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

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 10 Feb '14

10 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bb744d8d3d6a/ Changeset: bb744d8d3d6a Branch: stable User: dan Date: 2014-02-10 19:31:39 Summary: Fix for Dataset.set_total_size() when e.g. encountering a dead symlink. Affected #: 1 file diff -r dc067a95261dec2b8862162dbac3f61bffa69ec9 -r bb744d8d3d6a74872a7b42b511d087c16b1ee8b3 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1183,7 +1183,7 @@ self.total_size = self.file_size or 0 if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): for root, dirs, files in os.walk( self.extra_files_path ): - self.total_size += sum( [ os.path.getsize( os.path.join( root, file ) ) for file in files ] ) + self.total_size += sum( [ os.path.getsize( os.path.join( root, file ) ) for file in files if os.path.exists( os.path.join( root, file ) ) ] ) def has_data( self ): """Detects whether there is any data""" return self.get_size() > 0 https://bitbucket.org/galaxy/galaxy-central/commits/bb0f56f7c636/ Changeset: bb0f56f7c636 User: dan Date: 2014-02-10 19:32:35 Summary: merge Affected #: 1 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: dan: Fix for Dataset.set_total_size() when e.g. encountering a dead symlink.
by commits-noreply＠bitbucket.org 10 Feb '14

10 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ec9d31a8bc04/ Changeset: ec9d31a8bc04 User: dan Date: 2014-02-10 19:31:39 Summary: Fix for Dataset.set_total_size() when e.g. encountering a dead symlink. Affected #: 1 file diff -r 29ce93a13ac7c4a5d2b54e5e2c10960f30a350b3 -r ec9d31a8bc046fa2c682c0b220b7ecdbd014e38b lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1221,7 +1221,7 @@ self.total_size = self.file_size or 0 if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): for root, dirs, files in os.walk( self.extra_files_path ): - self.total_size += sum( [ os.path.getsize( os.path.join( root, file ) ) for file in files ] ) + self.total_size += sum( [ os.path.getsize( os.path.join( root, file ) ) for file in files if os.path.exists( os.path.join( root, file ) ) ] ) def has_data( self ): """Detects whether there is any data""" return self.get_size() > 0 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Close next-stable for release.
by commits-noreply＠bitbucket.org 10 Feb '14

10 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3fccf7610669/ Changeset: 3fccf7610669 Branch: next-stable User: natefoo Date: 2014-02-10 19:19:05 Summary: Close next-stable for release. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add a very simple example script that uses API to run data managers.
by commits-noreply＠bitbucket.org 10 Feb '14

10 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a5c0d860d190/ Changeset: a5c0d860d190 User: dan Date: 2014-02-10 17:59:58 Summary: Add a very simple example script that uses API to run data managers. Affected #: 1 file diff -r 1c14b0cdba15d8ffc2474a82aa3ca535e728f941 -r a5c0d860d19010309e8a8fd02f39c015c5315fe9 scripts/api/data_manager_example_execute.py --- /dev/null +++ b/scripts/api/data_manager_example_execute.py @@ -0,0 +1,106 @@ +#!/usr/bin/env python +##Dan Blankenberg +##Very simple example of using the API to run Data Managers +##Script makes the naive assumption that dbkey==sequence id, which in many cases is not true nor desired +##*** This script is not recommended for use as-is on a production server *** + +import os +import sys +import optparse +import urlparse +import time + +sys.path.insert( 0, os.path.dirname( __file__ ) ) + +from common import post, get + +DEFAULT_SLEEP_TIME = 3 +FETCH_GENOME_TOOL_ID = 'testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_fetch_genome_all_…' +BUILD_INDEX_TOOLS_ID = [ 'testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_index_builder…', + 'testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_bwa_index_builder…' ] + +def run_tool( tool_id, history_id, params, api_key, galaxy_url, wait=True, sleep_time=None, **kwargs ): + sleep_time = sleep_time or DEFAULT_SLEEP_TIME + tools_url = urlparse.urljoin( galaxy_url, 'api/tools' ) + payload = { + 'tool_id' : tool_id, + } + if history_id: + payload['history_id'] = history_id + payload[ 'inputs' ] = params + rval = post( api_key, tools_url, payload ) + if wait: + outputs = list( rval['outputs'] ) + while outputs: + finished_datasets = [] + for i, dataset_dict in enumerate( outputs ): + if dataset_is_terminal( dataset_dict['id'], api_key=api_key, galaxy_url=galaxy_url ): + finished_datasets.append( i ) + for i in reversed( finished_datasets ): + outputs.pop( 0 ) + if wait and outputs: + time.sleep( sleep_time ) + + return rval + +def get_dataset_state( hda_id, api_key, galaxy_url ): + datasets_url = urlparse.urljoin( galaxy_url, 'api/datasets/%s' % hda_id ) + dataset_info = get( api_key, datasets_url ) + return dataset_info['state'] + +def dataset_is_terminal( hda_id, api_key, galaxy_url ): + dataset_state = get_dataset_state( hda_id, api_key, galaxy_url ) + return dataset_state in [ 'ok', 'error' ] + +if __name__ == '__main__': + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '-k', '--key', dest='api_key', action='store', type="string", default=None, help='API Key.' ) + parser.add_option( '-u', '--url', dest='base_url', action='store', type="string", default='http://localhost:8080', help='Base URL of Galaxy Server' ) + parser.add_option( '-d', '--dbkey', dest='dbkeys', action='append', type="string", default=[], help='List of dbkeys to download and Index' ) + parser.add_option( '-s', '--sleep_time', dest='sleep_time', action='store', type="int", default=DEFAULT_SLEEP_TIME, help='How long to sleep between check loops' ) + (options, args) = parser.parse_args() + + #check options + assert options.api_key is not None, ValueError( 'You must specify an API key.' ) + assert options.dbkeys, ValueError( 'You must specify at least one dbkey to use.' ) + + #check user is admin + configuration_options = get( options.api_key, urlparse.urljoin( options.base_url, 'api/configuration' ) ) + if 'library_import_dir' not in configuration_options: #hack to check if is admin user + print "Warning: Data Managers are only available to admin users. The API Key provided does not appear to belong to an admin user. Will attempt to run anyway." + + #Fetch Genomes + dbkeys = {} + for dbkey in options.dbkeys: + if dbkey not in dbkeys: + dbkeys[ dbkey ] = run_tool( FETCH_GENOME_TOOL_ID, None, { 'dbkey':dbkey, 'reference_source|reference_source_selector': 'ucsc', 'reference_source|requested_dbkey': dbkey }, options.api_key, options.base_url, wait=False ) + else: + "dbkey (%s) was specified more than once, skipping additional specification." % ( dbkey ) + + print 'Genomes Queued for downloading.' + + #Start indexers + indexing_tools = [] + while dbkeys: + for dbkey, value in dbkeys.items(): + if dataset_is_terminal( value['outputs'][0]['id'], options.api_key, options.base_url ): + del dbkeys[ dbkey ] + for tool_id in BUILD_INDEX_TOOLS_ID: + indexing_tools.append( run_tool( tool_id, None, { 'all_fasta_source':dbkey }, options.api_key, options.base_url, wait=False ) ) + if dbkeys: + time.sleep( options.sleep_time ) + + print 'All genomes downloaded and indexers now queued.' + + #Wait for indexers to finish + while indexing_tools: + for i, indexing_tool_value in enumerate( indexing_tools ): + if dataset_is_terminal( indexing_tool_value['outputs'][0]['id'], options.api_key, options.base_url ): + print 'Finished:', indexing_tool_value + del indexing_tools[i] + break + if indexing_tools: + time.sleep( options.sleep_time ) + + print 'All indexers have been run, please check results.' 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 10 Feb '14

10 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f957eec387a0/ Changeset: f957eec387a0 Branch: next-stable User: greg Date: 2014-02-10 17:33:51 Summary: Fixes for the tool shed's install and test framework. Affected #: 3 files diff -r aea2ff5acd6805ad10db0442cc159f7e4e67a541 -r f957eec387a07f5dc7acceff2124a8ef2edac6f8 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -285,15 +285,17 @@ break return version -def get_missing_repository_dependencies( repository ): +def get_missing_repository_dependencies( repository, all_missing_repository_dependencies=None ): """ Return the entire list of missing repository dependencies for the received repository. The entire dependency tree will be inspected. """ + if all_missing_repository_dependencies is None: + all_missing_repository_dependencies = [] print 'Checking revision %s of repository %s owned by %s for missing repository dependencies.' % \ ( repository.changeset_revision, repository.name, repository.owner ) - missing_repository_dependencies = repository.missing_repository_dependencies - for missing_required_repository in missing_repository_dependencies: + all_missing_repository_dependencies.extend( repository.missing_repository_dependencies ) + for missing_required_repository in repository.missing_repository_dependencies: print 'Revision %s of required repository %s owned by %s has status %s.' % \ ( missing_required_repository.changeset_revision, missing_required_repository.name, @@ -301,24 +303,28 @@ missing_required_repository.status ) for repository_dependency in repository.repository_dependencies: if repository_dependency.missing_repository_dependencies: - missing_repository_dependencies.extend( get_missing_repository_dependencies( repository_dependency ) ) - return missing_repository_dependencies + all_missing_repository_dependencies.extend( get_missing_repository_dependencies( repository_dependency, + all_missing_repository_dependencies ) ) + return