_dependencies_tup ) + valid_repository_dependency_tups.append( repository_dependency_tup ) else: # Append the error_message to the repository dependencies tuple. - toolshed, name, owner, changeset_revision = repository_dependencies_tup - repository_dependencies_tup = ( toolshed, name, owner, changeset_revision, error_message ) - invalid_repository_dependencies_tups.append( repository_dependencies_tup ) - if invalid_repository_dependencies_tups: - invalid_repository_dependencies_dict[ 'repository_dependencies' ] = invalid_repository_dependencies_tups + toolshed, name, owner, changeset_revision, prior_installation_required = repository_dependency_tup + repository_dependency_tup = ( toolshed, name, owner, changeset_revision, prior_installation_required, error_message ) + invalid_repository_dependency_tups.append( repository_dependency_tup ) + if invalid_repository_dependency_tups: + invalid_repository_dependencies_dict[ 'repository_dependencies' ] = invalid_repository_dependency_tups metadata_dict[ 'invalid_repository_dependencies' ] = invalid_repository_dependencies_dict - if valid_repository_dependencies_tups: - valid_repository_dependencies_dict[ 'repository_dependencies' ] = valid_repository_dependencies_tups + if valid_repository_dependency_tups: + valid_repository_dependencies_dict[ 'repository_dependencies' ] = valid_repository_dependency_tups metadata_dict[ 'repository_dependencies' ] = valid_repository_dependencies_dict return metadata_dict, error_message @@ -765,8 +766,8 @@ # We have an invalid complex repository dependency, so mark the tool dependency as invalid. tool_dependency_is_valid = False # Append the error message to the invalid repository dependency tuple. - toolshed, name, owner, changeset_revision = repository_dependency_tup - repository_dependency_tup = ( toolshed, name, owner, changeset_revision, message ) + toolshed, name, owner, changeset_revision, prior_installation_required = repository_dependency_tup + repository_dependency_tup = ( toolshed, name, owner, changeset_revision, prior_installation_required, message ) invalid_repository_dependency_tups.append( repository_dependency_tup ) error_message = '%s %s' % ( error_message, message ) elif elem.tag == 'set_environment': @@ -1044,11 +1045,12 @@ sa_session = app.model.context.current is_valid = True error_message = '' - toolshed = repository_elem.attrib[ 'toolshed' ] - name = repository_elem.attrib[ 'name' ] - owner = repository_elem.attrib[ 'owner' ] - changeset_revision = repository_elem.attrib[ 'changeset_revision' ] - repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) + toolshed = repository_elem.get( 'toolshed' ) + name = repository_elem.get( 'name' ) + owner = repository_elem.get( 'owner' ) + changeset_revision = repository_elem.get( 'changeset_revision' ) + prior_installation_required = repository_elem.get( 'prior_installation_required', False ) + repository_dependency_tup = ( toolshed, name, owner, changeset_revision, prior_installation_required ) user = None repository = None if app.name == 'galaxy': @@ -1058,20 +1060,16 @@ # repository_elem, we know it is valid. repository = suc.get_repository_for_dependency_relationship( app, toolshed, name, owner, changeset_revision ) if repository: - return repository_dependencies_tup, is_valid, error_message + return repository_dependency_tup, is_valid, error_message else: # Send a request to the tool shed to retrieve appropriate additional changeset revisions with which the repository may have been installed. - #try: - # Hopefully the tool shed is accessible. text = get_updated_changeset_revisions_from_tool_shed( toolshed, name, owner, changeset_revision ) - #except: - # text = None if text: updated_changeset_revisions = util.listify( text ) for updated_changeset_revision in updated_changeset_revisions: repository = suc.get_repository_for_dependency_relationship( app, toolshed, name, owner, updated_changeset_revision ) if repository: - return repository_dependencies_tup, is_valid, error_message + return repository_dependency_tup, is_valid, error_message # We'll currently default to setting the repository dependency definition as invalid if an installed repository cannot be found. # This may not be ideal because the tool shed may have simply been inaccessible when metadata was being generated for the installed # tool shed repository. @@ -1079,7 +1077,7 @@ ( toolshed, name, owner, changeset_revision ) log.debug( error_message ) is_valid = False - return repository_dependencies_tup, is_valid, error_message + return repository_dependency_tup, is_valid, error_message else: # We're in the tool shed. if suc.tool_shed_is_this_tool_shed( toolshed ): @@ -1093,7 +1091,7 @@ error_message += "because the owner is invalid. " log.debug( error_message ) is_valid = False - return repository_dependencies_tup, is_valid, error_message + return repository_dependency_tup, is_valid, error_message try: repository = sa_session.query( app.model.Repository ) \ .filter( and_( app.model.Repository.table.c.name == name, @@ -1105,7 +1103,7 @@ error_message += "because the name is invalid. " log.debug( error_message ) is_valid = False - return repository_dependencies_tup, is_valid, error_message + return repository_dependency_tup, is_valid, error_message # Find the specified changeset revision in the repository's changelog to see if it's valid. found = False repo = hg.repository( suc.get_configured_ui(), repository.repo_path( app ) ) @@ -1120,15 +1118,15 @@ error_message += "because the changeset revision is invalid. " log.debug( error_message ) is_valid = False - return repository_dependencies_tup, is_valid, error_message + return repository_dependency_tup, is_valid, error_message else: # Repository dependencies are currently supported within a single tool shed. error_message = "Repository dependencies are currently supported only within the same tool shed. Ignoring repository dependency definition " error_message += "for tool shed %s, name %s, owner %s, changeset revision %s. " % ( toolshed, name, owner, changeset_revision ) log.debug( error_message ) is_valid = False - return repository_dependencies_tup, is_valid, error_message - return repository_dependencies_tup, is_valid, error_message + return repository_dependency_tup, is_valid, error_message + return repository_dependency_tup, is_valid, error_message def is_downloadable( metadata_dict ): # NOTE: although repository README files are considered Galaxy utilities, they have no effect on determining if a revision is installable. @@ -1851,13 +1849,15 @@ repository_dependencies_dict = metadata.get( 'invalid_repository_dependencies', None ) for repository_dependency_tup in repository_dependency_tups: if is_valid: - tool_shed, name, owner, changeset_revision = repository_dependency_tup + tool_shed, name, owner, changeset_revision, prior_installation_required = repository_dependency_tup else: - tool_shed, name, owner, changeset_revision, error_message = repository_dependency_tup + tool_shed, name, owner, changeset_revision, prior_installation_required, error_message = repository_dependency_tup + prior_installation_required = util.asbool( str( prior_installation_required ) ) rd_key = container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=tool_shed, repository_name=name, repository_owner=owner, - changeset_revision=changeset_revision ) + changeset_revision=changeset_revision, + prior_installation_required=prior_installation_required ) if repository_dependencies_dict: if rd_key in repository_dependencies_dict: repository_dependencies = repository_dependencies_dict[ rd_key ] diff -r d62c5edf1ef265000740cac2949f90c9b175db6c -r 715dc4f4c8e218f50d08eb81dc1b3ef0453860a5 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -33,7 +33,8 @@ if key in [ 'root_key', 'description' ]: continue dependent_repository = None - dependent_toolshed, dependent_name, dependent_owner, dependent_changeset_revision = container_util.get_components_from_key( key ) + dependent_toolshed, dependent_name, dependent_owner, dependent_changeset_revision, dependent_prior_installation_required = \ + container_util.get_components_from_key( key ) for tsr in tool_shed_repositories: # Get the the tool_shed_repository defined by name, owner and changeset_revision. This is the repository that will be # dependent upon each of the tool shed repositories contained in val. @@ -47,7 +48,8 @@ # Process each repository_dependency defined for the current dependent repository. for repository_dependency_components_list in val: required_repository = None - rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_dependency_components_list + rd_toolshed, rd_name, rd_owner, rd_changeset_revision, prior_installation_required = \ + suc.parse_repository_dependency_tuple( repository_dependency_components_list ) # Get the the tool_shed_repository defined by rd_name, rd_owner and rd_changeset_revision. This is the repository that will be # required by the current dependent_repository. # TODO: Check tool_shed_repository.tool_shed as well when repository dependencies across tool sheds is supported. @@ -244,7 +246,8 @@ if invalid_repository_dependencies_dict: invalid_repository_dependencies = invalid_repository_dependencies_dict[ 'invalid_repository_dependencies' ] for repository_dependency_tup in invalid_repository_dependencies: - toolshed, name, owner, changeset_revision, error = repository_dependency_tup + toolshed, name, owner, changeset_revision, prior_installation_required, error = \ + suc.parse_repository_dependency_tuple( repository_dependency_tup, contains_error=True ) if error: message = '%s ' % str( error ) return message @@ -253,7 +256,8 @@ return container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=toolshed_base_url, repository_name=repository.name, repository_owner=repository.user.username, - changeset_revision=repository_metadata.changeset_revision ) + changeset_revision=repository_metadata.changeset_revision, + prior_installation_required=False ) def get_repository_dependencies_for_changeset_revision( trans, repository, repository_metadata, toolshed_base_url, key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, @@ -320,7 +324,7 @@ for key_rd_dict in key_rd_dicts: key = key_rd_dict.keys()[ 0 ] repository_dependency = key_rd_dict[ key ] - rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_dependency + rd_toolshed, rd_name, rd_owner, rd_changeset_revision, rd_prior_installation_required = suc.parse_repository_dependency_tuple( repository_dependency ) if suc.tool_shed_is_this_tool_shed( rd_toolshed ): repository = suc.get_repository_by_name_and_owner( trans.app, rd_name, rd_owner ) if repository: @@ -342,16 +346,17 @@ changeset_revision ) if repository_metadata: new_key_rd_dict = {} - new_key_rd_dict[ key ] = [ rd_toolshed, rd_name, rd_owner, repository_metadata.changeset_revision ] + new_key_rd_dict[ key ] = [ rd_toolshed, rd_name, rd_owner, repository_metadata.changeset_revision, rd_prior_installation_required ] # We have the updated changset revision. updated_key_rd_dicts.append( new_key_rd_dict ) else: - toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key ) + toolshed, repository_name, repository_owner, repository_changeset_revision, prior_installation_required = \ + container_util.get_components_from_key( key ) message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \ ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) ) log.debug( message ) else: - toolshed, repository_name, repository_owner, repository_changeset_revision = container_util.get_components_from_key( key ) + toolshed, repository_name, repository_owner, repository_changeset_revision, prior_installation_required = container_util.get_components_from_key( key ) message = "The revision %s defined for repository %s owned by %s is invalid, so repository dependencies defined for repository %s will be ignored." % \ ( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ), str( repository_name ) ) log.debug( message ) @@ -397,7 +402,7 @@ def handle_key_rd_dicts_for_repository( trans, current_repository_key, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, circular_repository_dependencies ): key_rd_dict = repository_key_rd_dicts.pop( 0 ) repository_dependency = key_rd_dict[ current_repository_key ] - toolshed, name, owner, changeset_revision = repository_dependency + toolshed, name, owner, changeset_revision, prior_installation_required = suc.parse_repository_dependency_tuple( repository_dependency ) if suc.tool_shed_is_this_tool_shed( toolshed ): required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) required_repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, @@ -444,7 +449,7 @@ circular_repository_dependencies=circular_repository_dependencies ) def in_all_repository_dependencies( repository_key, repository_dependency, all_repository_dependencies ): - """Return True if { repository_key :repository_dependency } is in all_repository_dependencies.""" + """Return True if { repository_key : repository_dependency } is in all_repository_dependencies.""" for key, val in all_repository_dependencies.items(): if key != repository_key: continue @@ -455,7 +460,7 @@ def in_circular_repository_dependencies( repository_key_rd_dict, circular_repository_dependencies ): """ Return True if any combination of a circular dependency tuple is the key : value pair defined in the received repository_key_rd_dict. This - means that each circular dependency tuple is converted into the key : value pair for vomparision. + means that each circular dependency tuple is converted into the key : value pair for comparison. """ for tup in circular_repository_dependencies: rd_0, rd_1 = tup @@ -468,7 +473,8 @@ return False def