March 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jmchilton: Update LWR client through LWR commit 2fec198.
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc67550cf28a/ Changeset: dc67550cf28a User: jmchilton Date: 2014-03-26 16:00:22 Summary: Update LWR client through LWR commit 2fec198. Makes parsing LWR host more robust - auto-adding http to beginning and trailing / if needed. Also makes LWR runn compatible with forthcoming job metrics pull request and pulls in Python 3 fix for job_script module. Affected #: 3 files diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/lwr_client/interface.py --- a/lib/galaxy/jobs/runners/lwr_client/interface.py +++ b/lib/galaxy/jobs/runners/lwr_client/interface.py @@ -36,8 +36,13 @@ def __init__(self, destination_params, transport): self.transport = transport - self.remote_host = destination_params.get("url") - assert self.remote_host is not None, "Failed to determine url for LWR client." + remote_host = destination_params.get("url") + assert remote_host is not None, "Failed to determine url for LWR client." + if not remote_host.endswith("/"): + remote_host = "%s/" % remote_host + if not remote_host.startswith("http"): + remote_host = "http://%s" % remote_host + self.remote_host = remote_host self.private_key = destination_params.get("private_token", None) def execute(self, command, args={}, data=None, input_path=None, output_path=None): diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/lwr_client/staging/down.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/down.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/down.py @@ -14,7 +14,7 @@ # this pattern picks up attiditional files to copy back - such as those # associated with multiple outputs and metadata configuration. Set to .* to just # copy everything -COPY_FROM_WORKING_DIRECTORY_PATTERN = compile(r"primary_.*|galaxy.json|metadata_.*|dataset_\d+\.dat|dataset_\d+_files.+") +COPY_FROM_WORKING_DIRECTORY_PATTERN = compile(r"primary_.*|galaxy.json|metadata_.*|dataset_\d+\.dat|__instrument_.*|dataset_\d+_files.+") def finish_job(client, cleanup_job, job_completed_normally, client_outputs, lwr_outputs): diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/util/job_script/__init__.py --- a/lib/galaxy/jobs/runners/util/job_script/__init__.py +++ b/lib/galaxy/jobs/runners/util/job_script/__init__.py @@ -2,11 +2,11 @@ from pkg_resources import resource_string DEFAULT_JOB_FILE_TEMPLATE = Template( - resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh') + resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh').decode('UTF-8') ) SLOTS_STATEMENT_CLUSTER_DEFAULT = \ - resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh') + resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh').decode('UTF-8') SLOTS_STATEMENT_SINGLE = """ GALAXY_SLOTS="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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56be13c43a4e/ Changeset: 56be13c43a4e Branch: stable User: jmchilton Date: 2014-03-26 15:24:08 Summary: Fix NoneType exception when using LWR with old-style tool runner URLs. Affected #: 1 file diff -r 6007992cbcd3626cbed38b0e883f516b016f98be -r 56be13c43a4e8c1ad391eab212982659e4845d94 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -156,7 +156,8 @@ job_id = "%s_%s" % (job_id, job_wrapper.task_id) params = job_wrapper.job_destination.params.copy() for key, value in params.iteritems(): - params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) + if value: + params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) return self.get_client( params, job_id ) def get_client_from_state(self, job_state): https://bitbucket.org/galaxy/galaxy-central/commits/62146f92190c/ Changeset: 62146f92190c User: jmchilton Date: 2014-03-26 15:27:44 Summary: Merge latest stable. Affected #: 1 file diff -r 66c7385957303447c8f5bb96731945bba179c83a -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -220,7 +220,8 @@ job_id = "%s_%s" % (job_id, job_wrapper.task_id) params = job_wrapper.job_destination.params.copy() for key, value in params.iteritems(): - params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) + if value: + params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) return self.get_client( params, job_id ) def get_client_from_state(self, job_state): 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: davebgx: Add check to ensure that repositories cannot be created unless at least one category has been defined.
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/66c738595730/ Changeset: 66c738595730 User: davebgx Date: 2014-03-26 15:11:54 Summary: Add check to ensure that repositories cannot be created unless at least one category has been defined. Affected #: 1 file diff -r 561929fb2d7e827f20ea078904aeebe35173f3f9 -r 66c7385957303447c8f5bb96731945bba179c83a test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -2,6 +2,8 @@ repository_name = 'filtering_0000' repository_description = "Galaxy's filtering tool for test 0000" repository_long_description = "Long description of Galaxy's filtering tool for test 0000" +import logging +log = logging.getLogger( __name__ ) class TestBasicRepositoryFeatures( ShedTwillTestCase ): '''Test core repository features.''' @@ -24,12 +26,18 @@ assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email admin_user_private_role = self.test_db_util.get_private_role( admin_user ) - def test_0005_create_categories( self ): + def test_0005_create_repository_without_categories( self ): + '''Verify that a repository cannot be created unless at least one category has been defined.''' + strings_displayed = [ 'No categories have been configured in this instance of the Galaxy Tool Shed' ] + self.visit_url( '/repository/create_repository' ) + self.check_for_strings( strings_displayed=strings_displayed, strings_not_displayed=[] ) + + def test_0010_create_categories( self ): """Create categories for this test suite""" self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' ) self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' ) - def test_0010_create_repository( self ): + def test_0015_create_repository( self ): """Create the filtering repository""" self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) @@ -43,7 +51,7 @@ category_id=self.security.encode_id( category.id ), strings_displayed=strings_displayed ) - def test_0015_edit_repository( self ): + def test_0020_edit_repository( self ): """Edit the repository name, description, and long description""" repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) new_name = "renamed_filtering" @@ -51,20 +59,20 @@ new_long_description = "Edited long description" self.edit_repository_information( repository, repo_name=new_name, description=new_description, long_description=new_long_description ) - def test_0020_change_repository_category( self ): + def test_0025_change_repository_category( self ): """Change the categories associated with the filtering repository""" repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.edit_repository_categories( repository, categories_to_add=[ "Test 0000 Basic Repository Features 2" ], categories_to_remove=[ "Test 0000 Basic Repository Features 1" ] ) - def test_0025_grant_write_access( self ): + def test_0030_grant_write_access( self ): '''Grant write access to another user''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.grant_write_access( repository, usernames=[ common.test_user_2_name ] ) self.revoke_write_access( repository, common.test_user_2_name ) - def test_0030_upload_filtering_1_1_0( self ): + def test_0035_upload_filtering_1_1_0( self ): """Upload filtering_1.1.0.tar to the repository""" repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, @@ -77,7 +85,7 @@ strings_displayed=[], strings_not_displayed=[] ) - def test_0035_verify_repository( self ): + def test_0040_verify_repository( self ): '''Display basic repository pages''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) latest_changeset_revision = self.get_repository_tip( repository ) @@ -101,7 +109,7 @@ repository_name, strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision ] ) - def test_0040_alter_repository_states( self ): + def test_0045_alter_repository_states( self ): '''Test toggling the malicious and deprecated repository flags.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.logout() @@ -127,7 +135,7 @@ strings_displayed = [ 'Mark repository as deprecated', 'Upload files', 'Reset all repository metadata' ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) - def test_0045_display_repository_tip_file( self ): + def test_0050_display_repository_tip_file( self ): '''Display the contents of filtering.xml in the repository tip revision''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.display_repository_file_contents( repository=repository, @@ -136,7 +144,7 @@ strings_displayed=[ '1.1.0' ], strings_not_displayed=[] ) - def test_0050_upload_filtering_txt_file( self ): + def test_0055_upload_filtering_txt_file( self ): '''Upload filtering.txt file associated with tool version 1.1.0.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, @@ -150,7 +158,7 @@ strings_not_displayed=[] ) self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) - def test_0055_upload_filtering_test_data( self ): + def test_0060_upload_filtering_test_data( self ): '''Upload filtering test data.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, @@ -169,7 +177,7 @@ strings_not_displayed=[] ) self.check_repository_metadata( repository, tip_only=True ) - def test_0060_upload_filtering_2_2_0( self ): + def test_0065_upload_filtering_2_2_0( self ): '''Upload filtering version 2.2.0''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, @@ -182,7 +190,7 @@ strings_displayed=[], strings_not_displayed=[] ) - def test_0065_verify_filtering_repository( self ): + def test_0070_verify_filtering_repository( self ): '''Verify the new tool versions and repository metadata.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) category = self.test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' ) @@ -204,7 +212,7 @@ tool_page_strings_displayed=tool_page_strings_displayed ) self.check_repository_metadata( repository, tip_only=False ) - def test_0070_upload_readme_txt_file( self ): + def test_0075_upload_readme_txt_file( self ): '''Upload readme.txt file associated with tool version 2.2.0.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, @@ -223,26 +231,26 @@ strings_displayed=[ 'Readme file for filtering 1.1.0', 'This is a readme file.' ] ) - def test_0075_delete_readme_txt_file( self ): + def test_0080_delete_readme_txt_file( self ): '''Delete the readme.txt file.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.delete_files_from_repository( repository, filenames=[ 'readme.txt' ] ) self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=2 ) self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) - def test_0080_search_for_valid_filter_tool( self ): + def test_0085_search_for_valid_filter_tool( self ): '''Search for the filtering tool by tool ID, name, and version.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) tip_changeset = self.get_repository_tip( repository ) search_fields = dict( tool_id='Filter1', tool_name='filter', tool_version='2.2.0' ) self.search_for_valid_tools( search_fields=search_fields, strings_displayed=[ tip_changeset ], strings_not_displayed=[] ) - def test_0085_verify_repository_metadata( self ): + def test_0090_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.verify_unchanged_repository_metadata( repository ) - def test_0090_verify_reserved_repository_name_handling( self ): + def test_0095_verify_reserved_repository_name_handling( self ): '''Check that reserved repository names are handled correctly.''' category = self.test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' ) error_message = 'The term <b>repos</b> is a reserved word in the tool shed, so it cannot be used as a repository name.' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 25 Mar '14

25 Mar '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c4950bc66225/ Changeset: c4950bc66225 User: carlfeberhard Date: 2014-03-25 20:30:51 Summary: History API: show: add importable, username_and_slug to returned attributes, update: 1) allow setting importable and published, 2) published automatically makes a history importable, 3) in both cases slug is automatically set set_as_current: now correctly uses the HTTP method PUT (not POST), HDA API: all: histories that are importable and/or published now allow GET'ing the contents properly, create: you can now copy HDAs into your histories if the HDA and it's history are accessible Affected #: 7 files diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -773,7 +773,7 @@ class History( object, Dictifiable, UsesAnnotations, HasName ): dict_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' ) - dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged' ) + dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged', 'importable', 'slug' ) default_name = 'Unnamed history' def __init__( self, id=None, name=None, user=None ): diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -187,8 +187,11 @@ def validate_and_sanitize_basestring_list( self, key, val ): if not isinstance( val, list ): - raise ValueError( '%s must be a list: %s' %( key, str( type( val ) ) ) ) - return [ unicode( sanitize_html( t, 'utf-8', 'text/html' ), 'utf-8' ) for t in val ] + raise ValueError( '%s must be a list of strings: %s' %( key, str( type( val ) ) ) ) + try: + return [ unicode( sanitize_html( t, 'utf-8', 'text/html' ), 'utf-8' ) for t in val ] + except TypeError, type_err: + raise ValueError( '%s must be a list of strings: %s' %( key, str( type_err ) ) ) def validate_boolean( self, key, val ): if not isinstance( val, bool ): @@ -527,6 +530,10 @@ if not history_dict[ 'annotation' ]: history_dict[ 'annotation' ] = '' #TODO: item_slug url + if history_dict[ 'importable' ] and history_dict[ 'slug' ]: + #TODO: this should be in History (or a superclass of) + username_and_slug = ( '/' ).join(( 'u', history.user.username, 'h', history_dict[ 'slug' ] )) + history_dict[ 'username_and_slug' ] = username_and_slug hda_summaries = hda_dictionaries if hda_dictionaries else self.get_hda_summary_dicts( trans, history ) #TODO remove the following in v2 @@ -541,26 +548,69 @@ """ Changes history data using the given dictionary new_data. """ - # precondition: access of the history has already been checked + #precondition: ownership of the history has already been checked + #precondition: user is not None (many of these attributes require a user to set properly) + user = trans.get_user() + # published histories should always be importable + if 'published' in new_data and new_data[ 'published' ] and not history.importable: + new_data[ 'importable' ] = True # send what we can down into the model changed = history.set_from_dict( new_data ) + # the rest (often involving the trans) - do here - if 'annotation' in new_data.keys() and trans.get_user(): - history.add_item_annotation( trans.sa_session, trans.get_user(), history, new_data[ 'annotation' ] ) + #TODO: the next two could be an aspect/mixin + #TODO: also need a way to check whether they've changed - assume they have for now + if 'annotation' in new_data: + history.add_item_annotation( trans.sa_session, user, history, new_data[ 'annotation' ] ) changed[ 'annotation' ] = new_data[ 'annotation' ] - if 'tags' in new_data.keys() and trans.get_user(): - self.set_tags_from_list( trans, history, new_data[ 'tags' ], user=trans.user ) - # importable (ctrl.history.set_accessible_async) - # sharing/permissions? - # slugs? - # purged - duh duh duhhhhhhnnnnnnnnnn + + if 'tags' in new_data: + self.set_tags_from_list( trans, history, new_data[ 'tags' ], user=user ) + changed[ 'tags' ] = new_data[ 'tags' ] + + #TODO: sharing with user/permissions? if changed.keys(): trans.sa_session.flush() + # create a slug if none exists (setting importable to false should not remove the slug) + if 'importable' in changed and changed[ 'importable' ] and not history.slug: + self._create_history_slug( trans, history ) + return changed + def _create_history_slug( self, trans, history ): + #TODO: mixins need to die a quick, horrible death + # (this is duplicate from SharableMixin which can't be added to UsesHistory without exposing various urls) + cur_slug = history.slug + + # Setup slug base. + if cur_slug is None or cur_slug == "": + # Item can have either a name or a title. + item_name = history.name + slug_base = util.ready_name_for_url( item_name.lower() ) + else: + slug_base = cur_slug + + # Using slug base, find a slug that is not taken. If slug is taken, + # add integer to end. + new_slug = slug_base + count = 1 + while ( trans.sa_session.query( trans.app.model.History ) + .filter_by( user=history.user, slug=new_slug, importable=True ) + .count() != 0 ): + # Slug taken; choose a new slug based on count. This approach can + # handle numerous items with the same name gracefully. + new_slug = '%s-%i' % ( slug_base, count ) + count += 1 + + # Set slug and return. + trans.sa_session.add( history ) + history.slug = new_slug + trans.sa_session.flush() + return history.slug == cur_slug + class ExportsHistoryMixin: @@ -685,9 +735,9 @@ else: #TODO: do we really need the history? history = self.get_history( trans, history_id, - check_ownership=True, check_accessible=True, deleted=False ) + check_ownership=False, check_accessible=True, deleted=False ) hda = self.get_history_dataset_association( trans, history, id, - check_ownership=True, check_accessible=True ) + check_ownership=False, check_accessible=True ) return hda def get_hda_list( self, trans, hda_ids, check_ownership=True, check_accessible=False, check_state=True ): diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -6,20 +6,26 @@ import pkg_resources pkg_resources.require( "Paste" ) -from paste.httpexceptions import HTTPBadRequest, HTTPForbidden, HTTPInternalServerError, HTTPException + +from paste.httpexceptions import HTTPBadRequest +from paste.httpexceptions import HTTPForbidden +from paste.httpexceptions import HTTPInternalServerError +from paste.httpexceptions import HTTPException from galaxy import exceptions from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.web import _future_expose_api_raw as expose_api_raw -from galaxy.util import string_as_bool -from galaxy.util import restore_text + from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import UsesHistoryMixin from galaxy.web.base.controller import UsesTagsMixin from galaxy.web.base.controller import ExportsHistoryMixin from galaxy.web.base.controller import ImportsHistoryMixin + +from galaxy.util import string_as_bool +from galaxy.util import restore_text from galaxy.web import url_for import logging @@ -48,27 +54,22 @@ #TODO: query (by name, date, etc.) rval = [] deleted = string_as_bool( deleted ) - try: - if trans.user: - histories = self.get_user_histories( trans, user=trans.user, only_deleted=deleted ) - #for history in query: - for history in histories: - item = history.to_dict(value_mapper={'id': trans.security.encode_id}) - item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) - rval.append( item ) - elif trans.galaxy_session.current_history: - #No user, this must be session authentication with an anonymous user. - history = trans.galaxy_session.current_history + if trans.user: + histories = self.get_user_histories( trans, user=trans.user, only_deleted=deleted ) + + for history in histories: item = history.to_dict(value_mapper={'id': trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) - rval.append(item) + rval.append( item ) - except Exception, e: - raise - rval = "Error in history API" - log.error( rval + ": %s" % str(e) ) - trans.response.status = 500 + elif trans.galaxy_session.current_history: + #No user, this