June 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: guerler: scratchbook: hide on disable
by commits-noreply＠bitbucket.org 01 Jul '13

01 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9ddb3130b98d/ Changeset: 9ddb3130b98d User: guerler Date: 2013-07-01 01:29:04 Summary: scratchbook: hide on disable Affected #: 2 files diff -r 27a8341736452288e7324559ff74df38abaa3931 -r 9ddb3130b98d450ca2be3f447f171ff5f192b8a1 static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -123,8 +123,8 @@ this.event_initialize(); // add - $(".galaxy-frame-active").tooltip({title: "Enable/Disable Scratchbook"}); - $(".galaxy-frame-load").tooltip({title: "Show/Hide Scratchbook"}); + //$(".galaxy-frame-active").tooltip({title: "Enable/Disable Scratchbook"}); + //$(".galaxy-frame-load").tooltip({title: "Show/Hide Scratchbook"}); // catch window resize event var self = this; @@ -218,7 +218,7 @@ if (this.event.type === null) return; - // prevent text selection + // prevent e.preventDefault(); // identify frame @@ -340,6 +340,9 @@ if (this.event.type !== null) return; + // prevent + e.preventDefault(); + // get frame var frame = this.event_get_frame(e.target); var self = this; @@ -375,7 +378,7 @@ if (this.event.type !== null) return; - // prevent text selection + // prevent e.preventDefault(); // get frame @@ -413,7 +416,7 @@ if (this.event.type !== null) return; - // prevent text selection + // prevent e.preventDefault(); // load panel @@ -427,7 +430,7 @@ if (this.event.type !== null) return; - // prevent text selection + // prevent e.preventDefault(); // load panel @@ -441,7 +444,7 @@ if (this.event.type !== null || !this.visible) return; - // prevent text selection + // prevent e.preventDefault(); // get wheel delta @@ -458,7 +461,7 @@ if (this.event.type !== null) return; - // prevent text selection + // prevent e.preventDefault(); // scroll up @@ -472,7 +475,7 @@ if (this.event.type !== null) return; - // prevent text selection + // prevent e.preventDefault(); // scroll down @@ -774,6 +777,10 @@ // untoggle $(".galaxy-frame-active .icon").removeClass("f-toggle"); + + // hide panel + if (this.visible) + this.panel_show_hide(); } else { // activate this.active = true; @@ -789,9 +796,6 @@ // adds and displays a new frame/window frame_new: function(options) { - // trigger mouse leave - $(document).trigger('mouseleave'); - // validate if (!this.active) { diff -r 27a8341736452288e7324559ff74df38abaa3931 -r 9ddb3130b98d450ca2be3f447f171ff5f192b8a1 static/style/blue/galaxy.frame.css --- a/static/style/blue/galaxy.frame.css +++ b/static/style/blue/galaxy.frame.css @@ -95,7 +95,7 @@ z-index : 34010; position : absolute; top : 6px; - right : 165px; + right : 170px; cursor : pointer; color : #BCC800; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: GCC2013 Advanced Tool and Data Source Configuration workshop: "The test framework uses tool_conf.xml.sample for reasons unknown and lost to time."