initialize_all_repository_dependencies( current_repository_key, repository_dependencies_dict, all_repository_dependencies ): - # Initialize the all_repository_dependencies dictionary. It's safe to assume that current_repository_key in this case will have a value. + """Initialize the all_repository_dependencies dictionary.""" + # It's safe to assume that current_repository_key in this case will have a value. all_repository_dependencies[ 'root_key' ] = current_repository_key all_repository_dependencies[ current_repository_key ] = [] # Store the value of the 'description' key only once, the first time through this recursive method. @@ -477,6 +483,7 @@ return all_repository_dependencies def in_key_rd_dicts( key_rd_dict, key_rd_dicts ): + """Return True if key_rd_dict is contained in the list of key_rd_dicts.""" k = key_rd_dict.keys()[ 0 ] v = key_rd_dict[ k ] for key_rd_dict in key_rd_dicts: @@ -513,7 +520,7 @@ return False def merge_missing_repository_dependencies_to_installed_container( containers_dict ): - """ Merge the list of missing repository dependencies into the list of installed repository dependencies.""" + """Merge the list of missing repository dependencies into the list of installed repository dependencies.""" missing_rd_container_root = containers_dict.get( 'missing_repository_dependencies', None ) if missing_rd_container_root: # The missing_rd_container_root will be a root folder containing a single sub_folder. @@ -542,6 +549,11 @@ def populate_repository_dependency_objects_for_processing( trans, current_repository_key, repository_dependencies_dict, key_rd_dicts_to_be_processed, handled_key_rd_dicts, circular_repository_dependencies, all_repository_dependencies ): + """ + The process that discovers all repository dependencies for a specified repository's changeset revision uses this method to populate the following items + for the current processing loop: filtered_current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies. + Each processing loop may discover more repository dependencies, so this method is repeatedly called until all repository dependencies have been discovered. + """ current_repository_key_rd_dicts = [] filtered_current_repository_key_rd_dicts = [] for rd in repository_dependencies_dict[ 'repository_dependencies' ]: @@ -602,6 +614,7 @@ return valid_repository_dependencies def remove_from_key_rd_dicts( key_rd_dict, key_rd_dicts ): + """Eliminate the key_rd_dict from the list of key_rd_dicts if it is contained in the list.""" k = key_rd_dict.keys()[ 0 ] v = key_rd_dict[ k ] clean_key_rd_dicts = [] @@ -618,11 +631,11 @@ clean_key_rd_dicts = [] key = key_rd_dicts[ 0 ].keys()[ 0 ] repository_tup = key.split( container_util.STRSEP ) - rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_tup + rd_toolshed, rd_name, rd_owner, rd_changeset_revision, rd_prior_installation_required = suc.parse_repository_dependency_tuple( repository_tup ) for key_rd_dict in key_rd_dicts: k = key_rd_dict.keys()[ 0 ] repository_dependency = key_rd_dict[ k ] - toolshed, name, owner, changeset_revision = repository_dependency + toolshed, name, owner, changeset_revision, prior_installation_required = suc.parse_repository_dependency_tuple( repository_dependency ) if rd_toolshed == toolshed and rd_name == name and rd_owner == owner: log.debug( "Removing repository dependency for repository %s owned by %s since it refers to a revision within itself." % ( name, owner ) ) else: @@ -631,44 +644,9 @@ clean_key_rd_dicts.append( new_key_rd_dict ) return clean_key_rd_dicts -def repository_dependencies_have_tool_dependencies( trans, repository_dependencies ): - rd_tups_processed = [] - for key, rd_tups in repository_dependencies.items(): - if key in [ 'root_key', 'description' ]: - continue - rd_tup = container_util.get_components_from_key( key ) - if rd_tup not in rd_tups_processed: - toolshed, name, owner, changeset_revision = rd_tup - repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, - trans.security.encode_id( repository.id ), - changeset_revision ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - if 'tool_dependencies' in metadata: - return True - rd_tups_processed.append( rd_tup ) - for rd_tup in rd_tups: - if rd_tup not in rd_tups_processed: - toolshed, name, owner, changeset_revision = rd_tup - repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, - trans.security.encode_id( repository.id ), - changeset_revision ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - if 'tool_dependencies' in metadata: - return True - rd_tups_processed.append( rd_tup ) - return False - def get_repository_dependency_as_key( repository_dependency ): - return container_util.generate_repository_dependencies_key_for_repository( repository_dependency[ 0 ], - repository_dependency[ 1 ], - repository_dependency[ 2 ], - repository_dependency[ 3 ] ) + tool_shed, name, owner, changeset_revision, prior_installation_required = suc.parse_repository_dependency_tuple( repository_dependency ) + return container_util.generate_repository_dependencies_key_for_repository( tool_shed, name, owner, changeset_revision, prior_installation_required ) def get_repository_dependency_by_repository_id( trans, decoded_repository_id ): return trans.sa_session.query( trans.model.RepositoryDependency ) \ diff -r d62c5edf1ef265000740cac2949f90c9b175db6c -r 715dc4f4c8e218f50d08eb81dc1b3ef0453860a5 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 @@ -272,8 +272,8 @@ def generate_clone_url_from_repo_info_tup( repo_info_tup ): """Generate teh URL for cloning a repositoyr given a tuple of toolshed, name, owner, changeset_revision.""" - # Example tuple: ['http://localhost:9009', 'blast_datatypes', 'test', '461a4216e8ab'] - toolshed, name, owner, changeset_revision = repo_info_tup + # Example tuple: ['http://localhost:9009', 'blast_datatypes', 'test', '461a4216e8ab', False] + toolshed, name, owner, changeset_revision, prior_installation_required = parse_repository_dependency_tuple( repo_info_tup ) # Don't include the changeset_revision in clone urls. return url_join( toolshed, 'repos', owner, name ) @@ -1019,6 +1019,28 @@ folder_contents.append( node ) return folder_contents +def parse_repository_dependency_tuple( repository_dependency_tuple, contains_error=False ): + if contains_error: + if len( repository_dependency_tuple ) == 5: + # Metadata should have been reset on the repository containing this repository_dependency definition. + tool_shed, name, owner, changeset_revision, error = repository_dependency_tuple + # Default prior_installation_required to False. + prior_installation_required = False + elif len( repository_dependency_tuple ) == 6: + toolshed, name, owner, changeset_revision, prior_installation_required, error = repository_dependency_tuple + prior_installation_required = util.asbool( str( prior_installation_required ) ) + return toolshed, name, owner, changeset_revision, prior_installation_required, error + else: + if len( repository_dependency_tuple ) == 4: + # Metadata should have been reset on the repository containing this repository_dependency definition. + tool_shed, name, owner, changeset_revision = repository_dependency_tuple + # Default prior_installation_required to False. + prior_installation_required = False + elif len( repository_dependency_tuple ) == 5: + tool_shed, name, owner, changeset_revision, prior_installation_required = repository_dependency_tuple + prior_installation_required = util.asbool( str( prior_installation_required ) ) + return tool_shed, name, owner, changeset_revision, prior_installation_required + def remove_dir( dir ): """Attempt to remove a directory from disk.""" if os.path.exists( dir ): @@ -1097,6 +1119,19 @@ trans.sa_session.add( repository ) trans.sa_session.flush() +def set_prior_installation_required( repository, required_repository ): + """Return True if the received required_repository must be installed before the received repository.""" + required_repository_tup = [ required_repository.tool_shed, required_repository.name, required_repository.owner, required_repository.changeset_revision ] + # Get the list of repository dependency tuples associated with the received repository where prior_installation_required is True. + required_rd_tups_that_must_be_installed = repository.requires_prior_installation_of + for required_rd_tup in required_rd_tups_that_must_be_installed: + # Repository dependency tuples in metadata include a prior_installation_required value, so strip it for comparision. + partial_required_rd_tup = required_rd_tup[ 0:4 ] + if partial_required_rd_tup == required_repository_tup: + # Return the boolean value of prior_installation_required, which defaults to False. + return required_rd_tup[ 4 ] + return False + def strip_path( fpath ): """Attempt to strip the path from a file name.""" if not fpath: diff -r d62c5edf1ef265000740cac2949f90c9b175db6c -r 715dc4f4c8e218f50d08eb81dc1b3ef0453860a5 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -513,8 +513,12 @@ else: installation_status = None repository_name = str( repository_dependency.repository_name ) + repository_owner = str( repository_dependency.repository_owner ) changeset_revision = str( repository_dependency.changeset_revision ) - repository_owner = str( repository_dependency.repository_owner ) + if prior_installation_required: + prior_installation_required_str = " <i>(prior install required)</i>" + else: + prior_installation_required_str = "" if trans.webapp.name == 'galaxy': if row_is_header: @@ -550,7 +554,7 @@ </${cell_type}> %else: <td style="padding-left: ${pad+20}px;"> - Repository <b>${repository_name | h}</b> revision <b>${changeset_revision | h}</b> owned by <b>${repository_owner | h}</b> + Repository <b>${repository_name | h}</b> revision <b>${changeset_revision | h}</b> owned by <b>${repository_owner | h}</b>${prior_installation_required_str} </td> %endif </tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d6ab0870547c/ Changeset: d6ab0870547c User: dannon Date: 2013-04-02 20:41:10 Summary: Library controller code cleanup, imports and spacing. Affected #: 1 file diff -r f03401b61bc6825131b163b9bb8cf1acf8ac48c3 -r d6ab0870547c5342b101d2a97513da699ef4ae39 lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -1,24 +1,27 @@ -import urllib, urllib2 +import logging +from galaxy import model, util +from galaxy import web +from galaxy.model.orm import and_, not_, or_ +from galaxy.web.base.controller import BaseUIController +from galaxy.web.framework.helpers import grids +from library_common import get_comptypes, lucene_search, whoosh_search -from galaxy.web.base.controller import * -from galaxy.web.framework.helpers import time_ago, iff, grids -from galaxy.model.orm import * -from galaxy.datatypes import sniff -from galaxy import model, util -from galaxy.util.odict import odict -from library_common import get_comptypes, lucene_search, whoosh_search log = logging.getLogger( __name__ ) + class LibraryListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, library ): return library.name + class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, library ): if library.description: return library.description return '' + # Grid definition title = "Data Libraries" model_class = model.Library @@ -45,8 +48,10 @@ num_rows_per_page = 50 preserve_state = False use_paging = True + def build_initial_query( self, trans, **kwargs ): return trans.sa_session.query( self.model_class ).filter( self.model_class.table.c.deleted == False ) + def apply_query_filter( self, trans, query, **kwd ): current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ] library_access_action = trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action @@ -65,8 +70,10 @@ # public libraries and restricted libraries accessible by the current user. return query.filter( or_( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ), trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) + + class Library( BaseUIController ): - + library_list_grid = LibraryListGrid() @web.expose https://bitbucket.org/galaxy/galaxy-central/commits/8a84382c5c33/ Changeset: 8a84382c5c33 User: dannon Date: 2013-04-02 20:41:55 Summary: Trim trailing whitespace. Affected #: 1 file diff -r d6ab0870547c5342b101d2a97513da699ef4ae39 -r 8a84382c5c339eee6c866301bae613bb4a2b0595 lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -38,8 +38,8 @@ attach_popup=False, filterable="advanced" ), ] - columns.append( grids.MulticolFilterColumn( "search dataset name, info, message, dbkey", - cols_to_filter=[ columns[0], columns[1] ], + columns.append( grids.MulticolFilterColumn( "search dataset name, info, message, dbkey", + cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -62,11 +62,11 @@ .filter( and_( trans.model.LibraryPermissions.table.c.action == library_access_action, trans.model.LibraryPermissions.table.c.role_id.in_( current_user_role_ids ) ) ) ] if not trans.user: - # Filter to get only public libraries, a library whose id + # Filter to get only public libraries, a library whose id # is not in restricted_library_ids is a public library return query.filter( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ) ) else: - # Filter to get libraries accessible by the current user, get both + # Filter to get libraries accessible by the current user, get both # public libraries and restricted libraries accessible by the current user. return query.filter( or_( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ), trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) https://bitbucket.org/galaxy/galaxy-central/commits/d62c5edf1ef2/ Changeset: d62c5edf1ef2 User: dannon Date: 2013-04-02 20:47:12 Summary: Merge Affected #: 6 files This diff is so big that we needed to truncate the remainder. 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.