must be session authentication with an anonymous user. + history = trans.galaxy_session.current_history + item = history.to_dict(value_mapper={'id': trans.security.encode_id}) + item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) + rval.append(item) + return rval @web.expose_api_anonymous @@ -92,7 +93,6 @@ :returns: detailed history information from :func:`galaxy.web.base.controller.UsesHistoryDatasetAssociationMixin.get_history_dict` """ - #TODO: GET /api/histories/{encoded_history_id}?as_archive=True #TODO: GET /api/histories/s/{username}/{slug} history_id = id deleted = string_as_bool( deleted ) @@ -116,7 +116,7 @@ except HTTPBadRequest, bad_req: trans.response.status = 400 - return str( bad_req ) + raise exceptions.MessageException( bad_req.detail ) except Exception, e: msg = "Error in history API at showing history detail: %s" % ( str( e ) ) @@ -444,7 +444,7 @@ continue if key in ( 'name', 'genome_build', 'annotation' ): validated_payload[ key ] = self.validate_and_sanitize_basestring( key, val ) - if key in ( 'deleted', 'published' ): + if key in ( 'deleted', 'published', 'importable' ): validated_payload[ key ] = self.validate_boolean( key, val ) elif key == 'tags': validated_payload[ key ] = self.validate_and_sanitize_basestring_list( key, val ) diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 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 @@ -2,20 +2,32 @@ API operations on the contents of a history. """ -import logging -from galaxy import exceptions, util, web -from galaxy.web.base.controller import ( BaseAPIController, url_for, - UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, - UsesLibraryMixinItems, UsesTagsMixin ) +from galaxy import exceptions +from galaxy import util +from galaxy import web + +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy.web import _future_expose_api_raw as expose_api_raw + +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin +from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.web.base.controller import UsesLibraryMixin +from galaxy.web.base.controller import UsesLibraryMixinItems +from galaxy.web.base.controller import UsesTagsMixin + +from galaxy.web.base.controller import url_for from galaxy.util.sanitize_html import sanitize_html +import logging log = logging.getLogger( __name__ ) class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, UsesLibraryMixinItems, UsesTagsMixin ): - @web.expose_api_anonymous + @expose_api_anonymous def index( self, trans, history_id, ids=None, **kwd ): """ index( self, trans, history_id, ids=None, **kwd ) @@ -52,7 +64,7 @@ history = trans.history # otherwise, check permissions for the history first else: - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) + history = self.get_history( trans, history_id, check_ownership=False, check_accessible=True ) # Allow passing in type or types - for continuity rest of methods # take in type - but this one can be passed multiple types and @@ -134,7 +146,7 @@ hda.history_id, hda.id, type( exc ), str( exc ) ) return self.get_hda_dict_with_error( trans, hda=hda, error_msg=str( exc ) ) - @web.expose_api_anonymous + @expose_api_anonymous def show( self, trans, id, history_id, **kwd ): """ show( self, trans, id, history_id, **kwd ) @@ -170,7 +182,7 @@ trans.response.status = 500 return msg - @web.expose_api + @expose_api def create( self, trans, history_id, payload, **kwd ): """ create( self, trans, history_id, payload, **kwd ) @@ -201,6 +213,8 @@ # retrieve history try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False ) + except exceptions.httpexceptions.HTTPException: + raise except Exception, e: # no way to tell if it failed bc of perms or other (all MessageExceptions) trans.response.status = 500 @@ -236,7 +250,8 @@ elif source == 'hda': try: #NOTE: user currently only capable of copying one of their own datasets - hda = self.get_dataset( trans, content ) + hda = self.get_dataset( trans, content, check_ownership=False, check_accessible=True ) + self.security_check( trans, hda.history, check_ownership=False, check_accessible=True ) except ( exceptions.httpexceptions.HTTPRequestRangeNotSatisfiable, exceptions.httpexceptions.HTTPBadRequest ), id_exc: # wot... @@ -259,7 +274,7 @@ trans.response.status = 501 return - @web.expose_api_anonymous + @expose_api_anonymous def update( self, trans, history_id, id, payload, **kwd ): """ update( self, trans, history_id, id, payload, **kwd ) @@ -306,6 +321,7 @@ if hda.history != trans.history: trans.response.status = 401 return { 'error': 'Anonymous users cannot edit datasets outside their current history' } + else: payload = self._validate_and_parse_update_payload( payload ) # only check_state if not deleting, otherwise cannot delete uploading files @@ -316,6 +332,7 @@ changed = self.set_hda_from_dict( trans, hda, payload ) if payload.get( 'deleted', False ): self.stop_hda_creating_job( hda ) + except Exception, exception: log.error( 'Update of history (%s), HDA (%s) failed: %s', history_id, id, str( exception ), exc_info=True ) @@ -330,7 +347,7 @@ return changed #TODO: allow anonymous del/purge and test security on this - @web.expose_api + @expose_api def delete( self, trans, history_id, id, purge=False, **kwd ): """ delete( self, trans, history_id, id, **kwd ) diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -165,8 +165,9 @@ parent_resources=dict( member_name='page', collection_name='pages' ) ) # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource + #webapp.mapper.connect( "set_as_current", "/api/histories/set_as_current/{id}", webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", - controller="histories", action="set_as_current", conditions=dict( method=["POST"] ) ) + controller="histories", action="set_as_current", conditions=dict( method=["PUT"] ) ) webapp.mapper.connect( "history_archive_export", "/api/histories/{id}/exports", controller="histories", action="archive_export", conditions=dict( method=[ "PUT" ] ) ) diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 static/scripts/mvc/history/current-history-panel.js --- a/static/scripts/mvc/history/current-history-panel.js +++ b/static/scripts/mvc/history/current-history-panel.js @@ -84,7 +84,10 @@ var panel = this, historyFn = function(){ // make this current and get history data with one call - return jQuery.post( galaxy_config.root + 'api/histories/' + historyId + '/set_as_current' ); + return jQuery.ajax({ + url : galaxy_config.root + 'api/histories/' + historyId + '/set_as_current', + method : 'PUT' + }); }; return this.loadHistoryWithHDADetails( historyId, attributes, historyFn ) .then(function( historyData, hdaData ){ diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 static/scripts/packed/mvc/history/current-history-panel.js --- a/static/scripts/packed/mvc/history/current-history-panel.js +++ b/static/scripts/packed/mvc/history/current-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-edit","mvc/history/history-panel","mvc/base-mvc"],function(b,f,c){var d=c.SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});d.storageKey=function e(){return("history-panel")};var a=f.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(g){g=g||{};this.preferences=new d(_.extend({id:d.storageKey()},_.pick(g,_.keys(d.prototype.defaults))));f.HistoryPanel.prototype.initialize.call(this,g)},loadCurrentHistory:function(h){var g=this;return this.loadHistoryWithHDADetails("current",h).then(function(j,i){g.trigger("current-history",g)})},switchToHistory:function(j,i){var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories/"+j+"/set_as_current")};return this.loadHistoryWithHDADetails(j,i,h).then(function(l,k){g.trigger("switched-history",g)})},createNewHistory:function(i){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,i,h).then(function(k,j){g.trigger("new-history",g)})},setModel:function(h,g,i){f.HistoryPanel.prototype.setModel.call(this,h,g,i);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpModelEventHandlers:function(){f.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(h,i,g){if((!h.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[h.id])}},this)},render:function(i,j){i=(i===undefined)?(this.fxSpeed):(i);var g=this,h;if(this.model){h=this.renderModel()}else{h=this.renderWithoutModel()}$(g).queue("fx",[function(k){if(i&&g.$el.is(":visible")){g.$el.fadeOut(i,k)}else{k()}},function(k){g.$el.empty();if(h){g.$el.append(h.children());g.renderBasedOnPrefs()}k()},function(k){if(i&&!g.$el.is(":visible")){g.$el.fadeIn(i,k)}else{k()}},function(k){if(j){j.call(this)}g.trigger("rendered",this);k()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.toggleSearchControls(0,true)}},_renderEmptyMsg:function(i){var h=this,g=h.$emptyMessage(i),j=$(".toolMenuContainer");if((_.isEmpty(h.hdaViews)&&!h.searchFor)&&(Galaxy&&Galaxy.upload&&j.size())){g.empty();g.html([_l("This history is empty. "),_l("You can "),'<a class="uploader-link" href="javascript:void(0)">',_l("load your own data"),"</a>",_l(" or "),'<a class="get-data-link" href="javascript:void(0)">',_l("get data from an external source"),"</a>"].join(""));g.find(".uploader-link").click(function(k){Galaxy.upload._eventShow(k)});g.find(".get-data-link").click(function(k){j.parent().scrollTop(0);j.find('span:contains("Get Data")').click()});g.show()}else{f.HistoryPanel.prototype._renderEmptyMsg.call(this,i)}return this},toggleSearchControls:function(h,g){var i=f.HistoryPanel.prototype.toggleSearchControls.call(this,h,g);this.preferences.set("searching",i)},_renderTags:function(g){var h=this;f.HistoryPanel.prototype._renderTags.call(this,g);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(i){h.preferences.set("tagsEditorShown",i.hidden)})},_renderAnnotation:function(g){var h=this;f.HistoryPanel.prototype._renderAnnotation.call(this,g);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(i){h.preferences.set("annotationEditorShown",i.hidden)})},connectToQuotaMeter:function(g){if(!g){return this}this.listenTo(g,"quota:over",this.showQuotaMessage);this.listenTo(g,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(g&&g.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var g=this.$el.find(".quota-message");if(g.is(":hidden")){g.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var g=this.$el.find(".quota-message");if(!g.is(":hidden")){g.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(g){if(!g){return this}this.on("new-storage",function(i,h){if(g&&i){g.findItemByHtml(_l("Include Deleted Datasets")).checked=i.get("show_deleted");g.findItemByHtml(_l("Include Hidden Datasets")).checked=i.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CurrentHistoryPanel:a}}); \ No newline at end of file +define(["mvc/dataset/hda-edit","mvc/history/history-panel","mvc/base-mvc"],function(b,f,c){var d=c.SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});d.storageKey=function e(){return("history-panel")};var a=f.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(g){g=g||{};this.preferences=new d(_.extend({id:d.storageKey()},_.pick(g,_.keys(d.prototype.defaults))));f.HistoryPanel.prototype.initialize.call(this,g)},loadCurrentHistory:function(h){var g=this;return this.loadHistoryWithHDADetails("current",h).then(function(j,i){g.trigger("current-history",g)})},switchToHistory:function(j,i){var g=this,h=function(){return jQuery.ajax({url:galaxy_config.root+"api/histories/"+j+"/set_as_current",method:"PUT"})};return this.loadHistoryWithHDADetails(j,i,h).then(function(l,k){g.trigger("switched-history",g)})},createNewHistory:function(i){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,i,h).then(function(k,j){g.trigger("new-history",g)})},setModel:function(h,g,i){f.HistoryPanel.prototype.setModel.call(this,h,g,i);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpModelEventHandlers:function(){f.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(h,i,g){if((!h.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[h.id])}},this)},render:function(i,j){i=(i===undefined)?(this.fxSpeed):(i);var g=this,h;if(this.model){h=this.renderModel()}else{h=this.renderWithoutModel()}$(g).queue("fx",[function(k){if(i&&g.$el.is(":visible")){g.$el.fadeOut(i,k)}else{k()}},function(k){g.$el.empty();if(h){g.$el.append(h.children());g.renderBasedOnPrefs()}k()},function(k){if(i&&!g.$el.is(":visible")){g.$el.fadeIn(i,k)}else{k()}},function(k){if(j){j.call(this)}g.trigger("rendered",this);k()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.toggleSearchControls(0,true)}},_renderEmptyMsg:function(i){var h=this,g=h.$emptyMessage(i),j=$(".toolMenuContainer");if((_.isEmpty(h.hdaViews)&&!h.searchFor)&&(Galaxy&&Galaxy.upload&&j.size())){g.empty();g.html([_l("This history is empty. "),_l("You can "),'<a class="uploader-link" href="javascript:void(0)">',_l("load your own data"),"</a>",_l(" or "),'<a class="get-data-link" href="javascript:void(0)">',_l("get data from an external source"),"</a>"].join(""));g.find(".uploader-link").click(function(k){Galaxy.upload._eventShow(k)});g.find(".get-data-link").click(function(k){j.parent().scrollTop(0);j.find('span:contains("Get Data")').click()});g.show()}else{f.HistoryPanel.prototype._renderEmptyMsg.call(this,i)}return this},toggleSearchControls:function(h,g){var i=f.HistoryPanel.prototype.toggleSearchControls.call(this,h,g);this.preferences.set("searching",i)},_renderTags:function(g){var h=this;f.HistoryPanel.prototype._renderTags.call(this,g);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(i){h.preferences.set("tagsEditorShown",i.hidden)})},_renderAnnotation:function(g){var h=this;f.HistoryPanel.prototype._renderAnnotation.call(this,g);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(i){h.preferences.set("annotationEditorShown",i.hidden)})},connectToQuotaMeter:function(g){if(!g){return this}this.listenTo(g,"quota:over",this.showQuotaMessage);this.listenTo(g,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(g&&g.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var g=this.$el.find(".quota-message");if(g.is(":hidden")){g.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var g=this.$el.find(".quota-message");if(!g.is(":hidden")){g.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(g){if(!g){return this}this.on("new-storage",function(i,h){if(g&&i){g.findItemByHtml(_l("Include Deleted Datasets")).checked=i.get("show_deleted");g.findItemByHtml(_l("Include Hidden Datasets")).checked=i.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CurrentHistoryPanel:a}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/79ab14af25e4/ Changeset: 79ab14af25e4 User: carlfeberhard Date: 2014-03-25 21:59:27 Summary: History/HDA API: begin normalizing exceptions and return codes; Browser testing: update and expand history/hda testing, add importable/published permissions testing, transfer upload functions to api module Affected #: 8 files diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -97,32 +97,32 @@ history_id = id deleted = string_as_bool( deleted ) - try: - if history_id == "most_recently_used": - if not trans.user or len( trans.user.galaxy_sessions ) <= 0: - return None - # Most recent active history for user sessions, not deleted - history = trans.user.galaxy_sessions[0].histories[-1].history + #try: + if history_id == "most_recently_used": + if not trans.user or len( trans.user.galaxy_sessions ) <= 0: + return None + # Most recent active history for user sessions, not deleted + history = trans.user.galaxy_sessions[0].histories[-1].history - elif history_id == "current": - history = trans.get_history( create=True ) + elif history_id == "current": + history = trans.get_history( create=True ) - else: - history = self.get_history( trans, history_id, check_ownership=False, - check_accessible=True, deleted=deleted ) + else: + history = self.get_history( trans, history_id, check_ownership=False, + check_accessible=True, deleted=deleted ) - history_data = self.get_history_dict( trans, history ) - history_data[ 'contents_url' ] = url_for( 'history_contents', history_id=history_id ) + history_data = self.get_history_dict( trans, history ) + history_data[ 'contents_url' ] = url_for( 'history_contents', history_id=history_id ) - except HTTPBadRequest, bad_req: - trans.response.status = 400 - raise exceptions.MessageException( bad_req.detail ) - - except Exception, e: - msg = "Error in history API at showing history detail: %s" % ( str( e ) ) - log.exception( msg ) - trans.response.status = 500 - return msg + #except HTTPBadRequest, bad_req: + # trans.response.status = 400 + # raise exceptions.MessageException( bad_req.detail ) + # + #except Exception, e: + # msg = "Error in history API at showing history detail: %s" % ( str( e ) ) + # log.exception( msg ) + # trans.response.status = 500 + # return msg return history_data diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/api-hda-tests.js --- a/test/casperjs/api-hda-tests.js +++ b/test/casperjs/api-hda-tests.js @@ -32,33 +32,12 @@ } spaceghost.user.loginOrRegisterUser( email, password ); -var uploadFilename = '1.sam', - uploadFilepath = '../../test-data/' + uploadFilename, - upload = {}; -spaceghost.thenOpen( spaceghost.baseUrl ).tools.uploadFile( uploadFilepath, function( uploadInfo ){ - upload = uploadInfo; +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + this.api.tools.thenUpload( spaceghost.api.histories.show( 'current' ).id, { + filepath: this.options.scriptDir + '/../../test-data/1.sam' + }); }); -function hasKeys( object, keysArray ){ - if( !utils.isObject( object ) ){ return false; } - for( var i=0; i<keysArray.length; i += 1 ){ - if( !object.hasOwnProperty( keysArray[i] ) ){ - spaceghost.debug( 'object missing key: ' + keysArray[i] ); - return false; - } - } - return true; -} - -function countKeys( object ){ - if( !utils.isObject( object ) ){ return 0; } - var count = 0; - for( var key in object ){ - if( object.hasOwnProperty( key ) ){ count += 1; } - } - return count; -} - // =================================================================== TESTS var summaryKeys = [ 'id', 'name', 'type', 'url' ], detailKeys = [ @@ -76,11 +55,8 @@ 'metadata_comment_lines', 'metadata_data_lines' ]; -spaceghost.historypanel.waitForHdas().then( function(){ +spaceghost.then( function(){ - var uploaded = this.historypanel.hdaElementInfoByTitle( uploadFilename ); - this.info( 'found uploaded hda: ' + uploaded.attributes.id ); - this.debug( 'uploaded hda: ' + this.jsonStr( uploaded ) ); // ------------------------------------------------------------------------------------------- INDEX this.test.comment( 'index should return a list of summary data for each hda' ); var histories = this.api.histories.index(), @@ -92,18 +68,17 @@ this.test.assert( hdaIndex.length >= 1, 'Has at least one hda' ); var firstHda = hdaIndex[0]; - this.test.assert( hasKeys( firstHda, summaryKeys ), 'Has the proper keys' ); + this.test.assert( this.hasKeys( firstHda, summaryKeys ), 'Has the proper keys' ); this.test.assert( this.api.isEncodedId( firstHda.id ), 'Id appears well-formed: ' + firstHda.id ); - this.test.assert( uploaded.text.indexOf( firstHda.name ) !