by commits-noreply＠bitbucket.org 30 Jun '13

30 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/27a834173645/ Changeset: 27a834173645 User: natefoo Date: 2013-06-30 16:04:58 Summary: GCC2013 Advanced Tool and Data Source Configuration workshop: "The test framework uses tool_conf.xml.sample for reasons unknown and lost to time." Use tool_conf.xml for running functional tests, rather than tool_conf.xml.sample. Affected #: 3 files diff -r 9c4b7f8d2f980ff69a0e7947c9360dd7154c65eb -r 27a8341736452288e7324559ff74df38abaa3931 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -65,6 +65,7 @@ " SAMPLES=" +tool_conf.xml.sample datatypes_conf.xml.sample universe_wsgi.ini.sample tool_data_table_conf.xml.sample diff -r 9c4b7f8d2f980ff69a0e7947c9360dd7154c65eb -r 27a8341736452288e7324559ff74df38abaa3931 run_functional_tests.sh --- a/run_functional_tests.sh +++ b/run_functional_tests.sh @@ -51,4 +51,3 @@ fi echo "'run_functional_tests.sh help' for help" -echo "Note: galaxy test framework uses tool_conf.xml.sample, not tool_conf.xml" diff -r 9c4b7f8d2f980ff69a0e7947c9360dd7154c65eb -r 27a8341736452288e7324559ff74df38abaa3931 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -129,7 +129,7 @@ # Exclude all files except test_toolbox.py. ignore_files = ( re.compile( r'^test_[adghlmsu]*' ), re.compile( r'^test_ta*' ) ) else: - tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml.sample' ) + tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml' ) galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', default_galaxy_test_file_dir ) if not os.path.isabs( galaxy_test_file_dir ): galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) 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: guerler: Scratchbook: Improve event handling
by commits-noreply＠bitbucket.org 30 Jun '13

30 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9c4b7f8d2f98/ Changeset: 9c4b7f8d2f98 User: guerler Date: 2013-06-30 09:27:29 Summary: Scratchbook: Improve event handling Affected #: 1 file diff -r d748871f160f9bf1b13df57d34a9f3cf13a9f947 -r 9c4b7f8d2f980ff69a0e7947c9360dd7154c65eb static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -375,6 +375,9 @@ if (this.event.type !== null) return; + // prevent text selection + e.preventDefault(); + // get frame var frame = this.event_get_frame(e.target); @@ -404,23 +407,29 @@ }, // show/hide panel - event_panel_load: function () + event_panel_load: function (e) { // check if (this.event.type !== null) return; + // prevent text selection + e.preventDefault(); + // load panel this.panel_show_hide(); }, // activate/disable panel - event_panel_active: function () + event_panel_active: function (e) { // check if (this.event.type !== null) return; + // prevent text selection + e.preventDefault(); + // load panel this.panel_active_disable(); }, @@ -432,6 +441,9 @@ if (this.event.type !== null || !this.visible) return; + // prevent text selection + e.preventDefault(); + // get wheel delta var delta = e.originalEvent.detail ? e.originalEvent.detail : e.originalEvent.wheelDelta / -3; @@ -440,23 +452,29 @@ }, // scroll up - event_panel_scroll_up: function() + event_panel_scroll_up: function(e) { // check if (this.event.type !== null) return; + // prevent text selection + e.preventDefault(); + // scroll up this.panel_scroll(-this.options.scroll); }, // scroll down - event_panel_scroll_down: function() + event_panel_scroll_down: function(e) { // check if (this.event.type !== null) return; + // prevent text selection + e.preventDefault(); + // scroll down this.panel_scroll(this.options.scroll); }, @@ -771,6 +789,9 @@ // adds and displays a new frame/window frame_new: function(options) { + // trigger mouse leave + $(document).trigger('mouseleave'); + // validate if (!this.active) { 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: guerler: Fix event handling, tooltip
by commits-noreply＠bitbucket.org 30 Jun '13

