galaxy-commits September 2013

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149 discussions

commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2dc56086d6dc/ Changeset: 2dc56086d6dc User: dorine Date: 2013-09-17 19:19:32 Summary: modified registration message Affected #: 1 file diff -r 48fad71361b3075c85c7d365dd52c106cabad73a -r 2dc56086d6dcf32fe76c39ee31bca3a8afbdc129 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -107,6 +107,9 @@ <input type="submit" name="create_user_button" value="Submit"/></div></form> + <div style="color: red; margin: 30px 0 10px 12px;"> + WARNING: Only one account per user is allowed. Creating multiple accounts will be detected and may result in termination of all related accounts. Please note that any violation of the <a style="color: red;" href="/static/terms.html" target="_blank">Terms and Conditions for use of this service</a> is cause for permanent suspension and data deletion. + </div></div></%def> https://bitbucket.org/galaxy/galaxy-central/commits/2d70646b76d1/ Changeset: 2d70646b76d1 User: dorine Date: 2013-09-17 20:41:09 Summary: modified registration message Affected #: 2 files diff -r 2dc56086d6dcf32fe76c39ee31bca3a8afbdc129 -r 2d70646b76d15e80c7918d79b00e66732f19e870 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -107,8 +107,8 @@ <input type="submit" name="create_user_button" value="Submit"/></div></form> - <div style="color: red; margin: 30px 0 10px 12px;"> - WARNING: Only one account per user is allowed. Creating multiple accounts will be detected and may result in termination of all related accounts. Please note that any violation of the <a style="color: red;" href="/static/terms.html" target="_blank">Terms and Conditions for use of this service</a> is cause for permanent suspension and data deletion. + <div class="alert alert-danger" style="margin: 30px 12px 12px 12px;"> + WARNING: Only one account per user is allowed. Creating multiple accounts will be detected and may result in termination of all related accounts. Please note that any violation of the <a href="${trans.app.config.get('terms_url', None)}">Terms and Conditions for use of this service</a> is cause for permanent suspension and data deletion. </div></div> diff -r 2dc56086d6dcf32fe76c39ee31bca3a8afbdc129 -r 2d70646b76d15e80c7918d79b00e66732f19e870 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -26,12 +26,13 @@ use = egg:Paste#http # The port on which to listen. -#port = 8080 +port = 8080 # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. #host = 127.0.0.1 +host = 0.0.0.0 # Use a threadpool for the web server instead of creating a thread for each # request. https://bitbucket.org/galaxy/galaxy-central/commits/7960d6872156/ Changeset: 7960d6872156 User: dorine Date: 2013-09-17 20:56:13 Summary: modified registration message Affected #: 1 file diff -r 2d70646b76d15e80c7918d79b00e66732f19e870 -r 7960d6872156bdea26de50c6701646847194cd80 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -26,13 +26,12 @@ use = egg:Paste#http # The port on which to listen. -port = 8080 +#port = 8080 # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. #host = 127.0.0.1 -host = 0.0.0.0 # Use a threadpool for the web server instead of creating a thread for each # request. https://bitbucket.org/galaxy/galaxy-central/commits/7fe444e0b76e/ Changeset: 7fe444e0b76e User: dorine Date: 2013-09-17 23:26:00 Summary: rephrased with 'please register only one account...' Affected #: 1 file diff -r 7960d6872156bdea26de50c6701646847194cd80 -r 7fe444e0b76ed05fe5e4855c910519699c3b6863 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -108,7 +108,7 @@ </div></form><div class="alert alert-danger" style="margin: 30px 12px 12px 12px;"> - WARNING: Only one account per user is allowed. Creating multiple accounts will be detected and may result in termination of all related accounts. Please note that any violation of the <a href="${trans.app.config.get('terms_url', None)}">Terms and Conditions for use of this service</a> is cause for permanent suspension and data deletion. + Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion. </div></div> https://bitbucket.org/galaxy/galaxy-central/commits/0c1ecb1f4190/ Changeset: 0c1ecb1f4190 User: martenson Date: 2013-09-23 20:58:23 Summary: Merged in dorine/galaxy-central_registrationmessage (pull request #221) modified registration message Affected #: 2 files diff -r 315b484fe81b99954c093b248859a16cd65b4164 -r 0c1ecb1f4190800abdb29b3a17fc2b9d8bd21eba templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -107,6 +107,9 @@ <input type="submit" name="create_user_button" value="Submit"/></div></form> + <div class="alert alert-danger" style="margin: 30px 12px 12px 12px;"> + Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion. + </div></div></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: HDA API: only fetch/return filepaths when user is admin or confing.expose_dataset_path=True (expensive operation)
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/315b484fe81b/ Changeset: 315b484fe81b User: carlfeberhard Date: 2013-09-23 20:32:36 Summary: HDA API: only fetch/return filepaths when user is admin or confing.expose_dataset_path=True (expensive operation) Affected #: 2 files diff -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 -r 315b484fe81b99954c093b248859a16cd65b4164 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1681,7 +1681,7 @@ rval += child.get_disk_usage( user ) return rval - def to_dict( self, view='collection' ): + def to_dict( self, view='collection', expose_dataset_path=False ): """ Return attributes of this HDA that are exposed using the API. """ @@ -1714,6 +1714,9 @@ for name, spec in hda.metadata.spec.items(): val = hda.metadata.get( name ) if isinstance( val, MetadataFile ): + # only when explicitly set: fetching filepaths can be expensive + if not expose_dataset_path: + continue val = val.file_name # If no value for metadata, look in datatype for metadata. elif val == None and hasattr( hda.datatype, name ): diff -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 -r 315b484fe81b99954c093b248859a16cd65b4164 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -583,7 +583,8 @@ """ #precondition: the user's access to this hda has already been checked #TODO:?? postcondition: all ids are encoded (is this really what we want at this level?) - hda_dict = hda.to_dict( view='element' ) + expose_dataset_path = trans.user_is_admin() or trans.app.config.expose_dataset_path + hda_dict = hda.to_dict( view='element', expose_dataset_path=expose_dataset_path ) hda_dict[ 'api_type' ] = "file" # Add additional attributes that depend on trans can hence must be added here rather than at the model level. @@ -599,7 +600,7 @@ #TODO: to_dict should really go AFTER this - only summary data return trans.security.encode_dict_ids( hda_dict ) - if trans.user_is_admin() or trans.app.config.expose_dataset_path: + if expose_dataset_path: hda_dict[ 'file_name' ] = hda.file_name hda_dict[ 'download_url' ] = url_for( 'history_contents_display', 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 23 Sep '13

23 Sep '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7fc48713b918/ Changeset: 7fc48713b918 User: dannon Date: 2013-09-23 19:12:34 Summary: Correctly use tool_conf.xml,shed_tool_conf.xml as the default tool config file entry (as shown in universe_wsgi.ini.sample) Affected #: 1 file diff -r d4c6a250afd03a942e70f04ee7da8335dfea476b -r 7fc48713b918011a814269e4a210471afc2f8ac2 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -63,7 +63,7 @@ elif 'tool_config_files' in kwargs: tcf = kwargs[ 'tool_config_files' ] else: - tcf = 'tool_conf.xml' + tcf = 'tool_conf.xml,shed_tool_conf.xml' self.tool_filters = listify( kwargs.get( "tool_filters", [] ) ) self.tool_label_filters = listify( kwargs.get( "tool_label_filters", [] ) ) self.tool_section_filters = listify( kwargs.get( "tool_section_filters", [] ) ) https://bitbucket.org/galaxy/galaxy-central/commits/87d9c0ca5a4f/ Changeset: 87d9c0ca5a4f User: dannon Date: 2013-09-23 19:12:45 Summary: Merge Affected #: 11 files diff -r 7fc48713b918011a814269e4a210471afc2f8ac2 -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -40,13 +40,14 @@ docutils = 0.7 drmaa = 0.4b3 elementtree = 1.2.6_20050316 -Fabric = 1.4.2 +Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 lrucache = 0.2 Mako = 0.4.1 nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 +paramiko = 1.11.1 Parsley = 1.1 Paste = 1.7.5.1 PasteDeploy = 1.5.0 diff -r 7fc48713b918011a814269e4a210471afc2f8ac2 -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -587,8 +587,10 @@ hda_dict[ 'api_type' ] = "file" # Add additional attributes that depend on trans can hence must be added here rather than at the model level. - - #NOTE: access is an expensive operation - removing it and adding the precondition of access is already checked + can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) + can_access_hda = ( trans.user_is_admin() or can_access_hda ) + if not can_access_hda: + return self.get_inaccessible_hda_dict( trans, hda ) hda_dict[ 'accessible' ] = True # ---- return here if deleted AND purged OR can't access @@ -634,6 +636,18 @@ return trans.security.encode_dict_ids( hda_dict ) + def get_inaccessible_hda_dict( self, trans, hda ): + return trans.security.encode_dict_ids({ + 'id' : hda.id, + 'history_id': hda.history.id, + 'hid' : hda.hid, + 'name' : hda.name, + 'state' : hda.state, + 'deleted' : hda.deleted, + 'visible' : hda.visible, + 'accessible': False + }) + def get_hda_dict_with_error( self, trans, hda, error_msg='' ): return trans.security.encode_dict_ids({ 'id' : hda.id, diff -r 7fc48713b918011a814269e4a210471afc2f8ac2 -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -309,7 +309,6 @@ # If deleting the current history, make a new current. if history == trans.get_history(): deleted_current = True - trans.get_or_create_default_history() trans.log_event( "History (%s) marked as deleted" % history.name ) n_deleted += 1 if purge and trans.app.config.allow_user_dataset_purge: @@ -339,6 +338,8 @@ part += " but the datasets were not removed from disk because that feature is not enabled in this Galaxy instance" message_parts.append( "%s. " % part ) if deleted_current: + #note: this needs to come after commits above or will use an empty history that was deleted above + trans.get_or_create_default_history() message_parts.append( "Your active history was deleted, a new empty history is now active. " ) status = INFO return ( status, " ".join( message_parts ) ) diff -r 7fc48713b918011a814269e4a210471afc2f8ac2 -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 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 @@ -973,9 +973,9 @@ flush_needed = True if flush_needed: trans.sa_session.flush() - message = "Repository '%s' has been created." % repository.name + message = "Repository <b>%s</b> has been created." % str( repository.name ) trans.response.send_redirect( web.url_for( controller='repository', - action='view_repository', + action='manage_repository', message=message, id=trans.security.encode_id( repository.id ) ) ) repository_type_select_field = rt_util.build_repository_type_select_field( trans ) diff -r 7fc48713b918011a814269e4a210471afc2f8ac2 -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -66,7 +66,10 @@ }; /** - * Sets up popupmenu rendering and binds options functions to the appropriate links + * Sets up popupmenu rendering and binds options functions to the appropriate links. + * initial_options is a dict with text describing the option pointing to either (a) a + * function to perform; or (b) another dict with two required keys, 'url' and 'action' (the + * function to perform. (b) is useful for exposing the underlying URL of the option. */ function make_popupmenu(button_element, initial_options) { /* Use the $.data feature to store options with the link element. @@ -92,7 +95,9 @@ } $.each( options, function( k, v ) { if (v) { - menu_element.append( $("<li></li>").append( $("<a href='#'></a>").html(k).click(v) ) ); + // Action can be either an anonymous function and a mapped dict. + var action = v.action || v; + menu_element.append( $("<li></li>").append( $("<a>").attr("href", v.url).html(k).click(action) ) ); } else { menu_element.append( $("<li></li>").addClass( "head" ).append( $("<a href='#'></a>").html(k) ) ); } @@ -164,43 +169,24 @@ options[ link.text() ] = null; } else { - options[ link.text() ] = function() { + options[ link.text() ] = { + url: href, + action: function() { - // if theres confirm text, send the dialog - if ( !confirmtext || confirm( confirmtext ) ) { - var f; - // relocate the center panel - if ( target === "_parent" ) { - window.parent.location = href; - - // relocate the entire window - } else if ( target === "_top" ) { - window.top.location = href; - - // Http request target is a window named demolocal on the local box - } else if ( target === "demo" ) { - if ( f === undefined || f.closed ) { - f = window.open( href,target ); - f.creator = self; + // if theres confirm text, send the dialog + if ( !confirmtext || confirm( confirmtext ) ) { + var f; + // Http request target is a window named demolocal on the local box + if ( target === "demo" ) { + if ( f === undefined || f.closed ) { + f = window.open( href,target ); + f.creator = self; + } + } - - // this panel or other, valid panels - } else { - // it may be that the button and menu href are not in the same frame: - // allow certain frame names to be used as a target - var other_valid_targets = [ - 'galaxy_main' - // following are blocked until needed - //'galaxy_tools', - //'galaxy_history' - ]; - if( ( target && ( target in window ) - && ( other_valid_targets.indexOf( target ) !== -1 ) ) ){ - window[ target ].location = href; - - // relocate this panel - } else { - window.location = href; + // For all other links, do the default action. + else { + link.trigger('click'); } } } diff -r 7fc48713b918011a814269e4a210471afc2f8ac2 -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -168,16 +168,17 @@ this.$overlay.show(); this.$dialog.show(); this.$overlay.addClass("in"); - // Fix min-width so that modal cannot shrink considerably if - // new content is loaded. + // Fix min-width so that modal cannot shrink considerably if new content is loaded. this.$body.css( "min-width", this.$body.width() ); - // Set max-height so that modal does not exceed window size. - // FIXME: this could perhaps be handled better using a container for the modal - // header-body-footer and setting max-height for the container. + // Set max-height so that modal does not exceed window size and is in middle of page. + // TODO: this could perhaps be handled better using CSS. this.