== -1, 'Title matches: ' + firstHda.name ); - // not caring about type or url here + this.test.assert( firstHda.name === '1.sam', 'Title matches: ' + firstHda.name ); // ------------------------------------------------------------------------------------------- SHOW this.test.comment( 'show should get an HDA details object' ); var hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); //this.debug( this.jsonStr( hdaShow ) ); - this.test.assert( hasKeys( hdaShow, detailKeys ), 'Has the proper keys' ); + this.test.assert( this.hasKeys( hdaShow, detailKeys ), 'Has the proper keys' ); //TODO: validate data in each hdaShow attribute... @@ -117,7 +92,7 @@ this.test.assert( hdaIndex.length >= 1, 'Has at least one hda' ); firstHda = hdaIndex[0]; - this.test.assert( hasKeys( firstHda, detailKeys ), 'Has the proper keys' ); + this.test.assert( this.hasKeys( firstHda, detailKeys ), 'Has the proper keys' ); //TODO??: validate data in firstHda attribute? we ASSUME it's from a common method as show... @@ -133,29 +108,21 @@ var returned = this.api.hdas.update( lastHistory.id, firstHda.id, { name : hdaShow.name }); - this.test.assert( countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); + this.test.assert( this.countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); this.test.comment( 'updating using a nonsense key should NOT fail with an error' ); returned = this.api.hdas.update( lastHistory.id, firstHda.id, { konamiCode : 'uuddlrlrba' }); - this.test.assert( countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); + this.test.assert( this.countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); this.test.comment( 'updating by attempting to change type should cause an error' ); - err = {}; - try { + this.api.assertRaises( function(){ returned = this.api.hdas.update( lastHistory.id, firstHda.id, { //name : false deleted : 'sure why not' }); - } catch( error ){ - err = error; - //this.debug( this.jsonStr( err ) ); - } - this.test.assert( !!err.message, "Error occurred: " + err.message ); - this.test.assert( err.status === 400, "Error status is 400: " + err.status ); - //TODO??: other type checks? - + }, 400, 'deleted must be a boolean', 'changing deleted type failed' ); // ........................................................................................... name this.test.comment( 'update should allow changing the name' ); @@ -330,25 +297,68 @@ // ------------------------------------------------------------------------------------------- ERRORS this.test.comment( 'create should error with "Please define the source" when the param "from_ld_id" is not used' ); - var errored = false; - try { - // sending an empty object won't work - var created = this.api.hdas.create( lastHistory.id, { bler: 'bler' } ); + this.api.assertRaises( function(){ + this.api.hdas.create( lastHistory.id, { bler: 'bler' } ); + }, 400, 'Please define the source', 'create with no source failed' ); - } catch( err ){ - errored = true; - this.test.assert( err.message.indexOf( 'Please define the source' ) !== -1, - 'Error has the proper message: ' + err.message ); - this.test.assert( err.status === 400, 'Error has the proper status code: ' + err.status ); - } - if( !errored ){ - this.test.fail( 'create without "from_ld_id" did not cause error' ); - } + this.test.comment( 'updating using a nonsense key should fail silently' ); + returned = this.api.hdas.update( lastHistory.id, hdaShow.id, { + konamiCode : 'uuddlrlrba' + }); + this.test.assert( returned.konamiCode === undefined, 'key was not set: ' + returned.konamiCode ); - //var returned = this.api.hdas.update( lastHistory.id, hdaIndex[0].id, { deleted: true, blerp: 'blerp' }); - //var returned = this.api.hdas.update( lastHistory.id, { deleted: true, blerp: 'blerp' }); - //this.debug( 'returned:' + this.jsonStr( returned ) ); - //this.debug( 'page:' + this.jsonStr( this.page ) ); + spaceghost.test.comment( 'A bad id should throw an error when using show' ); + this.api.assertRaises( function(){ + this.api.hdas.show( lastHistory.id, '1234123412341234' ); + }, 500, 'unable to decode', 'Bad Request with invalid id: show' ); + spaceghost.test.comment( 'A bad id should throw an error when using update' ); + this.api.assertRaises( function(){ + this.api.hdas.update( lastHistory.id, '1234123412341234', {} ); + }, 400, 'invalid literal for int', 'Bad Request with invalid id: update' ); + spaceghost.test.comment( 'A bad id should throw an error when using delete' ); + this.api.assertRaises( function(){ + this.api.hdas.delete_( lastHistory.id, '1234123412341234' ); + }, 500, 'invalid literal for int', 'Bad Request with invalid id: delete' ); + spaceghost.test.comment( 'A bad id should throw an error when using undelete' ); + + this.test.comment( 'updating by attempting to change type should cause an error' ); + [ 'name', 'annotation', 'genome_build', 'misc_info' ].forEach( function( key ){ + var updatedAttrs = {}; + updatedAttrs[ key ] = false; + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, updatedAttrs ); + }, 400, key + ' must be a string or unicode', 'type validation error' ); + }); + [ 'deleted', 'visible' ].forEach( function( key ){ + var updatedAttrs = {}; + updatedAttrs[ key ] = 'straaang'; + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, updatedAttrs ); + }, 400, key + ' must be a boolean', 'type validation error' ); + }); + [ 'you\'re it', [ true ] ].forEach( function( badVal ){ + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, { tags: badVal }); + }, 400, 'tags must be a list', 'type validation error' ); + }); + + // ------------------------------------------------------------------------------------------- DELETE + this.test.comment( 'calling delete on an hda should mark it as deleted but not change the history size' ); + lastHistory = this.api.histories.show( lastHistory.id ); + var sizeBeforeDelete = lastHistory.nice_size; + + returned = this.api.hdas.delete_( lastHistory.id, firstHda.id ); + //this.debug( this.jsonStr( returned ) ); + + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.deleted, 'hda is marked deleted' ); + lastHistory = this.api.histories.show( lastHistory.id ); + this.test.assert( lastHistory.nice_size === sizeBeforeDelete, 'history size has not changed' ); + + // by default, purging fails bc uni.ini:allow_user_dataset_purge=False + this.api.assertRaises( function(){ + returned = this.api.hdas.delete_( lastHistory.id, firstHda.id, { purge : true }); + }, 403, 'This instance does not allow user dataset purging', 'Purge failed' ); /* */ }); diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/api-history-permission-tests.js --- /dev/null +++ b/test/casperjs/api-history-permission-tests.js @@ -0,0 +1,303 @@ +/* Utility to load a specific page and output html, page text, or a screenshot + * Optionally wait for some time, text, or dom selector + */ +try { + //...if there's a better way - please let me know, universe + var scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} +spaceghost.start(); + + +// =================================================================== SET UP +var utils = require( 'utils' ); + +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} +var email2 = spaceghost.user.getRandomEmail(), + password2 = '123456'; +if( spaceghost.fixtureData.testUser2 ){ + email2 = spaceghost.fixtureData.testUser2.email; + password2 = spaceghost.fixtureData.testUser2.password; +} + +var inaccessibleHistory, accessibleHistory, publishedHistory, + inaccessibleHdas, accessibleHdas, publishedHdas, + accessibleLink; + +// =================================================================== TESTS +//// ------------------------------------------------------------------------------------------- create 3 histories +spaceghost.user.loginOrRegisterUser( email, password ); +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + // create three histories: make the 2nd importable (via the API), and the third published + + this.test.comment( 'importable, slug, and published should all be returned by show and initially off' ); + // make the current the inaccessible one + inaccessibleHistory = this.api.histories.show( 'current' ); + this.test.assert( this.hasKeys( inaccessibleHistory, [ 'id', 'name', 'slug', 'importable', 'published' ] ), + 'Has the proper keys' ); + this.test.assert( inaccessibleHistory.slug === null, + 'initial slug is null: ' + inaccessibleHistory.slug ); + this.test.assert( inaccessibleHistory.importable === false, + 'initial importable is false: ' + inaccessibleHistory.importable ); + this.test.assert( inaccessibleHistory.published === false, + 'initial published is false: ' + inaccessibleHistory.published ); + this.api.histories.update( inaccessibleHistory.id, { name: 'inaccessible' }); + + this.test.comment( 'Setting importable to true should create a slug, username_and_slug, and importable === true' ); + accessibleHistory = this.api.histories.create({ name: 'accessible' }); + var returned = this.api.histories.update( accessibleHistory.id, { + importable : true + }); + this.debug( this.jsonStr( returned ) ); + accessibleHistory = this.api.histories.show( accessibleHistory.id ); + this.test.assert( this.hasKeys( accessibleHistory, [ 'username_and_slug' ] ), + 'Has the proper keys' ); + this.test.assert( accessibleHistory.slug === 'accessible', + 'slug is not null: ' + accessibleHistory.slug ); + this.test.assert( accessibleHistory.importable, + 'importable is true: ' + accessibleHistory.importable ); + accessibleLink = 'u/' + email.replace( '@test.test', '' ) + '/h/accessible'; + this.test.assert( accessibleHistory.username_and_slug === accessibleLink, + 'username_and_slug is proper: ' + accessibleHistory.username_and_slug ); + + this.test.comment( 'Setting published to true should create make accessible and published === true' ); + publishedHistory = this.api.histories.create({ name: 'published' }); + returned = this.api.histories.update( publishedHistory.id, { + published : true + }); + this.debug( this.jsonStr( returned ) ); + publishedHistory = this.api.histories.show( publishedHistory.id ); + this.test.assert( this.hasKeys( publishedHistory, [ 'username_and_slug' ] ), + 'Has the proper keys' ); + this.test.assert( publishedHistory.published, + 'published is true: ' + publishedHistory.published ); + this.test.assert( publishedHistory.importable, + 'importable is true: ' + publishedHistory.importable ); + this.test.assert( publishedHistory.slug === 'published', + 'slug is not null: ' + publishedHistory.slug ); + accessibleLink = 'u/' + email.replace( '@test.test', '' ) + '/h/published'; + this.test.assert( publishedHistory.username_and_slug === accessibleLink, + 'username_and_slug is proper: ' + publishedHistory.username_and_slug ); + +}); + +//// ------------------------------------------------------------------------------------------- upload some files +spaceghost.then( function(){ + this.api.tools.thenUpload( inaccessibleHistory.id, { filepath: this.options.scriptDir + '/../../test-data/1.bed' }); + this.api.tools.thenUpload( accessibleHistory.id, { filepath: this.options.scriptDir + '/../../test-data/1.bed' }); + this.api.tools.thenUpload( publishedHistory.id, { filepath: this.options.scriptDir + '/../../test-data/1.bed' }); +}); +spaceghost.then( function(){ + // check that they're there + inaccessibleHdas = this.api.hdas.index( inaccessibleHistory.id ), + accessibleHdas = this.api.hdas.index( accessibleHistory.id ), + publishedHdas = this.api.hdas.index( publishedHistory.id ); + this.test.assert( inaccessibleHdas.length === 1, + 'uploaded file to inaccessible: ' + inaccessibleHdas.length ); + this.test.assert( accessibleHdas.length === 1, + 'uploaded file to accessible: ' + accessibleHdas.length ); + this.test.assert( publishedHdas.length === 1, + 'uploaded file to published: ' + publishedHdas.length ); +}); +spaceghost.user.logout(); + +//// ------------------------------------------------------------------------------------------- log in user2 +function ensureInaccessibility( history, hdas ){ + + this.test.comment( 'all four CRUD API calls should fail for user2 with history: ' + history.name ); + this.api.assertRaises( function(){ + this.api.histories.show( history.id ); + }, 400, 'History is not accessible to the current user', 'show failed with error' ); + this.api.assertRaises( function(){ + this.api.histories.create({ history_id : history.id }); + }, 403, 'History is not accessible to the current user', 'copy failed with error' ); + this.api.assertRaises( function(){ + this.api.histories.update( history.id, { deleted: true }); + }, 500, 'History is not owned by the current user', 'update failed with error' ); + this.api.assertRaises( function(){ + this.api.histories.delete_( history.id ); + }, 400, 'History is not owned by the current user', 'delete failed with error' ); + + this.test.comment( 'all four HDA CRUD API calls should fail for user2 with history: ' + history.name ); + this.api.assertRaises( function(){ + this.api.hdas.index( history.id ); + }, 500, 'History is not accessible to the current user', 'index failed with error' ); + this.api.assertRaises( function(){ + this.api.hdas.show( history.id, hdas[0].id ); + }, 500, 'History is not accessible to the current user', 'show failed with error' ); + this.api.assertRaises( function(){ + this.api.hdas.update( history.id, hdas[0].id, { deleted: true }); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'update failed with error' ); + this.api.assertRaises( function(){ + this.api.hdas.delete_( history.id, hdas[0].id ); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'delete failed with error' ); + + this.test.comment( 'Attempting to copy an accessible hda (default is accessible)' + + 'from an inaccessible history should fail' ); + this.api.assertRaises( function(){ + var returned = this.api.hdas.create( this.api.histories.show( 'current' ).id, { + source : 'hda', + content : hdas[0].id + }); + this.debug( this.jsonStr( returned ) ); + }, 403, 'History is not accessible to the current user', 'copy failed with error' ); + +} +spaceghost.user.loginOrRegisterUser( email2, password2 ); +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + + // ----------------------------------------------------------------------------------------- user2 + inaccessible + ensureInaccessibility.call( spaceghost, inaccessibleHistory, inaccessibleHdas ); + + // ----------------------------------------------------------------------------------------- user2 + accessible + this.test.comment( 'show should work for the importable history' ); + this.test.assert( this.api.histories.show( accessibleHistory.id ).id === accessibleHistory.id, + 'show worked' ); + + this.test.comment( 'create/copy should work for the importable history' ); + var returned = this.api.histories.create({ history_id : accessibleHistory.id }); + this.test.assert( returned.name === "Copy of '" + accessibleHistory.name + "'", + 'copied name matches: ' + returned.name ); + + this.test.comment( 'update should fail for the importable history' ); + this.api.assertRaises( function(){ + this.api.histories.update( accessibleHistory.id, { deleted: true }); + }, 500, 'History is not owned by the current user', 'update failed with error' ); + this.test.comment( 'delete should fail for the importable history' ); + this.api.assertRaises( function(){ + this.api.histories.delete_( accessibleHistory.id ); + }, 400, 'History is not owned by the current user', 'delete failed with error' ); + + this.test.comment( 'indexing should work for the contents of the importable history' ); + this.test.assert( this.api.hdas.index( accessibleHistory.id ).length === 1, + 'index worked' ); + this.test.comment( 'showing should work for the contents of the importable history' ); + this.test.assert( this.api.hdas.show( accessibleHistory.id, accessibleHdas[0].id ).id === accessibleHdas[0].id, + 'show worked' ); + this.test.comment( 'updating should fail for the contents of the importable history' ); + this.api.assertRaises( function(){ + this.api.hdas.update( accessibleHistory.id, accessibleHdas[0].id, { deleted: true }); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'update failed with error' ); + this.test.comment( 'deleting should fail for the contents of the importable history' ); + this.api.assertRaises( function(){ + this.api.hdas.delete_( accessibleHistory.id, accessibleHdas[0].id ); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'delete failed with error' ); + this.test.comment( 'copying a dataset from the importable history should work' ); + returned = this.api.hdas.create( this.api.histories.show( 'current' ).id, { + source : 'hda', + content : accessibleHdas[0].id + }); + this.test.assert( returned.name === accessibleHdas[0].name, 'successful copy from: ' + returned.name ); + + this.test.comment( 'copying a dataset into the importable history should fail' ); + this.api.assertRaises( function(){ + this.api.hdas.create( accessibleHistory.id, { + source : 'hda', + // should error before it checks the id + content : 'bler' + }); + }, 400, 'History is not owned by the current user', 'copy to failed' ); + + //// ----------------------------------------------------------------------------------------- user2 + published + this.test.comment( 'show should work for the published history' ); + this.test.assert( this.api.histories.show( publishedHistory.id ).id === publishedHistory.id, + 'show worked' ); + this.test.comment( 'create/copy should work for the published history' ); + returned = this.api.histories.create({ history_id : publishedHistory.id }); + this.test.assert( returned.name === "Copy of '" + publishedHistory.name + "'", + 'copied name matches: ' + returned.name ); + this.test.comment( 'update should fail for the published history' ); + this.api.assertRaises( function(){ + this.api.histories.update( publishedHistory.id, { deleted: true }); + }, 500, 'History is not owned by the current user', 'update failed with error' ); + this.test.comment( 'delete should fail for the published history' ); + this.api.assertRaises( function(){ + this.api.histories.delete_( publishedHistory.id ); + }, 400, 'History is not owned by the current user', 'delete failed with error' ); + + this.test.comment( 'indexing should work for the contents of the published history' ); + this.test.assert( this.api.hdas.index( publishedHistory.id ).length === 1, + 'index worked' ); + this.test.comment( 'showing should work for the contents of the published history' ); + this.test.assert( this.api.hdas.show( publishedHistory.id, publishedHdas[0].id ).id === publishedHdas[0].id, + 'show worked' ); + this.test.comment( 'updating should fail for the contents of the published history' ); + this.api.assertRaises( function(){ + this.api.hdas.update( publishedHistory.id, publishedHdas[0].id, { deleted: true }); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'update failed with error' ); + this.test.comment( 'deleting should fail for the contents of the published history' ); + this.api.assertRaises( function(){ + this.api.hdas.delete_( publishedHistory.id, publishedHdas[0].id ); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'delete failed with error' ); + + this.test.comment( 'copying a dataset from the published history should work' ); + returned = this.api.hdas.create( this.api.histories.show( 'current' ).id, { + source : 'hda', + content : publishedHdas[0].id + }); + this.test.assert( returned.name === publishedHdas[0].name, 'successful copy from: ' + returned.name ); + + this.test.comment( 'copying a dataset into the published history should fail' ); + this.api.assertRaises( function(){ + this.api.hdas.create( publishedHistory.id, { + source : 'hda', + // should error before it checks the id + content : 'bler' + }); + }, 400, 'History is not owned by the current user', 'copy to failed' ); +}); +spaceghost.user.logout(); + + +//// ------------------------------------------------------------------------------------------- user1 revoke perms +spaceghost.user.loginOrRegisterUser( email, password ); +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + this.test.comment( 'revoking perms should prevent access' ); + this.api.histories.update( accessibleHistory.id, { + importable : false + }); + var returned = this.api.histories.show( accessibleHistory.id ); + this.test.assert( !returned.importable, 'now not importable' ); + this.test.assert( !returned.published, '(still not published)' ); + this.test.assert( !!returned.slug, '(slug still set) ' + returned.slug ); + + this.api.histories.update( publishedHistory.id, { + importable : false, + published : false + }); + returned = this.api.histories.show( publishedHistory.id ); + this.test.assert( !returned.importable, 'now not importable' ); + this.test.assert( !returned.published, 'now not published' ); + this.test.assert( !!returned.slug, '(slug still set) ' + returned.slug ); +}); +spaceghost.user.logout(); + + +//// ------------------------------------------------------------------------------------------- user2 retry perms +spaceghost.user.loginOrRegisterUser( email2, password2 ); +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + ensureInaccessibility.call( spaceghost, accessibleHistory, accessibleHdas ); + ensureInaccessibility.call( spaceghost, publishedHistory, publishedHdas ); +}); + +// =================================================================== +spaceghost.run( function(){ +}); diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/api-history-tests.js --- a/test/casperjs/api-history-tests.js +++ b/test/casperjs/api-history-tests.js @@ -33,25 +33,6 @@ } spaceghost.user.loginOrRegisterUser( email, password ); -function hasKeys( object, keysArray ){ - if( !utils.isObject( object ) ){ return false; } - for( var i=0; i<keysArray.length; i += 1 ){ - if( !object.hasOwnProperty( keysArray[i] ) ){ - spaceghost.debug( 'object missing key: ' + keysArray[i] ); - return false; - } - } - return true; -} - -function countKeys( object ){ - if( !utils.isObject( object ) ){ return 0; } - var count = 0; - for( var key in object ){ - if( object.hasOwnProperty( key ) ){ count += 1; } - } - return count; -} // =================================================================== TESTS spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ @@ -64,7 +45,7 @@ this.test.assert( historyIndex.length >= 1, 'Has at least one history' ); var firstHistory = historyIndex[0]; - this.test.assert( hasKeys( firstHistory, [ 'id', 'name', 'url' ] ), 'Has the proper keys' ); + this.test.assert( this.hasKeys( firstHistory, [ 'id', 'name', 'url' ] ), 'Has the proper keys' ); this.test.assert( this.api.isEncodedId( firstHistory.id ), 'Id appears well-formed' ); @@ -72,7 +53,7 @@ this.test.comment( 'show should get a history details object' ); var historyShow = this.api.histories.show( firstHistory.id ); //this.debug( this.jsonStr( historyShow ) ); - this.test.assert( hasKeys( historyShow, [ + this.test.assert( this.hasKeys( historyShow, [ 'id', 'name', 'annotation', 'nice_size', 'contents_url', 'state', 'state_details', 'state_ids' ]), 'Has the proper keys' ); @@ -83,8 +64,8 @@ 'ok', 'paused', 'queued', 'running', 'setting_metadata', 'upload' ], state_details = historyShow.state_details, state_ids = historyShow.state_ids; - this.test.assert( hasKeys( state_details, states ), 'state_details has the proper keys' ); - this.test.assert( hasKeys( state_ids, states ), 'state_ids has the proper keys' ); + this.test.assert( this.hasKeys( state_details, states ), 'state_details has the proper keys' ); + this.test.assert( this.hasKeys( state_ids, states ), 'state_ids has the proper keys' ); var state_detailsAreNumbers = true; state_idsAreArrays = true; states.forEach( function( state ){ @@ -103,20 +84,19 @@ this.test.assert( this.api.histories.show( this.api.histories.index()[0].id ).id === firstHistory.id, 'combining function calls works' ); - // test server bad id protection - this.test.comment( 'A bad id to show should throw an error' ); - this.assertRaises( function(){ - this.api.histories.show( '1234123412341234' ); - }, '400 Bad Request', 'Raises an exception' ); + this.test.comment( 'Calling show with "current" should return the current history' ); + this.test.assert( this.api.histories.show( 'current' ).id === historyShow.id, 'current returned same id' ); // ------------------------------------------------------------------------------------------- CREATE - this.test.comment( 'Calling create should create a new history and allow setting the name' ); + this.test.comment( 'Calling create should create a new history and allow setting the name and making it current' ); var newHistoryName = 'Created History', - createdHistory = this.api.histories.create({ name: newHistoryName }); + createdHistory = this.api.histories.create({ name: newHistoryName, current: true }); //this.debug( 'returned from create:\n' + this.jsonStr( createdHistory ) ); this.test.assert( createdHistory.name === newHistoryName, "Name of created history (from create) is correct: " + createdHistory.name ); + this.test.assert( this.api.histories.show( 'current' ).id === createdHistory.id, + "was made current" ); // check the index var newFirstHistory = this.api.histories.index()[0]; @@ -156,50 +136,25 @@ "Undeletion returned 'OK' - even though that's not a great, informative response: " + undeletedHistory ); newFirstHistory = this.api.histories.index()[0]; - this.debug( 'newFirstHistory:\n' + this.jsonStr( newFirstHistory ) ); + //this.debug( 'newFirstHistory:\n' + this.jsonStr( newFirstHistory ) ); this.test.assert( newFirstHistory.id === createdHistory.id, "Id of last history (from index) DOES appear after undeletion: " + newFirstHistory.id ); //TODO: show, deleted flag //TODO: delete, purge flag + + + // ------------------------------------------------------------------------------------------- set_as_current + this.test.comment( 'calling set_as_current on a non-current history will make it current' ); + this.test.assert( this.api.histories.show( 'current' ).id !== historyShow.id, historyShow.id + ' is not current' ); + var returned = this.api.histories.set_as_current( historyShow.id ); + this.debug( this.jsonStr( returned ) ); + this.test.assert( this.api.histories.show( 'current' ).id === historyShow.id, 'made current' ); + this.api.histories.set_as_current( newFirstHistory.id ); + + // ------------------------------------------------------------------------------------------- UPDATE - // ........................................................................................... idiot proofing - this.test.comment( 'updating to the current value should return no value (no change)' ); - historyShow = this.api.histories.show( newFirstHistory.id ); - var returned = this.api.histories.update( newFirstHistory.id, { - name : historyShow.name - }); - this.test.assert( countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); - - this.test.comment( 'updating using a nonsense key should fail silently' ); - var err = null; - try { - returned = this.api.histories.update( newFirstHistory.id, { - konamiCode : 'uuddlrlrba' - }); - } catch( error ){ - err = error; - //this.debug( this.jsonStr( err ) ); - } - this.test.assert( err === null, "No error occurred: " + this.jsonStr( err ) ); - - this.test.comment( 'updating by attempting to change type should cause an error' ); - err = {}; - try { - returned = this.api.histories.update( newFirstHistory.id, { - //name : false - deleted : 'sure why not' - }); - } catch( error ){ - err = error; - //this.debug( this.jsonStr( err ) ); - } - this.test.assert( !!err.message, "Error occurred: " + err.message ); - this.test.assert( err.status === 400, "Error status is 400: " + err.status ); - //TODO??: other type checks? - - // ........................................................................................... name this.test.comment( 'update should allow changing the name' ); returned = this.api.histories.update( newFirstHistory.id, { @@ -339,8 +294,58 @@ // ------------------------------------------------------------------------------------------- ERRORS - //TODO: make sure expected errors are being passed back (but no permissions checks here - different suite) - // bad ids: index, show, update, delete, undelete + // ........................................................................................... idiot proofing + this.test.comment( 'updating to the current value should return no value (no change)' ); + historyShow = this.api.histories.show( newFirstHistory.id ); + returned = this.api.histories.update( newFirstHistory.id, { + name : historyShow.name + }); + this.test.assert( this.countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); + + this.test.comment( 'updating using a nonsense key should fail silently' ); + returned = this.api.histories.update( newFirstHistory.id, { + konamiCode : 'uuddlrlrba' + }); + this.test.assert( returned.konamiCode === undefined, 'key was not set: ' + returned.konamiCode ); + + // test server bad id protection + spaceghost.test.comment( 'A bad id should throw an error' ); + this.api.assertRaises( function(){ + this.api.histories.show( '1234123412341234' ); + }, 400, 'unable to decode', 'Bad Request with invalid id: show' ); + spaceghost.test.comment( 'A bad id should throw an error when using update' ); + this.api.assertRaises( function(){ + this.api.histories.update( '1234123412341234', {} ); + }, 500, 'unable to decode', 'Bad Request with invalid id: update' ); + spaceghost.test.comment( 'A bad id should throw an error when using delete' ); + this.api.assertRaises( function(){ + this.api.histories.delete_( '1234123412341234' ); + }, 400, 'unable to decode', 'Bad Request with invalid id: delete' ); + spaceghost.test.comment( 'A bad id should throw an error when using undelete' ); + this.api.assertRaises( function(){ + this.api.histories.undelete( '1234123412341234' ); + }, 400, 'unable to decode', 'Bad Request with invalid id: undelete' ); + + this.test.comment( 'updating by attempting to change type should cause an error' ); + [ 'name', 'annotation' ].forEach( function( key ){ + var updatedAttrs = {}; + updatedAttrs[ key ] = false; + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.histories.update( newFirstHistory.id, updatedAttrs ); + }, 400, key + ' must be a string or unicode', 'type validation error' ); + }); + [ 'deleted', 'importable', 'published' ].forEach( function( key ){ + var updatedAttrs = {}; + updatedAttrs[ key ] = 'straaang'; + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.histories.update( newFirstHistory.id, updatedAttrs ); + }, 400, key + ' must be a boolean', 'type validation error' ); + }); + [ 'you\'re it', [ true ] ].forEach( function( badVal ){ + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.histories.update( newFirstHistory.id, { tags: badVal }); + }, 400, 'tags must be a list', 'type validation error' ); + }); /* */ //this.debug( this.jsonStr( historyShow ) ); diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/casperjs_runner.py --- a/test/casperjs/casperjs_runner.py +++ b/test/casperjs/casperjs_runner.py @@ -81,6 +81,7 @@ """ # debugging flag - set to true to have casperjs tests output with --verbose=true and --logLevel=debug + #debug = True debug = False # bit of a hack - this is the beginning of the last string when capserjs --verbose=true --logLevel=debug # use this to get subprocess to stop waiting for output @@ -191,6 +192,7 @@ except ValueError, val_err: if str( val_err ) == 'No JSON object could be decoded': log.debug( '(error parsing returned JSON from casperjs, dumping stdout...)\n:%s', stdout_output ) + return HeadlessJSJavascriptError( 'see log for details' ) else: raise @@ -375,19 +377,29 @@ class Test_04_HDAs( CasperJSTestCase ): """Tests for HistoryDatasetAssociation fetching, rendering, and modeling. """ - def test_00_HDA_states( self ): - """Test structure rendering of HDAs in all the possible HDA states - """ - self.run_js_script( 'hda-state-tests.js' ) + #def test_00_HDA_states( self ): + # """Test structure rendering of HDAs in all the possible HDA states + # """ + # self.run_js_script( 'hda-state-tests.js' ) class Test_05_API( CasperJSTestCase ): """Tests for API functionality and security. """ - def test_00_history_api( self ): - """Test history API. + #def test_00_history_api( self ): + # """Test history API. + # """ + # self.run_js_script( 'api-history-tests.js' ) + + def test_01_hda_api( self ): + """Test HDA API. """ - self.run_js_script( 'api-history-tests.js' ) + self.run_js_script( 'api-hda-tests.js' ) + + def test_02_history_permissions_api( self ): + """Test API permissions for importable, published histories. + """ + self.run_js_script( 'api-history-permission-tests.js' ) # ==================================================================== MAIN diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -75,12 +75,63 @@ if( resp.status !== 200 ){ // grrr... this doesn't lose the \n\r\t //throw new APIError( resp.responseText.replace( /[\s\n\r\t]+/gm, ' ' ).replace( /"/, '' ) ); - this.spaceghost.debug( 'api error response status code: ' + resp.status ); + this.spaceghost.debug( 'API error: code: ' + resp.status + ', responseText: ' + resp.responseText ); + this.spaceghost.debug( '\t responseJSON: ' + this.spaceghost.jsonStr( resp.responseJSON ) ); throw new APIError( resp.responseText, resp.status ); } return JSON.parse( resp.responseText ); }; +// =================================================================== TESTING +/** Checks whether fn raises an error with a message that contains a status and given string. + * NOTE: DOES NOT work with steps. @see SpaceGhost#assertStepsRaise + * @param {Function} testFn a function that may throw an error + * @param {Integer} statusExpected the HTTP status code expected + * @param {String} errMsgContains some portion of the correct error msg + * @private + */ +API.prototype._APIRaises = function _APIRaises( testFn, statusExpected, errMsgContains ){ + var failed = false; + try { + testFn.call( this.spaceghost ); + } catch( err ){ + this.spaceghost.debug( err.name + ': ' + err.status ); + this.spaceghost.debug( err.message ); + if( ( err.name === 'APIError' ) + && ( err.status && err.status === statusExpected ) + && ( err.message.indexOf( errMsgContains ) !== -1 ) ){ + failed = true; + + // re-raise other, non-searched-for errors + } else { + throw err; + } + } + return failed; +}; + +/** Simple assert raises. + * NOTE: DOES NOT work with steps. @see SpaceGhost#assertStepsRaise + * @param {Function} testFn a function that may throw an error + * @param {Integer} statusExpected the HTTP status code expected + * @param {String} errMsgContains some portion of the correct error msg + * @param {String} msg assertion message to display + */ +API.prototype.assertRaises = function assertRaises( testFn, statusExpected, errMsgContains, msg ){ + return this.spaceghost.test.assert( this._APIRaises( testFn, statusExpected, errMsgContains ), msg ); +}; + +/** Simple assert does not raise. + * NOTE: DOES NOT work with steps. @see SpaceGhost#assertStepsRaise + * @param {Function} testFn a function that may throw an error + * @param {Integer} statusExpected the HTTP status code expected + * @param {String} errMsgContains some portion of the correct error msg + * @param {String} msg assertion message to display + */ +API.prototype.assertDoesntRaise = function assertDoesntRaise( testFn, statusExpected, errMsgContains, msg ){ + return this.spaceghost.test.assert( !this._APIRaises( testFn, statusExpected, errMsgContains ), msg ); +}; + // =================================================================== MISC API.prototype.isEncodedId = function isEncodedId( id ){ if( typeof id !== 'string' ){ return false; } @@ -164,7 +215,8 @@ create : 'api/histories', delete_ : 'api/histories/%s', undelete: 'api/histories/deleted/%s/undelete', - update : 'api/histories/%s' + update : 'api/histories/%s', + set_as_current : 'api/histories/%s/set_as_current' }; HistoriesAPI.prototype.index = function index( deleted ){ @@ -179,7 +231,7 @@ HistoriesAPI.prototype.show = function show( id, deleted ){ this.api.spaceghost.info( 'histories.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); - id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); + id = ( id === 'most_recently_used' || id === 'current' )?( id ):( this.api.ensureId( id ) ); deleted = deleted || false; return this.api._ajax( utils.format( this.urlTpls.show, id ), { data : { deleted: deleted } @@ -217,7 +269,7 @@ }); }; -HistoriesAPI.prototype.update = function create( id, payload ){ +HistoriesAPI.prototype.update = function update( id, payload ){ this.api.spaceghost.info( 'histories.update: ' + id + ',' + this.api.spaceghost.jsonStr( payload ) ); // py.payload <-> ajax.data @@ -231,6 +283,15 @@ }); }; +HistoriesAPI.prototype.set_as_current = function set_as_current( id ){ + this.api.spaceghost.info( 'histories.set_as_current: ' + id ); + id = this.api.ensureId( id ); + + return this.api._ajax( utils.format( this.urlTpls.set_as_current, id ), { + type : 'PUT' + }); +}; + // =================================================================== HDAS var HDAAPI = function HDAAPI( api ){ @@ -297,6 +358,23 @@ }); }; +HDAAPI.prototype.delete_ = function create( historyId, id, purge ){ + this.api.spaceghost.info( 'hdas.delete_: ' + [ historyId, id ] ); + historyId = this.api.ensureId( historyId ); + id = this.api.ensureId( id ); + + // have to attach like GET param - due to body loss in jq + url = utils.format( this.urlTpls.update, historyId, id ); + if( purge ){ + url += '?purge=True'; + } + return this.api._ajax( url, { + type : 'DELETE' + }); +}; + +//TODO: delete_ + // =================================================================== TOOLS var ToolsAPI = function HDAAPI( api ){ @@ -350,6 +428,218 @@ }); }; +//ToolsAPI.prototype.uploadByForm = function upload( historyId, options ){ +// this.api.spaceghost.debug( '-------------------------------------------------' ); +// this.api.spaceghost.info( 'tools.upload: ' + [ historyId, '(contents)', this.api.spaceghost.jsonStr( options ) ] ); +// this.api.ensureId( historyId ); +// options = options || {}; +// +// this.api.spaceghost.evaluate( function( url ){ +// var html = [ +// '<form action="', url, '" method="post" enctype="multipart/form-data">', +// '<input type="file" name="files_0|file_data">', +// '<input type="hidden" name="tool_id" />', +// '<input type="hidden" name="history_id" />', +// '<input type="hidden" name="inputs" />', +// '<button type="submit">Submit</button>', +// '</form>' +// ]; +// document.write( html.join('') ); +// //document.getElementsByTagName( 'body' )[0].innerHTML = html.join(''); +// }, utils.format( this.urlTpls.create ) ); +// +// this.api.spaceghost.fill( 'form', { +// 'files_0|file_data' : '1.txt', +// 'tool_id' : 'upload1', +// 'history_id' : historyId, +// 'inputs' : JSON.stringify({ +// 'file_type' : 'auto', +// 'files_0|type' : 'upload_dataset', +// 'to_posix_lines' : true, +// 'space_to_tabs' : false, +// 'dbkey' : '?' +// }) +// }, true ); +// // this causes the page to switch...I think +//}; + +/** paste a file - either from a string (options.paste) or from a filesystem file (options.filepath) */ +ToolsAPI.prototype.uploadByPaste = function upload( historyId, options ){ + this.api.spaceghost.info( 'tools.upload: ' + [ historyId, this.api.spaceghost.jsonStr( options ) ] ); + this.api.ensureId( historyId ); + options = options || {}; + + var inputs = { + 'files_0|NAME' : options.name || 'Test Dataset', + 'dbkey' : options.dbkey || '?', + 'file_type' : options.ext || 'auto' + }; + if( options.filepath ){ + var fs = require( 'fs' ); + inputs[ 'files_0|url_paste' ] = fs.read( options.filepath ); + + } else if( options.paste ){ + inputs[ 'files_0|url_paste' ] = options.paste; + } + if( options.posix ){ + inputs[ 'files_0|to_posix_lines' ] = 'Yes'; + } + if( options.tabs ){ + inputs[ 'files_0|space_to_tab' ] = 'Yes'; + } + return this.api._ajax( utils.format( this.urlTpls.create ), { + type : 'POST', + data : { + tool_id : 'upload1', + upload_type : 'upload_dataset', + history_id : historyId, + inputs : inputs + } + }); +}; + +/** post a file to the upload1 tool over ajax */ +ToolsAPI.prototype.upload = function upload( historyId, options ){ + this.api.spaceghost.info( 'tools.upload: ' + [ historyId, this.api.spaceghost.jsonStr( options ) ] ); + this.api.ensureId( historyId ); + options = options || {}; + + // We can post an upload using jquery and formdata (see below), the more + // difficult part is attaching the file without user intervention. + // To do this we need to (unfortunately) create a form phantom can attach the file to first. + this.api.spaceghost.evaluate( function(){ + $( 'body' ).append( '<input type="file" name="casperjs-upload-file" />' ); + }); + this.api.spaceghost.page.uploadFile( 'input[name="casperjs-upload-file"]', options.filepath ); + + var inputs = { + 'file_type' : options.ext || 'auto', + 'files_0|type' : 'upload_dataset', + 'dbkey' : options.dbkey || '?' + }; + if( options.posix ){ + inputs[ 'files_0|to_posix_lines' ] = 'Yes'; + } + if( options.tabs ){ + inputs[ 'files_0|space_to_tab' ] = 'Yes'; + } + var response = this.api.spaceghost.evaluate( function( url, historyId, inputs ){ + var file = $( 'input[name="casperjs-upload-file"]' )[0].files[0], + formData = new FormData(), + response; + + formData.append( 'files_0|file_data', file ); + formData.append( 'history_id', historyId ); + formData.append( 'tool_id', 'upload1' ); + formData.append( 'inputs', JSON.stringify( inputs ) ); + $.ajax({ + url : url, + async : false, + type : 'POST', + data : formData, + // when sending FormData don't have jq process or cache the data + cache : false, + contentType : false, + processData : false, + // if we don't add this, payload isn't processed as JSON + headers : { 'Accept': 'application/json' } + }).done(function( resp ){ + response = resp; + }); + // this works only bc jq is async + return response; + }, utils.format( this.urlTpls.create ), historyId, inputs ); + + if( !response ){ + throw new APIError( 'Failed to upload: ' + options.filepath, 0 ); + } + + return response; +}; + +/** amount of time allowed to upload a file (before erroring) */ +ToolsAPI.prototype.DEFAULT_UPLOAD_TIMEOUT = 12000; + +/** add two casperjs steps - upload a file, wait for the job to complete, and run 'then' when they are */ +ToolsAPI.prototype.thenUpload = function thenUpload( historyId, options, then ){ + var spaceghost = this.api.spaceghost, + uploadedId; + + spaceghost.then( function(){ + var returned = this.api.tools.upload( historyId, options ); + this.debug( 'returned: ' + this.jsonStr( returned ) ); + uploadedId = returned.outputs[0].id; + this.debug( 'uploadedId: ' + uploadedId ); + }); + + spaceghost.then( function(){ + this.waitFor( + function testHdaState(){ + var hda = spaceghost.api.hdas.show( historyId, uploadedId ); + spaceghost.debug( spaceghost.jsonStr( hda.state ) ); + return !