all_missing_repository_dependencies -def get_missing_tool_dependencies( repository ): +def get_missing_tool_dependencies( repository, all_missing_tool_dependencies=None ): """ Return the entire list of missing tool dependencies for the received repository. The entire dependency tree will be inspected. """ + if all_missing_tool_dependencies is None: + all_missing_tool_dependencies = [] print 'Checking revision %s of repository %s owned by %s for missing tool dependencies.' % \ ( repository.changeset_revision, repository.name, repository.owner ) - missing_tool_dependencies = repository.missing_tool_dependencies - for missing_tool_dependency in missing_tool_dependencies: + all_missing_tool_dependencies.extend( repository.missing_tool_dependencies ) + for missing_tool_dependency in repository.missing_tool_dependencies: print 'Tool dependency %s version %s has status %s.' % \ ( missing_tool_dependency.name, missing_tool_dependency.version, missing_tool_dependency.status ) for repository_dependency in repository.repository_dependencies: - if repository_dependency.includes_tool_dependencies: - missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency ) ) - return missing_tool_dependencies + if repository_dependency.missing_tool_dependencies: + all_missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency, + all_missing_tool_dependencies ) ) + return all_missing_tool_dependencies def get_repositories_to_install( tool_shed_url, test_framework ): """ @@ -950,29 +956,23 @@ repository_identifier_tup, install_and_test_statistics_dict, tool_test_results_dict ) - response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dependencies_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print'\n=============================================================' + save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) else: # The required repository's installation failed. tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = str( required_repository.error_message ) params = dict( test_install_error=True, do_not_test=False ) - response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dependencies_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print'\n=============================================================' + save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) else: print 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ ( changeset_revision, name, owner ) @@ -1059,26 +1059,26 @@ changeset_revision = repository_dict.get( 'changeset_revision', None ) if name is None or owner is None or changeset_revision is None: print 'Entries for name, owner or changeset_revision missing from repository_dict %s' % repository_dict - return {} - name = str( name ) - owner = str( owner ) - changeset_revision = str( changeset_revision ) - print '\n=============================================================' - print 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( tool_test_results_dict ) ) - print 'Updating tool_test_results for repository_metadata id %s.' % metadata_revision_id - tool_test_results_dicts.insert( 0, tool_test_results_dict ) - params[ 'tool_test_results' ] = tool_test_results_dicts - # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. - params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' - url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) - print 'url: ', url - print 'params: ', params - try: - return update( tool_shed_api_key, url, params, return_formatted=False ) - except Exception, e: - log.exception( 'Error updating tool_test_results for repository_metadata id %s:\n%s' % \ - ( str( metadata_revision_id ), str( e ) ) ) - return {} - else: - return {} + else: + name = str( name ) + owner = str( owner ) + changeset_revision = str( changeset_revision ) + print '\n=============================================================\n' + print 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( tool_test_results_dict ) ) + print 'Updating tool_test_results for repository_metadata id %s.' % metadata_revision_id + tool_test_results_dicts.insert( 0, tool_test_results_dict ) + params[ 'tool_test_results' ] = tool_test_results_dicts + # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. + params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' + url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) + print 'url: ', url + print 'params: ', params + try: + response_from_update = update( tool_shed_api_key, url, params, return_formatted=False ) + print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_from_update ) ) + print '\n=============================================================\n' + except Exception, e: + log.exception( 'Error updating tool_test_results for repository_metadata id %s:\n%s' % \ + ( str( metadata_revision_id ), str( e ) ) ) diff -r aea2ff5acd6805ad10db0442cc159f7e4e67a541 -r