$body.css( "max-height", - // 2* to provide buffer between bottom of modal and bottom of page. - $(window).height() - 2 * this.$dialog.offset().top - - this.$footer.outerHeight() - this.$header.outerHeight()); + $(window).height() - + this.$footer.outerHeight() - + this.$header.outerHeight() - + parseInt( this.$dialog.css( "padding-top" ), 10 ) - + parseInt( this.$dialog.css( "padding-bottom" ), 10 ) + ); } // Callback on init if ( callback ) { diff -r 7fc48713b918011a814269e4a210471afc2f8ac2 -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -756,6 +756,7 @@ .btn.active,.btn:active{color:inherit} .dropdown-menu{max-width:auto} input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex} +.modal-body{overflow:auto} .nav-tabs{margin-bottom:15px} a{text-decoration:underline} label{font-weight:normal} @@ -1388,9 +1389,9 @@ div.historyItem-setting_metadata{background:#ffc}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif)} div.historyItem-upload{background:#a6e4f7}div.historyItem-upload .state-icon{background-image:url(data_upload.gif)} div.historyItem-queued{background:#eee}div.historyItem-queued .state-icon{background-image:url(sprite-history-states.png);background-position:0px -45px;width:15px;height:15px;height:15px} -div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60} -div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-paused .state-icon:before{content:"\f04c"} -div.historyItem-new .state-icon{font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-new .state-icon:before{content:"\f071"} +div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60}div.historyItem-noPermission .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-noPermission .state-icon:before{content:"\f05e"} +div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-paused .state-icon:before{content:"\f04c"} +div.historyItem-new .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-new .state-icon:before{content:"\f071"} div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important} div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px} div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px} diff -r 7fc48713b918011a814269e4a210471afc2f8ac2 -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -1509,11 +1509,19 @@ filter: alpha(opacity=60); -moz-opacity: .60; opacity: .60; + .state-icon { + line-height: 16px; + .fa-icon(); + &:before { + content: "\f05e"; + } + } } div.historyItem-paused { background: @state-paused-bg; .state-icon { + line-height: 16px; .fa-icon(); &:before { content: "\f04c"; @@ -1523,6 +1531,7 @@ div.historyItem-new { .state-icon { + line-height: 16px; .fa-icon(); &:before { content: "\f071"; diff -r 7fc48713b918011a814269e4a210471afc2f8ac2 -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 static/style/src/less/galaxy_bootstrap/overrides.less --- a/static/style/src/less/galaxy_bootstrap/overrides.less +++ b/static/style/src/less/galaxy_bootstrap/overrides.less @@ -32,6 +32,9 @@ // Modal -- wider by default, scroll like Trello /* + +NOTE: these styles do not currently work. + .modal { position: absolute; top: 50px; @@ -54,6 +57,11 @@ } */ +// Scroll modal body. +.modal-body { + overflow: auto; +} + // Tabs -- border color is hardcoded in navs.less, change to @btnBorder here .nav-tabs { diff -r 7fc48713b918011a814269e4a210471afc2f8ac2 -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 test/functional/test_get_data.py --- a/test/functional/test_get_data.py +++ b/test/functional/test_get_data.py @@ -22,7 +22,7 @@ """ # in order to remove a lot of boiler plate - and not have cascading errors history = get_latest_history_for_user( user ) - self.delete_current_history() + self.delete_history( id=self.security.encode_id( history.id ) ) self.is_history_empty() return get_latest_history_for_user( user ) diff -r 7fc48713b918011a814269e4a210471afc2f8ac2 -r 87d9c0ca5a4f8ba1f73411ac7f9c23f59ce2cac4 test/tool_shed/functional/test_0440_deleting_dependency_definitions.py --- a/test/tool_shed/functional/test_0440_deleting_dependency_definitions.py +++ b/test/tool_shed/functional/test_0440_deleting_dependency_definitions.py @@ -74,7 +74,7 @@ description='Description of Deleted Dependency Definitions category for test 0440' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - strings_displayed = [ "Repository 'column_maker_0440' has been created" ] + strings_displayed = [ "Repository <b>column_maker_0440</b> has been created" ] repository = self.get_or_create_repository( name=column_repository_name, description=column_repository_description, long_description=column_repository_long_description, @@ -99,7 +99,7 @@ category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - strings_displayed = [ "Repository 'convert_chars_0440' has been created" ] + strings_displayed = [ "Repository <b>convert_chars_0440</b> has been created" ] repository = self.get_or_create_repository( name=convert_repository_name, description=convert_repository_description, long_description=convert_repository_long_description, @@ -182,7 +182,7 @@ category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - strings_displayed = [ "Repository 'bwa_package_0440' has been created" ] + strings_displayed = [ "Repository <b>bwa_package_0440</b> has been created" ] repository = self.get_or_create_repository( name=bwa_package_repository_name, description=bwa_package_repository_description, long_description=bwa_package_repository_long_description, @@ -208,7 +208,7 @@ category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - strings_displayed = [ "Repository 'bwa_base_0440' has been created" ] + strings_displayed = [ "Repository <b>bwa_base_0440</b> has been created" ] repository = self.get_or_create_repository( name=bwa_base_repository_name, description=bwa_base_repository_description, long_description=bwa_base_repository_long_description, @@ -291,7 +291,7 @@ category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - strings_displayed = [ "Repository 'bwa_tool_dependency_0440' has been created" ] + strings_displayed = [ "Repository <b>bwa_tool_dependency_0440</b> has been created" ] repository = self.get_or_create_repository( name=bwa_tool_dependency_repository_name, description=bwa_tool_dependency_repository_description, long_description=bwa_tool_dependency_repository_long_description, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Add paramiko egg, which fabric 1.7 depends on.
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8045e137464f/ Changeset: 8045e137464f User: Dave Bouvier Date: 2013-09-23 17:43:06 Summary: Add paramiko egg, which fabric 1.7 depends on. Affected #: 1 file diff -r 45abde58ef552a6838d9cbfbe2b00351bb7dd825 -r 8045e137464ff14bec24ce574649e152b168eff3 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -47,6 +47,7 @@ nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 +paramiko = 1.11.1 Parsley = 1.1 Paste = 1.7.5.1 PasteDeploy = 1.5.0 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.

1 0

commit/galaxy-central: Dave Bouvier: Upgrade Fabric egg to 1.7.0.
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/45abde58ef55/ Changeset: 45abde58ef55 User: Dave Bouvier Date: 2013-09-23 17:04:52 Summary: Upgrade Fabric egg to 1.7.0. Affected #: 1 file diff -r 216c01ce66250f453425175d97094525b90f9108 -r 45abde58ef552a6838d9cbfbe2b00351bb7dd825 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -40,7 +40,7 @@ docutils = 0.7 drmaa = 0.4b3 elementtree = 1.2.6_20050316 -Fabric = 1.4.2 +Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 lrucache = 0.2 Mako = 0.4.1 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: greg: Redirect to "manage" rather than "view" when creating a new repository in the too shed.
by commits-noreply＠bitbucket.org 23 Sep '13

23 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/216c01ce6625/ Changeset: 216c01ce6625 User: greg Date: 2013-09-23 16:10:05 Summary: Redirect to "manage" rather than "view" when creating a new repository in the too shed. Affected #: 2 files diff -r 66d484a18d198725ab5f388d4e538ac86d9f081b -r 216c01ce66250f453425175d97094525b90f9108 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 @@ -973,9 +973,9 @@ flush_needed = True if flush_needed: trans.sa_session.flush() - message = "Repository '%s' has been created." % repository.name + message = "Repository <b>%s</b> has been created." % str( repository.name ) trans.response.send_redirect( web.url_for( controller='repository', - action='view_repository', + action='manage_repository', message=message, id=trans.security.encode_id( repository.id ) ) ) repository_type_select_field = rt_util.build_repository_type_select_field( trans ) diff -r 66d484a18d198725ab5f388d4e538ac86d9f081b -r 216c01ce66250f453425175d97094525b90f9108 test/tool_shed/functional/test_0440_deleting_dependency_definitions.py --- a/test/tool_shed/functional/test_0440_deleting_dependency_definitions.py +++ b/test/tool_shed/functional/test_0440_deleting_dependency_definitions.py @@ -74,7 +74,7 @@ description='Description of Deleted Dependency Definitions category for test 0440' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - strings_displayed = [ "Repository 'column_maker_0440' has been created" ] + strings_displayed = [ "Repository <b>column_maker_0440</b> has been created" ] repository = self.get_or_create_repository( name=column_repository_name, description=column_repository_description, long_description=column_repository_long_description, @@ -99,7 +99,7 @@ category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - strings_displayed = [ "Repository 'convert_chars_0440' has been created" ] + strings_displayed = [ "Repository <b>convert_chars_0440</b> has been created" ] repository = self.get_or_create_repository( name=convert_repository_name, description=convert_repository_description, long_description=convert_repository_long_description, @@ -182,7 +182,7 @@ category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - strings_displayed = [ "Repository 'bwa_package_0440' has been created" ] + strings_displayed = [ "Repository <b>bwa_package_0440</b> has been created" ] repository = self.get_or_create_repository( name=bwa_package_repository_name, description=bwa_package_repository_description, long_description=bwa_package_repository_long_description, @@ -208,7 +208,7 @@ category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - strings_displayed = [ "Repository 'bwa_base_0440' has been created" ] + strings_displayed = [ "Repository <b>bwa_base_0440</b> has been created" ] repository = self.get_or_create_repository( name=bwa_base_repository_name, description=bwa_base_repository_description, long_description=bwa_base_repository_long_description, @@ -291,7 +291,7 @@ category = test_db_util.get_category_by_name( 'Test 0440 Deleted Dependency Definitions' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - strings_displayed = [ "Repository 'bwa_tool_dependency_0440' has been created" ] + strings_displayed = [ "Repository <b>bwa_tool_dependency_0440</b> has been created" ] repository = self.get_or_create_repository( name=bwa_tool_dependency_repository_name, description=bwa_tool_dependency_repository_description, long_description=bwa_tool_dependency_repository_long_description, 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: 3 new changesets
by commits-noreply＠bitbucket.org 21 Sep '13

21 Sep '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b8b8a4e16d49/ Changeset: b8b8a4e16d49 User: jgoecks Date: 2013-09-20 19:37:57 Summary: Modal dialog fixes: (a) scroll when necessary and (b) set maximum height so modal does not overflow viewing window. Affected #: 6 files diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -168,16 +168,17 @@ this.$overlay.show(); this.$dialog.show(); this.$overlay.addClass("in"); - // Fix min-width so that modal cannot shrink considerably if - // new content is loaded. + // Fix min-width so that modal cannot shrink considerably if new content is loaded. this.$body.css( "min-width", this.$body.width() ); - // Set max-height so that modal does not exceed window size. - // FIXME: this could perhaps be handled better using a container for the modal - // header-body-footer and setting max-height for the container. + // Set max-height so that modal does not exceed window size and is in middle of page. + // TODO: this could perhaps be handled better using CSS. this.$body.css( "max-height", - // 2* to provide buffer between bottom of modal and bottom of page. - $(window).height() - 2 * this.$dialog.offset().top - - this.$footer.outerHeight() - this.$header.outerHeight()); + $(window).height() - + this.$footer.outerHeight() - + this.$header.outerHeight() - + parseInt( this.$dialog.css( "padding-top" ), 10 ) - + parseInt( this.