1 0

commit/galaxy-central: carlfeberhard: That went well. (rollback changes to backbone, backbone-relational, and handlebars.runtime to not break every possible thing)
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/23fd5251f5ec/ Changeset: 23fd5251f5ec User: carlfeberhard Date: 2013-04-02 20:41:29 Summary: That went well. (rollback changes to backbone, backbone-relational, and handlebars.runtime to not break every possible thing) Affected #: 6 files This diff is so big that we needed to truncate the remainder. 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.

1 0

commit/galaxy-central: dannon: api/users import cleanup
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f03401b61bc6/ Changeset: f03401b61bc6 User: dannon Date: 2013-04-02 20:36:50 Summary: api/users import cleanup Affected #: 1 file diff -r 8effd49e233eccfb0cc4f11cc1ff67da13cbb655 -r f03401b61bc6825131b163b9bb8cf1acf8ac48c3 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -2,10 +2,9 @@ API operations on User objects. """ import logging +from paste.httpexceptions import HTTPBadRequest, HTTPNotImplemented +from galaxy import util, web from galaxy.web.base.controller import BaseAPIController, url_for -from galaxy import web, util -from elementtree.ElementTree import XML -from paste.httpexceptions import * log = logging.getLogger( __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.

1 0

commit/galaxy-central: dannon: api/histories import cleanup, remove unused Params cruft.
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8effd49e233e/ Changeset: 8effd49e233e User: dannon Date: 2013-04-02 20:35:18 Summary: api/histories import cleanup, remove unused Params cruft. Affected #: 1 file diff -r c554d8795650fc155b2b2610bed3fe4f1e31c1f1 -r 8effd49e233eccfb0cc4f11cc1ff67da13cbb655 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -1,19 +1,11 @@ """ API operations on a history. """ -import logging, os, string, shutil, urllib, re, socket -from cgi import escape, FieldStorage -from galaxy import util, datatypes, jobs, web, util +import logging +from galaxy import web, util from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin from galaxy.web import url_for -from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.orm import * -import galaxy.datatypes -from galaxy.util.bunch import Bunch - -import pkg_resources -pkg_resources.require( "Routes" ) -import routes +from galaxy.model.orm import desc log = logging.getLogger( __name__ ) @@ -59,7 +51,6 @@ Displays information about a history. """ history_id = id - params = util.Params( kwd ) deleted = util.string_as_bool( deleted ) # try to load the history, by most_recently_used or the given id @@ -91,7 +82,6 @@ POST /api/histories Creates a new history. """ - params = util.Params( payload ) hist_name = None if payload.get( 'name', None ): hist_name = util.restore_text( payload['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.

1 0

commit/galaxy-central: carlfeberhard: update js libs: underscore 1.3.1 -> 1.4.4, backbone 0.9.2 -> 1.0, backbone-relational 0.5.0 -> 0.8.0, handlebars 1.0.beta.6 -> 1.0.rc1
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c554d8795650/ Changeset: c554d8795650 User: carlfeberhard Date: 2013-04-02 20:27:23 Summary: update js libs: underscore 1.3.1 -> 1.4.4, backbone 0.9.2 -> 1.0, backbone-relational 0.5.0 -> 0.8.0, handlebars 1.0.beta.6 -> 1.0.rc1 Affected #: 8 files This diff is so big that we needed to truncate the remainder. 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.