30 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d748871f160f/ Changeset: d748871f160f User: guerler Date: 2013-06-30 08:34:19 Summary: Fix event handling, tooltip Affected #: 1 file diff -r 019ad31c3c2502005846dadc5c0457bbb6f80712 -r d748871f160f9bf1b13df57d34a9f3cf13a9f947 static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -91,8 +91,8 @@ $(this.el).append(this.frame_template_menu()); // load load button - $(this.el_header).append(this.frame_template_load()); - + $(this.el_header).append(this.frame_template_header()); + // // define shadow frame // @@ -121,7 +121,11 @@ // link events this.event_initialize(); - + + // add + $(".galaxy-frame-active").tooltip({title: "Enable/Disable Scratchbook"}); + $(".galaxy-frame-load").tooltip({title: "Show/Hide Scratchbook"}); + // catch window resize event var self = this; $(window).resize(function () @@ -162,7 +166,6 @@ {*/ this.events = { // global page events - 'mousedown' : 'event_frame_mouse_down', 'mousemove' : 'event_frame_mouse_move', 'mouseup' : 'event_frame_mouse_up', 'mouseleave' : 'event_frame_mouse_up', @@ -170,13 +173,14 @@ 'DOMMouseScroll' : 'event_panel_scroll', // events fixed to elements - 'mousedown .f-close' : 'event_frame_close', - 'mousedown .f-pin' : 'event_frame_lock', + 'mousedown .galaxy-frame' : 'event_frame_mouse_down', 'mousedown .galaxy-frame-active' : 'event_panel_active', 'mousedown .galaxy-frame-load' : 'event_panel_load', 'mousedown .galaxy-frame-background' : 'event_panel_load', 'mousedown .galaxy-frame-scroll-up' : 'event_panel_scroll_up', - 'mousedown .galaxy-frame-scroll-down' : 'event_panel_scroll_down' + 'mousedown .galaxy-frame-scroll-down' : 'event_panel_scroll_down', + 'mousedown .f-close' : 'event_frame_close', + 'mousedown .f-pin' : 'event_frame_lock' }; /*} else { this.events = { @@ -197,9 +201,6 @@ // drag start event_frame_mouse_down: function (e) { - // prevent text selection - e.preventDefault(); - // skip if event is already active if (this.event.type !== null) return; @@ -212,11 +213,14 @@ // check for resize event if ($(e.target).hasClass('f-resize')) this.event.type = 'resize'; - + // skip if no event has to be handled if (this.event.type === null) return; - + + // prevent text selection + e.preventDefault(); + // identify frame this.event.target = this.event_get_frame(e.target); @@ -1044,13 +1048,13 @@ }, // fill load button template - frame_template_load: function() + frame_template_header: function() { return '<div class="galaxy-frame-load f-corner">' + '<div class="number f-corner">0</div>' + '<div class="icon fa-icon-2x"></div>' + - '</div>'+ - '<div class="galaxy-frame-active f-corner">' + + '</div>' + + '<div class="galaxy-frame-active f-corner" style="position: absolute; top: 8px;">' + '<div class="icon fa-icon-2x fa-icon-th"></div>' + '</div>'; }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 30 Jun '13

30 Jun '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bf69f8db6dbb/ Changeset: bf69f8db6dbb Branch: stable User: dannon Date: 2013-05-30 17:23:29 Summary: Add specific ami functionality (via GET param) to cloudlaunch. Prevent existing instance selection when using a share string. Affected #: 2 files diff -r be47a7f089f91c4b72c0c5f89182a62589389e1f -r bf69f8db6dbb1fd7c6ec16fb97b2e7c763f2ab55 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -35,8 +35,8 @@ BaseUIController.__init__(self, app) @web.expose - def index(self, trans, share_string=None): - return trans.fill_template("cloud/index.mako", default_keypair = DEFAULT_KEYPAIR, share_string=share_string) + def index(self, trans, share_string=None, ami=None): + return trans.fill_template("cloud/index.mako", default_keypair = DEFAULT_KEYPAIR, share_string=share_string, ami=ami) @web.expose def get_account_info(self, trans, key_id, secret, **kwargs): @@ -92,7 +92,7 @@ return to_json_string(account_info) @web.expose - def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, zone=None, **kwargs): + def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=DEFAULT_AMI, zone=None, **kwargs): ec2_error = None try: # Create security group & key pair used when starting an instance @@ -113,11 +113,14 @@ user_provided_data['password'] = password if share_string: user_provided_data['share_string'] = share_string + rs = run_instance(ec2_conn=ec2_conn, + image_id = ami, user_provided_data=user_provided_data, key_name=kp_name, security_groups=[sg_name], - placement=zone) + placement=zone + ) if rs: instance = rs.instances[0] ct = 0 @@ -266,7 +269,7 @@ return None, None return kp.name, kp.material -def run_instance(ec2_conn, user_provided_data, image_id=DEFAULT_AMI, +def run_instance(ec2_conn, user_provided_data, image_id=None, kernel_id=None, ramdisk_id=None, key_name=DEFAULT_KEYPAIR, placement=None, security_groups=['CloudMan']): """ Start an instance. If instance start was OK, return the ResultSet object diff -r be47a7f089f91c4b72c0c5f89182a62589389e1f -r bf69f8db6dbb1fd7c6ec16fb97b2e7c763f2ab55 templates/webapps/galaxy/cloud/index.mako --- a/templates/webapps/galaxy/cloud/index.mako +++ b/templates/webapps/galaxy/cloud/index.mako @@ -202,12 +202,14 @@ </div><div id="hidden_options"> + %if not share_string: <div id='existing_instance_wrapper' style="display:none;" class="form-row"><label for="id_existing_instance">Instances in your account</label><select name="existing_instance" id="id_existing_instance"></select><input id='id_zone' type='hidden' name='zone' value=''/></div> + %endif <div id='cluster_name_wrapper' class="form-row"><label for="id_cluster_name">Cluster Name</label><input type="text" size="40" class="text-and-autocomplete-select" name="cluster_name" id="id_cluster_name"/><br/> @@ -244,6 +246,10 @@ </div> %endif + %if ami: + <input type='hidden' name='ami' value='${ami}'/> + %endif + <div class="form-row"><label for="id_instance_type">Instance Type</label><select name="instance_type" id="id_instance_type"> https://bitbucket.org/galaxy/galaxy-central/commits/51c57629182d/ Changeset: 51c57629182d Branch: stable User: dannon Date: 2013-05-31 17:55:46 Summary: Add bucket_default userData (param-based only) to cloudlaunch. Affected #: 2 files diff -r bf69f8db6dbb1fd7c6ec16fb97b2e7c763f2ab55 -r 51c57629182d2a77e5ddfe2742919a2412d42898 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -35,8 +35,12 @@ BaseUIController.__init__(self, app) @web.expose - def index(self, trans, share_string=None, ami=None): - return trans.fill_template("cloud/index.mako", default_keypair = DEFAULT_KEYPAIR, share_string=share_string, ami=ami) + def index(self, trans, share_string=None, ami=None, bucket_default = None): + return trans.fill_template("cloud/index.mako", + default_keypair = DEFAULT_KEYPAIR, + share_string=share_string, + ami=ami, + bucket_default=bucket_default) @web.expose def get_account_info(self, trans, key_id, secret, **kwargs): @@ -92,7 +96,7 @@ return to_json_string(account_info) @web.expose - def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=DEFAULT_AMI, zone=None, **kwargs): + def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=DEFAULT_AMI, zone=None, bucket_default=None, **kwargs): ec2_error = None try: # Create security group & key pair used when starting an instance @@ -113,6 +117,8 @@ user_provided_data['password'] = password if share_string: user_provided_data['share_string'] = share_string + if bucket_default: + user_provided_data['bucket_default'] = bucket_default rs = run_instance(ec2_conn=ec2_conn, image_id = ami, diff -r bf69f8db6dbb1fd7c6ec16fb97b2e7c763f2ab55 -r 51c57629182d2a77e5ddfe2742919a2412d42898 templates/webapps/galaxy/cloud/index.mako --- a/templates/webapps/galaxy/cloud/index.mako +++ b/templates/webapps/galaxy/cloud/index.mako @@ -250,6 +250,10 @@ <input type='hidden' name='ami' value='${ami}'/> %endif + %if bucket_default: + <input type='hidden' name='bucket_default' value='${bucket_default}'/> + %endif + <div class="form-row"><label for="id_instance_type">Instance Type</label><select name="instance_type" id="id_instance_type"> https://bitbucket.org/galaxy/galaxy-central/commits/64bc5a64b19e/ Changeset: 64bc5a64b19e Branch: stable User: dannon Date: 2013-06-30 07:26:31 Summary: Make default ami configurable via universe Affected #: 3 files diff -r 51c57629182d2a77e5ddfe2742919a2412d42898 -r 64bc5a64b19ea3161f95e74702cc1d44fb50e4e3 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -251,6 +251,7 @@ self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) # Cloud configuration options self.enable_cloud_launch = string_as_bool( kwargs.get( 'enable_cloud_launch', False ) ) + self.cloudlaunch_default_ami = kwargs.get( 'cloudlaunch_default_ami', 'ami-118bfc78' ) # Galaxy messaging (AMQP) configuration options self.amqp = {} try: diff -r 51c57629182d2a77e5ddfe2742919a2412d42898 -r 64bc5a64b19ea3161f95e74702cc1d44fb50e4e3 lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -26,7 +26,6 @@ PKEY_PREFIX = 'gxy_pkey' DEFAULT_KEYPAIR = 'cloudman_keypair' -DEFAULT_AMI = 'ami-da58aab3' class CloudController(BaseUIController): @@ -96,7 +95,7 @@ return