$dialog.css( "padding-bottom" ), 10 ) + ); } // Callback on init if ( callback ) { diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -756,6 +756,7 @@ .btn.active,.btn:active{color:inherit} .dropdown-menu{max-width:auto} input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex} +.modal-body{overflow:auto} .nav-tabs{margin-bottom:15px} a{text-decoration:underline} label{font-weight:normal} diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/style/blue/sprite-fugue.png Binary file static/style/blue/sprite-fugue.png has changed diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/style/blue/sprite-history-buttons.png Binary file static/style/blue/sprite-history-buttons.png has changed diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/style/blue/sprite-history-states.png Binary file static/style/blue/sprite-history-states.png has changed diff -r cb95dad5175ec10cf191bddcaf2e1d115546dd7c -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 static/style/src/less/galaxy_bootstrap/overrides.less --- a/static/style/src/less/galaxy_bootstrap/overrides.less +++ b/static/style/src/less/galaxy_bootstrap/overrides.less @@ -32,6 +32,9 @@ // Modal -- wider by default, scroll like Trello /* + +NOTE: these styles do not currently work. + .modal { position: absolute; top: 50px; @@ -54,6 +57,11 @@ } */ +// Scroll modal body. +.modal-body { + overflow: auto; +} + // Tabs -- border color is hardcoded in navs.less, change to @btnBorder here .nav-tabs { https://bitbucket.org/galaxy/galaxy-central/commits/23abd7b603c8/ Changeset: 23abd7b603c8 User: jgoecks Date: 2013-09-20 20:01:49 Summary: Popup menu implementation: (a) use trigger rather than reimplementing anchor functionality and (b) set URLs for menu options for clarity and utility. Affected #: 1 file diff -r b8b8a4e16d4923f2cad4e10f39acf8d9131c9471 -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -66,7 +66,10 @@ }; /** - * Sets up popupmenu rendering and binds options functions to the appropriate links + * Sets up popupmenu rendering and binds options functions to the appropriate links. + * initial_options is a dict with text describing the option pointing to either (a) a + * function to perform; or (b) another dict with two required keys, 'url' and 'action' (the + * function to perform. (b) is useful for exposing the underlying URL of the option. */ function make_popupmenu(button_element, initial_options) { /* Use the $.data feature to store options with the link element. @@ -92,7 +95,9 @@ } $.each( options, function( k, v ) { if (v) { - menu_element.append( $("<li></li>").append( $("<a href='#'></a>").html(k).click(v) ) ); + // Action can be either an anonymous function and a mapped dict. + var action = v.action || v; + menu_element.append( $("<li></li>").append( $("<a>").attr("href", v.url).html(k).click(action) ) ); } else { menu_element.append( $("<li></li>").addClass( "head" ).append( $("<a href='#'></a>").html(k) ) ); } @@ -164,43 +169,24 @@ options[ link.text() ] = null; } else { - options[ link.text() ] = function() { + options[ link.text() ] = { + url: href, + action: function() { - // if theres confirm text, send the dialog - if ( !confirmtext || confirm( confirmtext ) ) { - var f; - // relocate the center panel - if ( target === "_parent" ) { - window.parent.location = href; - - // relocate the entire window - } else if ( target === "_top" ) { - window.top.location = href; - - // Http request target is a window named demolocal on the local box - } else if ( target === "demo" ) { - if ( f === undefined || f.closed ) { - f = window.open( href,target ); - f.creator = self; + // if theres confirm text, send the dialog + if ( !confirmtext || confirm( confirmtext ) ) { + var f; + // Http request target is a window named demolocal on the local box + if ( target === "demo" ) { + if ( f === undefined || f.closed ) { + f = window.open( href,target ); + f.creator = self; + } + } - - // this panel or other, valid panels - } else { - // it may be that the button and menu href are not in the same frame: - // allow certain frame names to be used as a target - var other_valid_targets = [ - 'galaxy_main' - // following are blocked until needed - //'galaxy_tools', - //'galaxy_history' - ]; - if( ( target && ( target in window ) - && ( other_valid_targets.indexOf( target ) !== -1 ) ) ){ - window[ target ].location = href; - - // relocate this panel - } else { - window.location = href; + // For all other links, do the default action. + else { + link.trigger('click'); } } } https://bitbucket.org/galaxy/galaxy-central/commits/66d484a18d19/ Changeset: 66d484a18d19 User: jgoecks Date: 2013-09-21 04:50:51 Summary: Automated merge. Affected #: 34 files diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -209,6 +209,7 @@ if self.nginx_upload_store: self.nginx_upload_store = os.path.abspath( self.nginx_upload_store ) self.object_store = kwargs.get( 'object_store', 'disk' ) + self.object_store_check_old_style = string_as_bool( kwargs.get( 'object_store_check_old_style', False ) ) self.object_store_cache_path = resolve_path( kwargs.get( "object_store_cache_path", "database/object_store_cache" ), self.root ) # Handle AWS-specific config options for backward compatibility if kwargs.get( 'aws_access_key', None) is not None: diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -25,7 +25,7 @@ from galaxy.datatypes.metadata import MetadataCollection from galaxy.model.item_attrs import Dictifiable, UsesAnnotations from galaxy.security import get_permitted_actions -from galaxy.util import is_multi_byte, nice_size, Params, restore_text, send_mail +from galaxy.util import asbool, is_multi_byte, nice_size, Params, restore_text, send_mail from galaxy.util.bunch import Bunch from galaxy.util.hash_util import new_secure_hash from galaxy.web.framework.helpers import to_unicode @@ -34,6 +34,7 @@ WorkflowMappingField) from sqlalchemy.orm import object_session from sqlalchemy.sql.expression import func +from tool_shed.util import common_util log = logging.getLogger( __name__ ) @@ -3463,7 +3464,28 @@ @property def has_repository_dependencies( self ): if self.metadata: - return 'repository_dependencies' in self.metadata + repository_dependencies_dict = self.metadata.get( 'repository_dependencies', {} ) + repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) + # [["http://localhost:9009", "package_libgtextutils_0_6", "test", "e2003cbf18cd", "True", "True"]] + for rd_tup in repository_dependencies: + tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ + common_util.parse_repository_dependency_tuple( rd_tup ) + if not asbool( only_if_compiling_contained_td ): + return True + return False + + @property + def has_repository_dependencies_only_if_compiling_contained_td( self ): + if self.metadata: + repository_dependencies_dict = self.metadata.get( 'repository_dependencies', {} ) + repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) + # [["http://localhost:9009", "package_libgtextutils_0_6", "test", "e2003cbf18cd", "True", "True"]] + for rd_tup in repository_dependencies: + tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ + common_util.parse_repository_dependency_tuple( rd_tup ) + if not asbool( only_if_compiling_contained_td ): + return False + return True return False @property @@ -3695,10 +3717,14 @@ @property def tuples_of_repository_dependencies_needed_for_compiling_td( self ): - """Return this repository's repository dependencies that are necessary only for compiling this repository's tool dependencies.""" + """ + Return tuples defining this repository's repository dependencies that are necessary only for compiling this repository's tool + dependencies. + """ rd_tups_of_repositories_needed_for_compiling_td = [] - if self.has_repository_dependencies: - rd_tups = self.metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] + if self.metadata: + repository_dependencies = self.metadata.get( 'repository_dependencies', None ) + rd_tups = repository_dependencies[ 'repository_dependencies' ] for rd_tup in rd_tups: if len( rd_tup ) == 6: tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -198,6 +198,7 @@ super(DiskObjectStore, self).__init__(config, file_path=file_path, extra_dirs=extra_dirs) self.file_path = file_path or config.file_path self.config = config + self.check_old_style = config.object_store_check_old_style self.extra_dirs['job_work'] = config.job_working_directory self.extra_dirs['temp'] = config.new_file_path if extra_dirs is not None: @@ -264,14 +265,13 @@ return os.path.abspath(path) def exists(self, obj, **kwargs): - path = self._construct_path(obj, old_style=True, **kwargs) - # For backward compatibility, check root path first; otherwise, construct - # and check hashed path - if os.path.exists(path): - return True - else: - path = self._construct_path(obj, **kwargs) - return os.path.exists(path) + if self.check_old_style: + path = self._construct_path(obj, old_style=True, **kwargs) + # For backward compatibility, check root path first; otherwise, construct + # and check hashed path + if os.path.exists(path): + return True + return os.path.exists(self._construct_path(obj, **kwargs)) def create(self, obj, **kwargs): if not self.exists(obj, **kwargs): @@ -320,13 +320,13 @@ return content def get_filename(self, obj, **kwargs): - path = self._construct_path(obj, old_style=True, **kwargs) - # For backward compatibility, check root path first; otherwise, construct - # and return hashed path - if os.path.exists(path): - return path - else: - return self._construct_path(obj, **kwargs) + if self.check_old_style: + path = self._construct_path(obj, old_style=True, **kwargs) + # For backward compatibility, check root path first; otherwise, construct + # and return hashed path + if os.path.exists(path): + return path + return self._construct_path(obj, **kwargs) def update_from_file(self, obj, file_name=None, create=False, **kwargs): """ `create` parameter is not used in this implementation """ diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -587,8 +587,10 @@ hda_dict[ 'api_type' ] = "file" # Add additional attributes that depend on trans can hence must be added here rather than at the model level. - - #NOTE: access is an expensive operation - removing it and adding the precondition of access is already checked + can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) + can_access_hda = ( trans.user_is_admin() or can_access_hda ) + if not can_access_hda: + return self.get_inaccessible_hda_dict( trans, hda ) hda_dict[ 'accessible' ] = True # ---- return here if deleted AND purged OR can't access @@ -634,6 +636,18 @@ return trans.security.encode_dict_ids( hda_dict ) + def get_inaccessible_hda_dict( self, trans, hda ): + return trans.security.encode_dict_ids({ + 'id' : hda.id, + 'history_id': hda.history.id, + 'hid' : hda.hid, + 'name' : hda.name, + 'state' : hda.state, + 'deleted' : hda.deleted, + 'visible' : hda.visible, + 'accessible': False + }) + def get_hda_dict_with_error( self, trans, hda, error_msg='' ): return trans.security.encode_dict_ids({ 'id' : hda.id, diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -198,7 +198,10 @@ if page_num == 0: # Show all rows in page. total_num_rows = query.count() + # persistant page='all' page_num = 1 + #page_num = 'all' + #extra_url_args['page'] = page_num num_pages = 1 else: # Show a limited number of rows. Before modifying query, get the total number of rows that query diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b 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 @@ -235,8 +235,15 @@ # get file destination file_destination = dataset.get_file_name() + # check if the directory exists + dn = os.path.dirname(file_destination) + if not os.path.exists(dn): + os.makedirs(dn) + + # get file and directory names + fn = os.path.basename(content.filename) + # save file locally - fn = os.path.basename(content.filename) open(file_destination, 'wb').write(content.file.read()) # log diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -812,7 +812,7 @@ status = kwd.get( 'status', 'done' ) shed_tool_conf = kwd.get( 'shed_tool_conf', None ) tool_shed_url = kwd[ 'tool_shed_url' ] - # Handle repository dependencies. + # Handle repository dependencies, which do not include those that are required only for compiling a dependent repository's tool dependencies. has_repository_dependencies = util.string_as_bool( kwd.get( 'has_repository_dependencies', False ) ) install_repository_dependencies = kwd.get( 'install_repository_dependencies', '' ) # Every repository will be installed into the same tool panel section or all will be installed outside of any sections. @@ -1061,7 +1061,7 @@ repository_clone_url, metadata, trans.model.ToolShedRepository.installation_status.NEW, - tool_shed_repository.installed_changeset_revision, + tool_shed_repository.changeset_revision, tool_shed_repository.owner, tool_shed_repository.dist_to_shed ) ctx_rev = suc.get_ctx_rev( trans.app, @@ -1320,7 +1320,6 @@ missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None ) repository_name = dependencies_for_repository_dict.get( 'name', None ) repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None ) - if installed_repository_dependencies or missing_repository_dependencies: has_repository_dependencies = True else: diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -309,7 +309,6 @@ # If deleting the current history, make a new current. if history == trans.get_history(): deleted_current = True - trans.get_or_create_default_history() trans.log_event( "History (%s) marked as deleted" % history.name ) n_deleted += 1 if purge and trans.app.config.allow_user_dataset_purge: @@ -339,6 +338,8 @@ part += " but the datasets were not removed from disk because that feature is not enabled in this Galaxy instance" message_parts.append( "%s. " % part ) if deleted_current: + #note: this needs to come after commits above or will use an empty history that was deleted above + trans.get_or_create_default_history() message_parts.append( "Your active history was deleted, a new empty history is now active. " ) status = INFO return ( status, " ".join( message_parts ) ) diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -73,6 +73,7 @@ "changeset_revision": "3a08cc21466f", "downloadable": true, "has_repository_dependencies": false, + "has_repository_dependencies_only_if_compiling_contained_td": false, "id": "f9cad7b01a472135", "includes_datatypes": false, "includes_tool_dependencies": false, @@ -125,7 +126,8 @@ action='show', id=encoded_repository_metadata_id ) # Get the repo_info_dict for installing the repository. - repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, has_repository_dependencies = \ + repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \ + has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ repository_util.get_repo_info_dict( trans, encoded_repository_id, changeset_revision ) return repository_dict, repository_metadata_dict, repo_info_dict else: diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b 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 @@ -1343,32 +1343,36 @@ def get_changeset_revision_and_ctx_rev( self, trans, **kwd ): """Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated.""" def has_galaxy_utilities( repository_metadata ): - includes_data_managers = False - includes_datatypes = False - includes_tools = False - includes_tools_for_display_in_tool_panel = False - has_repository_dependencies = False - includes_tool_dependencies = False - includes_workflows = False + has_galaxy_utilities_dict = dict( includes_data_managers=False, + includes_datatypes=False, + includes_tools=False, + includes_tools_for_display_in_tool_panel=False, + has_repository_dependencies=False, + has_repository_dependencies_only_if_compiling_contained_td=False, + includes_tool_dependencies=False, + includes_workflows=False ) if repository_metadata: includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel metadata = repository_metadata.metadata if metadata: if 'data_manager' in metadata: - includes_data_managers = True + has_galaxy_utilities_dict[ 'includes_data_managers' ] = True if 'datatypes' in metadata: - includes_datatypes = True + has_galaxy_utilities_dict[ 'includes_datatypes' ] = True if 'tools' in metadata: - includes_tools = True + has_galaxy_utilities_dict[ 'includes_tools' ] = True if 'tool_dependencies' in metadata: - includes_tool_dependencies = True - if 'repository_dependencies' in metadata: - has_repository_dependencies = True + has_galaxy_utilities_dict[ 'includes_tool_dependencies' ] = True + repository_dependencies_dict = metadata.get( 'repository_dependencies', {} ) + repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) + has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ + suc.get_repository_dependency_types( repository_dependencies ) + has_galaxy_utilities_dict[ 