( hda.state === 'upload' || hda.state === 'queued' || hda.state === 'running' ); + }, + function _then(){ + spaceghost.info( 'upload finished: ' + uploadedId ); + if( then ){ + then.call( spaceghost, uploadedId ); + } + //var hda = spaceghost.api.hdas.show( historyId, uploadedId ); + //spaceghost.debug( spaceghost.jsonStr( hda ) ); + }, + function timeout(){ + throw new APIError( 'timeout uploading file', 408 ); + }, + options.timeout || spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT + ); + }); + return spaceghost; +}; + +/** add two casperjs steps - upload multiple files (described in optionsArray) and wait for all jobs to complete */ +ToolsAPI.prototype.thenUploadMultiple = function thenUploadMultiple( historyId, optionsArray, then ){ + var spaceghost = this.api.spaceghost, + uploadedIds = []; + + this.api.spaceghost.then( function(){ + var spaceghost = this; + optionsArray.forEach( function( options ){ + var returned = spaceghost.api.tools.upload( historyId, options ); + spaceghost.debug( 'uploaded:' + spaceghost.jsonStr( returned ) ); + uploadedIds.push( returned.outputs[0].id ); + }); + }); + + // wait for every hda to finish running - IOW, don't use uploadedIds + this.api.spaceghost.then( function(){ + this.debug( this.jsonStr( uploadedIds ) ); + this.waitFor( + function testHdaStates(){ + var hdas = spaceghost.api.hdas.index( historyId ), + running = hdas.filter( function( hda ){ + return ( hda.state === 'upload' || hda.state === 'queued' || hda.state === 'running' ); + }).map( function( hda ){ + return hda.id; + }); + //spaceghost.debug( 'still uploading: ' + spaceghost.jsonStr( running ) ); + return running.length === 0; + }, + function _then(){ + var hdas = spaceghost.api.hdas.index( historyId ); + spaceghost.debug( spaceghost.jsonStr( hdas ) ); + if( then ){ + then.call( spaceghost, uploadedIds ); + } + }, + function timeout(){ + throw new APIError( 'timeout uploading files', 408 ); + }, + ( options.timeout || spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ) * optionsArray.length + ); + }); + return spaceghost; +}; + // =================================================================== WORKFLOWS var WorkflowsAPI = function WorkflowsAPI( api ){ @@ -495,7 +785,7 @@ }; -// =================================================================== HISTORIES +// =================================================================== VISUALIZATIONS var VisualizationsAPI = function VisualizationsAPI( api ){ this.api = api; }; diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -280,6 +280,9 @@ User.prototype.getRandomEmail = function getRandomEmail( username, domain ){ username = username || 'test'; domain = domain || 'test.test'; - return username + Date.now() + '@' + domain; + var number = Math.ceil( Math.random() * 10000000000000 ); + // doesn't work so well when creating two users at once + //var number = Date.now(); + return username + number + '@' + domain; }; diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -886,6 +886,30 @@ this.test.assert( classes.indexOf( className ) === -1, msg ); }; +/** Return true if object has all keys in keysArray (useful in API testing of return values). + * @param {Object} object the object to test + * @param {String[]} keysArray an array of expected keys + */ +SpaceGhost.prototype.hasKeys = function hasKeys( object, keysArray ){ + if( !utils.isObject( object ) ){ return false; } + for( var i=0; i<keysArray.length; i += 1 ){ + if( !object.hasOwnProperty( keysArray[i] ) ){ + return false; + } + } + return true; +}; + +/** Returns count of keys in object. */ +SpaceGhost.prototype.countKeys = function countKeys( object ){ + if( !utils.isObject( object ) ){ return 0; } + var count = 0; + for( var key in object ){ + if( object.hasOwnProperty( key ) ){ count += 1; } + } + return count; +}; + // =================================================================== CONVENIENCE /** Wraps casper.getElementInfo in try, returning null if element not found instead of erroring. https://bitbucket.org/galaxy/galaxy-central/commits/561929fb2d7e/ Changeset: 561929fb2d7e User: carlfeberhard Date: 2014-03-25 22:00:03 Summary: merge Affected #: 3 files diff -r 79ab14af25e4182dac99ecad3918ed653c50f272 -r 561929fb2d7e827f20ea078904aeebe35173f3f9 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1106,6 +1106,10 @@ }); // For vertical alignment, track mouse with simple line. + // Fixes needed for this to work: + // (a) make work with embedded visualizations; + // (b) seems to get stuck on tile overlaps. + /* var mouse_tracker_div = $('<div/>').addClass('mouse-pos').appendTo(parent_element); // Show tracker only when hovering over view. @@ -1125,6 +1129,7 @@ mouse_tracker_div.hide(); } ); + */ this.add_label_track( new LabelTrack( this, { content_div: this.top_labeltrack } ) ); this.add_label_track( new LabelTrack( this, { content_div: this.nav_labeltrack } ) ); @@ -3053,14 +3058,21 @@ var tile_drawn = $.Deferred(); track.tile_cache.set_elt(key, tile_drawn); $.when.apply($, get_tile_data()).then( function() { - // If deferred objects ever show up in tile data, that is likely because a - // Deferred-subsetting interaction failed. Specifically, a Deferred for a superset - // was returned but then couldn't be used). It's not clear whether this will happen - // in practice, and currently the code doesn't handle it. It could probably handle it - // by recursively calling draw_helper. var tile_data = get_tile_data(), tracks_data = tile_data, seq_data; + + // Deferreds may show up here if trying to fetch a subset of data from a superset data chunk + // that cannot be subsetted. This may occur if the superset has a message. If there is a + // Deferred, try again from the top. NOTE: this condition could (should?) be handled by the + // GenomeDataManager in visualization module. + if (_.find(tile_data, function(d) { return util.is_deferred(d); })) { + track.tile_cache.set_elt(key, undefined); + $.when(track.draw_helper(region, w_scale, options)).then(function(tile) { + tile_drawn.resolve(tile); + }); + return; + } // If sequence data is available, subset to get only data in region. if (view.reference_track) { diff -r 79ab14af25e4182dac99ecad3918ed653c50f272 -r 561929fb2d7e827f20ea078904aeebe35173f3f9 static/scripts/viz/trackster/util.js --- a/static/scripts/viz/trackster/util.js +++ b/static/scripts/viz/trackster/util.js @@ -1,6 +1,13 @@ define(function(){ /** + * Helper to determine if object is jQuery deferred. + */ +var is_deferred = function ( d ) { + return ('promise' in d); +}; + +/** * Implementation of a server-state based deferred. Server is repeatedly polled, and when * condition is met, deferred is resolved. */ @@ -109,6 +116,7 @@ }; return { + is_deferred: is_deferred, ServerStateDeferred : ServerStateDeferred, get_random_color : get_random_color }; diff -r 79ab14af25e4182dac99ecad3918ed653c50f272 -r 561929fb2d7e827f20ea078904aeebe35173f3f9 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -86,14 +86,6 @@ }); }; - -/** - * Helper to determine if object is jQuery deferred. - */ -var is_deferred = function ( d ) { - return ('promise' in d); -}; - // --------- Models --------- /** @@ -380,11 +372,10 @@ * Get data from dataset. */ get_data: function(region, mode, resolution, extra_params) { - // Look for entry and return if it's a deferred or if data available is compatible with mode. var entry = this.get_elt(region); if ( entry && - ( is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) { + ( util_mod.is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) { return entry; } @@ -405,12 +396,12 @@ // This entry has data in the requested range. Return if data // is compatible and can be subsetted. entry = obj_cache[entry_region.toString()]; - if ( is_deferred(entry) || + if ( util_mod.is_deferred(entry) || ( this.get('data_mode_compatible')(entry, mode) && this.get('can_subset')(entry) ) ) { this.move_key_to_end(entry_region, i); // If there's data, subset it. - if ( !is_deferred(entry) ) { + if ( !util_mod.is_deferred(entry) ) { var subset_entry = this.subset_entry(entry, region); this.set(region, subset_entry); entry = subset_entry; 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: Jeremy Goecks: Trackster: (a) fix bug when trying to subset from supersets with messages; (b) display vertical placeholder until bugs are resolved.
by commits-noreply＠bitbucket.org 25 Mar '14

25 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/47211cedc8d0/ Changeset: 47211cedc8d0 User: Jeremy Goecks Date: 2014-03-25 20:41:40 Summary: Trackster: (a) fix bug when trying to subset from supersets with messages; (b) display vertical placeholder until bugs are resolved. Affected #: 3 files diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r 47211cedc8d0db9a3d9189bc2d3bfa7e3fe11b86 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1106,6 +1106,10 @@ }); // For vertical alignment, track mouse with simple line. + // Fixes needed for this to work: + // (a) make work with embedded visualizations; + // (b) seems to get stuck on tile overlaps. + /* var mouse_tracker_div = $('<div/>').addClass('mouse-pos').appendTo(parent_element); // Show tracker only when hovering over view. @@ -1125,6 +1129,7 @@ mouse_tracker_div.hide(); } ); + */ this.add_label_track( new LabelTrack( this, { content_div: this.top_labeltrack } ) ); this.add_label_track( new LabelTrack( this, { content_div: this.nav_labeltrack } ) ); @@ -3053,14 +3058,21 @@ var tile_drawn = $.Deferred(); track.tile_cache.set_elt(key, tile_drawn); $.when.apply($, get_tile_data()).then( function() { - // If deferred objects ever show up in tile data, that is likely because a - // Deferred-subsetting interaction failed. Specifically, a Deferred for a superset - // was returned but then couldn't be used). It's not clear whether this will happen - // in practice, and currently the code doesn't handle it. It could probably handle it - // by recursively calling draw_helper. var tile_data = get_tile_data(), tracks_data = tile_data, seq_data; + + // Deferreds may show up here if trying to fetch a subset of data from a superset data chunk + // that cannot be subsetted. This may occur if the superset has a message. If there is a + // Deferred, try again from the top. NOTE: this condition could (should?) be handled by the + // GenomeDataManager in visualization module. + if (_.find(tile_data, function(d) { return util.is_deferred(d); })) { + track.tile_cache.set_elt(key, undefined); + $.when(track.draw_helper(region, w_scale, options)).then(function(tile) { + tile_drawn.resolve(tile); + }); + return; + } // If sequence data is available, subset to get only data in region. if (view.reference_track) { diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r 47211cedc8d0db9a3d9189bc2d3bfa7e3fe11b86 static/scripts/viz/trackster/util.js --- a/static/scripts/viz/trackster/util.js +++ b/static/scripts/viz/trackster/util.js @@ -1,6 +1,13 @@ define(function(){ /** + * Helper to determine if object is jQuery deferred. + */ +var is_deferred = function ( d ) { + return ('promise' in d); +}; + +/** * Implementation of a server-state based deferred. Server is repeatedly polled, and when * condition is met, deferred is resolved. */ @@ -109,6 +116,7 @@ }; return { + is_deferred: is_deferred, ServerStateDeferred : ServerStateDeferred, get_random_color : get_random_color }; diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r 47211cedc8d0db9a3d9189bc2d3bfa7e3fe11b86 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -86,14 +86,6 @@ }); }; - -/** - * Helper to determine if object is jQuery deferred. - */ -var is_deferred = function ( d ) { - return ('promise' in d); -}; - // --------- Models --------- /** @@ -380,11 +372,10 @@ * Get data from dataset. */ get_data: function(region, mode, resolution, extra_params) { - // Look for entry and return if it's a deferred or if data available is compatible with mode. var entry = this.get_elt(region); if ( entry && - ( is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) { + ( util_mod.is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) { return entry; } @@ -405,12 +396,12 @@ // This entry has data in the requested range. Return if data // is compatible and can be subsetted. entry = obj_cache[entry_region.toString()]; - if ( is_deferred(entry) || + if ( util_mod.is_deferred(entry) || ( this.get('data_mode_compatible')(entry, mode) && this.get('can_subset')(entry) ) ) { this.move_key_to_end(entry_region, i); // If there's data, subset it. - if ( !is_deferred(entry) ) { + if ( !util_mod.is_deferred(entry) ) { var subset_entry = this.subset_entry(entry, region); this.set(region, subset_entry); entry = subset_entry; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Ui/Upload: Close modal on escape
by commits-noreply＠bitbucket.org 25 Mar '14

25 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4d2f3398ad6d/ Changeset: 4d2f3398ad6d User: guerler Date: 2014-03-25 19:01:26 Summary: Ui/Upload: Close modal on escape Affected #: 2 files diff -r 208533b58c7e135e99a74e7cf5183a63020b3341 -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 static/scripts/mvc/ui/ui-modal.js --- a/static/scripts/mvc/ui/ui-modal.js +++ b/static/scripts/mvc/ui/ui-modal.js @@ -115,7 +115,7 @@ this.$el.remove(); // remove escape event - $(document).off('keyup'); + $(document).off('keyup.ui-modal'); } // create new element @@ -157,13 +157,11 @@ // bind additional closing events if (this.options.closing_events) { // bind the ESC key to hide() function - if (!this.options.buttons.Pause){ // don't bind for the upload modal because of the side effects with system modal for file choosing - $(document).on('keyup', function(e) { - if (e.keyCode == 27) { - self.hide(); - } - }); - } + $(document).on('keyup.ui-modal', function(e) { + if (e.keyCode == 27) { + self.hide(); + } + }); // hide modal if background is clicked this.$el.find('.modal-backdrop').on('click', function() { self.hide(); }); diff -r 208533b58c7e135e99a74e7cf5183a63020b3341 -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 static/scripts/packed/mvc/ui/ui-modal.js --- a/static/scripts/packed/mvc/ui/ui-modal.js +++ b/static/scripts/packed/mvc/ui/ui-modal.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:true,height:null,width:null,closing_events:false},buttonList:{},initialize:function(c){if(c){this._create(c)}},show:function(c){this.initialize(c);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.visible=false;this.$el.fadeOut("fast")},enableButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).prop("disabled",false)},disableButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).prop("disabled",true)},showButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).show()},hideButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).hide()},getButton:function(c){var d=this.buttonList[c];return this.$buttons.find("#"+d)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var d=this;this.options=_.defaults(e,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove();$(document).off("keyup")}this.setElement(this._template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){this.buttonList={};var c=0;$.each(this.options.buttons,function(f,h){var g="button-"+c++;d.$buttons.append($('<button id="'+g+'"></button>').text(f).click(h)).append(" ");d.buttonList[f]=g})}else{this.$footer.hide()}$(this.elMain).append($(this.el));if(this.options.closing_events){if(!this.options.buttons.Pause){$(document).on("keyup",function(f){if(f.keyCode==27){d.hide()}})}this.$el.find(".modal-backdrop").on("click",function(){d.hide()})}},_template:function(c){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+c+'</h4></div><div class="modal-body" style="position: static;"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:true,height:null,width:null,closing_events:false},buttonList:{},initialize:function(c){if(c){this._create(c)}},show:function(c){this.initialize(c);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.visible=false;this.$el.fadeOut("fast")},enableButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).prop("disabled",false)},disableButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).prop("disabled",true)},showButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).show()},hideButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).hide()},getButton:function(c){var d=this.buttonList[c];return this.$buttons.find("#"+d)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var d=this;this.options=_.defaults(e,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove();$(document).off("keyup.ui-modal")}this.setElement(this._template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){this.buttonList={};var c=0;$.each(this.options.buttons,function(f,h){var g="button-"+c++;d.$buttons.append($('<button id="'+g+'"></button>').text(f).click(h)).append(" ");d.buttonList[f]=g})}else{this.$footer.hide()}$(this.elMain).append($(this.el));if(this.options.closing_events){$(document).on("keyup.ui-modal",function(f){if(f.keyCode==27){d.hide()}});this.$el.find(".modal-backdrop").on("click",function(){d.hide()})}},_template:function(c){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+c+'</h4></div><div class="modal-body" style="position: static;"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Fix server error when attempting to create a repository before any categories have been created.