to_json_string(account_info) @web.expose - def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=DEFAULT_AMI, zone=None, bucket_default=None, **kwargs): + def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, ami=None, zone=None, bucket_default=None, **kwargs): ec2_error = None try: # Create security group & key pair used when starting an instance @@ -120,6 +119,9 @@ if bucket_default: user_provided_data['bucket_default'] = bucket_default + if not ami: + ami = trans.app.config.cloudlaunch_default_ami + rs = run_instance(ec2_conn=ec2_conn, image_id = ami, user_provided_data=user_provided_data, diff -r 51c57629182d2a77e5ddfe2742919a2412d42898 -r 64bc5a64b19ea3161f95e74702cc1d44fb50e4e3 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -316,9 +316,10 @@ # Note that this requires java > 1.4 for executing yuicompressor.jar #pack_scripts = False -# Enable Cloud Launch +# Cloud Launch #enable_cloud_launch = False +#cloudlaunch_default_ami = ami-118bfc78 # -- Advanced proxy features Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 28 Jun '13

28 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/be47a7f089f9/ Changeset: be47a7f089f9 Branch: stable User: jgoecks Date: 2013-06-28 21:26:27 Summary: Enhance multi-value select parsing to split on all whitespace; this fixes a bug that prevents multi-value selects from being used in workflows due to web browsers using \r\n for newline designation. Affected #: 1 file diff -r 8c663e656f64a60dac55979841947e78ce23a473 -r be47a7f089f91c4b72c0c5f89182a62589389e1f lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -703,7 +703,10 @@ value = None else: if not isinstance( value, list ): - value = value.split( "\n" ) + # Split on all whitespace. This not only provides flexibility + # in interpreting values but also is needed because many browsers + # use \r\n to separate lines. + value = value.split() return UnvalidatedValue( value ) legal_values = self.get_legal_values( trans, context ) if isinstance( value, list ): https://bitbucket.org/galaxy/galaxy-central/commits/019ad31c3c25/ Changeset: 019ad31c3c25 User: jgoecks Date: 2013-06-28 21:28:01 Summary: Automated merge of stable branch. Affected #: 1 file diff -r b89b721a0b3db47cdeddef35f03ce4c2ffcb47b5 -r 019ad31c3c2502005846dadc5c0457bbb6f80712 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -703,7 +703,10 @@ value = None else: if not isinstance( value, list ): - value = value.split( "\n" ) + # Split on all whitespace. This not only provides flexibility + # in interpreting values but also is needed because many browsers + # use \r\n to separate lines. + value = value.split() return UnvalidatedValue( value ) legal_values = self.get_legal_values( trans, context ) if isinstance( value, list ): 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: Adam Brenner: Replaced "binary" with "package" for eXpress according to my listsrv report of not picking up the correct environmental variables.
by commits-noreply＠bitbucket.org 28 Jun '13

28 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b89b721a0b3d/ Changeset: b89b721a0b3d User: Adam Brenner Date: 2013-06-27 22:50:57 Summary: Replaced "binary" with "package" for eXpress according to my listsrv report of not picking up the correct environmental variables. http://dev.list.galaxyproject.org/Tool-Dependency-Check-for-eXpress-require… Signed-off-by: Adam Brenner <aebrenne(a)uci.edu> Affected #: 1 file diff -r 4227472b7640e6689d13d428949be363b4bbc637 -r b89b721a0b3db47cdeddef35f03ce4c2ffcb47b5 tools/ngs_rna/express_wrapper.xml --- a/tools/ngs_rna/express_wrapper.xml +++ b/tools/ngs_rna/express_wrapper.xml @@ -1,7 +1,7 @@ <tool id="express" name="eXpress" version="1.1.1"><description>Quantify the abundances of a set of target sequences from sampled subsequences</description><requirements> - <requirement type="binary">eXpress</requirement> + <requirement type="package">eXpress</requirement></requirements><command> express --no-update-check @@ -122,4 +122,4 @@ - If you choose to use to calculate the covariance between targets and outputs, an other output would be : varcov.xprs. </help> -</tool> \ No newline at end of file +</tool> 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: When repairing a repository via the browser, display the ordered list of repositories that will be inspected and repaired.