'has_repository_dependencies' ] = has_repository_dependencies + has_galaxy_utilities_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = \ + has_repository_dependencies_only_if_compiling_contained_td if 'workflows' in metadata: - includes_workflows = True - return includes_data_managers, includes_datatypes, includes_tools, includes_tools_for_display_in_tool_panel, includes_tool_dependencies, has_repository_dependencies, includes_workflows - message = kwd.get( 'message', '' ) - status = kwd.get( 'status', 'done' ) + has_galaxy_utilities_dict[ 'includes_workflows' ] = True + return has_galaxy_utilities_dict name = kwd.get( 'name', None ) owner = kwd.get( 'owner', None ) changeset_revision = kwd.get( 'changeset_revision', None ) @@ -1376,8 +1380,15 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) - includes_data_managers, includes_datatypes, includes_tools, includes_tools_for_display_in_tool_panel, includes_tool_dependencies, has_repository_dependencies, includes_workflows = \ - has_galaxy_utilities( repository_metadata ) + has_galaxy_utilities_dict = has_galaxy_utilities( repository_metadata ) + includes_data_managers = has_galaxy_utilities_dict[ 'includes_data_managers' ] + includes_datatypes = has_galaxy_utilities_dict[ 'includes_datatypes' ] + includes_tools = has_galaxy_utilities_dict[ 'includes_tools' ] + includes_tools_for_display_in_tool_panel = has_galaxy_utilities_dict[ 'includes_tools_for_display_in_tool_panel' ] + includes_tool_dependencies = has_galaxy_utilities_dict[ 'includes_tool_dependencies' ] + has_repository_dependencies = has_galaxy_utilities_dict[ 'has_repository_dependencies' ] + has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] + includes_workflows = has_galaxy_utilities_dict[ 'includes_workflows' ] repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) # Default to the received changeset revision and ctx_rev. @@ -1392,6 +1403,7 @@ includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies, has_repository_dependencies=has_repository_dependencies, + has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td, includes_workflows=includes_workflows ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. @@ -1407,6 +1419,7 @@ for changeset in repo.changelog: includes_tools = False has_repository_dependencies = False + has_repository_dependencies_only_if_compiling_contained_td = False changeset_hash = str( repo.changectx( changeset ) ) ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) if update_to_changeset_hash: @@ -1414,8 +1427,15 @@ trans.security.encode_id( repository.id ), changeset_hash ) if update_to_repository_metadata: - includes_data_managers, includes_datatypes, includes_tools, includes_tools_for_display_in_tool_panel, includes_tool_dependencies, has_repository_dependencies, includes_workflows = \ - has_galaxy_utilities( update_to_repository_metadata ) + has_galaxy_utilities_dict = has_galaxy_utilities( repository_metadata ) + includes_data_managers = has_galaxy_utilities_dict[ 'includes_data_managers' ] + includes_datatypes = has_galaxy_utilities_dict[ 'includes_datatypes' ] + includes_tools = has_galaxy_utilities_dict[ 'includes_tools' ] + includes_tools_for_display_in_tool_panel = has_galaxy_utilities_dict[ 'includes_tools_for_display_in_tool_panel' ] + includes_tool_dependencies = has_galaxy_utilities_dict[ 'includes_tool_dependencies' ] + has_repository_dependencies = has_galaxy_utilities_dict[ 'has_repository_dependencies' ] + has_repository_dependencies_only_if_compiling_contained_td = has_galaxy_utilities_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] + includes_workflows = has_galaxy_utilities_dict[ 'includes_workflows' ] # We found a RepositoryMetadata record. if changeset_hash == repository.tip( trans.app ): # The current ctx is the repository tip, so use it. @@ -1435,6 +1455,7 @@ update_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies update_dict[ 'includes_workflows' ] = includes_workflows update_dict[ 'has_repository_dependencies' ] = has_repository_dependencies + update_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = has_repository_dependencies_only_if_compiling_contained_td update_dict[ 'changeset_revision' ] = str( latest_changeset_revision ) update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() ) return encoding_util.tool_shed_encode( update_dict ) @@ -1611,14 +1632,18 @@ includes_tools = False includes_tools_for_display_in_tool_panel = False has_repository_dependencies = False + has_repository_dependencies_only_if_compiling_contained_td = False includes_tool_dependencies = False repo_info_dicts = [] for tup in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ): repository_id, changeset_revision = tup - repo_info_dict, cur_includes_tools, cur_includes_tool_dependencies, cur_includes_tools_for_display_in_tool_panel, cur_has_repository_dependencies = \ + repo_info_dict, cur_includes_tools, cur_includes_tool_dependencies, cur_includes_tools_for_display_in_tool_panel, \ + cur_has_repository_dependencies, cur_has_repository_dependencies_only_if_compiling_contained_td = \ repository_util.get_repo_info_dict( trans, repository_id, changeset_revision ) if cur_has_repository_dependencies and not has_repository_dependencies: has_repository_dependencies = True + if cur_has_repository_dependencies_only_if_compiling_contained_td and not has_repository_dependencies_only_if_compiling_contained_td: + has_repository_dependencies_only_if_compiling_contained_td = True if cur_includes_tools and not includes_tools: includes_tools = True if cur_includes_tool_dependencies and not includes_tool_dependencies: @@ -1629,6 +1654,7 @@ return dict( includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, has_repository_dependencies=has_repository_dependencies, + has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td, includes_tool_dependencies=includes_tool_dependencies, repo_info_dicts=repo_info_dicts ) @@ -1708,7 +1734,9 @@ tool_version_dicts = [] for changeset in repo.changelog: current_changeset_revision = str( repo.changectx( changeset ) ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), current_changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + current_changeset_revision ) if repository_metadata and repository_metadata.tool_versions: tool_version_dicts.append( repository_metadata.tool_versions ) if current_changeset_revision == changeset_revision: @@ -1766,22 +1794,30 @@ includes_workflows = True readme_files_dict = readme_util.build_readme_files_dict( metadata ) # See if the repo_info_dict was populated with repository_dependencies or tool_dependencies. + has_repository_dependencies = False + has_repository_dependencies_only_if_compiling_contained_td = False + includes_tool_dependencies = False for name, repo_info_tuple in repo_info_dict.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tuple ) - if repository_dependencies: - has_repository_dependencies = True - else: - has_repository_dependencies = False - if tool_dependencies: - includes_tool_dependencies = True - else: - includes_tool_dependencies = False + if not has_repository_dependencies or not has_repository_dependencies_only_if_compiling_contained_td or not includes_tool_dependencies: + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + for rd_key, rd_tups in repository_dependencies.items(): + if rd_key in [ 'root_key', 'description' ]: + continue + curr_has_repository_dependencies, curr_has_repository_dependencies_only_if_compiling_contained_td = \ + suc.get_repository_dependency_types( rd_tups ) + if curr_has_repository_dependencies and not has_repository_dependencies: + has_repository_dependencies = True + if curr_has_repository_dependencies_only_if_compiling_contained_td and not has_repository_dependencies_only_if_compiling_contained_td: + has_repository_dependencies_only_if_compiling_contained_td = True + if tool_dependencies and not includes_tool_dependencies: + includes_tool_dependencies = True return dict( includes_data_managers=includes_data_managers, includes_datatypes=includes_datatypes, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, has_repository_dependencies=has_repository_dependencies, + has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td, includes_tool_dependencies=includes_tool_dependencies, includes_workflows=includes_workflows, readme_files_dict=readme_files_dict, @@ -2434,7 +2470,9 @@ try: commands.remove( repo.ui, repo, selected_file, force=True ) except Exception, e: - log.debug( "Error removing files using the mercurial API, so trying a different approach, the error was: %s" % str( e )) + log.debug( "Error removing the following file using the mercurial API:\n %s" % str( selected_file ) ) + log.debug( "The error was: %s" % str( e )) + log.debug( "Attempting to remove the file using a different approach." ) relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) repo.dirstate.remove( relative_selected_file ) repo.dirstate.write() diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -253,6 +253,7 @@ self.time_last_tested = time_last_tested self.tool_test_results = tool_test_results self.has_repository_dependencies = has_repository_dependencies + # We don't consider the special case has_repository_dependencies_only_if_compiling_contained_td here. self.includes_datatypes = includes_datatypes self.includes_tools = includes_tools self.includes_tool_dependencies = includes_tool_dependencies diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b 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 @@ -234,10 +234,10 @@ else: includes_tools = False includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel - if 'repository_dependencies' in metadata: - has_repository_dependencies = True - else: - has_repository_dependencies = False + repository_dependencies_dict = metadata.get( 'repository_dependencies', {} ) + repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) + has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ + suc.get_repository_dependency_types( repository_dependencies ) if 'tool_dependencies' in metadata: includes_tool_dependencies = True else: @@ -246,6 +246,7 @@ # Here's where we may have to handle enhancements to the callers. See above comment. includes_tools = False has_repository_dependencies = False + has_repository_dependencies_only_if_compiling_contained_td = False includes_tool_dependencies = False includes_tools_for_display_in_tool_panel = False ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) @@ -259,7 +260,8 @@ repository_metadata=repository_metadata, tool_dependencies=None, repository_dependencies=None ) - return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, has_repository_dependencies + return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \ + has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td def get_repository_components_for_installation( encoded_tsr_id, encoded_tsr_ids, repo_info_dicts, tool_panel_section_keys ): """ @@ -311,6 +313,7 @@ includes_tool_dependencies = update_dict.get( 'includes_tool_dependencies', False ) includes_workflows = update_dict.get( 'includes_workflows', False ) has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False ) + has_repository_dependencies_only_if_compiling_contained_td = update_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) changeset_revision = update_dict.get( 'changeset_revision', None ) ctx_rev = update_dict.get( 'ctx_rev', None ) changeset_revision_dict[ 'includes_data_managers' ] = includes_data_managers @@ -320,6 +323,7 @@ changeset_revision_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies changeset_revision_dict[ 'includes_workflows' ] = includes_workflows changeset_revision_dict[ 'has_repository_dependencies' ] = has_repository_dependencies + changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = has_repository_dependencies_only_if_compiling_contained_td changeset_revision_dict[ 'changeset_revision' ] = changeset_revision changeset_revision_dict[ 'ctx_rev' ] = ctx_rev except Exception, e: @@ -331,6 +335,7 @@ changeset_revision_dict[ 'includes_tool_dependencies' ] = False changeset_revision_dict[ 'includes_workflows' ] = False changeset_revision_dict[ 'has_repository_dependencies' ] = False + changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = False changeset_revision_dict[ 'changeset_revision' ] = None changeset_revision_dict[ 'ctx_rev' ] = None return changeset_revision_dict diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b 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 @@ -394,7 +394,7 @@ if not binary_installed: print 'Binary installation did not occur, so proceeding with install and compile recipe.' # Make sure to reset for installation if attempt at binary installation resulted in an error. - if tool_dependency.status != app.model.ToolDependency.installation_status.NEW: + if tool_dependency.status != app.model.ToolDependency.installation_status.NEVER_INSTALLED: removed, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency ) install_via_fabric( app, tool_dependency, diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b 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 @@ -12,6 +12,7 @@ from tool_shed.util import encoding_util from tool_shed.util import data_manager_util from tool_shed.util import datatype_util +from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import xml_util from tool_shed.galaxy_install.tool_dependencies.install_util import install_package @@ -69,16 +70,28 @@ Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated with the repository defined by the received repo_info_dict. """ + repository = None + installed_rd = {} + installed_td = {} + missing_rd = {} + missing_td = {} name = repo_info_dict.keys()[ 0 ] repo_info_tuple = repo_info_dict[ name ] - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \ + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tuple ) + if tool_dependencies: + if not includes_tool_dependencies: + includes_tool_dependencies = True + # Inspect the tool_dependencies dictionary to separate the installed and missing tool dependencies. We don't add to installed_td + # and missing_td here because at this point they are empty. + installed_td, missing_td = get_installed_and_missing_tool_dependencies( trans, tool_shed_url, tool_dependencies ) + # In cases where a repository dependency is required only for compiling a dependent repository's tool dependency, the value of + # repository_dependencies will be an empty dictionary here. if repository_dependencies: # We have a repository with one or more defined repository dependencies. missing_td = {} - # Handle the scenario where a repository was installed, then uninstalled and an error occurred during the re-installation process. - # In this case, a record for the repository will exist in the database with the status of 'New'. - repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision ) + if not repository: + repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision ) if repository and repository.metadata: installed_rd, missing_rd = get_installed_and_missing_repository_dependencies( trans, repository ) else: @@ -86,73 +99,70 @@ # Discover all repository dependencies and retrieve information for installing them. all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False ) + has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False ) includes_tools = all_repo_info_dict.get( 'includes_tools', False ) required_repo_info_dicts = all_repo_info_dict.get( 'all_repo_info_dicts', [] ) # Display tool dependencies defined for each of the repository dependencies. if required_repo_info_dicts: - all_tool_dependencies = {} + required_tool_dependencies = {} for rid in required_repo_info_dicts: for name, repo_info_tuple in rid.