by commits-noreply＠bitbucket.org 25 Mar '14

25 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/208533b58c7e/ Changeset: 208533b58c7e User: davebgx Date: 2014-03-25 18:25:19 Summary: Fix server error when attempting to create a repository before any categories have been created. Affected #: 1 file diff -r cab5878ce755b1736d09a9a74e419eddb12c0f2d -r 208533b58c7e135e99a74e7cf5183a63020b3341 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 @@ -950,7 +950,7 @@ categories = suc.get_categories( trans ) if not categories: message = 'No categories have been configured in this instance of the Galaxy Tool Shed. ' - message += 'An administrator needs to create some via the Administrator control panel before creating repositories.', + message += 'An administrator needs to create some via the Administrator control panel before creating repositories.' status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Improve fit and chart state handling, recalculate chart only if neccessary
by commits-noreply＠bitbucket.org 25 Mar '14

25 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cab5878ce755/ Changeset: cab5878ce755 User: guerler Date: 2014-03-25 13:35:20 Summary: Charts: Improve fit and chart state handling, recalculate chart only if neccessary Affected #: 9 files diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -(function(){var e=this,t=e._,n={},r=Array.prototype,i=Object.prototype,s=Function.prototype,o=r.push,u=r.slice,a=r.concat,f=i.toString,l=i.hasOwnProperty,c=r.forEach,h=r.map,p=r.reduce,d=r.reduceRight,v=r.filter,m=r.every,g=r.some,y=r.indexOf,b=r.lastIndexOf,w=Array.isArray,E=Object.keys,S=s.bind,x=function(e){if(e 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this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&(this.options.buttons.Pause||$(document).on("keyup",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()})}},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}},s.cleanup(t),t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{s._refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"ok",state_info:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},ready:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n),alert("Error loading data:\n"+e.responseText)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.state("ok","Loaded previously saved visualization."),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({height:300,initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template()));var r=this;this.chart.on("redraw",function(){r._draw(r.chart)})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_draw:function(e){var t=this;if(!e.ready()){this.app.log("viewport:_drawChart()","Invalid attempt to draw chart before completion.");return}this.svg&&this.svg.remove(),this.svg=document.createElementNS("http://www.w3.org/2000/svg","svg"),this.svg.setAttribute("height",this.height),this.$el.append(this.svg),this.svg=d3.select(this.$el.find("svg")[0]),e.off("change:state"),e.on("change:state",function(){var n=t.$el.find("#info"),r=n.find("#icon");r.removeClass(),n.show(),n.find("#text").html(e.get("state_info"));var i=e.get("state");switch(i){case"ok":n.hide();break;case"failed":r.addClass("fa fa-warning");break;default:r.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var n=e.get("type"),r=this.app.types.get(n),t=this;require(["plugin/charts/"+n+"/"+n],function(n){var i=new n(t.app,{svg:t.svg});r.execute?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(e,t._defaultRequestDictionary(e))}):i.draw(e,t._defaultRequestDictionary(e))})},_template:function(){return'<div><div id="info" style="text-align: center; margin-top: 20px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-gear",tooltip:"Customize Chart",title:"Customize",onclick:function(){s._wait(s.app.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");e&&(e=" - "+e),this.portlet.title("Charts"+e)},_wait:function(e,t){if(e.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. 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t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var 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n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&(this.options.buttons.Pause||$(document).on("keyup",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}},t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{s._refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},drawable:function(){return this.get("state")=="ok"||this.get("state")=="failed"||this.get("state")=="initialized"},editable:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.state("ok","Loaded previously saved visualization."),this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template()));var r=this;this.chart.on("redraw",function(){r._create_svg(),r._draw(r.chart)}),this.chart.on("change:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":r.chart.trigger("drawable"),e.hide();break;case"failed":r.chart.trigger("drawable"),t.addClass("fa fa-warning");break;case"initialized":r.chart.trigger("drawable"),t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_create_svg:function(){this.svg&&this.svg.remove(),this.$el.append($(this._template_svg())),this.svg=d3.select(this.$el.find("svg")[0])},_draw:function(e){var t=this;if(!e.drawable()){e.off("drawable"),e.on("drawable",function(){t.chart.off("drawable"),e.drawable()&&t._draw(e)});return}e.state("wait","Please wait...");var n=e.get("type"),r=this.app.types.get(n);if(!r.execute||r.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+n+"/"+n],function(n){var i=new n(t.app,{svg:t.svg});r.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){this.app.storage.save(),i.draw(e,t._defaultRequestDictionary(e))}):i.draw(e,t._defaultRequestDictionary(e)):i.draw(e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={groups:[]};t.execute?n.id=e.get("dataset_id_job"):n.id=e.get("dataset_id");var r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n},_template:function(){return'<div style="height: 100%; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_svg:function(){return'<svg style="height: calc(100% - 80px)"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-gear",tooltip:"Customize Chart",title:"Customize",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){if(e.editable())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata..."),this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("initialized","Metadata initialized...")})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}});var u=this;this.table=new t.View({header:!1,onconfirm:function(e){u.chart.groups.length>0?u.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){u.app.modal.hide()},Continue:function(){u.app.modal.hide(),u.table.value(e)}}}):u.table.value(e)},onchange:function(e){u.chart.groups.reset(),u.chart.settings.clear(),u.chart.set({type:e})},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"});var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),h.execute?this.table.add(h.title+" (requires processing)"):this.table.add(h.title),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.app.config.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel(),this.chart.trigger("redraw"),this.app.storage.save()}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_tick:{init:".3"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el),this.storage.load()?(this.go("viewer"),this.chart.trigger("redraw")):this.go("editor")},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/charts/histogram/histogram.js --- a/config/plugins/visualizations/charts/static/charts/histogram/histogram.js +++ b/config/plugins/visualizations/charts/static/charts/histogram/histogram.js @@ -13,9 +13,6 @@ // render draw : function(chart, request_dictionary) { - // update request dataset id - request_dictionary.id = chart.get('dataset_id_job'); - // configure request var index = 0; for (var i in request_dictionary.groups) { diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/library/jobs.js --- a/config/plugins/visualizations/charts/static/library/jobs.js +++ b/config/plugins/visualizations/charts/static/library/jobs.js @@ -17,12 +17,15 @@ cleanup: function(chart) { // cleanup previous dataset file var previous = chart.get('dataset_id_job'); - if (previous) { + if (previous != '') { var self = this; Utils.request('PUT', config.root + 'api/histories/none/contents/' + previous, { deleted: true }, function() { // update galaxy history self._refreshHdas(); }); + + // reset id + chart.set('dataset_id_job', ''); } }, @@ -53,9 +56,6 @@ } } - // cleanup - self.cleanup(chart); - // set chart state chart.state('submit', 'Sending job request...'); diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/library/storage.js --- a/config/plugins/visualizations/charts/static/library/storage.js +++ b/config/plugins/visualizations/charts/static/library/storage.js @@ -77,7 +77,6 @@ this.vis.save() .fail(function(xhr, status, message) { console.error(xhr, status, message); - alert( 'Error loading data:\n' + xhr.responseText ); }) .then(function(response) { if (response && response.id) { @@ -110,6 +109,9 @@ // reset status this.chart.state('ok', 'Loaded previously saved visualization.'); + // reset modified flag + this.chart.set('modified', false); + // return return true; } diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/models/chart.js --- a/config/plugins/visualizations/charts/static/models/chart.js +++ b/config/plugins/visualizations/charts/static/models/chart.js @@ -7,12 +7,15 @@ { // defaults defaults : { - id : null, - title : '', - type : '', - date : null, - state : 'ok', - state_info : '' + id : null, + title : '', + type : '', + date : null, + state : '', + state_info : '', + modified : false, + dataset_id : '', + dataset_id_job : '' }, // initialize @@ -56,7 +59,11 @@ this.set('state', value); }, - ready: function() { + drawable: function() { + return (this.get('state') == 'ok') || (this.get('state') == 'failed') || (this.get('state') == 'initialized'); + }, + + editable: function() { return (this.get('state') == 'ok') || (this.get('state') == 'failed'); } }); diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/views/editor.js --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -222,10 +222,7 @@ // refresh title _refreshTitle: function() { var title = this.chart.get('title'); - if (title) { - title = ' - ' + title; - } - this.portlet.title('Charts' + title); + this.portlet.title(title); }, // update @@ -280,6 +277,9 @@ // update titles this._refreshGroupKey(); + + // reset + this.chart.set('modified', true); }, // remove group diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -98,6 +98,7 @@ gid : id, onchange : function(value) { self.group.set(this.gid, value); + self.chart.set('modified', true); }, value : value, wait : true @@ -112,6 +113,9 @@ list[id] = select; } + // loading + this.chart.state('wait', 'Loading metadata...'); + // get dataset this.app.datasets.request({id : dataset_id}, function(dataset) { // configure columns @@ -133,6 +137,9 @@ list[key].update(self.columns); list[key].show(); } + + // loading + self.chart.state('initialized', 'Metadata initialized...'); }); }, diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/views/viewer.js --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -32,7 +32,7 @@ title : 'Customize', onclick : function() { // attempt to load chart editor - self._wait (self.app.chart, function() { + self._wait (self.chart, function() { self.app.go('editor'); }); } @@ -41,7 +41,7 @@ } }); - // append view port + // append portlet this.portlet.append(this.viewport_view.$el); // set element @@ -71,23 +71,20 @@ // refresh title _refreshTitle: function() { var title = this.chart.get('title'); - if (title) { - title = ' - ' + title; - } - this.portlet.title('Charts' + title); + this.portlet.title(title); }, // wait for chart to be ready _wait: function(chart, callback) { // get chart - if (chart.ready()) { + if (chart.editable()) { callback(); } else { // show modal var self = this; this.app.modal.show({ title : 'Please wait!', - body : 'Your chart is currently being processed. Please wait...', + body : 'Your chart is currently being processed. Please wait and try again.', buttons : { 'Close' : function() {self.app.modal.hide();}, 'Retry' : function() { diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -5,9 +5,6 @@ // widget return Backbone.View.extend( { - // height - height : 300, - // initialize initialize: function(app, options) { @@ -26,8 +23,48 @@ // events var self = this; this.chart.on('redraw', function() { + // create svg element + self._create_svg(); + + // initialize self._draw(self.chart); }); + + // link status handler + this.chart.on('change:state', function() { + // get info element + var $info = self.$el.find('#info'); + + // get icon + var $icon = $info.find('#icon'); + + // remove icon + $icon.removeClass(); + + // show info + $info.show(); + $info.find('#text').html(self.chart.get('state_info')); + + // check status + var state = self.chart.get('state'); + switch (state) { + case 'ok': + self.chart.trigger('drawable'); + $info.hide(); + break; + case 'failed': + self.chart.trigger('drawable'); + $icon.addClass('fa fa-warning'); + break; + case 'initialized': + self.chart.trigger('drawable'); + $icon.addClass('fa fa-warning'); + break; + default: + $icon.addClass('fa fa-spinner fa-spin'); + break; + } + }); }, // show @@ -40,62 +77,36 @@ this.$el.hide(); }, - // add - _draw: function(chart) { - // link this - var self = this; - - // check - if (!chart.ready()) { - this.app.log('viewport:_drawChart()', 'Invalid attempt to draw chart before completion.'); - return; - } - + // create + _create_svg: function() { // clear svg if (this.svg) { this.svg.remove(); } // create - this.svg = document.createElementNS('http://www.w3.org/2000/svg', 'svg'); - this.svg.setAttribute('height', this.height); - this.$el.append(this.svg); + this.$el.append($(this._template_svg())); // find svg element this.svg = d3.select(this.$el.find('svg')[0]); - - // clear all previous handlers (including redraw listeners) - chart.off('change:state'); + }, + + // add + _draw: function(chart) { + // link this + var self = this; - // link status handler - chart.on('change:state', function() { - // get info element - var $info = self.$el.find('#info'); - - // get icon - var $icon = $info.find('#icon'); - - // remove icon - $icon.removeClass(); - - // show info - $info.show(); - $info.find('#text').html(chart.get('state_info')); - - // check status - var state = chart.get('state'); - switch (state) { - case 'ok': - $info.hide(); - break; - case 'failed': - $icon.addClass('fa fa-warning'); - break; - default: - $icon.addClass('fa fa-spinner fa-spin'); - break; - } - }); + // proceed once chart is drawable + if (!chart.drawable()) { + chart.off('drawable'); + chart.on('drawable', function() { + self.chart.off('drawable'); + if (chart.drawable()) { + self._draw(chart); + } + }); + return; + } // set chart state chart.state('wait', 'Please wait...'); @@ -104,6 +115,16 @@ var chart_type = chart.get('type'); var chart_settings = this.app.types.get(chart_type); + // clean up data if there is any from previous jobs + if (!chart_settings.execute || + (chart_settings.execute && chart.get('modified'))) { + // reset jobs + this.app.jobs.cleanup(chart); + + // reset modified flag + chart.set('modified', false); + } + // create chart view var self = this; require(['plugin/charts/' + chart_type + '/' + chart_type], function(ChartView) { @@ -112,25 +133,26 @@ // request data if (chart_settings.execute) { - self.app.jobs.submit(chart, self._defaultSettingsString(chart), self._defaultRequestString(chart), function() { + if (chart.get('dataset_id_job') == '') { + // submit job + self.app.jobs.submit(chart, self._defaultSettingsString(chart), self._defaultRequestString(chart), function() { + // save + this.app.storage.save(); + + // draw + view.draw(chart, self._defaultRequestDictionary(chart)); + }); + } else { + // load data into view view.draw(chart, self._defaultRequestDictionary(chart)); - }); + } } else { + // load data into view view.draw(chart, self._defaultRequestDictionary(chart)); } }); }, - // template - _template: function() { - return '<div>' + - '<div id="info" style="text-align: center; margin-top: 20px;">' + - '<span id="icon" style="font-size: 1.2em; display: inline-block;"/>' + - '<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>' + - '</div>' + - '</div>'; - }, - // create default chart request _defaultRequestString: function(chart) { @@ -175,10 +197,16 @@ // configure request var request_dictionary = { - id : chart.get('dataset_id'), - groups : [] + groups : [] }; + // update request dataset id + if (chart_settings.execute) { + request_dictionary.id = chart.get('dataset_id_job'); + } else { + request_dictionary.id = chart.get('dataset_id'); + } + // add groups to data request var group_index = 0; chart.groups.each(function(group) { @@ -198,7 +226,23 @@ // return return request_dictionary; - } + }, + + // template + _template: function() { + return '<div style="height: 100%; min-height: 50px;">' + + '<div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;">' + + '<span id="icon" style="font-size: 1.2em; display: inline-block;"/>' + + '<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>' + + '</div>' + + '</div>'; + }, + + // template svg element + _template_svg: function() { + return '<svg style="height: calc(100% - 80px)"/>'; + }, + }); }); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Refactor tool error / bug reporting. Allow reporting errors via biostar in addition to existing email functionality.