1 0

commit/galaxy-central: carlfeberhard: pack_scripts.py: have yuicompressor use utf-8 as the charset; remove unused packed scripts; update d3.js from 2.9.2 to 3.1.4
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1207f1c95e70/ Changeset: 1207f1c95e70 User: carlfeberhard Date: 2013-04-02 20:20:55 Summary: pack_scripts.py: have yuicompressor use utf-8 as the charset; remove unused packed scripts; update d3.js from 2.9.2 to 3.1.4 Affected #: 8 files This diff is so big that we needed to truncate the remainder. 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1c92aed71881/ Changeset: 1c92aed71881 Branch: stable User: inithello Date: 2013-04-02 19:34:25 Summary: Enable scrolling for the left panel in the tool shed. Fix for determining if a repository dependency can be added to a container. Affected #: 3 files diff -r 9264cf7148c08082d0706c0cf4b74f6a9332dc4d -r 1c92aed71881e3a15648e3be9478a69f76c50498 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -85,10 +85,9 @@ for kr_dict in key_rd_dicts: key = kr_dict.keys()[ 0 ] if key == k: - val = kr_dict[ key ] - for repository_dependency in val: - if repository_dependency[ 0:3 ] == partial_rd: - return False + repository_dependency = kr_dict[ key ] + if repository_dependency[ 0:3 ] == partial_rd: + return False return True def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, install_repository_dependencies=False, diff -r 9264cf7148c08082d0706c0cf4b74f6a9332dc4d -r 1c92aed71881e3a15648e3be9478a69f76c50498 templates/webapps/tool_shed/admin/index.mako --- a/templates/webapps/tool_shed/admin/index.mako +++ b/templates/webapps/tool_shed/admin/index.mako @@ -40,7 +40,7 @@ <div class="unified-panel-header" unselectable="on"><div class='unified-panel-header-inner'>Administration</div></div> - <div class="page-container" style="padding: 10px;"> + <div class="unified-panel-body" style="padding: 10px; overflow: auto;"><div class="toolMenu"><div class="toolSectionList"><div class="toolSectionTitle"> diff -r 9264cf7148c08082d0706c0cf4b74f6a9332dc4d -r 1c92aed71881e3a15648e3be9478a69f76c50498 templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -41,7 +41,7 @@ <div class="unified-panel-header" unselectable="on"><div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools | h} valid tools on ${trans.app.shed_counter.generation_time | h}</div></div> - <div class="page-container" style="padding: 10px;"> + <div class="unified-panel-body" style="padding: 10px; overflow: auto;"><div class="toolMenu"><div class="toolSectionList"> %if user_id or repository_id: https://bitbucket.org/galaxy/galaxy-central/commits/f9d8a99135ce/ Changeset: f9d8a99135ce User: inithello Date: 2013-04-02 19:34:53 Summary: Pull in changes from stable branch. Affected #: 3 files diff -r fe538afce7d41adec8c60f197c226e92702225f4 -r f9d8a99135ce4be3ae55459ecf177a382fe4c93a lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -85,10 +85,9 @@ for kr_dict in key_rd_dicts: key = kr_dict.keys()[ 0 ] if key == k: - val = kr_dict[ key ] - for repository_dependency in val: - if repository_dependency[ 0:3 ] == partial_rd: - return False + repository_dependency = kr_dict[ key ] + if repository_dependency[ 0:3 ] == partial_rd: + return False return True def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, install_repository_dependencies=False, diff -r fe538afce7d41adec8c60f197c226e92702225f4 -r f9d8a99135ce4be3ae55459ecf177a382fe4c93a templates/webapps/tool_shed/admin/index.mako --- a/templates/webapps/tool_shed/admin/index.mako +++ b/templates/webapps/tool_shed/admin/index.mako @@ -40,7 +40,7 @@ <div class="unified-panel-header" unselectable="on"><div class='unified-panel-header-inner'>Administration</div></div> - <div class="page-container" style="padding: 10px;"> + <div class="unified-panel-body" style="padding: 10px; overflow: auto;"><div class="toolMenu"><div class="toolSectionList"><div class="toolSectionTitle"> diff -r fe538afce7d41adec8c60f197c226e92702225f4 -r f9d8a99135ce4be3ae55459ecf177a382fe4c93a templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -41,7 +41,7 @@ <div class="unified-panel-header" unselectable="on"><div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools | h} valid tools on ${trans.app.shed_counter.generation_time | h}</div></div> - <div class="page-container" style="padding: 10px;"> + <div class="unified-panel-body" style="padding: 10px; overflow: auto;"><div class="toolMenu"><div class="toolSectionList"> %if user_id or repository_id: 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.

1 0

commit/galaxy-central: inithello: Fix for adding new entries to a tool data table that is already present in app.tool_data_tables.
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fe538afce7d4/ Changeset: fe538afce7d4 User: inithello Date: 2013-04-02 17:47:38 Summary: Fix for adding new entries to a tool data table that is already present in app.tool_data_tables. Affected #: 1 file diff -r eea87f210c46b6bc9cc7e82e0f12c13bfa6f1e5e -r fe538afce7d41adec8c60f197c226e92702225f4 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -59,6 +59,11 @@ if table.name not in self.data_tables: self.data_tables[ table.name ] = table log.debug( "Loaded tool data table '%s'", table.name ) + else: + for table_row in table.data: + # FIXME: This does not account for an entry with the same unique build ID, but a different path. + if table_row not in self.data_tables[ table.name ].data: + self.data_tables[ table.name ].data.append( table_row ) return table_elems def add_new_entries_from_config_file( self, config_filename, tool_data_path, shed_tool_data_table_config, persist=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.

1 0

commit/galaxy-central: carlfeberhard: fix simple-galaxy.js util in browser test section
by commits-noreply＠bitbucket.org 02 Apr '13

02 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eea87f210c46/ Changeset: eea87f210c46 User: carlfeberhard Date: 2013-04-02 16:50:56 Summary: fix simple-galaxy.js util in browser test section Affected #: 1 file diff -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 -r eea87f210c46b6bc9cc7e82e0f12c13bfa6f1e5e test/casperjs/utils/simple-galaxy.js --- a/test/casperjs/utils/simple-galaxy.js +++ b/test/casperjs/utils/simple-galaxy.js @@ -1,1 +1,65 @@ -/Users/carleberhard/explore/phantom-casper/simple-galaxy.js \ No newline at end of file +/* Utility to load a specific page and output html, page text, or a screenshot + * Optionally wait for some time, text, or dom selector + */ +try { + //...if there's a better way - please let me know, universe + var scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} + +spaceghost.start(); + +// Use the --url to load a specific page (e.g. --url="http://localhost:8080/history") +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + + // options for waiting before output/screenshot: + // --waitMs=<some number of Ms> --> wait some number of Ms before output + // --waitForText=<some text> --> wait for some text to be rendered before output + // --waitForSelector=<css selector> --> wait for some DOM to be rendered before output + if( 'waitMs' in spaceghost.cli.options ){ + spaceghost.wait( spaceghost.cli.get( 'waitMs' ) ); + + } else if( 'waitForText' in spaceghost.cli.options ){ + spaceghost.waitForText( spaceghost.cli.get( 'waitForText' ) ); + + } else if( 'waitForSelector' in spaceghost.cli.options ){ + spaceghost.waitForSelector( spaceghost.cli.get( 'waitForSelector' ) ); + } + + // --capture=<myscreenshot.png> --> capture a screenshot of the page + // --html --> output the html of the page + // (if not --html) --> output the text of the page + spaceghost.then( function(){ + if( 'capture' in spaceghost.cli.options ){ + var sshotFilename = spaceghost.cli.get( 'capture' ); + spaceghost.debug( 'screenshot stored at: ' + sshotFilename ); + spaceghost.capture( sshotFilename ); + + } else { + if( spaceghost.cli.args.indexOf( 'html' ) != -1 ){ + spaceghost.debugHTML(); + + } else { + spaceghost.debugPage(); + } + } + }); + +}); + +spaceghost.run( 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: clements: New RST files describing Sphinx doc for tool shed changes.
by commits-noreply＠bitbucket.org 01 Apr '13