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, rid_installed_td = \ + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, rid_repository_dependencies, rid_tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tuple ) - if rid_installed_td: - for td_key, td_dict in rid_installed_td.items(): - if td_key not in all_tool_dependencies: - all_tool_dependencies[ td_key ] = td_dict - if all_tool_dependencies: - if installed_td is None: - installed_td = {} - else: - # Move all tool dependencies to the missing_tool_dependencies container. - for td_key, td_dict in installed_td.items(): - if td_key not in missing_td: - missing_td[ td_key ] = td_dict - installed_td = {} + if rid_tool_dependencies: + for td_key, td_dict in rid_tool_dependencies.items(): + if td_key not in required_tool_dependencies: + required_tool_dependencies[ td_key ] = td_dict + if required_tool_dependencies: # Discover and categorize all tool dependencies defined for this repository's repository dependencies. - required_tool_dependencies, required_missing_tool_dependencies = \ - get_installed_and_missing_tool_dependencies_for_new_install( trans, all_tool_dependencies ) - if required_tool_dependencies: + required_installed_td, required_missing_td = get_installed_and_missing_tool_dependencies( trans, + tool_shed_url, + required_tool_dependencies ) + if required_installed_td: if not includes_tool_dependencies: includes_tool_dependencies = True - for td_key, td_dict in required_tool_dependencies.items(): + for td_key, td_dict in required_installed_td.items(): if td_key not in installed_td: installed_td[ td_key ] = td_dict - if required_missing_tool_dependencies: + if required_missing_td: if not includes_tool_dependencies: includes_tool_dependencies = True - for td_key, td_dict in required_missing_tool_dependencies.items(): + for td_key, td_dict in required_missing_td.items(): if td_key not in missing_td: missing_td[ td_key ] = td_dict else: - # We have a single repository with no defined repository dependencies. + # We have a single repository with (possibly) no defined repository dependencies. all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False ) + has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False ) includes_tools = all_repo_info_dict.get( 'includes_tools', False ) required_repo_info_dicts = all_repo_info_dict.get( 'all_repo_info_dicts', [] ) - installed_rd = None - missing_rd = None - missing_td = None - dependencies_for_repository_dict = dict( changeset_revision=changeset_revision, - has_repository_dependencies=has_repository_dependencies, - includes_tool_dependencies=includes_tool_dependencies, - includes_tools=includes_tools, - includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, - installed_repository_dependencies=installed_rd, - installed_tool_dependencies=installed_td, - missing_repository_dependencies=missing_rd, - missing_tool_dependencies=missing_td, - name=name, - repository_owner=repository_owner ) + dependencies_for_repository_dict = \ + dict( changeset_revision=changeset_revision, + has_repository_dependencies=has_repository_dependencies, + has_repository_dependencies_only_if_compiling_contained_td=has_repository_dependencies_only_if_compiling_contained_td, + includes_tool_dependencies=includes_tool_dependencies, + includes_tools=includes_tools, + includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, + installed_repository_dependencies=installed_rd, + installed_tool_dependencies=installed_td, + missing_repository_dependencies=missing_rd, + missing_tool_dependencies=missing_td, + name=name, + repository_owner=repository_owner ) return dependencies_for_repository_dict def get_installed_and_missing_repository_dependencies( trans, repository ): """ Return the installed and missing repository dependencies for a tool shed repository that has a record in the Galaxy database, but - may or may not be installed. In this case, the repository dependencies are associated with the repository in the database. + may or may not be installed. In this case, the repository dependencies are associated with the repository in the database. Do not + include a repository dependency if it is required only to compile a tool dependency defined for the dependent repository since these + special kinds of repository dependencies are really a dependency of the dependent repository's contained tool dependency, and only if + that tool dependency requires compilation. """ missing_repository_dependencies = {} installed_repository_dependencies = {} @@ -166,7 +176,14 @@ for tsr in repository.repository_dependencies: prior_installation_required = suc.set_prior_installation_required( repository, tsr ) only_if_compiling_contained_td = suc.set_only_if_compiling_contained_td( repository, tsr ) - rd_tup = [ tsr.tool_shed, tsr.name, tsr.owner, tsr.changeset_revision, prior_installation_required, only_if_compiling_contained_td, tsr.id, tsr.status ] + rd_tup = [ tsr.tool_shed, + tsr.name, + tsr.owner, + tsr.changeset_revision, + prior_installation_required, + only_if_compiling_contained_td, + tsr.id, + tsr.status ] if tsr.status == trans.model.ToolShedRepository.installation_status.INSTALLED: installed_rd_tups.append( rd_tup ) else: @@ -184,7 +201,7 @@ 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. + # dictionaries for proper display parsing. root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed, repository.name, repository.owner, @@ -210,7 +227,7 @@ installed_repository_dependencies = {} missing_rd_tups = [] installed_rd_tups = [] - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \ + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tuple ) if repository_dependencies: description = repository_dependencies[ 'description' ] @@ -228,7 +245,7 @@ # tuple looks like: ( description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td ) tmp_clone_url = suc.generate_clone_url_from_repo_info_tup( rd_tup ) 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 ) + repository, installed_changeset_revision = suc.repository_was_previously_installed( trans, tool_shed, name, tmp_repo_info_tuple ) if repository: new_rd_tup = [ tool_shed, name, @@ -273,29 +290,46 @@ missing_repository_dependencies[ 'description' ] = description return installed_repository_dependencies, missing_repository_dependencies -def get_installed_and_missing_tool_dependencies_for_new_install( trans, all_tool_dependencies ): +def get_installed_and_missing_tool_dependencies( trans, tool_shed_url, tool_dependencies_dict ): """Return the lists of installed tool dependencies and missing tool dependencies for a set of repositories being installed into Galaxy.""" - # FIXME: confirm that this method currently populates and returns only missing tool dependencies. If so, this method should be enhanced to search for - # installed tool dependencies defined as complex repository dependency relationships. - if all_tool_dependencies: - tool_dependencies = {} - missing_tool_dependencies = {} - for td_key, val in all_tool_dependencies.items(): - # Set environment tool dependencies are a list, set each member to never installed. + installed_tool_dependencies = {} + missing_tool_dependencies = {} + if tool_dependencies_dict: + for td_key, val in tool_dependencies_dict.items(): + # Default the status to NEVER_INSTALLED. + tool_dependency_status = trans.model.ToolDependency.installation_status.NEVER_INSTALLED + # Set environment tool dependencies are a list. if td_key == 'set_environment': new_val = [] for requirement_dict in val: - requirement_dict[ 'status' ] = trans.model.ToolDependency.installation_status.NEVER_INSTALLED + # {'repository_name': 'xx', 'name': 'bwa', 'version': '0.5.9', 'repository_owner': 'yy', 'changeset_revision': 'zz', 'type': 'package'} + tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type( trans.app, + requirement_dict.get( 'name', None ), + requirement_dict.get( 'version', None ), + requirement_dict.get( 'type', 'package' ) ) + if tool_dependency: + tool_dependency_status = tool_dependency.status + requirement_dict[ 'status' ] = tool_dependency_status new_val.append( requirement_dict ) - missing_tool_dependencies[ td_key ] = new_val + if tool_dependency_status in [ trans.model.ToolDependency.installation_status.INSTALLED ]: + installed_tool_dependencies[ td_key ] = new_val + else: + missing_tool_dependencies[ td_key ] = new_val else: - # Since we have a new install, missing tool dependencies have never been installed. - val[ 'status' ] = trans.model.ToolDependency.installation_status.NEVER_INSTALLED + # The val dictionary looks something like this: + # {'repository_name': 'xx', 'name': 'bwa', 'version': '0.5.9', 'repository_owner': 'yy', 'changeset_revision': 'zz', 'type': 'package'} + tool_dependency = tool_dependency_util.get_tool_dependency_by_name_version_type( trans.app, + val.get( 'name', None ), + val.get( 'version', None ), + val.get( 'type', 'package' ) ) + if tool_dependency: + tool_dependency_status = tool_dependency.status + val[ 'status' ] = tool_dependency_status + if tool_dependency_status in [ trans.model.ToolDependency.installation_status.INSTALLED ]: + installed_tool_dependencies[ td_key ] = val + else: missing_tool_dependencies[ td_key ] = val - else: - tool_dependencies = None - missing_tool_dependencies = None - return tool_dependencies, missing_tool_dependencies + return installed_tool_dependencies, missing_tool_dependencies def get_required_repo_info_dicts( trans, tool_shed_url, repo_info_dicts ): """ @@ -328,7 +362,9 @@ toolshed, name, owner, changeset_revision = container_util.get_components_from_key( key ) components_list = [ toolshed, name, owner, changeset_revision ] only_if_compiling_contained_td = 'False' - # Skip listing a repository dependency if it is required only to compile a tool dependency defined for the dependent repository. + # Skip listing a repository dependency if it is required only to compile a tool dependency defined for the dependent repository since + # in this case, the repository dependency is really a dependency of the dependent repository's contained tool dependency, and only if + # that tool dependency requires compilation. if not util.asbool( only_if_compiling_contained_td ): if components_list not in required_repository_tups: required_repository_tups.append( components_list ) @@ -337,8 +373,8 @@ only_if_compiling_contained_td = components_list[ 5 ] except: only_if_compiling_contained_td = 'False' - # TODO: Fix this to display the tool dependency if only_if_compiling_contained_td is True, but clarify that installation may not - # happen. + # Skip listing a repository dependency if it is required only to compile a tool dependency defined for the dependent repository + # (see above comment). if not util.asbool( only_if_compiling_contained_td ): if components_list not in required_repository_tups: required_repository_tups.append( components_list ) diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/util/common_util.py --- a/lib/tool_shed/util/common_util.py +++ b/lib/tool_shed/util/common_util.py @@ -1,3 +1,4 @@ +import logging import os import urllib2 from galaxy.util import json @@ -5,6 +6,8 @@ from tool_shed.util import encoding_util from tool_shed.util import xml_util +log = logging.getLogger( __name__ ) + REPOSITORY_OWNER = 'devteam' def accumulate_tool_dependencies( tool_shed_accessible, tool_dependencies, all_tool_dependencies ): diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -280,13 +280,16 @@ def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ): """Create or update a repository_metadatqa record in the tool shed.""" has_repository_dependencies = False + has_repository_dependencies_only_if_compiling_contained_td = False includes_datatypes = False includes_tools = False includes_tool_dependencies = False includes_workflows = False if metadata_dict: - if 'repository_dependencies' in metadata_dict: - has_repository_dependencies = True + repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) + has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ + suc.get_repository_dependency_types( repository_dependencies ) if 'datatypes' in metadata_dict: includes_datatypes = True if 'tools' in metadata_dict: @@ -295,7 +298,11 @@ includes_tool_dependencies = True if 'workflows' in metadata_dict: includes_workflows = True - downloadable = has_repository_dependencies or includes_datatypes or includes_tools or includes_tool_dependencies or includes_workflows + if has_repository_dependencies or has_repository_dependencies_only_if_compiling_contained_td or includes_datatypes or \ + includes_tools or includes_tool_dependencies or includes_workflows: + downloadable = True + else: + downloadable = False repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: # A repository metadata record already exists with the received changeset_revision, so we don't need to check the skip_tool_test table. @@ -1851,10 +1858,13 @@ repository_metadata.includes_datatypes = True else: repository_metadata.includes_datatypes = False - if 'repository_dependencies' in metadata_dict: - repository_metadata.has_repository_dependencies = True - else: - repository_metadata.has_repository_dependencies = False + # We don't store information about the special type of repository dependency that is needed only for compiling a tool dependency + # defined for the dependent repository. + repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) + has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ + suc.get_repository_dependency_types( repository_dependencies ) + repository_metadata.has_repository_dependencies = has_repository_dependencies if 'tool_dependencies' in metadata_dict: repository_metadata.includes_tool_dependencies = True else: diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b 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 @@ -139,6 +139,7 @@ # repository dependencies are not to be installed, only those items contained in the received repo_info_dicts list will be processed. if is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ) or install_repository_dependencies: if installed_tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR, + trans.model.ToolShedRepository.installation_status.NEW, trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: # The current tool shed repository is not currently installed, so we can update it's record in the database. can_update = True diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b 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 @@ -868,6 +868,31 @@ .first() return None +def get_repository_dependency_types( repository_dependencies ): + """ + Inspect the received list of repository_dependencies tuples and return boolean values for has_repository_dependencies and + has_repository_dependencies_only_if_compiling_contained_td. + """ + # Set has_repository_dependencies, which will be True only if at least one repository_dependency is defined with the value of + # only_if_compiling_contained_td as False. + has_repository_dependencies = False + for rd_tup in repository_dependencies: + tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ + common_util.parse_repository_dependency_tuple( rd_tup ) + if not asbool( only_if_compiling_contained_td ): + has_repository_dependencies = True + break + # Set has_repository_dependencies_only_if_compiling_contained_td, which will be True only if at least one repository_dependency is + # defined with the value of only_if_compiling_contained_td as True. + has_repository_dependencies_only_if_compiling_contained_td = False + for rd_tup in repository_dependencies: + tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ + common_util.parse_repository_dependency_tuple( rd_tup ) + if asbool( only_if_compiling_contained_td ): + has_repository_dependencies_only_if_compiling_contained_td = True + break + return has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td + def get_repository_for_dependency_relationship( app, tool_shed, name, owner, changeset_revision ): """Return an installed tool_shed_repository database record that is defined by either the current changeset revision or the installed_changeset_revision.""" # This method is used only in Galaxy, not the tool shed. @@ -1389,14 +1414,23 @@ def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple ): """ - Handle the case where the repository was previously installed using an older changeset_revsion, but later the repository was updated - in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one - that was previously installed. We'll look in the database instead of on disk since the repository may be uninstalled. + Find out if a repository is already installed into Galaxy - there are several scenarios where this is necessary. For example, this method + will handle the case where the repository was previously installed using an older changeset_revsion, but later the repository was updated + in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one that was + previously installed. We'll look in the database instead of on disk since the repository may be currently uninstalled. """ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ get_repo_info_tuple_contents( repo_info_tuple ) tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) - # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset + # See if we can locate the repository using the value of changeset_revision. + tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( trans.app, + tool_shed, + repository_name, + repository_owner, + changeset_revision ) + if tool_shed_repository: + return tool_shed_repository, changeset_revision + # Get all previous changeset revisions from the tool shed for the repository back to, but excluding, the previous valid changeset # revision to see if it was previously installed using one of them. url = url_join( tool_shed_url, 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ @@ -1410,14 +1444,14 @@ repository_name, repository_owner, previous_changeset_revision ) - if tool_shed_repository and tool_shed_repository.status not in [ trans.model.ToolShedRepository.installation_status.NEW ]: + if tool_shed_repository: return tool_shed_repository, previous_changeset_revision return None, None def reset_previously_installed_repository( trans, repository ): """ Reset the atrributes of a tool_shed_repository that was previsouly installed. The repository will be in some state other than with a - status of INSTALLED, so all atributes will be set to the default (NEW( state. This will enable the repository to be freshly installed. + status of INSTALLED, so all atributes will be set to the default NEW state. This will enable the repository to be freshly installed. """ repository.deleted = False repository.tool_shed_status = None diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -258,6 +258,14 @@ app.model.ToolDependency.table.c.type == type ) ) \ .first() +def get_tool_dependency_by_name_version_type( app, name, version, type ): + sa_session = app.model.context.current + return sa_session.query( app.model.ToolDependency ) \ + .filter( and_( app.model.ToolDependency.table.c.name == name, + app.model.ToolDependency.table.c.version == version, + app.model.ToolDependency.table.c.type == type ) ) \ + .first() + def get_tool_dependency_by_name_version_type_repository( app, repository, name, version, type ): sa_session = app.model.context.current return sa_session.query( app.model.ToolDependency ) \ diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -962,7 +962,7 @@ suc.config_elems_to_xml_file( trans.app, config_elems, shed_tool_conf, tool_path ) def remove_from_tool_panel( trans, repository, shed_tool_conf, uninstall ): - """A tool shed repository is being deactivated or uninstalled so handle tool panel alterations accordingly.""" + """A tool shed repository is being deactivated or uninstalled, so handle tool panel alterations accordingly.""" # Determine where the tools are currently defined in the tool panel and store this information so the tools can be displayed # in the same way when the repository is activated or reinstalled. tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository ) diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -472,7 +472,7 @@ go_to_URL(); return; } - + // If there's an operation, do POST; otherwise, do GET. var method = (grid.get('operation') ? "POST" : "GET" ); $('.loading-elt-overlay').show(); // Show overlay to indicate loading and prevent user actions. @@ -565,4 +565,4 @@ // return return true; -} \ No newline at end of file +} diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -77,13 +77,25 @@ // link functions $.each(options.buttons, function(name, value) { - footer.append($('<button></button>').text(name).click(value)).append(" "); + footer.append($('<button id="' + String(name).toLowerCase() + '"></button>').text(name).click(value)).append(" "); }); } else // default close button footer.append($('<button></button>').text('Close').click(function() { self.hide() })).append(" "); }, + // enable buttons + enable: function(name) + { + $(this.el).find('#' + String(name).toLowerCase()).prop('disabled', false); + }, + + // disable buttons + disable: function(name) + { + $(this.el).find('#' + String(name).toLowerCase()).prop('disabled', true); + }, + /* HTML TEMPLATES */ diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -1,5 +1,5 @@ /* - galaxy upload v1.0 + galaxy upload */ // dependencies @@ -14,12 +14,20 @@ // button button_show : null, - // file counter - file_counter: 0, + // upload mod + uploadbox: null, // initialize initialize : function() { + // wait for galaxy history panel (workaround due to the use of iframes) + if (!Galaxy.currHistoryPanel) + { + var self = this; + window.setTimeout(function() { self.initialize() }, 500) + return; + } + // add activate icon var self = this; this.button_show = new mod_master.GalaxyMasterIcon ( @@ -37,87 +45,252 @@ // events events : { - 'mouseover' : 'event_mouseover', - 'mouseleave' : 'event_mouseleave' + 'mouseover' : 'event_mouseover', + 'mouseleave' : 'event_mouseleave' }, // mouse over event_mouseover : function (e) { - $('#galaxy-upload-box').addClass('highlight'); }, // mouse left event_mouseleave : function (e) { - $('#galaxy-upload-box').removeClass('highlight'); }, // start - event_start : function(index, file, message) + event_announce : function(index, file, message) { + // hide info + this.uploadbox.info().hide(); + // make id - var id = '#galaxy-upload-file-' + index; + var id = '#upload-' + index; - // add tag - $('#galaxy-upload-box').append(this.template_file(id)); + // add upload item + $(this.el).append(this.template_file(id)); + + // scroll to bottom + $(this.el).scrollTop($(this.el).prop('scrollHeight')); + + // access upload item + var it = this.get_upload_item(index); + + // fade in + it.fadeIn(); // update title - $('#galaxy-upload-file-' + index).find('.title').html(file.name); + it.find('.title').html(file.name); + // configure select field + it.find('#extension').select2( + { + placeholder: 'Auto-detect', + width: 'copy', + ajax: { + url: "http://www.weighttraining.com/sm/search", + dataType: 'jsonp', + quietMillis: 100, + data: function(term, page) + { + return { + types: ["exercise"], + limit: -1, + term: term + }; + }, + results: function(data, page) + { + return { results: data.results.exercise } + } + }, + formatResult: function(exercise) + { + return "<div class='select2-user-result'>" + exercise.term + "</div>"; + }, + formatSelection: function(exercise) + { + return exercise.term; + }, + initSelection : function (element, callback) + { + var elementText = $(element).attr('data-init-text'); + callback({"term":elementText}); + } + }); + + // add functionality to remove button + var self = this; + it.find('.remove').on('click', function() { self.event_remove (index) }); + // initialize progress this.event_progress(index, file, 0); - // update counter - this.file_counter++; - this.refresh(); + // update button status + this.modal.enable('Upload'); + this.modal.enable('Reset'); + }, + + // start + event_initialize : function(index, file, message) + { + // update on screen counter + this.button_show.number(message); + + // get element + var it = this.get_upload_item(index); + + // read in configuration + var data = { + source : "upload", + space_to_tabs : it.find('#space_to_tabs').is(':checked'), + extension : it.find('#extension').val() + } + + // return additional data to be send with file + return data; }, // progress event_progress : function(index, file, message) { - // get progress bar - var el = $('#galaxy-upload-file-' + index); + // get element + var it = this.get_upload_item(index); // get value var percentage = parseInt(message); // update progress - el.find('.progress').css({ width : percentage + '%' }); + it.find('.progress-bar').css({ width : percentage + '%' }); // update info - el.find('.info').html(percentage + '% of ' + this.size_to_string (file.size)); + it.find('.info').html(percentage + '% of ' + this.size_to_string (file.size)); }, // end event_success : function(index, file, message) - { + { + // get element + var it = this.get_upload_item(index); + + // update progress frame + it.addClass('panel-success'); + it.removeClass('panel-default'); + // update galaxy history Galaxy.currHistoryPanel.refresh(); - // update counter - this.file_counter--; - this.refresh(); + // make sure progress is shown correctly + this.event_progress(index, file, 100); + + // update on screen counter + this.button_show.number(''); }, // end event_error : function(index, file, message) { - // get file box - var el = $('#galaxy-upload-file-' + index); + // get element + var it = this.get_upload_item(index); // update progress frame - el.find('.progress-frame').addClass('failed'); + it.addClass('panel-danger'); + it.removeClass('panel-default'); - // update error message - el.find('.error').html("<strong>Failed:</strong> " + message); - - // update progress + // remove progress bar + it.find('.progress').remove(); + + // write error message + it.find('.error').html('<strong>Failed:</strong> ' + message); + + // make sure progress is shown correctly this.event_progress(index, file, 0); - // update counter - this.file_counter--; - this.refresh(); + // update on screen counter + this.button_show.number(''); + }, + + // start upload process + event_upload : function() + { + // hide configuration + $(this.el).find('.panel-body').hide(); + + // switch icon + $(this.el).find('.remove').each(function() + { + $(this).removeClass('fa-icon-trash'); + $(this).addClass('fa-icon-caret-down'); + }); + + // update button status + this.modal.disable('Upload'); + + // configure url + var current_history = Galaxy.currHistoryPanel.model.get('id'); + this.uploadbox.configure({url : galaxy_config.root + "api/histories/" + current_history + "/contents"}); + + // initiate upload procedure in plugin + this.uploadbox.upload(); + }, + + // remove all + event_reset : function() + { + // remove from screen + var panels = $(this.el).find('.panel'); + var self = this; + panels.fadeOut({complete: function() + { + // remove panels + panels.remove(); + + // show on screen info + self.uploadbox.info().fadeIn(); + }}); + + // update button status + this.modal.disable('Upload'); + this.modal.disable('Reset'); + + // remove from queue + this.uploadbox.reset(); + }, + + // remove item from upload list + event_remove : function(index) + { + // remove + var self = this; + var it = this.get_upload_item(index); + + // fade out and update button status + it.fadeOut({complete: function() + { + // remove from screen + it.remove(); + + // remove from queue + self.uploadbox.remove(index); + + // update reset button + if ($(self.el).find('.panel').length > 0) + self.modal.enable('Reset'); + else { + // disable reset button + self.modal.disable('Reset'); + + // show on screen info + self.uploadbox.info().fadeIn(); + } + + // update upload button + if (self.uploadbox.length() > 0) + self.modal.enable('Upload'); + else + self.modal.disable('Upload'); + }}); }, // show/hide upload frame @@ -126,14 +299,6 @@ // prevent default e.preventDefault(); - // wait for galaxy history panel (workaround due to the use of iframes) - if (!Galaxy.currHistoryPanel) - { - var self = this; - window.setTimeout(function() { self.event_show(e) }, 200) - return; - } - // create modal if (!this.modal) { @@ -142,44 +307,45 @@ this.modal = new mod_modal.GalaxyModal( { title : 'Upload files from your local drive', - body : this.template(), + body : this.template('upload-box'), buttons : { - 'Close' : function() {self.modal.hide()} + 'Select' : function() {self.uploadbox.select()}, + 'Upload' : function() {self.event_upload()}, + 'Reset' : function() {self.event_reset()}, + 'Close' : function() {self.modal.hide()} } }); - // get current history - var current_history = Galaxy.currHistoryPanel.model.get('id'); - + // set element + this.setElement('#upload-box'); + // file upload var self = this; - $('#galaxy-upload-box').uploadbox( + this.uploadbox = this.