by commits-noreply＠bitbucket.org 24 Mar '14

24 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ec715604b476/ Changeset: ec715604b476 User: dan Date: 2014-03-24 21:19:35 Summary: Refactor tool error / bug reporting. Allow reporting errors via biostar in addition to existing email functionality. Affected #: 5 files diff -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c -r ec715604b476c47703b90385062a6ec482cfd302 lib/galaxy/tools/errors.py --- /dev/null +++ b/lib/galaxy/tools/errors.py @@ -0,0 +1,121 @@ +""" +Functionality for dealing with tool errors. +""" +import string +from galaxy import model, util, web + +error_report_template = """ +GALAXY TOOL ERROR REPORT +------------------------ + +This error report was sent from the Galaxy instance hosted on the server +"${host}" +----------------------------------------------------------------------------- +This is in reference to dataset id ${dataset_id} from history id ${history_id} +----------------------------------------------------------------------------- +You should be able to view the history containing the related history item + +${hid}: ${history_item_name} + +by logging in as a Galaxy admin user to the Galaxy instance referenced above +and pointing your browser to the following link. + +${history_view_link} +----------------------------------------------------------------------------- +The user '${email}' provided the following information: + +${message} +----------------------------------------------------------------------------- +job id: ${job_id} +tool id: ${job_tool_id} +job pid or drm id: ${job_runner_external_id} +----------------------------------------------------------------------------- +job command line: +${job_command_line} +----------------------------------------------------------------------------- +job stderr: +${job_stderr} +----------------------------------------------------------------------------- +job stdout: +${job_stdout} +----------------------------------------------------------------------------- +job info: +${job_info} +----------------------------------------------------------------------------- +job traceback: +${job_traceback} +----------------------------------------------------------------------------- +(This is an automated message). +""" + +class ErrorReporter( object ): + def __init__( self, hda, app ): + # Get the dataset + sa_session = app.model.context + if not isinstance( hda, model.HistoryDatasetAssociation ): + try: + hda = sa_session.query( model.HistoryDatasetAssociation ).get( hda ) + except: + hda = sa_session.query( model.HistoryDatasetAssociation ).get( app.security.decode_id( hda ) ) + assert isinstance( hda, model.HistoryDatasetAssociation ), ValueError( "Bad value provided for HDA (%s)." % ( hda ) ) + self.hda = hda + # Get the associated job + self.job = hda.creating_job + self.app = app + self.tool_id = self.job.tool_id + self.report = None + def _can_access_dataset( self, user ): + if user: + roles = user.all_roles() + else: + roles = [] + return self.app.security_agent.can_access_dataset( roles, self.hda.dataset ) + def create_report( self, email='', message='', **kwd ): + hda = self.hda + job = self.job + host = web.url_for( '/', qualified=True ) + history_view_link = web.url_for( controller="history", action="view", id=self.app.security.encode_id( hda.history_id ), qualified=True ) + # Build the email message + self.report = string.Template( error_report_template ) \ + .safe_substitute( host=host, + dataset_id=hda.dataset_id, + history_id=hda.history_id, + hid=hda.hid, + history_item_name=hda.get_display_name(), + history_view_link=history_view_link, + job_id=job.id, + job_tool_id=job.tool_id, + job_runner_external_id=job.job_runner_external_id, + job_command_line=job.command_line, + job_stderr=util.unicodify( job.stderr ), + job_stdout=util.unicodify( job.stdout ), + job_info=util.unicodify( job.info ), + job_traceback=util.unicodify( job.traceback ), + email=email, + message=util.unicodify( message ) ) + def _send_report( self, user, email=None, message=None, **kwd ): + return self.report + def send_report( self, user, email=None, message=None, **kwd ): + if self.report is None: + self.create_report( email=email, message=message, **kwd ) + return self._send_report( user, email=email, message=message, **kwd ) + +class EmailErrorReporter( ErrorReporter ): + def _send_report( self, user, email=None, message=None, **kwd ): + smtp_server = self.app.config.smtp_server + assert smtp_server, ValueError( "Mail is not configured for this galaxy instance" ) + to_address = self.app.config.error_email_to + assert to_address, ValueError( "Error reporting has been disabled for this galaxy instance" ) + + frm = to_address + # Check email a bit + email = email or '' + email = email.strip() + parts = email.split() + if len( parts ) == 1 and len( email ) > 0 and self._can_access_dataset( user ): + to = to_address + ", " + email + else: + to = to_address + subject = "Galaxy tool error report from %s" % email + # Send it + return util.send_mail( frm, to, subject, self.report, self.app.config ) diff -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c -r ec715604b476c47703b90385062a6ec482cfd302 lib/galaxy/util/biostar.py --- a/lib/galaxy/util/biostar.py +++ b/lib/galaxy/util/biostar.py @@ -7,6 +7,7 @@ import re from unicodedata import normalize from galaxy.web.base.controller import url_for +from galaxy.tools.errors import ErrorReporter _punct_re = re.compile(r'[\t !"#$%&\'()*\-/<=>?(a)\[\\\]^_`{|},.]+') @@ -27,6 +28,8 @@ # Slugifying from Armin Ronacher (http://flask.pocoo.org/snippets/5/) def slugify(text, delim=u'-'): """Generates an slightly worse ASCII-only slug.""" + if not isinstance( text, unicode ): + text = unicode( text ) result = [] for word in _punct_re.split(text.lower()): word = normalize('NFKD', word).encode('ascii', 'ignore') @@ -63,7 +66,7 @@ Generate a reasonable biostar tag for a tool. """ #Biostar can now handle tags with spaces, do we want to generate tags differently now? - return slugify( unicode( tool.name ), delim='-' ) + return slugify( tool.name, delim='-' ) def populate_tag_payload( payload=None, tool=None ): if payload is None: @@ -119,3 +122,18 @@ delete_cookie( trans, trans.app.config.biostar_key_name ) return get_biostar_url( trans.app, biostar_action='log_out' ) return None + +class BiostarErrorReporter( ErrorReporter ): + def _send_report( self, user, email=None, message=None, **kwd ): + assert biostar_enabled( self.app ), ValueError( "Biostar is not configured for this galaxy instance" ) + assert self._can_access_dataset( user ), Exception( "You are not allowed to access this dataset." ) + tool_version_select_field, tools, tool = \ + self.app.toolbox.get_tool_components( self.tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True ) + payload = { 'title': 'Bug report on "%s" tool' % ( tool.name ), 'content': self.report.replace( '\n', '<br />' ), 'tag_val':slugify( 'bug report' ) } + #Get footer for email from here + payload2 = populate_tool_payload( tool=tool ) + if 'content' in payload2: + payload[ 'content' ] = "%s<br />%s" % ( payload['content'], payload2['content'] ) + if 'tag_val' in payload2: + payload[ 'tag_val' ] = ','.join( [ payload2[ 'tag_val' ], payload[ 'tag_val' ] ] ) + return payload diff -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c -r ec715604b476c47703b90385062a6ec482cfd302 lib/galaxy/webapps/galaxy/controllers/biostar.py --- a/lib/galaxy/webapps/galaxy/controllers/biostar.py +++ b/lib/galaxy/webapps/galaxy/controllers/biostar.py @@ -75,6 +75,19 @@ return self.biostar_question_redirect( trans, payload ) @web.expose + def biostar_tool_bug_report( self, trans, hda=None, email=None, message=None ): + """ + Generate a redirect to a Biostar site using external authentication to + pass Galaxy user information and information about a specific tool error. + """ + try: + error_reporter = biostar.BiostarErrorReporter( hda, trans.app ) + payload = error_reporter.send_report( trans.user, email=email, message=message ) + except Exception, e: + return error( str( e ) ) + return self.biostar_question_redirect( trans, payload=payload ) + + @web.expose def biostar_logout( self, trans ): """ Log out of biostar diff -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c -r ec715604b476c47703b90385062a6ec482cfd302 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -1,6 +1,5 @@ import logging import os -import string import tempfile import urllib import zipfile @@ -14,6 +13,7 @@ from galaxy.web.base.controller import BaseUIController, ERROR, SUCCESS, url_for, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesExtendedMetadataMixin from galaxy.web.framework.helpers import grids, iff, time_ago from galaxy.web.framework.helpers import to_unicode +from galaxy.tools.errors import EmailErrorReporter eggs.require( "Paste" ) import paste.httpexceptions @@ -27,51 +27,6 @@ except ImportError: pass - -error_report_template = """ -GALAXY TOOL ERROR REPORT ------------------------- - -This error report was sent from the Galaxy instance hosted on the server -"${host}" ------------------------------------------------------------------------------ -This is in reference to dataset id ${dataset_id} from history id ${history_id} ------------------------------------------------------------------------------ -You should be able to view the history containing the related history item - -${hid}: ${history_item_name} - -by logging in as a Galaxy admin user to the Galaxy instance referenced above -and pointing your browser to the following link. - -${history_view_link} ------------------------------------------------------------------------------ -The user '${email}' provided the following information: - -${message} ------------------------------------------------------------------------------ -job id: ${job_id} -tool id: ${job_tool_id} -job pid or drm id: ${job_runner_external_id} ------------------------------------------------------------------------------ -job command line: -${job_command_line} ------------------------------------------------------------------------------ -job stderr: -${job_stderr} ------------------------------------------------------------------------------ -job stdout: -${job_stdout} ------------------------------------------------------------------------------ -job info: -${job_info} ------------------------------------------------------------------------------ -job traceback: -${job_traceback} ------------------------------------------------------------------------------ -(This is an automated message). -""" - class HistoryDatasetAssociationListGrid( grids.Grid ): # Custom columns for grid. class HistoryColumn( grids.GridColumn ): @@ -197,50 +152,15 @@ except: exit_code = "Invalid dataset ID or you are not allowed to access this dataset" return exit_code + @web.expose def report_error( self, trans, id, email='', message="", **kwd ): - smtp_server = trans.app.config.smtp_server - if smtp_server is None: - return trans.show_error_message( "Mail is not configured for this galaxy instance" ) - to_address = trans.app.config.error_email_to - if to_address is None: - return trans.show_error_message( "Error reporting has been disabled for this galaxy instance" ) - # Get the dataset and associated job - hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) - job = hda.creating_job - # Get the name of the server hosting the Galaxy instance from which this report originated - host = trans.request.host - history_view_link = "%s/history/view?id=%s" % ( str( host ), trans.security.encode_id( hda.history_id ) ) - # Build the email message - body = string.Template( error_report_template ) \ - .safe_substitute( host=host, - dataset_id=hda.dataset_id, - history_id=hda.history_id, - hid=hda.hid, - history_item_name=hda.get_display_name(), - history_view_link=history_view_link, - job_id=job.id, - job_tool_id=job.tool_id, - job_runner_external_id=job.job_runner_external_id, - job_command_line=job.command_line, - job_stderr=util.unicodify( job.stderr ), - job_stdout=util.unicodify( job.stdout ), - job_info=util.unicodify( job.info ), - job_traceback=util.unicodify( job.traceback ), - email=email, - message=util.unicodify( message ) ) - frm = to_address - # Check email a bit - email = email.strip() - parts = email.split() - if len( parts ) == 1 and len( email ) > 0 and self._can_access_dataset( trans, hda ): - to = to_address + ", " + email - else: - to = to_address - subject = "Galaxy tool error report from %s" % email - # Send it + biostar_report = 'biostar' in str( kwd.get( 'submit_error_report') ).lower() + if biostar_report: + return trans.response.send_redirect( url_for( controller='biostar', action='biostar_tool_bug_report', hda=id, email=email, message=message ) ) try: - util.send_mail( frm, to, subject, body, trans.app.config ) + error_reporter = EmailErrorReporter( id, trans.app ) + error_reporter.send_report( user=trans.user, email=email, message=message ) return trans.show_ok_message( "Your error report has been sent" ) except Exception, e: return trans.show_error_message( "An error occurred sending the report by email: %s" % str( e ) ) diff -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c -r ec715604b476c47703b90385062a6ec482cfd302 templates/webapps/galaxy/dataset/errors.mako --- a/templates/webapps/galaxy/dataset/errors.mako +++ b/templates/webapps/galaxy/dataset/errors.mako @@ -71,7 +71,10 @@ <textarea name="message" rows="10" cols="40"></textarea></div><div class="form-row"> - <input type="submit" name="submit_error_report" value="Report"/> + <input type="submit" name="submit_error_report" value="Report" onclick="form.setAttribute('target', '_self');"/> + %if trans.app.config.biostar_url: + <input type="submit" name="submit_error_report" value="Post on Biostar" onclick="form.setAttribute('target', '_blank');"/> + %endif </div></form></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: correct for random error that happens during grunt build (this css modification is just randomly modified for some builds)
by commits-noreply＠bitbucket.org 24 Mar '14

24 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6e9354d1fbdf/ Changeset: 6e9354d1fbdf User: martenson Date: 2014-03-24 20:15:10 Summary: correct for random error that happens during grunt build (this css modification is just randomly modified for some builds) Affected #: 1 file diff -r 68d35caf407f367c3447a1a6675d6705c8daacf4 -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -41,7 +41,7 @@ body{font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:1.428571429;color:#333;background-color:#fff} input,button,select,textarea{font-family:inherit;font-size:inherit;line-height:inherit} button,input,select[multiple],textarea{background-image:none} -a{color:#5f6990;text-decoration:none}a:hover,a:focus{color:#404862;text-decoration:underline} +a{color:#303030;text-decoration:none}a:hover,a:focus{color:#0a0a0a;text-decoration:underline} a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} img{vertical-align:middle} .img-responsive{display:block;max-width:100%;height:auto} @@ -114,13 +114,13 @@ .col-xs-12{width:100%} @media (min-width:768px){.container{max-width:750px} .col-sm-1,.col-sm-2,.col-sm-3,.col-sm-4,.col-sm-5,.col-sm-6,.col-sm-7,.col-sm-8,.col-sm-9,.col-sm-10,.col-sm-11{float:left} .col-sm-1{width:8.333333333333332%} .col-sm-2{width:16.666666666666664%} .col-sm-3{width:25%} .col-sm-4{width:33.33333333333333%} .col-sm-5{width:41.66666666666667%} .col-sm-6{width:50%} .col-sm-7{width:58.333333333333336%} .col-sm-8{width:66.66666666666666%} .col-sm-9{width:75%} .col-sm-10{width:83.33333333333334%} .col-sm-11{width:91.66666666666666%} .col-sm-12{width:100%} .col-sm-push-1{left:8.333333333333332%} .col-sm-push-2{left:16.666666666666664%} .col-sm-push-3{left:25%} .col-sm-push-4{left:33.33333333333333%} .col-sm-push-5{left:41.66666666666667%} .col-sm-push-6{left:50%} .col-sm-push-7{left:58.333333333333336%} .col-sm-push-8{left:66.66666666666666%} .col-sm-push-9{left:75%} .col-sm-push-10{left:83.33333333333334%} .col-sm-push-11{left:91.66666666666666%} .col-sm-pull-1{right:8.333333333333332%} .col-sm-pull-2{right:16.666666666666664%} .col-sm-pull-3{right:25%} .col-sm-pull-4{right:33.33333333333333%} .col-sm-pull-5{right:41.66666666666667%} .col-sm-pull-6{right:50%} .col-sm-pull-7{right:58.333333333333336%} .col-sm-pull-8{right:66.66666666666666%} .col-sm-pull-9{right:75%} .col-sm-pull-10{right:83.33333333333334%} .col-sm-pull-11{right:91.66666666666666%} .col-sm-offset-1{margin-left:8.333333333333332%} .col-sm-offset-2{margin-left:16.666666666666664%} .col-sm-offset-3{margin-left:25%} .col-sm-offset-4{margin-left:33.33333333333333%} .col-sm-offset-5{margin-left:41.66666666666667%} .col-sm-offset-6{margin-left:50%} .col-sm-offset-7{margin-left:58.333333333333336%} .col-sm-offset-8{margin-left:66.66666666666666%} .col-sm-offset-9{margin-left:75%} .col-sm-offset-10{margin-left:83.33333333333334%} .col-sm-offset-11{margin-left:91.66666666666666%}}@media (min-width:992px){.container{max-width:970px} .col-md-1,.col-md-2,.col-md-3,.col-md-4,.col-md-5,.col-md-6,.col-md-7,.col-md-8,.col-md-9,.col-md-10,.col-md-11{float:left} .col-md-1{width:8.333333333333332%} .col-md-2{width:16.666666666666664%} .col-md-3{width:25%} .col-md-4{width:33.33333333333333%} .col-md-5{width:41.66666666666667%} .col-md-6{width:50%} .col-md-7{width:58.333333333333336%} .col-md-8{width:66.66666666666666%} .col-md-9{width:75%} .col-md-10{width:83.33333333333334%} .col-md-11{width:91.66666666666666%} .col-md-12{width:100%} .col-md-push-0{left:auto} .col-md-push-1{left:8.333333333333332%} .col-md-push-2{left:16.666666666666664%} .col-md-push-3{left:25%} .col-md-push-4{left:33.33333333333333%} .col-md-push-5{left:41.66666666666667%} .col-md-push-6{left:50%} .col-md-push-7{left:58.333333333333336%} .col-md-push-8{left:66.66666666666666%} .col-md-push-9{left:75%} .col-md-push-10{left:83.33333333333334%} .col-md-push-11{left:91.66666666666666%} .col-md-pull-0{right:auto} .col-md-pull-1{right:8.333333333333332%} .col-md-pull-2{right:16.666666666666664%} .col-md-pull-3{right:25%} .col-md-pull-4{right:33.33333333333333%} .col-md-pull-5{right:41.66666666666667%} .col-md-pull-6{right:50%} .col-md-pull-7{right:58.333333333333336%} .col-md-pull-8{right:66.66666666666666%} .col-md-pull-9{right:75%} .col-md-pull-10{right:83.33333333333334%} .col-md-pull-11{right:91.66666666666666%} .col-md-offset-0{margin-left:0} .col-md-offset-1{margin-left:8.333333333333332%} .col-md-offset-2{margin-left:16.666666666666664%} .col-md-offset-3{margin-left:25%} .col-md-offset-4{margin-left:33.33333333333333%} .col-md-offset-5{margin-left:41.66666666666667%} .col-md-offset-6{margin-left:50%} .col-md-offset-7{margin-left:58.333333333333336%} .col-md-offset-8{margin-left:66.66666666666666%} .col-md-offset-9{margin-left:75%} .col-md-offset-10{margin-left:83.33333333333334%} .col-md-offset-11{margin-left:91.66666666666666%}}@media (min-width:1200px){.container{max-width:1170px} .col-lg-1,.col-lg-2,.col-lg-3,.col-lg-4,.col-lg-5,.col-lg-6,.col-lg-7,.col-lg-8,.col-lg-9,.col-lg-10,.col-lg-11{float:left} .col-lg-1{width:8.333333333333332%} .col-lg-2{width:16.666666666666664%} .col-lg-3{width:25%} .col-lg-4{width:33.33333333333333%} .col-lg-5{width:41.66666666666667%} .col-lg-6{width:50%} .col-lg-7{width:58.333333333333336%} .col-lg-8{width:66.66666666666666%} .col-lg-9{width:75%} .col-lg-10{width:83.33333333333334%} .col-lg-11{width:91.66666666666666%} .col-lg-12{width:100%} .col-lg-push-0{left:auto} .col-lg-push-1{left:8.333333333333332%} .col-lg-push-2{left:16.666666666666664%} .col-lg-push-3{left:25%} .col-lg-push-4{left:33.33333333333333%} .col-lg-push-5{left:41.66666666666667%} .col-lg-push-6{left:50%} .col-lg-push-7{left:58.333333333333336%} .col-lg-push-8{left:66.66666666666666%} .col-lg-push-9{left:75%} .col-lg-push-10{left:83.33333333333334%} .col-lg-push-11{left:91.66666666666666%} .col-lg-pull-0{right:auto} .col-lg-pull-1{right:8.333333333333332%} .col-lg-pull-2{right:16.666666666666664%} .col-lg-pull-3{right:25%} .col-lg-pull-4{right:33.33333333333333%} .col-lg-pull-5{right:41.66666666666667%} .col-lg-pull-6{right:50%} .col-lg-pull-7{right:58.333333333333336%} .col-lg-pull-8{right:66.66666666666666%} .col-lg-pull-9{right:75%} .col-lg-pull-10{right:83.33333333333334%} .col-lg-pull-11{right:91.66666666666666%} .col-lg-offset-0{margin-left:0} .col-lg-offset-1{margin-left:8.333333333333332%} .col-lg-offset-2{margin-left:16.666666666666664%} .col-lg-offset-3{margin-left:25%} .col-lg-offset-4{margin-left:33.33333333333333%} .col-lg-offset-5{margin-left:41.66666666666667%} .col-lg-offset-6{margin-left:50%} .col-lg-offset-7{margin-left:58.333333333333336%} .col-lg-offset-8{margin-left:66.66666666666666%} .col-lg-offset-9{margin-left:75%} .col-lg-offset-10{margin-left:83.33333333333334%} .col-lg-offset-11{margin-left:91.66666666666666%}}table{max-width:100%;background-color:transparent} th{text-align:left} -.table{width:100%;margin-bottom:17px}.table