by commits-noreply＠bitbucket.org 27 Jun '13

27 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4227472b7640/ Changeset: 4227472b7640 User: greg Date: 2013-06-27 21:52:45 Summary: When repairing a repository via the browser, display the ordered list of repositories that will be inspected and repaired. Affected #: 2 files diff -r 43e609a791a13c37612e5e440d5890acc070a351 -r 4227472b7640e6689d13d428949be363b4bbc637 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 @@ -1147,8 +1147,6 @@ Inspect the repository dependency hierarchy for a specified repository and attempt to make sure they are all properly installed as well as each repository's tool dependencies. """ - # TODO: figure out how to handle installing repositories and tool dependencies consecutively since each redirects to an ajaxian grid. This - # is not a problem in that Galaxy API. message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) @@ -1160,15 +1158,27 @@ message=message, status=status ) ) tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + if kwd.get( 'repair_repository_button', False ): + repair_dict = kwd.get( 'repair_dict', None ) + if not repair_dict: + repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) + ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) + ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) + if ordered_tsr_ids and ordered_repo_info_dicts: + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='manage_repositories', + operation='repair', + ordered_tsr_ids=ordered_tsr_ids, + ordered_repo_info_dicts=ordered_repo_info_dicts ) ) + tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) - if ordered_tsr_ids and ordered_repo_info_dicts: - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='manage_repositories', - operation='repair', - ordered_tsr_ids=ordered_tsr_ids, - ordered_repo_info_dicts=ordered_repo_info_dicts ) ) + return trans.fill_template( 'admin/tool_shed_repository/repair_repository.mako', + repository=tool_shed_repository, + repair_dict=repair_dict, + message=message, + status=status ) @web.json def repository_installation_status_updates( self, trans, ids=None, status_list=None ): diff -r 43e609a791a13c37612e5e440d5890acc070a351 -r 4227472b7640e6689d13d428949be363b4bbc637 templates/admin/tool_shed_repository/repair_repository.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/repair_repository.mako @@ -0,0 +1,51 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" /> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "library" )} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} +</%def> + +${render_galaxy_repository_actions( repository )} + +%if message: + ${render_msg( message, status )} +%endif + +<div class="warningmessage"> + The following repositories will be inspected and repaired in the order listed to ensure each repository and all of it's tool dependencies are correctly + installed. Click <b>Repair</b> to inspect and repair these repositories. +</div> + +<div class="toolForm"> + <div class="toolFormTitle">Repair tool shed repository '${repository.name}'</div> + <br/><br/> + <form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ), repair_dict=repair_dict )}" method="post" > + <% ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) %> + <table class="grid"> + <tr><th bgcolor="#D8D8D8">Name</th><th bgcolor="#D8D8D8">Owner</th><th bgcolor="#D8D8D8">Changeset revision</th></tr> + %for repo_info_dict in ordered_repo_info_dicts: + <% + for name, repo_info_tuple in repo_info_dict.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple + break + %> + <tr> + <td>${name | h}</td> + <td>${repository_owner | h}</td> + <td>${changeset_revision | h}</td> + </tr> + %endfor + </table> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" name="repair_repository_button" value="Repair"/> + </div> + </form> + </div> +</div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Add VCF visualization support for dataset viewer
by commits-noreply＠bitbucket.org 27 Jun '13

27 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43e609a791a1/ Changeset: 43e609a791a1 User: guerler Date: 2013-06-27 20:35:37 Summary: Add VCF visualization support for dataset viewer Affected #: 1 file diff -r 507ac09f587d2e0c40c1d8f06ed385817a209626 -r 43e609a791a13c37612e5e440d5890acc070a351 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -120,7 +120,7 @@ initialize: function(options) { // load trackster button - (new TabularButtonTracksterView(options)).render(); + new TabularButtonTracksterView(options); }, render: function() @@ -252,23 +252,63 @@ // database key genome_build: null, + // data type + data_type: null, + // backbone initialize initialize: function (options) { - // verify that metadata exists - var metadata = options.model.attributes.metadata.attributes; - if (typeof metadata.chromCol === "undefined" || typeof metadata.startCol === "undefined" || typeof metadata.endCol === "undefined") - console.log("TabularButtonTrackster : Metadata for column identification is missing."); - else { - // read in columns - this.col.chrom = metadata.chromCol - 1; - this.col.start = metadata.startCol - 1; - this.col.end = metadata.endCol - 1; + // get options + var attributes = options.model.attributes; + var metadata = options.model.attributes.metadata.attributes; + + // check for datatype + if (typeof attributes.data_type !