$el.uploadbox( { - url : galaxy_config.root + "api/histories/" + current_history + "/contents", dragover : self.event_mouseover, dragleave : self.event_mouseleave, - start : function(index, file, message) { self.event_start(index, file, message) }, + announce : function(index, file, message) { self.event_announce(index, file, message) }, + initialize : function(index, file, message) { return self.event_initialize(index, file, message) }, success : function(index, file, message) { self.event_success(index, file, message) }, progress : function(index, file, message) { self.event_progress(index, file, message) }, error : function(index, file, message) { self.event_error(index, file, message) }, - data : {source : "upload"} }); - // set element - this.setElement('#galaxy-upload-box'); + // update button status + this.modal.disable('Upload'); + this.modal.disable('Reset'); } - + // show modal this.modal.show(); }, - // update counter - refresh: function () + // get upload item + get_upload_item: function(index) { - if (this.file_counter > 0) - this.button_show.number(this.file_counter); - else - this.button_show.number(''); + // get element + return $(this.el).find('#upload-' + index); }, // to string @@ -197,21 +363,32 @@ }, // load html template - template: function() + template: function(id) { - return '<form id="galaxy-upload-box" class="galaxy-upload-box"></form>'; + return '<div id="' + id + '" class="upload-box"></div>'; }, // load html template template_file: function(id) { - return '<div id="' + id.substr(1) + '" class="file corner-soft shadow">' + - '<div class="title"></div>' + - '<div class="error"></div>' + - '<div class="progress-frame corner-soft">' + - '<div class="progress"></div>' + + return '<div id="' + id.substr(1) + '" class="panel panel-default">' + + '<div class="panel-heading">' + + '<h5 class="title"></h5>' + + '<h5 class="info"></h5>' + + '<div class="remove fa-icon-trash"></div>' + '</div>' + - '<div class="info"></div>' + + '<div class="panel-body">' + + '<div class="menu">' + + //'<input id="extension" type="hidden" width="10px"/> ' + + '<span><input id="space_to_tabs" type="checkbox">Convert spaces to tabs</input></span>' + + '</div>' + + '</div>' + + '<div class="panel-footer">' + + '<div class="progress">' + + '<div class="progress-bar progress-bar-success"></div>' + + '</div>' + + '<h6 class="error"></h6>' + + '</div>' + '</div>'; } }); diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/packed/galaxy.upload.js --- a/static/scripts/packed/galaxy.upload.js +++ b/static/scripts/packed/galaxy.upload.js @@ -1,1 +1,1 @@ -define(["utils/galaxy.css","galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(c,b,d){var a=Backbone.View.extend({modal:null,button_show:null,file_counter:0,initialize:function(){c.load_file("static/style/galaxy.upload.css");var e=this;this.button_show=new d.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(f){$("#galaxy-upload-box").addClass("galaxy-upload-highlight")},event_mouseleave:function(f){$("#galaxy-upload-box").removeClass("galaxy-upload-highlight")},event_start:function(e,f,g){var h="#galaxy-upload-file-"+e;$("#galaxy-upload-box").append(this.template_file(h));$("#galaxy-upload-file-"+e).find(".title").html(f.name);this.event_progress(e,f,0);this.file_counter++;this.refresh()},event_progress:function(f,g,i){var h=$("#galaxy-upload-file-"+f);var e=parseInt(i);h.find(".progress").css({width:e+"%"});h.find(".info").html(e+"% of "+this.size_to_string(g.size))},event_success:function(e,f,g){Galaxy.currHistoryPanel.refresh();this.file_counter--;this.refresh()},event_error:function(e,f,h){var g=$("#galaxy-upload-file-"+e);g.find(".progress-frame").addClass("failed");g.find(".error").html("<strong>Failed:</strong> "+h);this.event_progress(e,f,0);this.file_counter--;this.refresh()},event_show:function(h){h.preventDefault();if(!Galaxy.currHistoryPanel){var g=this;window.setTimeout(function(){g.event_show(h)},200);return}if(!this.modal){this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template()});var f=Galaxy.currHistoryPanel.model.get("id");var g=this;$("#galaxy-upload-box").uploadbox({url:galaxy_config.root+"api/histories/"+f+"/contents",dragover:g.event_mouseover,dragleave:g.event_mouseleave,start:function(e,i,j){g.event_start(e,i,j)},success:function(e,i,j){g.event_success(e,i,j)},progress:function(e,i,j){g.event_progress(e,i,j)},error:function(e,i,j){g.event_error(e,i,j)},data:{source:"upload"}});this.setElement("#galaxy-upload-box")}this.modal.show()},refresh:function(){if(this.file_counter>0){this.button_show.number(this.file_counter)}else{this.button_show.number("")}},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{e=e*10;f="b"}}}}return"<strong>"+(Math.round(e)/10)+"</strong> "+f},template:function(){return'<form id="galaxy-upload-box" class="galaxy-upload-box galaxy-corner"></form>'},template_file:function(e){return'<div id="'+e.substr(1)+'" class="galaxy-upload-file galaxy-corner-soft galaxy-shadow"><div class="title"></div><div class="error"></div><div class="progress-frame galaxy-corner-soft"><div class="progress"></div></div><div class="info"></div></div>'}});return{GalaxyUpload:a}}); \ No newline at end of file +define(["galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c){var a=Backbone.View.extend({modal:null,button_show:null,file_counter:0,initialize:function(){var d=this;this.button_show=new c.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){d.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(d){$("#galaxy-upload-box").addClass("highlight")},event_mouseleave:function(d){$("#galaxy-upload-box").removeClass("highlight")},event_start:function(d,e,f){var g="#galaxy-upload-file-"+d;$("#galaxy-upload-box").append(this.template_file(g));$("#galaxy-upload-file-"+d).find(".title").html(e.name);this.event_progress(d,e,0);this.file_counter++;this.refresh()},event_progress:function(e,f,h){var g=$("#galaxy-upload-file-"+e);var d=parseInt(h);g.find(".progress").css({width:d+"%"});g.find(".info").html(d+"% of "+this.size_to_string(f.size))},event_success:function(d,e,f){Galaxy.currHistoryPanel.refresh();this.file_counter--;this.refresh()},event_error:function(d,e,g){var f=$("#galaxy-upload-file-"+d);f.find(".progress-frame").addClass("failed");f.find(".error").html("<strong>Failed:</strong> "+g);this.event_progress(d,e,0);this.file_counter--;this.refresh()},event_show:function(g){g.preventDefault();if(!Galaxy.currHistoryPanel){var f=this;window.setTimeout(function(){f.event_show(g)},200);return}if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template(),buttons:{Close:function(){f.modal.hide()}}});var d=Galaxy.currHistoryPanel.model.get("id");var f=this;$("#galaxy-upload-box").uploadbox({url:galaxy_config.root+"api/histories/"+d+"/contents",dragover:f.event_mouseover,dragleave:f.event_mouseleave,start:function(e,h,i){f.event_start(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},data:{source:"upload"}});this.setElement("#galaxy-upload-box")}this.modal.show()},refresh:function(){if(this.file_counter>0){this.button_show.number(this.file_counter)}else{this.button_show.number("")}},size_to_string:function(d){var e="";if(d>=100000000000){d=d/100000000000;e="TB"}else{if(d>=100000000){d=d/100000000;e="GB"}else{if(d>=100000){d=d/100000;e="MB"}else{if(d>=100){d=d/100;e="KB"}else{d=d*10;e="b"}}}}return"<strong>"+(Math.round(d)/10)+"</strong> "+e},template:function(){return'<form id="galaxy-upload-box" class="galaxy-upload-box"></form>'},template_file:function(d){return'<div id="'+d.substr(1)+'" class="file corner-soft shadow"><div class="title"></div><div class="error"></div><div class="progress-frame corner-soft"><div class="progress"></div></div><div class="info"></div></div>'}});return{GalaxyUpload:a}}); \ No newline at end of file diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(f,b,c,a){var d=this;$(f).each(function(){var g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/delete_icon.png").click(function(){$.each(g.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(this).offset().top-2,left:$(this).offset().left-h.width(),"padding-right":$(this).width()}).show()}});d.input_terminals[b]=g})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions,f.multiple);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions,j.multiple);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b=false;var a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if($.isArray(h)){$.each(h,function(m,k){var n=wf.nodes[k.id];var o=new Connector();o.connect(n.output_terminals[k.output_name],d.input_terminals[i]);o.redraw()})}else{var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_config.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",galaxy_config.root+"static/images/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",galaxy_config.root+"static/images/delete_icon_dark.png")},function(){$(this).attr("src",galaxy_config.root+"static/images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(f,b,c,a){var d=this;$(f).each(function(){var g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='button'></div>").append($("<div/>").addClass("fa-icon-button fa-icon-remove").click(function(){$.each(g.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(this).offset().top-2,left:$(this).offset().left-h.width(),"padding-right":$(this).width()}).show()}});d.input_terminals[b]=g})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions,f.multiple);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions,j.multiple);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b=false;var a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if($.isArray(h)){$.each(h,function(m,k){var n=wf.nodes[k.id];var o=new Connector();o.connect(n.output_terminals[k.output_name],d.input_terminals[i]);o.redraw()})}else{var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_config.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<div>").addClass("fa-icon-button fa-icon-remove").click(function(b){g.destroy()}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -1,5 +1,5 @@ /* - galaxy upload lib v1.0 - uses FileReader, FormData and XMLHttpRequest + galaxy upload lib - uses FileReader, FormData and XMLHttpRequest */ ;(function($) { @@ -11,67 +11,71 @@ { url : '', paramname : 'content', - maxfilesize : 2048, - data : {}, + maxfilesize : 250, dragover : function() {}, dragleave : function() {}, + announce : function() {}, initialize : function() {}, - start : function() {}, progress : function() {}, success : function() {}, error : function(index, file, message) { alert(message); }, error_browser : "Your browser does not support drag-and-drop file uploads.", - error_filesize : "This file is too large. Please use an FTP client to upload it.", - error_default : "The upload failed. Please make sure the file is available and accessible.", - text_default : "Drag&drop files here or click to browse your local drive.", - text_degrade : "Click here to browse your local drive. <br><br>Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+." + error_filesize : "This file is too large (>250MB). Please use an FTP client to upload it.", + error_default : "Please make sure the file is available.", + text_default : "Drag&drop files into this box or click 'Select' to select files!", + text_degrade : "Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+." } - // global file queue - var queue = []; + // options + var opts = {}; + + // file queue + var queue = {}; - // global counter for file being currently processed - var queue_index = -1; + // counter for file being currently processed + var queue_index = 0; - // global queue status + // queue length + var queue_length = 0; + + // indicates if queue is currently running var queue_status = false; + // element + var el = null; + // attach to element $.fn.uploadbox = function(options) { // parse options - var opts = $.extend({}, default_opts, options); + opts = $.extend({}, default_opts, options); // compatibility var mode = window.File && window.FileReader && window.FormData && window.XMLHttpRequest; + // element + el = this; + // append upload button - this.append('<input id="uploadbox_input" type="file" style="display: none" multiple>'); - this.append('<div id="uploadbox_info"></div>'); + el.append('<input id="uploadbox_input" type="file" style="display: none" multiple>'); + el.append('<div id="uploadbox_info"></div>'); // set info text if (mode) - this.find('#uploadbox_info').html(opts.text_default); + el.find('#uploadbox_info').html(opts.text_default); else - this.find('#uploadbox_info').html(opts.text_degrade); + el.find('#uploadbox_info').html(opts.text_degrade); // attach events - this.on('drop', drop); - this.on('dragover', dragover); - this.on('dragleave', dragleave); - - // attach click event - this.on('click', function(e) - { - e.stopPropagation(); - $('#uploadbox_input').trigger(e); - }); + el.on('drop', drop); + el.on('dragover', dragover); + el.on('dragleave', dragleave); // attach change event $('#uploadbox_input').change(function(e) { - var files = e.target.files; - upload(files); + // add files to queue + add(e.target.files); }); // drop event @@ -81,11 +85,8 @@ if(!e.dataTransfer) return; - // get files from event - var files = e.dataTransfer.files; - - // start upload - upload(files); + // add files to queue + add(e.dataTransfer.files); // prevent default e.preventDefault(); @@ -98,14 +99,14 @@ function dragover(e) { e.preventDefault(); - opts.dragover.call(this, e); + opts.dragover.call(e); } // drag leave function dragleave(e) { e.stopPropagation(); - opts.dragleave.call(this, e); + opts.dragleave.call(e); } // progress @@ -117,39 +118,61 @@ } // respond to an upload request - function upload(files) + function add(files) { - // get current queue size - var queue_sofar = queue.length; + // add new files to queue + for (var i = 0; i < files.length; i++) + { + // new identifier + var index = String(++queue_index); - // add new files to queue - for (var index = 0; index < files.length; index++) - queue.push(files[index]); + // add to queue + queue[index] = files[i]; - // tell client about new uploads - for (var index = queue_sofar; index < queue.length; index++) - opts.start(index, queue[index], ""); + // increase counter + queue_length++; - // initiate processing loop if process