01 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/71a9abf4b651/ Changeset: 71a9abf4b651 User: clements Date: 2013-04-01 23:49:17 Summary: New RST files describing Sphinx doc for tool shed changes. Affected #: 16 files diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/galaxy.webapps.tool_shed.api.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.api.rst @@ -0,0 +1,19 @@ +api Package +=========== + +:mod:`repositories` Module +-------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.repositories + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_revisions` Module +---------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.repository_revisions + :members: + :undoc-members: + :show-inheritance: + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/galaxy.webapps.tool_shed.controllers.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst @@ -0,0 +1,59 @@ +controllers Package +=================== + +:mod:`controllers` Package +-------------------------- + +.. automodule:: galaxy.webapps.tool_shed.controllers + :members: + :undoc-members: + :show-inheritance: + +:mod:`admin` Module +------------------- + +.. automodule:: galaxy.webapps.tool_shed.controllers.admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`hg` Module +---------------- + +.. automodule:: galaxy.webapps.tool_shed.controllers.hg + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository` Module +------------------------ + +.. automodule:: galaxy.webapps.tool_shed.controllers.repository + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_review` Module +------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.controllers.repository_review + :members: + :undoc-members: + :show-inheritance: + +:mod:`upload` Module +-------------------- + +.. automodule:: galaxy.webapps.tool_shed.controllers.upload + :members: + :undoc-members: + :show-inheritance: + +:mod:`user` Module +------------------ + +.. automodule:: galaxy.webapps.tool_shed.controllers.user + :members: + :undoc-members: + :show-inheritance: + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst @@ -0,0 +1,27 @@ +middleware Package +================== + +:mod:`middleware` Package +------------------------- + +.. automodule:: galaxy.webapps.tool_shed.framework.middleware + :members: + :undoc-members: + :show-inheritance: + +:mod:`hg` Module +---------------- + +.. automodule:: galaxy.webapps.tool_shed.framework.middleware.hg + :members: + :undoc-members: + :show-inheritance: + +:mod:`remoteuser` Module +------------------------ + +.. automodule:: galaxy.webapps.tool_shed.framework.middleware.remoteuser + :members: + :undoc-members: + :show-inheritance: + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/galaxy.webapps.tool_shed.framework.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst @@ -0,0 +1,18 @@ +framework Package +================= + +:mod:`framework` Package +------------------------ + +.. automodule:: galaxy.webapps.tool_shed.framework + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.tool_shed.framework.middleware + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst @@ -0,0 +1,11 @@ +migrate Package +=============== + +:mod:`check` Module +------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.check + :members: + :undoc-members: + :show-inheritance: + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/galaxy.webapps.tool_shed.model.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.rst @@ -0,0 +1,26 @@ +model Package +============= + +:mod:`model` Package +-------------------- + +.. automodule:: galaxy.webapps.tool_shed.model + :members: + :undoc-members: + :show-inheritance: + +:mod:`mapping` Module +--------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.mapping + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.tool_shed.model.migrate + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/galaxy.webapps.tool_shed.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.rst @@ -0,0 +1,47 @@ +tool_shed Package +================= + +:mod:`tool_shed` Package +------------------------ + +.. automodule:: galaxy.webapps.tool_shed + :members: + :undoc-members: + :show-inheritance: + +:mod:`app` Module +----------------- + +.. automodule:: galaxy.webapps.tool_shed.app + :members: + :undoc-members: + :show-inheritance: + +:mod:`buildapp` Module +---------------------- + +.. automodule:: galaxy.webapps.tool_shed.buildapp + :members: + :undoc-members: + :show-inheritance: + +:mod:`config` Module +-------------------- + +.. automodule:: galaxy.webapps.tool_shed.config + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.tool_shed.api + galaxy.webapps.tool_shed.controllers + galaxy.webapps.tool_shed.framework + galaxy.webapps.tool_shed.model + galaxy.webapps.tool_shed.security + galaxy.webapps.tool_shed.util + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/galaxy.webapps.tool_shed.security.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.security.rst @@ -0,0 +1,11 @@ +security Package +================ + +:mod:`security` Package +----------------------- + +.. automodule:: galaxy.webapps.tool_shed.security + :members: + :undoc-members: + :show-inheritance: + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/galaxy.webapps.tool_shed.util.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.util.rst @@ -0,0 +1,35 @@ +util Package +============ + +:mod:`common_util` Module +------------------------- + +.. automodule:: galaxy.webapps.tool_shed.util.common_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`container_util` Module +---------------------------- + +.. automodule:: galaxy.webapps.tool_shed.util.container_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`hgweb_config` Module +-------------------------- + +.. automodule:: galaxy.webapps.tool_shed.util.hgweb_config + :members: + :undoc-members: + :show-inheritance: + +:mod:`shed_statistics` Module +----------------------------- + +.. automodule:: galaxy.webapps.tool_shed.util.shed_statistics + :members: + :undoc-members: + :show-inheritance: + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/tool_shed.galaxy_install.grids.rst --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.grids.rst @@ -0,0 +1,11 @@ +grids Package +============= + +:mod:`admin_toolshed_grids` Module +---------------------------------- + +.. automodule:: tool_shed.galaxy_install.grids.admin_toolshed_grids + :members: + :undoc-members: + :show-inheritance: + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/tool_shed.galaxy_install.migrate.rst --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.migrate.rst @@ -0,0 +1,19 @@ +migrate Package +=============== + +:mod:`check` Module +------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.check + :members: + :undoc-members: + :show-inheritance: + +:mod:`common` Module +-------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.common + :members: + :undoc-members: + :show-inheritance: + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/tool_shed.galaxy_install.rst --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.rst @@ -0,0 +1,44 @@ +galaxy_install Package +====================== + +:mod:`galaxy_install` Package +----------------------------- + +.. automodule:: tool_shed.galaxy_install + :members: + :undoc-members: + :show-inheritance: + +:mod:`install_manager` Module +----------------------------- + +.. automodule:: tool_shed.galaxy_install.install_manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_util` Module +----------------------------- + +.. automodule:: tool_shed.galaxy_install.repository_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`update_manager` Module +---------------------------- + +.. automodule:: tool_shed.galaxy_install.update_manager + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + tool_shed.galaxy_install.grids + tool_shed.galaxy_install.migrate + tool_shed.galaxy_install.tool_dependencies + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst @@ -0,0 +1,27 @@ +tool_dependencies Package +========================= + +:mod:`common_util` Module +------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.common_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`fabric_util` Module +------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.fabric_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`install_util` Module +-------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.install_util + :members: + :undoc-members: + :show-inheritance: + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/tool_shed.grids.rst --- /dev/null +++ b/doc/source/lib/tool_shed.grids.rst @@ -0,0 +1,35 @@ +grids Package +============= + +:mod:`admin_grids` Module +------------------------- + +.. automodule:: tool_shed.grids.admin_grids + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_grids` Module +------------------------------ + +.. automodule:: tool_shed.grids.repository_grids + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_review_grids` Module +------------------------------------- + +.. automodule:: tool_shed.grids.repository_review_grids + :members: + :undoc-members: + :show-inheritance: + +:mod:`util` Module +------------------ + +.. automodule:: tool_shed.grids.util + :members: + :undoc-members: + :show-inheritance: + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/tool_shed.rst --- /dev/null +++ b/doc/source/lib/tool_shed.rst @@ -0,0 +1,20 @@ +tool_shed Package +================= + +:mod:`tool_shed_registry` Module +-------------------------------- + +.. automodule:: tool_shed.tool_shed_registry + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + tool_shed.galaxy_install + tool_shed.grids + tool_shed.util + diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 71a9abf4b651f4373f48ea5450ba06b90e56fc11 doc/source/lib/tool_shed.util.rst --- /dev/null +++ b/doc/source/lib/tool_shed.util.rst @@ -0,0 +1,107 @@ +util Package +============ + +:mod:`common_install_util` Module +--------------------------------- + +.. automodule:: tool_shed.util.common_install_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`common_util` Module +------------------------- + +.. automodule:: tool_shed.util.common_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`data_manager_util` Module +------------------------------- + +.. automodule:: tool_shed.util.data_manager_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`datatype_util` Module +--------------------------- + +.. automodule:: tool_shed.util.datatype_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`encoding_util` Module +--------------------------- + +.. automodule:: tool_shed.util.encoding_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`metadata_util` Module +--------------------------- + +.. automodule:: tool_shed.util.metadata_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`readme_util` Module +------------------------- + +.. automodule:: tool_shed.util.readme_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository_dependency_util` Module +---------------------------------------- + +.. automodule:: tool_shed.util.repository_dependency_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`review_util` Module +------------------------- + +.. automodule:: tool_shed.util.review_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`shed_util_common` Module +------------------------------ + +.. automodule:: tool_shed.util.shed_util_common + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_dependency_util` Module +---------------------------------- + +.. automodule:: tool_shed.util.tool_dependency_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_util` Module +----------------------- + +.. automodule:: tool_shed.util.tool_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflow_util` Module +--------------------------- + +.. automodule:: tool_shed.util.workflow_util + :members: + :undoc-members: + :show-inheritance: + 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.

1 0

commit/galaxy-central: natefoo: Close the next-stable branch.
by commits-noreply＠bitbucket.org 01 Apr '13

01 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a97c69f46c07/ Changeset: a97c69f46c07 Branch: next-stable User: natefoo Date: 2013-04-01 18:35:49 Summary: Close the next-stable branch. Affected #: 0 files 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.

1 0

commit/galaxy-central: james_taylor: biostar: bugfix for display name of anonymous users
by commits-noreply＠bitbucket.org 01 Apr '13

01 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/249b62c192b5/ Changeset: 249b62c192b5 User: james_taylor Date: 2013-04-01 20:01:56 Summary: biostar: bugfix for display name of anonymous users Affected #: 1 file diff -r c8cd70be284ebc129412ec030e4041c4bff342d3 -r 249b62c192b57cd142144e00d0483f3ca75af894 lib/galaxy/webapps/galaxy/controllers/biostar.py --- a/lib/galaxy/webapps/galaxy/controllers/biostar.py +++ b/lib/galaxy/webapps/galaxy/controllers/biostar.py @@ -81,7 +81,7 @@ else: encoded = trans.security.encode_id( trans.galaxy_session.id ) payload['username'] = "anon-" + encoded - payload['display_name'] = "Anonymous Galaxy User %d" % encoded[0:8] + payload['display_name'] = "Anonymous Galaxy User" data, digest = encode_data( trans.app.config.biostar_key, payload ) return trans.response.send_redirect( url_for( trans.app.config.biostar_url, data=data, digest=digest, name=trans.app.config.biostar_key_name, action=biostar_action ) ) 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.