thead>tr>th,.table tbody>tr>th,.table tfoot>tr>th,.table thead>tr>td,.table tbody>tr>td,.table tfoot>tr>td{padding:8px;line-height:1.428571429;vertical-align:top;border-top:1px solid #bfbfbf} -.table thead>tr>th{vertical-align:bottom;border-bottom:2px solid #bfbfbf} +.table{width:100%;margin-bottom:17px}.table thead>tr>th,.table tbody>tr>th,.table tfoot>tr>th,.table thead>tr>td,.table tbody>tr>td,.table tfoot>tr>td{padding:8px;line-height:1.428571429;vertical-align:top;border-top:1px solid #d6b161} +.table thead>tr>th{vertical-align:bottom;border-bottom:2px solid #d6b161} .table caption+thead tr:first-child th,.table colgroup+thead tr:first-child th,.table thead:first-child tr:first-child th,.table caption+thead tr:first-child td,.table colgroup+thead tr:first-child td,.table thead:first-child tr:first-child td{border-top:0} -.table tbody+tbody{border-top:2px solid #bfbfbf} +.table tbody+tbody{border-top:2px solid #d6b161} .table .table{background-color:#fff} .table-condensed thead>tr>th,.table-condensed tbody>tr>th,.table-condensed tfoot>tr>th,.table-condensed thead>tr>td,.table-condensed tbody>tr>td,.table-condensed tfoot>tr>td{padding:5px} -.table-bordered{border:1px solid #bfbfbf}.table-bordered>thead>tr>th,.table-bordered>tbody>tr>th,.table-bordered>tfoot>tr>th,.table-bordered>thead>tr>td,.table-bordered>tbody>tr>td,.table-bordered>tfoot>tr>td{border:1px solid #bfbfbf} +.table-bordered{border:1px solid #d6b161}.table-bordered>thead>tr>th,.table-bordered>tbody>tr>th,.table-bordered>tfoot>tr>th,.table-bordered>thead>tr>td,.table-bordered>tbody>tr>td,.table-bordered>tfoot>tr>td{border:1px solid #d6b161} .table-bordered>thead>tr>th,.table-bordered>thead>tr>td{border-bottom-width:2px} .table-striped>tbody>tr:nth-child(odd)>td,.table-striped>tbody>tr:nth-child(odd)>th{background-color:#f9f9f9} .table-hover>tbody>tr:hover>td,.table-hover>tbody>tr:hover>th{background-color:#f5f5f5} @@ -133,7 +133,7 @@ .table-hover>tbody>tr>td.danger:hover,.table-hover>tbody>tr>th.danger:hover,.table-hover>tbody>tr.danger:hover>td,.table-hover>tbody>tr.danger:hover>th{background-color:#f7b0ae;border-color:#c61913} .table>thead>tr>td.warning,.table>tbody>tr>td.warning,.table>tfoot>tr>td.warning,.table>thead>tr>th.warning,.table>tbody>tr>th.warning,.table>tfoot>tr>th.warning,.table>thead>tr.warning>td,.table>tbody>tr.warning>td,.table>tfoot>tr.warning>td,.table>thead>tr.warning>th,.table>tbody>tr.warning>th,.table>tfoot>tr.warning>th{background-color:#fce1ba;border-color:#e28709} .table-hover>tbody>tr>td.warning:hover,.table-hover>tbody>tr>th.warning:hover,.table-hover>tbody>tr.warning:hover>td,.table-hover>tbody>tr.warning:hover>th{background-color:#fbd6a2;border-color:#c97908} -@media (max-width:768px){.table-responsive{width:100%;margin-bottom:15px;overflow-y:hidden;overflow-x:scroll;-ms-overflow-style:-ms-autohiding-scrollbar;border:1px solid #bfbfbf;-webkit-overflow-scrolling:touch}.table-responsive>.table{margin-bottom:0;background-color:#fff}.table-responsive>.table>thead>tr>th,.table-responsive>.table>tbody>tr>th,.table-responsive>.table>tfoot>tr>th,.table-responsive>.table>thead>tr>td,.table-responsive>.table>tbody>tr>td,.table-responsive>.table>tfoot>tr>td{white-space:nowrap} .table-responsive>.table-bordered{border:0}.table-responsive>.table-bordered>thead>tr>th:first-child,.table-responsive>.table-bordered>tbody>tr>th:first-child,.table-responsive>.table-bordered>tfoot>tr>th:first-child,.table-responsive>.table-bordered>thead>tr>td:first-child,.table-responsive>.table-bordered>tbody>tr>td:first-child,.table-responsive>.table-bordered>tfoot>tr>td:first-child{border-left:0} .table-responsive>.table-bordered>thead>tr>th:last-child,.table-responsive>.table-bordered>tbody>tr>th:last-child,.table-responsive>.table-bordered>tfoot>tr>th:last-child,.table-responsive>.table-bordered>thead>tr>td:last-child,.table-responsive>.table-bordered>tbody>tr>td:last-child,.table-responsive>.table-bordered>tfoot>tr>td:last-child{border-right:0} .table-responsive>.table-bordered>thead>tr:last-child>th,.table-responsive>.table-bordered>tbody>tr:last-child>th,.table-responsive>.table-bordered>tfoot>tr:last-child>th,.table-responsive>.table-bordered>thead>tr:last-child>td,.table-responsive>.table-bordered>tbody>tr:last-child>td,.table-responsive>.table-bordered>tfoot>tr:last-child>td{border-bottom:0}}fieldset{padding:0;margin:0;border:0} +@media (max-width:768px){.table-responsive{width:100%;margin-bottom:15px;overflow-y:hidden;overflow-x:scroll;-ms-overflow-style:-ms-autohiding-scrollbar;border:1px solid #d6b161;-webkit-overflow-scrolling:touch}.table-responsive>.table{margin-bottom:0;background-color:#fff}.table-responsive>.table>thead>tr>th,.table-responsive>.table>tbody>tr>th,.table-responsive>.table>tfoot>tr>th,.table-responsive>.table>thead>tr>td,.table-responsive>.table>tbody>tr>td,.table-responsive>.table>tfoot>tr>td{white-space:nowrap} .table-responsive>.table-bordered{border:0}.table-responsive>.table-bordered>thead>tr>th:first-child,.table-responsive>.table-bordered>tbody>tr>th:first-child,.table-responsive>.table-bordered>tfoot>tr>th:first-child,.table-responsive>.table-bordered>thead>tr>td:first-child,.table-responsive>.table-bordered>tbody>tr>td:first-child,.table-responsive>.table-bordered>tfoot>tr>td:first-child{border-left:0} .table-responsive>.table-bordered>thead>tr>th:last-child,.table-responsive>.table-bordered>tbody>tr>th:last-child,.table-responsive>.table-bordered>tfoot>tr>th:last-child,.table-responsive>.table-bordered>thead>tr>td:last-child,.table-responsive>.table-bordered>tbody>tr>td:last-child,.table-responsive>.table-bordered>tfoot>tr>td:last-child{border-right:0} .table-responsive>.table-bordered>thead>tr:last-child>th,.table-responsive>.table-bordered>tbody>tr:last-child>th,.table-responsive>.table-bordered>tfoot>tr:last-child>th,.table-responsive>.table-bordered>thead>tr:last-child>td,.table-responsive>.table-bordered>tbody>tr:last-child>td,.table-responsive>.table-bordered>tfoot>tr:last-child>td{border-bottom:0}}fieldset{padding:0;margin:0;border:0} legend{display:block;width:100%;padding:0;margin-bottom:17px;font-size:18px;line-height:inherit;color:#333;border:0;border-bottom:1px solid #bfbfbf} label{display:inline-block;margin-bottom:5px;font-weight:bold} input[type="search"]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box} @@ -148,7 +148,7 @@ .form-control::-moz-placeholder{color:#999} .form-control:-ms-input-placeholder{color:#999} .form-control::-webkit-input-placeholder{color:#999} -.form-control{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #bfbfbf;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} +.form-control{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} .form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee} textarea.form-control{height:auto} .form-group{margin-bottom:15px} @@ -202,9 +202,9 @@ .btn-info{color:#fff;background-color:#3186a0;border-color:#010304}.btn-info:hover,.btn-info:focus,.btn-info:active,.btn-info.active,.open .dropdown-toggle.btn-info{color:#fff;background-color:#276c81;border-color:#000} .btn-info:active,.btn-info.active,.open .dropdown-toggle.btn-info{background-image:none} .btn-info.disabled,.btn-info[disabled],fieldset[disabled] .btn-info,.btn-info.disabled:hover,.btn-info[disabled]:hover,fieldset[disabled] .btn-info:hover,.btn-info.disabled:focus,.btn-info[disabled]:focus,fieldset[disabled] .btn-info:focus,.btn-info.disabled:active,.btn-info[disabled]:active,fieldset[disabled] .btn-info:active,.btn-info.disabled.active,.btn-info[disabled].active,fieldset[disabled] .btn-info.active{background-color:#3186a0;border-color:#010304} -.btn-link{color:#5f6990;font-weight:normal;cursor:pointer;border-radius:0}.btn-link,.btn-link:active,.btn-link[disabled],fieldset[disabled] .btn-link{background-color:transparent;-webkit-box-shadow:none;box-shadow:none} +.btn-link{color:#303030;font-weight:normal;cursor:pointer;border-radius:0}.btn-link,.btn-link:active,.btn-link[disabled],fieldset[disabled] .btn-link{background-color:transparent;-webkit-box-shadow:none;box-shadow:none} .btn-link,.btn-link:hover,.btn-link:focus,.btn-link:active{border-color:transparent} -.btn-link:hover,.btn-link:focus{color:#404862;text-decoration:underline;background-color:transparent} +.btn-link:hover,.btn-link:focus{color:#0a0a0a;text-decoration:underline;background-color:transparent} .btn-link[disabled]:hover,fieldset[disabled] .btn-link:hover,.btn-link[disabled]:focus,fieldset[disabled] .btn-link:focus{color:#999;text-decoration:none} .btn-lg{padding:8px 14px;font-size:15px;line-height:1.33;border-radius:5px} .btn-sm,.btn-xs{padding:3px 8px;font-size:11px;line-height:1.5;border-radius:2px} @@ -486,7 +486,7 @@ textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon,textarea.input-group-sm>.input-group-btn>.btn{height:auto} .input-group-addon,.input-group-btn,.input-group .form-control{display:table-cell}.input-group-addon:not(:first-child):not(:last-child),.input-group-btn:not(:first-child):not(:last-child),.input-group .form-control:not(:first-child):not(:last-child){border-radius:0} .input-group-addon,.input-group-btn{width:1%;white-space:nowrap;vertical-align:middle} -.input-group-addon{padding:4px 10px;font-size:12px;font-weight:normal;line-height:1;text-align:center;background-color:#eee;border:1px solid #bfbfbf;border-radius:3px}.input-group-addon.input-sm{padding:3px 8px;font-size:11px;border-radius:2px} +.input-group-addon{padding:4px 10px;font-size:12px;font-weight:normal;line-height:1;text-align:center;background-color:#eee;border:1px solid #aaa;border-radius:3px}.input-group-addon.input-sm{padding:3px 8px;font-size:11px;border-radius:2px} .input-group-addon.input-lg{padding:8px 14px;font-size:15px;border-radius:5px} .input-group-addon input[type="radio"],.input-group-addon input[type="checkbox"]{margin-top:0} .input-group .form-control:first-child,.input-group-addon:first-child,.input-group-btn:first-child>.btn,.input-group-btn:first-child>.dropdown-toggle,.input-group-btn:last-child>.btn:not(:last-child):not(.dropdown-toggle){border-bottom-right-radius:0;border-top-right-radius:0} @@ -502,7 +502,7 @@ .nav:after{clear:both} .nav>li{position:relative;display:block}.nav>li>a{position:relative;display:block;padding:4px 10px}.nav>li>a:hover,.nav>li>a:focus{text-decoration:none;background-color:#eee} .nav>li.disabled>a{color:#999}.nav>li.disabled>a:hover,.nav>li.disabled>a:focus{color:#999;text-decoration:none;background-color:transparent;cursor:not-allowed} -.nav .open>a,.nav .open>a:hover,.nav .open>a:focus{background-color:#eee;border-color:#5f6990} +.nav .open>a,.nav .open>a:hover,.nav .open>a:focus{background-color:#eee;border-color:#303030} .nav .nav-divider{height:1px;margin:7.5px 0;overflow:hidden;background-color:#e5e5e5} .nav>li>a>img{max-width:none} .nav-tabs{border-bottom:1px solid #bfbfbf}.nav-tabs>li{float:left;margin-bottom:-1px}.nav-tabs>li>a{margin-right:2px;line-height:1.428571429;border:1px solid transparent;border-radius:3px 3px 0 0}.nav-tabs>li>a:hover{border-color:#eee #eee #bfbfbf} @@ -526,8 +526,8 @@ .tabbable:after{clear:both} .tab-content>.tab-pane,.pill-content>.pill-pane{display:none} .tab-content>.active,.pill-content>.active{display:block} -.nav .caret{border-top-color:#5f6990;border-bottom-color:#5f6990} -.nav a:hover .caret{border-top-color:#404862;border-bottom-color:#404862} +.nav .caret{border-top-color:#303030;border-bottom-color:#303030} +.nav a:hover .caret{border-top-color:#0a0a0a;border-bottom-color:#0a0a0a} .nav-tabs .dropdown-menu{margin-top:-1px;border-top-right-radius:0;border-top-left-radius:0} .navbar{position:relative;z-index:1000;min-height:33px;margin-bottom:17px;border:1px solid transparent}.navbar:before,.navbar:after{content:" ";display:table;} .navbar:after{clear:both} @@ -617,7 +617,7 @@ .badge{display:inline-block;min-width:10px;padding:3px 7px;font-size:11px;font-weight:bold;color:#fff;line-height:1;vertical-align:baseline;white-space:nowrap;text-align:center;background-color:#999;border-radius:10px}.badge:empty{display:none} a.badge:hover,a.badge:focus{color:#fff;text-decoration:none;cursor:pointer} .btn .badge{position:relative;top:-1px} -a.list-group-item.active>.badge,.nav-pills>.active>a>.badge{color:#5f6990;background-color:#fff} +a.list-group-item.active>.badge,.nav-pills>.active>a>.badge{color:#303030;background-color:#fff} .nav-pills>li>a>.badge{margin-left:3px} .jumbotron{padding:30px;margin-bottom:30px;font-size:18px;font-weight:200;line-height:2.1428571435;color:inherit;background-color:#eee}.jumbotron h1{line-height:1;color:inherit} .jumbotron p{line-height:1.4} @@ -672,7 +672,7 @@ .panel>.list-group .list-group-item:last-child{border-bottom:0} .panel-heading+.list-group .list-group-item:first-child{border-top-width:0} .panel>.table{margin-bottom:0} -.panel>.panel-body+.table{border-top:1px solid #bfbfbf} +.panel>.panel-body+.table{border-top:1px solid #d6b161} .panel-heading{padding:10px 15px;border-bottom:1px solid transparent;border-top-right-radius:2px;border-top-left-radius:2px} .panel-title{margin-top:0;margin-bottom:0;font-size:14px}.panel-title>a{color:inherit} .panel-footer{padding:10px 15px;background-color:#f5f5f5;border-top:1px solid #bfbfbf;border-bottom-right-radius:2px;border-bottom-left-radius:2px} @@ -1454,7 +1454,7 @@ select{padding:2px;font-size:12px;line-height:1.428571429} select,input,textarea{font:inherit} .form-row select,.form-row textarea,.form-row input[type="text"],.form-row input[type="file"],.form-row input[type="password"]{max-width:90%} -textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:1.428571429;border:1px solid #bfbfbf;padding:3px} +textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:1.428571429;border:1px solid #aaa;padding:3px} input[type="submit"],button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;white-space:normal;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}input[type="submit"]:focus,button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} input[type="submit"]:hover,button:hover,input[type="submit"]:focus,button:focus{color:#333;text-decoration:none} input[type="submit"]:active,button:active,input[type="submit"].active,button.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} @@ -1465,7 +1465,7 @@ input[type="submit"].btn-primary,button.btn-primary{color:#fff;background-color:#5f6990;border-color:#0e0f15}input[type="submit"].btn-primary:hover,button.btn-primary:hover,input[type="submit"].btn-primary:focus,button.btn-primary:focus,input[type="submit"].btn-primary:active,button.btn-primary:active,input[type="submit"].btn-primary.active,button.btn-primary.active,.open .dropdown-toggleinput[type="submit"].btn-primary,.open .dropdown-togglebutton.btn-primary{color:#fff;background-color:#4e5777;border-color:#000} input[type="submit"].btn-primary:active,button.btn-primary:active,input[type="submit"].btn-primary.active,button.btn-primary.active,.open .dropdown-toggleinput[type="submit"].btn-primary,.open .dropdown-togglebutton.btn-primary{background-image:none} input[type="submit"].btn-primary.disabled,button.btn-primary.disabled,input[type="submit"].btn-primary[disabled],button.btn-primary[disabled],fieldset[disabled] input[type="submit"].btn-primary,fieldset[disabled] button.btn-primary,input[type="submit"].btn-primary.disabled:hover,button.btn-primary.disabled:hover,input[type="submit"].btn-primary[disabled]:hover,button.btn-primary[disabled]:hover,fieldset[disabled] input[type="submit"].btn-primary:hover,fieldset[disabled] button.btn-primary:hover,input[type="submit"].btn-primary.disabled:focus,button.btn-primary.disabled:focus,input[type="submit"].btn-primary[disabled]:focus,button.btn-primary[disabled]:focus,fieldset[disabled] input[type="submit"].btn-primary:focus,fieldset[disabled] button.btn-primary:focus,input[type="submit"].btn-primary.disabled:active,button.btn-primary.disabled:active,input[type="submit"].btn-primary[disabled]:active,button.btn-primary[disabled]:active,fieldset[disabled] input[type="submit"].btn-primary:active,fieldset[disabled] button.btn-primary:active,input[type="submit"].btn-primary.disabled.active,button.btn-primary.disabled.active,input[type="submit"].btn-primary[disabled].active,button.btn-primary[disabled].active,fieldset[disabled] input[type="submit"].btn-primary.active,fieldset[disabled] button.btn-primary.active{background-color:#5f6990;border-color:#0e0f15} -.search-query{display:inline-block;padding:4px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #bfbfbf;padding-left:14px !important;padding-right:14px;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto} +.search-query{display:inline-block;padding:4px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #aaa;padding-left:14px !important;padding-right:14px;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto} .search-query:focus{border-color:rgba(24,132,218,0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);outline:0;outline:thin dotted \9;} .search-spinner{position:absolute;display:none;right:6px;top:9px} #search-clear-btn{position:absolute;right:6px;top:5px;display:block;font-size:1.4em;text-decoration:none;color:#888;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}#search-clear-btn:before{content:"\f057"} @@ -1506,9 +1506,9 @@ table.tabletip th{white-space:nowrap;border-bottom:1px solid #444;padding-right:3px} table.tabletip td{border-bottom:1px solid #ddd} table.tabletip tbody tr:hover td{background-color:#eee} -table.colored{border-top:solid #bfbfbf 1px;border-bottom:solid #bfbfbf 1px} +table.colored{border-top:solid #d6b161 1px;border-bottom:solid #d6b161 1px} table.colored td,table.colored th{text-align:left;padding:5px;line-height:1.428571429} -table.colored tr.header{background:#ebd9b2;color:#000;background-repeat:repeat-x;background-position:top;border-bottom:solid #bfbfbf 1px;font-weight:bold} +table.colored tr.header{background:#ebd9b2;color:#000;background-repeat:repeat-x;background-position:top;border-bottom:solid #d6b161 1px;font-weight:bold} table.colored tr{background:#fff} table.colored tr.odd_row{background:#f9f9f9} div.debug{margin:10px;padding:5px;background:#FFFF99;border:solid #FFFF33 1px;color:black} @@ -1519,7 +1519,7 @@ .grid tbody td{line-height:1.428571429;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px} .grid tbody td:empty{padding:0} .grid thead tr{height:2em} -.grid thead th{line-height:1.428571429;background:#ebd9b2;color:#000;border-top:solid #bfbfbf 1px;border-bottom:solid #bfbfbf 1px;padding:5px;text-align:left;white-space:nowrap} +.grid thead th{line-height:1.428571429;background:#ebd9b2;color:#000;border-top:solid #d6b161 1px;border-bottom:solid #d6b161 1px;padding:5px;text-align:left;white-space:nowrap} .grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px} .grid .current{background-color:#EEEEFF} .count-box{min-width:1.1em;padding:5px;border-width:1px;border-style:solid;text-align:center;display:inline-block} @@ -1618,7 +1618,7 @@ .icon-btn-group .icon-btn:only-child{margin:0px;border-radius:3px} .search-input .search-query{width:100%;padding-right:24px} .search-input .search-clear,.search-input .search-loading{position:relative;display:inline-block;float:right;margin-top:-23px;margin-right:4px;font-size:1.4em;line-height:23px;color:grey} -.search-input .search-clear:hover{color:#5f6990} +.search-input .search-clear:hover{color:#303030} #history-refresh-button,#history-options-button{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;padding:0px} .history-panel .dataset{border:1px solid #bfbfbf}.history-panel .dataset .vertical-spacing{margin-bottom:8px} .history-panel .dataset .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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