== "undefined") + this.data_type = attributes.data_type; + else + console.log("TabularButtonTrackster : Data type missing."); + + // check for bed-file format + if (this.data_type == "bed") + { + // verify that metadata exists + if (typeof metadata.chromCol !== "undefined" || typeof metadata.startCol !== "undefined" || typeof metadata.endCol !== "undefined") + { + // read in columns + this.col.chrom = metadata.chromCol - 1; + this.col.start = metadata.startCol - 1; + this.col.end = metadata.endCol - 1; + } else + console.log("TabularButtonTrackster : Bed-file metadata incomplete."); + } + + // check for vcf-file format + if (this.data_type == "vcf") + { + // search array + function search (str, array) + { + for (var j = 0; j < array.length; j++) + if (array[j].match(str)) return j; + return -1; + }; + + // load + this.col.chrom = search("Chrom", metadata.column_names); + this.col.start = search("Pos", metadata.column_names); + this.col.end = null; + + // verify that metadata exists + if (this.col.chrom == -1 || this.col.start == -1) + console.log("TabularButtonTrackster : VCF-file metadata incomplete."); } // check if(this.col.chrom === null) + { + console.log("TabularButtonTrackster : Chromosome column undefined."); return; + } // get dataset id if (typeof options.model.attributes.id === "undefined") @@ -285,6 +325,19 @@ // get genome_build / database key if (typeof options.model.attributes.genome_build !== "undefined") this.genome_build = options.model.attributes.genome_build; + + // render the icon from template + var btn_viz = new IconButtonView({ model : new IconButton({ + title : 'Visualize', + icon_class : 'chart_curve', + id : 'btn_viz' + })}); + + // add it to the screen + this.$el.append(btn_viz.render().$el); + + // hide the button + $('#btn_viz').hide(); }, // backbone events @@ -297,29 +350,39 @@ // show button btn_viz_show: function (e) { + // is numeric + function is_numeric(n) + { + return !isNaN(parseFloat(n)) && isFinite(n); + }; + // check if(this.col.chrom === null) return; - + // get selected data line var row = $(e.target).parent(); - + // verify that location has been found var chrom = row.children().eq(this.col.chrom).html(); var start = row.children().eq(this.col.start).html(); - var end = row.children().eq(this.col.end).html(); - if (chrom !== "" && start !== "" && end !== "") + + // end is optional + var end = this.col.end ? row.children().eq(this.col.end).html() : start; + + // double check location + if (!chrom.match("^#") && chrom !== "" && is_numeric(start)) { // get target gene region var btn_viz_pars = { dataset_id : this.dataset_id, gene_region : chrom + ":" + start + "-" + end }; - + // get button position var offset = row.offset(); var left = offset.left - 10; - var top = offset.top; + var top = offset.top - $(window).scrollTop(); // update css $('#btn_viz').css({'position': 'fixed', 'top': top + 'px', 'left': left + 'px'}); @@ -328,6 +391,9 @@ // show the button $('#btn_viz').show(); + } else { + // hide the button + $('#btn_viz').hide(); } }, @@ -401,24 +467,7 @@ }); return false; }; - }, - - // render frame - render: function() - { - // render the icon from template - var btn_viz = new IconButtonView({ model : new IconButton({ - title : 'Visualize', - icon_class : 'chart_curve', - id : 'btn_viz' - })}); - - // add it to the screen - this.$el.append(btn_viz.render().$el); - - // hide the button - $('#btn_viz').hide(); - } + } }); // -- Utility functions. -- Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 27 Jun '13

27 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8c663e656f64/ Changeset: 8c663e656f64 Branch: stable User: jgoecks Date: 2013-06-27 18:11:21 Summary: Fix unicode issues in page editor. Affected #: 1 file diff -r 53f9bc7009f4c7c93177eb1f71d014e822b43640 -r 8c663e656f64a60dac55979841947e78ce23a473 templates/webapps/galaxy/page/editor.mako --- a/templates/webapps/galaxy/page/editor.mako +++ b/templates/webapps/galaxy/page/editor.mako @@ -782,7 +782,7 @@ </div><div class="unified-panel-body"> - <textarea name="page_content">${page.latest_revision.content.decode('utf-8')}</textarea> + <textarea name="page_content">${util.unicodify( page.latest_revision.content) }</textarea></div></%def> https://bitbucket.org/galaxy/galaxy-central/commits/507ac09f587d/ Changeset: 507ac09f587d User: jgoecks Date: 2013-06-27 18:12:07 Summary: Automated merge of stable branch. Affected #: 3 files diff -r e1955f57e73a8ce096bf77fd6c9d0e0ad8c5f086 -r 507ac09f587d2e0c40c1d8f06ed385817a209626 templates/webapps/galaxy/page/editor.mako --- a/templates/webapps/galaxy/page/editor.mako +++ b/templates/webapps/galaxy/page/editor.mako @@ -782,7 +782,7 @@ </div><div class="unified-panel-body"> - <textarea name="page_content">${page.latest_revision.content.decode('utf-8')}</textarea> + <textarea name="page_content">${util.unicodify( page.latest_revision.content) }</textarea></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.

1 0