1 0

commit/galaxy-central: carlfeberhard: api: history_contents.show, datasets.show add both types of display app links for consistency
by commits-noreply＠bitbucket.org 01 Apr '13

01 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c8cd70be284e/ Changeset: c8cd70be284e User: carlfeberhard Date: 2013-04-01 18:28:44 Summary: api: history_contents.show, datasets.show add both types of display app links for consistency Affected #: 2 files diff -r f97689cd28c4e3dd516d277dee1000af33a98d67 -r c8cd70be284ebc129412ec030e4041c4bff342d3 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -53,6 +53,9 @@ # Default: return dataset as dict. if hda_ldda == 'hda': rval = self.get_hda_dict( trans, dataset ) + # add these to match api/history_contents.py, show + rval[ 'display_types' ] = self.get_old_display_applications( trans, dataset ) + rval[ 'display_apps' ] = self.get_display_apps( trans, dataset ) else: rval = dataset.get_api_value() diff -r f97689cd28c4e3dd516d277dee1000af33a98d67 -r c8cd70be284ebc129412ec030e4041c4bff342d3 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -142,6 +142,8 @@ check_ownership=True, check_accessible=True ) hda_dict = self.get_hda_dict( trans, hda ) + hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) + hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) except Exception, e: msg = "Error in history API at listing dataset: %s" % ( str(e) ) 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.

1 0

commit/galaxy-central: carlfeberhard: pack scripts
by commits-noreply＠bitbucket.org 01 Apr '13

01 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f97689cd28c4/ Changeset: f97689cd28c4 User: carlfeberhard Date: 2013-04-01 17:20:18 Summary: pack scripts Affected #: 7 files diff -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b -r f97689cd28c4e3dd516d277dee1000af33a98d67 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return 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h=a.text(),k,j;if(e){k=$("<textarea/>").attr({rows:c,cols:d}).text($.trim(h)).keyup(function(m){if(m.keyCode===27){i(h)}});j=$("<button/>").text("Done").click(function(){i(k.val());return false})}else{k=$("<input type='text'/>").attr({value:$.trim(h),size:d}).blur(function(){i(h)}).keyup(function(m){if(m.keyCode===27){$(this).trigger("blur")}else{if(m.keyCode===13){i($(this).val())}}})}a.text("");a.append(k);if(j){a.append(j)}k.focus();k.select();l.stopPropagation()});if(f){a.attr("title",f).tooltip()}return a};function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input 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a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return 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HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with 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a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.show()}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a="This is a new dataset and not all of its data are available yet";b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(c,d){var b=_.without(_.keys(d.changes),["display_apps","display_types"]);if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("View data");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.show()}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a="This is a new dataset and not all of its data are available yet";b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file diff -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b -r f97689cd28c4e3dd516d277dee1000af33a98d67 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true)});f.error(function(h,g,i){alert("("+h.status+") Unable to purge this dataset:\n"+i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file +var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true)});f.error(function(h,g,i){alert("("+h.status+") Unable to purge this dataset:\n"+i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file diff -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b -r f97689cd28c4e3dd516d277dee1000af33a98d67 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",b,a,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return(this.isDeletedOrPurged()||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",b,a,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return(this.isDeletedOrPurged()||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a=this.get("hid")+' :"'+this.get("name")+'",'+a}return"HDA("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},set:function(a){var b=this;if(!a||!_.isArray(a)){return}a.forEach(function(c){var d=b.get(c.id);if(d){d.set(c)}})},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file diff -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b -r f97689cd28c4e3dd516d277dee1000af33a98d67 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server:")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,f);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates();this.updateDisplayApplications()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}this.hdas.bind("state:ready",function(d,f,c){if(d.get("force_history_refresh")){var e=this;setTimeout(function(){e.stateUpdater()},History.UPDATE_DELAY)}},this)},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server:")+"\n"+e);c.log("stateUpdater error:",e,"responseText:",f.responseText)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,f);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(e,d,f){c.hdas.set(e)},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){var f="Error fetching display applications, "+a+":"+(g.responseText||e);Galaxy.show_modal("History panel error",f,{Ok:function(){Galaxy.hide_modal()}});this.log(f)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b -r f97689cd28c4e3dd516d277dee1000af33a98d67 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("state:ready",function(c,d,b){if((!c.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(c.get("id"))}},this);this.model.hdas.bind("state:ready",function(c,d,b){if(c.get("force_history_refresh")){window.location.reload()}},this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("state:ready",function(c,d,b){if((!c.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(c.get("id"))}},this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b -r f97689cd28c4e3dd516d277dee1000af33a98d67 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var af=[];for(var ad=0;ad<this.drawables.length;ad++){af.push(this.drawables[ad].name)}var ae=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"}],saved_values:ac.prefs,onchange:function(){track.request_redraw(false,true)}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new x.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new Y.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag,10)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,genome:new x.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),af={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,ao){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;aq=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ap=[],ai=function(ar){return(ar&&"track" in ar)};while((ac*S*ag)<ah){var am=this._get_tile_bounds(ac,ag),an=this.draw_helper(ad,am,ag,this.tiles_div,aq);if(ai(an)){ap.push(an)}else{ak=false}ac+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ap,ae,aq,ao)}},postdraw_actions:function(ad,ae,ag,ac){var af=ab.find(ad,function(ah){return ah.has_icons});if(af){ab.each(ad,function(ah){if(!ah.has_icons){ah.html_elt.css("padding-top",D)}})}},draw_helper:function(ac,af,ar,ah,ai,ao){var an=this,aw=this._gen_tile_cache_key(ai,af);if(!ao){ao={}}var av=(ac?undefined:an.tile_cache.get_elt(aw));if(av){an.show_tile(av,ah,ai);return av}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}else{aj=view.reference_track.data_manager.subset_entry(aj,af)}}if(al){q(at,ao.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),au=af.get("start"),ad=af.get("end"),ap=Math.ceil((ad-au)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ap);ae.width=ap;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var av=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(av!==undefined){an.tile_cache.set_elt(aw,av);an.show_tile(av,ah,ai)}return av}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,ah,av,aj,al,at){var aq=this,aB=this._gen_tile_cache_key(al,ah);if(!at){at={}}var aA=(ad?undefined:aq.tile_cache.get_elt(aB));if(aA){aq.show_tile(aA,aj,al);return aA}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(ah,aq.mode,av,aq.data_url_extra_params);if(V(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ah,aq.mode,av,view.reference_track.data_url_extra_params);if(V(am)){ao=false}}ak.push(am)}if(ao){q(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ay=ah.get("start"),ae=ah.get("end"),az=0,ar=Math.ceil((ae-ay)*al)+this.left_offset,ap=0,af=[],ax;var ac=0;for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);az=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];am=ak[az+1];aA=aq.draw_tile(aw,au,af[ax],av,ah,al,am)}this.tile_cache.set_elt(aB,aA);this.show_tile(aA,aj,al);return aA}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();return M.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new L.LinePainter(al.data,af,ai,this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.data)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)}});var t=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof O){var ap=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var af=[];for(var ad=0;ad<this.drawables.length;ad++){af.push(this.drawables[ad].name)}var ae=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"}],saved_values:ac.prefs,onchange:function(){track.request_redraw(false,true)}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new x.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new Y.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag,10)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,genome:new x.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),af={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,ao){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;aq=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ap=[],ai=function(ar){return(ar&&"track" in ar)};while((ac*S*ag)<ah){var am=this._get_tile_bounds(ac,ag),an=this.draw_helper(ad,am,ag,this.tiles_div,aq);if(ai(an)){ap.push(an)}else{ak=false}ac+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ap,ae,aq,ao)}},postdraw_actions:function(ad,ae,ag,ac){var af=ab.find(ad,function(ah){return ah.has_icons});if(af){ab.each(ad,function(ah){if(!ah.has_icons){ah.html_elt.css("padding-top",D)}})}},draw_helper:function(ac,af,ar,ah,ai,ao){var an=this,aw=this._gen_tile_cache_key(ai,af);if(!ao){ao={}}var av=(ac?undefined:an.tile_cache.get_elt(aw));if(av){an.show_tile(av,ah,ai);return av}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}else{aj=view.reference_track.data_manager.subset_entry(aj,af)}}if(al){q(at,ao.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),au=af.get("start"),ad=af.get("end"),ap=Math.ceil((ad-au)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ap);ae.width=ap;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var av=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(av!==undefined){an.tile_cache.set_elt(aw,av);an.show_tile(av,ah,ai)}return av}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,ah,av,aj,al,at){var aq=this,aB=this._gen_tile_cache_key(al,ah);if(!at){at={}}var aA=(ad?undefined:aq.tile_cache.get_elt(aB));if(aA){aq.show_tile(aA,aj,al);return aA}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(ah,aq.mode,av,aq.data_url_extra_params);if(V(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ah,aq.mode,av,view.reference_track.data_url_extra_params);if(V(am)){ao=false}}ak.push(am)}if(ao){q(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ay=ah.get("start"),ae=ah.get("end"),az=0,ar=Math.ceil((ae-ay)*al)+this.left_offset,ap=0,af=[],ax;var ac=0;for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);az=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];am=ak[az+1];aA=aq.draw_tile(aw,au,af[ax],av,ah,al,am)}this.tile_cache.set_elt(aB,aA);this.show_tile(aA,aj,al);return aA}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();return M.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new L.LinePainter(al.data,af,ai,this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.data)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)}});var t=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof O){var ap=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: history panel: load display applications via ajax, update on force_history_refresh instead of reloading frame
by commits-noreply＠bitbucket.org 01 Apr '13