loop is not running already - if (!queue_status) - process(); + // announce + opts.announce(index, queue[index], ""); + } } + // remove entry from queue + function remove(index) + { + if (queue[index]) + { + // remove from queue + delete queue[index]; + + // update counter + queue_length--; + } + } + // process an upload, recursive function process() { - // check if for files - if (queue_index + 1 == queue.length) + // get an identifier from the queue + var index = -1; + for (var key in queue) { - queue_status = false; - return; + index = key; + break; } - // set status - queue_status = true; + // validate + if (queue_length == 0) + return; - // identify current index - var index = ++queue_index; + // get current file from queue + var file = queue[index]; + + // remove from queue + remove(index) + + // start + var data = opts.initialize(index, file, length); // add file to queue try @@ -158,50 +181,45 @@ var reader = new FileReader(); // identify maximum file size - var file = queue[index]; var filesize = file.size; var maxfilesize = 1048576 * opts.maxfilesize; - + // set index reader.index = index; if (filesize < maxfilesize) { - // link loadend is always called at the end - reader.onloadend = function(e) + // link load + reader.onload = function(e) { - send(index, file) + send(index, file, data) }; // link error reader.onerror = function(e) { - opts.error(index, file, opts.error_default); - queue_status = false; + error(index, file, opts.error_default); }; // read data reader.readAsDataURL(file); } else { // skip file - opts.error(index, file, opts.error_filesize); - - // restart process - process(); + error(index, file, opts.error_filesize); } } catch (err) { // parse error - opts.error(index, file, err); + error(index, file, err); } } // send file - function send (index, file) + function send (index, file, data) { // construct form data var formData = new FormData(); - for (var key in opts.data) - formData.append(key, opts.data[key]); + for (var key in data) + formData.append(key, data[key]); formData.append(opts.paramname, file, file.name); // prepare request @@ -237,22 +255,94 @@ // pass any error to the error option if (xhr.status < 200 || xhr.status > 299) { + // format error + var text = xhr.statusText; + if (!xhr.statusText) + text = opts.error_default; + // request error - opts.error(index, file, xhr.statusText + " (Server Code " + xhr.status + ")"); - - // reset status - queue_status = false; - } else { + error(index, file, text + " (Server Code " + xhr.status + ")"); + } else // parse response - opts.success(index, file, response); - - // upload next file - process(); - } + success(index, file, response); } } - // return - return this; + // success + function success (index, file, msg) + { + // parse message + opts.success(index, file, msg); + + // restart process after success + process(); + } + + // error + function error (index, file, err) + { + // parse error + opts.error(index, file, err); + + // restart process after error + process(); + } + + /* + public interface + */ + + // open file browser for selection + function select() + { + $('#uploadbox_input').trigger('click'); + } + + // remove all entries from queue + function reset(index) + { + for (index in queue) + remove(index); + } + + // initiate upload process + function upload() + { + if (!queue_status) + process(); + } + + // current queue length + function length() + { + return queue_length; + } + + // set options + function configure(options) + { + // update current configuration + opts = $.extend({}, opts, options); + + // return new configuration + return opts; + } + + // visibility of on screen information + function info() + { + return el.find('#uploadbox_info'); + } + + // export functions + return { + 'select' : select, + 'remove' : remove, + 'upload' : upload, + 'reset' : reset, + 'length' : length, + 'configure' : configure, + 'info' : info + }; } })(jQuery); \ No newline at end of file diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1123,15 +1123,12 @@ .galaxy-frame .frame .f-close{right:5px;top:1px} .galaxy-frame .frame .f-pin{left:6px;top:1px} .galaxy-frame .frame .f-resize{background:#fff;width:16px;height:16px;color:#2c3143;right:0px;bottom:0px;text-align:center;line-height:16px;border:0px} -.galaxy-upload-box{width:100%;height:200px;max-height:200px;padding:10px 0px 0px 0px;text-align:center;cursor:pointer;overflow:scroll;font-size:12px;line-height:1.428571429;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf}.galaxy-upload-box .corner-soft{-moz-border-radius:3px;border-radius:3px} -.galaxy-upload-box .shadow{-webkit-box-shadow:0 0 2px rgba(0,0,0,0.3)} -.galaxy-upload-box .highlight{border:1px dashed #333} -.galaxy-upload-box .file{position:relative;margin:5px 20px 5px 20px;border:1px solid #bfbfbf;color:#333}.galaxy-upload-box .file .title{margin:3px 130px 0px 5px;text-align:left;overflow:hidden;border:0px} -.galaxy-upload-box .file .progress-frame{border:0px;margin:0px 5px 3px 5px;height:7px;background:#bfbfbf} -.galaxy-upload-box .file .progress{background:#5cb85c;height:100%;width:0%} -.galaxy-upload-box .file .failed{background:#d9534f} -.galaxy-upload-box .file .error{font-size:11px;text-align:left;overflow:hidden;margin:0px 5px 0px 5px} -.galaxy-upload-box .file .info{position:absolute;top:4px;right:5px;font-size:11px;text-align:right;overflow:hidden;max-width:100px;max-height:12px} +.upload-box{width:100%;height:250px;max-height:250px;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:20px}.upload-box .panel{display:none}.upload-box .panel .panel-heading{position:relative;height:19px;padding:5px}.upload-box .panel .panel-heading .title{position:absolute;top:2px;font-weight:normal;text-align:left;margin:0px;max-width:300px;overflow:hidden} +.upload-box .panel .panel-heading .info{position:absolute;top:3px;font-weight:normal;right:20px;text-align:right;margin:0px} +.upload-box .panel .panel-heading .remove{position:absolute;cursor:pointer;top:0px;right:3px} +.upload-box .panel .panel-body{position:relative;padding:5px} +.upload-box .panel .panel-footer{position:relative;height:20px;padding:0px}.upload-box .panel .panel-footer .progress{height:10px;margin:5px} +.upload-box .panel .panel-footer .error{font-weight:normal;margin:2px} .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:before,.clear:after{content:" ";display:table;} @@ -1392,9 +1389,9 @@ div.historyItem-setting_metadata{background:#ffc}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif)} div.historyItem-upload{background:#a6e4f7}div.historyItem-upload .state-icon{background-image:url(data_upload.gif)} div.historyItem-queued{background:#eee}div.historyItem-queued .state-icon{background-image:url(sprite-history-states.png);background-position:0px -45px;width:15px;height:15px;height:15px} -div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60} -div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-paused .state-icon:before{content:"\f04c"} -div.historyItem-new .state-icon{font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-new .state-icon:before{content:"\f071"} +div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60}div.historyItem-noPermission .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-noPermission .state-icon:before{content:"\f05e"} +div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-paused .state-icon:before{content:"\f04c"} +div.historyItem-new .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-new .state-icon:before{content:"\f071"} div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important} div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px} div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px} diff -r 23abd7b603c873e6e59fe0f73e53210cf45aaa72 -r 66d484a18d198725ab5f388d4e538ac86d9f081b static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -1509,11 +1509,19 @@ filter: alpha(opacity=60); -moz-opacity: .60; opacity: .60; + .state-icon { + line-height: 16px; + .fa-icon(); + &:before { + content: "\f05e"; + } + } } div.historyItem-paused { background: @state-paused-bg; .state-icon { + line-height: 16px; .fa-icon(); &:before { content: "\f04c"; @@ -1523,6 +1531,7 @@ div.historyItem-new { .state-icon { + line-height: 16px; .fa-icon(); &:before { content: "\f071"; 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.

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commit/galaxy-central: carlfeberhard: Style: add icon to inaccessible hda state, tweak vertical align of fa-icon state icons
by commits-noreply＠bitbucket.org 20 Sep '13

20 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/96c27525741b/ Changeset: 96c27525741b User: carlfeberhard Date: 2013-09-20 22:58:32 Summary: Style: add icon to inaccessible hda state, tweak vertical align of fa-icon state icons Affected #: 2 files diff -r c23fb89215ce1d36f23d4806fd04a8153fe6fbe6 -r 96c27525741b7d8773ade063e9cd829b03be211f static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1388,9 +1388,9 @@ div.historyItem-setting_metadata{background:#ffc}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif)} div.historyItem-upload{background:#a6e4f7}div.historyItem-upload .state-icon{background-image:url(data_upload.gif)} div.historyItem-queued{background:#eee}div.historyItem-queued .state-icon{background-image:url(sprite-history-states.png);background-position:0px -45px;width:15px;height:15px;height:15px} -div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60} -div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-paused .state-icon:before{content:"\f04c"} -div.historyItem-new .state-icon{font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-new .state-icon:before{content:"\f071"} +div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60}div.historyItem-noPermission .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-noPermission .state-icon:before{content:"\f05e"} +div.historyItem-paused{background:#d9edf7}div.historyItem-paused .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-paused .state-icon:before{content:"\f04c"} +div.historyItem-new .state-icon{line-height:16px;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}div.historyItem-new .state-icon:before{content:"\f071"} div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important} div.historyItemButtons{float:right}div.historyItemButtons .icon-button.display{background-image:url(sprite-history-buttons.png);background-position:0px -48px;width:16px;height:16px} div.historyItemButtons .icon-button.display:hover{background-image:url(sprite-history-buttons.png);background-position:0px -64px;width:16px;height:16px} diff -r c23fb89215ce1d36f23d4806fd04a8153fe6fbe6 -r 96c27525741b7d8773ade063e9cd829b03be211f static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -1509,11 +1509,19 @@ filter: alpha(opacity=60); -moz-opacity: .60; opacity: .60; + .state-icon { + line-height: 16px; + .fa-icon(); + &:before { + content: "\f05e"; + } + } } div.historyItem-paused { background: @state-paused-bg; .state-icon { + line-height: 16px; .fa-icon(); &:before { content: "\f04c"; @@ -1523,6 +1531,7 @@ div.historyItem-new { .state-icon { + line-height: 16px; .fa-icon(); &:before { content: "\f071"; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: HDA API: re-add accessibility check
by commits-noreply＠bitbucket.org 20 Sep '13

20 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c23fb89215ce/ Changeset: c23fb89215ce User: carlfeberhard Date: 2013-09-20 22:12:53 Summary: HDA API: re-add accessibility check Affected #: 1 file diff -r 3fc486ee887aec89a75097477ba7a4acff0ced1b -r c23fb89215ce1d36f23d4806fd04a8153fe6fbe6 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -587,8 +587,10 @@ hda_dict[ 'api_type' ] = "file" # Add additional attributes that depend on trans can hence must be added here rather than at the model level. - - #NOTE: access is an expensive operation - removing it and adding the precondition of access is already checked + can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) + can_access_hda = ( trans.user_is_admin() or can_access_hda ) + if not can_access_hda: + return self.get_inaccessible_hda_dict( trans, hda ) hda_dict[ 'accessible' ] = True # ---- return here if deleted AND purged OR can't access @@ -634,6 +636,18 @@ return trans.security.encode_dict_ids( hda_dict ) + def get_inaccessible_hda_dict( self, trans, hda ): + return trans.security.encode_dict_ids({ + 'id' : hda.id, + 'history_id': hda.history.id, + 'hid' : hda.hid, + 'name' : hda.name, + 'state' : hda.state, + 'deleted' : hda.deleted, + 'visible' : hda.visible, + 'accessible': False + }) + def get_hda_dict_with_error( self, trans, hda, error_msg='' ): return trans.security.encode_dict_ids({ 'id' : hda.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: carlfeberhard: Saved histories: fix new history creation when deleting a current, empty history
by commits-noreply＠bitbucket.org 20 Sep '13

20 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3fc486ee887a/ Changeset: 3fc486ee887a User: carlfeberhard Date: 2013-09-20 20:46:26 Summary: Saved histories: fix new history creation when deleting a current, empty history Affected #: 2 files diff -r d4c6a250afd03a942e70f04ee7da8335dfea476b -r 3fc486ee887aec89a75097477ba7a4acff0ced1b lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -309,7 +309,6 @@ # If deleting the current history, make a new current. if history == trans.get_history(): deleted_current = True - trans.get_or_create_default_history() trans.log_event( "History (%s) marked as deleted" % history.name ) n_deleted += 1 if purge and trans.app.config.allow_user_dataset_purge: @@ -339,6 +338,8 @@ part += " but the datasets were not removed from disk because that feature is not enabled in this Galaxy instance" message_parts.append( "%s. " % part ) if deleted_current: + #note: this needs to come after commits above or will use an empty history that was deleted above + trans.get_or_create_default_history() message_parts.append( "Your active history was deleted, a new empty history is now active. " ) status = INFO return ( status, " ".join( message_parts ) ) diff -r d4c6a250afd03a942e70f04ee7da8335dfea476b -r 3fc486ee887aec89a75097477ba7a4acff0ced1b test/functional/test_get_data.py --- a/test/functional/test_get_data.py +++ b/test/functional/test_get_data.py @@ -22,7 +22,7 @@ """ # in order to remove a lot of boiler plate - and not have cascading errors history = get_latest_history_for_user( user ) - self.delete_current_history() + self.delete_history( id=self.security.encode_id( history.id ) ) self.is_history_empty() return get_latest_history_for_user( user ) 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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galaxy-commits September 2013