01 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/375abd0dad7e/ Changeset: 375abd0dad7e User: carlfeberhard Date: 2013-04-01 17:10:08 Summary: history panel: load display applications via ajax, update on force_history_refresh instead of reloading frame Affected #: 10 files diff -r 15a5683a73457b6adf81651f32e2d5605c81c0e3 -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -364,8 +364,8 @@ if meta_files: hda_dict[ 'meta_files' ] = meta_files - hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) - hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) + #hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) + #hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) hda_dict[ 'visualizations' ] = hda.get_visualizations() # ---- return here if deleted @@ -899,8 +899,6 @@ hda_dicts = [] for hda_tuple in query.all(): hda_dict = dict( zip( column_keys, hda_tuple ) ) - #if hda_dict[ 'job_state' ] not in [ None, 'ok' ]: - # print hda_dict[ 'hid' ], hda_dict[ 'name' ], hda_dict[ 'job_state' ] hda_dict[ 'history_id' ] = history.id trans.security.encode_dict_ids( hda_dict ) hda_dicts.append( hda_dict ) diff -r 15a5683a73457b6adf81651f32e2d5605c81c0e3 -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -55,7 +55,11 @@ if encoded_hda_id in ids: #TODO: share code with show try: - rval.append( self.get_hda_dict( trans, hda ) ) + hda_dict = self.get_hda_dict( trans, hda ) + hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) + hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) + #rval.append( self.get_hda_dict( trans, hda ) ) + rval.append( hda_dict ) except Exception, exc: # don't fail entire list if hda err's, record and move on diff -r 15a5683a73457b6adf81651f32e2d5605c81c0e3 -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -24,6 +24,7 @@ return history.get_display_name() class HistoryListGrid( grids.Grid ): + # Custom column types class DatasetsByStateColumn( grids.GridColumn, UsesHistoryMixin ): def get_value( self, trans, grid, history ): @@ -56,6 +57,7 @@ elif history.deleted: return "deleted" return "" + def sort( self, trans, query, ascending, column_name=None ): if ascending: query = query.order_by( self.model_class.table.c.purged.asc(), self.model_class.table.c.update_time.desc() ) @@ -63,7 +65,6 @@ query = query.order_by( self.model_class.table.c.purged.desc(), self.model_class.table.c.update_time.desc() ) return query - # Grid definition title = "Saved Histories" model_class = model.History @@ -105,12 +106,15 @@ preserve_state = False use_async = True use_paging = True + def get_current_item( self, trans, **kwargs ): return trans.get_history() + def apply_query_filter( self, trans, query, **kwargs ): return query.filter_by( user=trans.user, importing=False ) class SharedHistoryListGrid( grids.Grid ): + # Custom column types class DatasetsByStateColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): @@ -122,9 +126,11 @@ else: rval.append( '' ) return rval + class SharedByColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): return history.user.email + # Grid definition title = "Histories shared with you by others" model_class = model.History @@ -143,8 +149,10 @@ grids.GridOperation( "Unshare" ) ] standard_filters = [] + def build_initial_query( self, trans, **kwargs ): return trans.sa_session.query( self.model_class ).join( 'users_shared_with' ) + def apply_query_filter( self, trans, query, **kwargs ): return query.filter( model.HistoryUserShareAssociation.user == trans.user ) @@ -172,17 +180,21 @@ key="free-text-search", visible=False, filterable="standard" ) ) operations = [] + def build_initial_query( self, trans, **kwargs ): # Join so that searching history.user makes sense. return trans.sa_session.query( self.model_class ).join( model.User.table ) + def apply_query_filter( self, trans, query, **kwargs ): # A public history is published, has a slug, and is not deleted. return query.filter( self.model_class.published == True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False ) -class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings, UsesHistoryMixin ): +class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings, + UsesHistoryMixin, UsesHistoryDatasetAssociationMixin ): @web.expose def index( self, trans ): return "" + @web.expose def list_as_xml( self, trans ): """XML history list for functional tests""" @@ -282,6 +294,7 @@ trans.sa_session.flush() # Render the list view return self.stored_list_grid( trans, status=status, message=message, **kwargs ) + def _list_delete( self, trans, histories, purge=False ): """Delete histories""" n_deleted = 0 @@ -331,6 +344,7 @@ message_parts.append( "Your active history was deleted, a new empty history is now active. " ) status = INFO return ( status, " ".join( message_parts ) ) + def _list_undelete( self, trans, histories ): """Undelete histories""" n_undeleted = 0 @@ -359,6 +373,7 @@ message_parts.append( "%d histories have already been purged and cannot be undeleted." % n_already_purged ) status = WARNING return status, "".join( message_parts ) + def _list_switch( self, trans, histories ): """Switch to a new different history""" new_history = histories[0] @@ -1062,6 +1077,7 @@ elif history not in histories_for_sharing[ send_to_user ]: histories_for_sharing[ send_to_user ].append( history ) return self._share_histories( trans, user, send_to_err, histories=histories_for_sharing ) + def _get_histories_and_users( self, trans, user, id, email ): if not id: # Default to the current history @@ -1087,6 +1103,7 @@ else: send_to_err += "%s is not a valid Galaxy user. " % email_address return histories, send_to_users, send_to_err + def _populate( self, trans, histories_for_sharing, other, send_to_err ): # This method will populate the histories_for_sharing dictionary with the users and # histories in other, eliminating histories that have already been shared with the @@ -1110,6 +1127,7 @@ elif history not in histories_for_sharing[ send_to_user ]: histories_for_sharing[ send_to_user ].append( history ) return histories_for_sharing, send_to_err + def _populate_restricted( self, trans, user, histories, send_to_users, action, send_to_err, unique=False ): # The user may be attempting to share histories whose datasets cannot all be accessed by other users. # If this is the case, the user sharing the histories can: @@ -1196,6 +1214,7 @@ else: cannot_change[ send_to_user ][ history ].append( hda ) return can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err + def _share_histories( self, trans, user, send_to_err, histories={} ): # histories looks like: { userA: [ historyX, historyY ], userB: [ historyY ] } msg = "" @@ -1314,3 +1333,47 @@ def get_item( self, trans, id ): return self.get_history( trans, id ) + + @web.json + def get_display_application_links( self, trans, hda_ids=None ): + """Returns external display application JSON data for all/given + HDAs within the current history. + """ + try: + history = trans.get_history() + #TODO: allow id for more flexibility? (the following doesn't work if anonymous...) + #history = self.get_history( trans, id, check_ownership=True, check_accessible=True, deleted=None ) + if hda_ids: + unencoded_hda_ids = [ trans.security.decode_id( hda_id ) for hda_id in util.listify( hda_ids ) ] + #TODO: this gets all - should narrow query by using hda_ids here - no way with this current method + hdas = self.get_history_datasets( trans, history, show_deleted=False, show_hidden=True, show_purged=False ) + + except Exception, exc: + log.error( 'Error get_display_application_links (%s): %s', hda_ids, str( exc ) ) + trans.response.status = 500 + return str( exc ) + + hda_display_links = [] + for hda in hdas: + # only get requested hdas + if hda_ids and hda.id not in unencoded_hda_ids: + continue + + hda_link_data = { 'id': trans.security.encode_id( hda.id ) } + # don't bail on entire list if one hda has an error; record and move on + try: + # 'old style': must be enabled in config (see universe_wsgi.ini) + if trans.app.config.enable_old_display_applications: + hda_link_data[ 'display_types' ] = self.get_old_display_applications( trans, hda ) + + # 'new style' + hda_link_data[ 'display_apps' ] = self.get_display_apps( trans, hda ) + + except Exception, exc: + log.error( 'Error getting display applications, hda (%s): %s', hda_link_data[ 'id' ], str( exc ) ) + hda_link_data[ 'error' ] = str( exc ) + + hda_display_links.append( hda_link_data ) + + trans.response.set_content_type( 'application/json' ) + return hda_display_links diff -r 15a5683a73457b6adf81651f32e2d5605c81c0e3 -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -98,8 +98,8 @@ @web.expose def history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, hda_id=None, **kwd ): - """ - Display the current history, creating a new history if necessary. + """Display the current history, creating a new history if necessary. + NOTE: No longer accepts "id" or "template" options for security reasons. """ params = util.Params( kwd ) @@ -165,6 +165,7 @@ datasets = hda_dictionaries return trans.stream_template_mako( history_panel_template, + #return trans.fill_template_mako( history_panel_template, history = history, annotation = self.get_item_annotation_str( trans.sa_session, trans.user, history ), datasets = datasets, diff -r 15a5683a73457b6adf81651f32e2d5605c81c0e3 -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -1,6 +1,8 @@ //define([ // "../mvc/base-mvc" //], function(){ + +/* global BaseView, LoggableMixin, HistoryDatasetAssociation, HDABaseView */ //============================================================================== /** @class Read only view for HistoryDatasetAssociation. * @name HDABaseView @@ -44,7 +46,21 @@ this.expanded = attributes.expanded || false; // re-render the entire view on any model change - this.model.bind( 'change', this.render , this ); + //this.model.bind( 'change', this.render , this ); + this.model.bind( 'change', function( event, changed ){ + //var withoutDisplayApps = _.omit( changed, [ 'display_apps', 'display_types' ] ); + var nonDisplayAppChanges = _.without( _.keys( changed.changes ), [ 'display_apps', 'display_types' ] ); + + if( nonDisplayAppChanges.length ){ + this.render(); + + //TODO: need a better handler for these sorts of rendering exceptions + } else { + if( this.expanded ){ + this._render_displayApps(); + } + } + }, this ); //this.bind( 'all', function( event ){ // this.log( event ); @@ -291,28 +307,38 @@ }, // ......................................................................... other elements - /** Render links to external genome display applications (igb, gbrowse, etc.). + /** Render the area for display application links. * @returns {jQuery} rendered DOM */ + _render_displayAppArea : function(){ + return $( '<div/>' ).addClass( 'display-apps' ); + }, + + /** Render links to external genome display applications (igb, gbrowse, etc.). + * @param {jQuery} $parent the jq node to search for .display-apps and render into to (defaults to this.$el) + */ //TODO: not a fan of the style on these - _render_displayApps : function(){ - if( !this.model.hasData() ){ return null; } - - var displayAppsDiv = $( '<div/>' ).addClass( 'display-apps' ); - if( !_.isEmpty( this.model.get( 'display_types' ) ) ){ + _render_displayApps : function( $parent ){ + $parent = $parent || this.$el; + var $displayAppsDiv = $parent.find( 'div.display-apps' ), + display_types = this.model.get( 'display_types' ), + display_apps = this.model.get( 'display_apps' ); + + if( ( !this.model.hasData() ) + || ( !$parent || !$parent.length ) + || ( !$displayAppsDiv.length ) ){ + return; + } + + $displayAppsDiv.html( null ); + if( !_.isEmpty( display_types ) ){ //this.log( this + 'display_types:', this.model.get( 'urls' ).display_types ); - //TODO:?? does this ever get used? - displayAppsDiv.append( - HDABaseView.templates.displayApps({ displayApps : this.model.get( 'display_types' ) }) - ); + $displayAppsDiv.append( HDABaseView.templates.displayApps({ displayApps : display_types }) ); } - if( !_.isEmpty( this.model.get( 'display_apps' ) ) ){ + if( !_.isEmpty( display_apps ) ){ //this.log( this + 'display_apps:', this.model.get( 'urls' ).display_apps ); - displayAppsDiv.append( - HDABaseView.templates.displayApps({ displayApps : this.model.get( 'display_apps' ) }) - ); + $displayAppsDiv.append( HDABaseView.templates.displayApps({ displayApps : display_apps }) ); } - return displayAppsDiv; }, /** Render the data peek. @@ -526,7 +552,8 @@ ])); parent.append( '<div class="clear"/>' ); - parent.append( this._render_displayApps() ); + parent.append( this._render_displayAppArea() ); + this._render_displayApps( parent ); parent.append( this._render_peek() ); }, diff -r 15a5683a73457b6adf81651f32e2d5605c81c0e3 -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -404,6 +404,7 @@ * @see HDABaseView#_render_body_ok */ _render_body_ok : function( parent ){ + //TODO: should call super somehow and insert the needed... // most common state renderer and the most complicated parent.append( this._render_hdaSummary() ); @@ -434,7 +435,8 @@ parent.append( this._render_tagArea() ); parent.append( this._render_annotationArea() ); - parent.append( this._render_displayApps() ); + parent.append( this._render_displayAppArea() ); + this._render_displayApps( parent ); parent.append( this._render_peek() ); }, diff -r 15a5683a73457b6adf81651f32e2d5605c81c0e3 -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -152,9 +152,9 @@ toString : function(){ var nameAndId = this.get( 'id' ) || ''; if( this.get( 'name' ) ){ - nameAndId += ':"' + this.get( 'name' ) + '"'; + nameAndId = this.get( 'hid' ) + ' :"' + this.get( 'name' ) + '",' + nameAndId; } - return 'HistoryDatasetAssociation(' + nameAndId + ')'; + return 'HDA(' + nameAndId + ')'; } }); @@ -300,8 +300,25 @@ return idList; }, + /** Set ea + * Precondition: each data_array object must have an id + * @param {Object[]} data_array an array of attribute objects to update the models with + * @see HistoryDatasetAssociation#set + */ + set : function( data_array ){ + var collection = this; + if( !data_array || !_.isArray( data_array ) ){ return; } + + //TODO: remove when updated backbone >= 1.0 + data_array.forEach( function( hda_data ){ + var model = collection.get( hda_data.id ); + if( model ){ + model.set( hda_data ); + } + }); + }, + /** Update (fetch) the data of the hdas with the given ids. - * @param {String} historyId the id of the history containing this collection * @param {String[]} ids an array of hda ids to update * @returns {HistoryDatasetAssociation[]} hda models that were updated * @see HistoryDatasetAssociation#fetch diff -r 15a5683a73457b6adf81651f32e2d5605c81c0e3 -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -59,6 +59,8 @@ if( _.isArray( initialHdas ) ){ this.hdas.reset( initialHdas ); this.checkForUpdates(); + //TODO: don't call if force_history_refresh + this.updateDisplayApplications(); // handle errors in initialHdas //TODO: errors from the api shouldn't be plain strings... @@ -68,6 +70,18 @@ } } + // if an hda moves into the ready state and has the force_history_refresh flag (often via tool.xml) + // then: refresh the panel + this.hdas.bind( 'state:ready', function( hda, newState, oldState ){ + if( hda.get( 'force_history_refresh' ) ){ + //TODO: could poll jobs here... + var history = this; + setTimeout( function(){ + history.stateUpdater(); + }, History.UPDATE_DELAY ); + } + }, this ); + // events //this.on( 'change', function( currModel, changedList ){ // this.log( this + ' has changed:', currModel, changedList ); @@ -290,6 +304,35 @@ history.hdas.trigger( 'add', hdaDataList ); }, + /** Update (from controller) the display application link data of the hdas with the given ids. + * @param {String[]} ids an array of hda ids to update (optional, defaults to all hdas) + * @returns {HistoryDatasetAssociation[]} hda models that were updated + */ + updateDisplayApplications : function( ids ){ + this.log( this + 'updateDisplayApplications:', ids ); + var history = this, + // data = { id: this.get( 'id' ) }; + //if( ids && _.isArray( ids ) ){ data.hda_ids = ids.join( ',' ); } + data = ( ids && _.isArray( ids ) )?({ hda_ids : ids.join( ',' ) }):({}); + + //TODO: hardcoded + history.log( this + ': fetching display application data' ); + jQuery.ajax( 'history/get_display_application_links', { + data : data, + success : function( data, status, xhr ){ + history.hdas.set( data ); + }, + error : function( xhr, status, error ){ + if( !( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ) ){ + var msg = 'Error fetching display applications, ' + ids + ':' + ( xhr.responseText || error ); + Galaxy.show_modal( 'History panel error', + msg, { 'Ok': function(){ Galaxy.hide_modal(); } }); + this.log( msg ); + } + } + }); + }, + toString : function(){ var nameString = ( this.get( 'name' ) )? ( ',' + this.get( 'name' ) ) : ( '' ); diff -r 15a5683a73457b6adf81651f32e2d5605c81c0e3 -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -126,14 +126,6 @@ } }, this ); - // if an hda moves into the ready state and has the force_history_refresh flag (often via tool.xml) - // then: refresh the panel - this.model.hdas.bind( 'state:ready', function( hda, newState, oldState ){ - if( hda.get( 'force_history_refresh' ) ){ - window.location.reload(); - } - }, this ); - //this.bind( 'all', function(){ // this.log( arguments ); //}, this ); diff -r 15a5683a73457b6adf81651f32e2d5605c81c0e3 -r 375abd0dad7e9e52c9ca2f94cd37b6da96b4156b templates/webapps/galaxy/root/alternate_history.mako --- a/templates/webapps/galaxy/root/alternate_history.mako +++ b/templates/webapps/galaxy/root/alternate_history.mako @@ -285,6 +285,9 @@ top.Galaxy.$rightPanel = top.Galaxy.$rightPanel || $( top.document ).find( 'div#right' ); //modals + top.Galaxy.show_modal = top.show_modal; + top.Galaxy.hide_modal = top.hide_modal; + // other base functions // global backbone models 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 commits-noreply＠bitbucket.org 29 Mar '13

29 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/74ecac39ebd7/ Changeset: 74ecac39ebd7 Branch: next-stable User: greg Date: 2013-03-29 18:02:18 Summary: Fix missing import in tool shed's hg middleware controller. Affected #: 1 file diff -r a5cedd31d98e0af9b80843ed7e0c987a6b04cda1 -r 74ecac39ebd7da2df71f7e31c796dd270a7063b6 lib/galaxy/webapps/tool_shed/framework/middleware/hg.py --- a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py +++ b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py @@ -7,6 +7,7 @@ from paste.httpheaders import AUTH_TYPE from paste.httpheaders import REMOTE_USER +from galaxy.util import asbool from galaxy.webapps.tool_shed import model from galaxy.util.hash_util import new_secure_hash import mercurial.__version__ https://bitbucket.org/galaxy/galaxy-central/commits/15a5683a7345/ Changeset: 15a5683a7345 User: greg Date: 2013-03-29 18:03:58 Summary: Merged next-stable Affected #: 1 file diff -r 4f4f7bd74074090bd0192e76e361d42d9db70060 -r 15a5683a73457b6adf81651f32e2d5605c81c0e3 lib/galaxy/webapps/tool_shed/framework/middleware/hg.py --- a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py +++ b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py @@ -7,6 +7,7 @@ from paste.httpheaders import AUTH_TYPE from paste.httpheaders import REMOTE_USER +from galaxy.util import asbool from galaxy.webapps.tool_shed import model from galaxy.util.hash_util import new_secure_hash import mercurial.__version__ 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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