f957eec387a07f5dc7acceff2124a8ef2edac6f8 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -195,16 +195,12 @@ # If this repository is being skipped, register the reason. tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) else: # See if the repository was installed in a previous test. repository = install_and_test_base_util.get_repository( name, owner, changeset_revision ) @@ -223,16 +219,12 @@ tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message params = dict( test_install_error=True, do_not_test=False ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) else: # The repository was successfully installed. print 'Installation succeeded for revision %s of repository %s owned by %s.' % \ @@ -243,6 +235,9 @@ # missing test components. if 'missing_test_components' not in tool_test_results_dict: tool_test_results_dict[ 'missing_test_components' ] = [] + # Hopefully we'll be able to run functional tests defined for tools contained in the repository - we'll + # assume so as the default. + can_run_functional_tests = True # Populate the installation containers (success and error) for the repository's immediate dependencies # (the entire dependency tree is not handled here). params, install_and_test_statistics_dict, tool_test_results_dict = \ @@ -254,16 +249,18 @@ if params.get( 'test_install_error', False ): # The repository was successfully installed, but one or more dependencies had installation errors, # so we'll populate the test result containers since we cannot execute any tests. - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print'\n=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) + # We cannot run functional tests for contained tools due to dependency installation errors. + print 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ + ( changeset_revision, name, owner ) + print 'because one or more dependencies has installation errors.' + can_run_functional_tests = False + remove_tests( app ) # Populate the installation containers (success or error) for the repository's immediate repository # dependencies whose containers are not yet populated. install_and_test_base_util.populate_install_containers_for_repository_dependencies( app, @@ -271,63 +268,67 @@ encoded_repository_metadata_id, install_and_test_statistics_dict, can_update_tool_shed ) - # Execute the contained tool's functional tests only if the repository's entire dependency - # tree is successfully installed. - missing_repository_dependencies = install_and_test_base_util.get_missing_repository_dependencies( repository ) - missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) - if missing_repository_dependencies or missing_tool_dependencies: - print 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ - ( changeset_revision, name, owner ) - print 'because one or more dependencies has installation errors.' - # The repository was installed successfully, but one or more dependencies had installation errors. Since - # we cannot test the tools due to these errors, we'll remove tests and tools were created during the repository - # installation process so nose will not discover them and attempt to execute them. - remove_tests( app ) - else: - print 'Revision %s of repository %s owned by %s installed successfully, so running tool tests.' % \ - ( changeset_revision, name, owner ) - # Generate the shed_tools_dict that specifies the location of test data contained within this repository. - # and configure and run functional tests for this repository. This is equivalent to - # sh run_functional_tests.sh -installed - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) - # Find the path to the test-data directory within the installed repository. - has_test_data, shed_tools_dict = \ - parse_tool_panel_config( galaxy_shed_tool_conf_file, - from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) - # If the repository has a test-data directory we write the generated shed_tools_dict to a temporary - # file so the functional test framework can find it. - # TODO: Eliminate the need for this shed_tools_dict since it grows large over the course of each test run. - # If it cannot be eliminated altogether, reinitialize it with each new repository install so at this point - # it contains only entries for the current repository dependency hierarchy being tested. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) - print 'Saved generated shed_tools_dict to %s\nContents: %s' % ( galaxy_shed_tools_dict, shed_tools_dict ) - try: - install_and_test_statistics_dict = test_repository_tools( app, - repository, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - install_and_test_statistics_dict ) - except Exception, e: - exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) - log.exception( exception_message ) - tool_test_results_dict[ 'failed_tests' ].append( exception_message ) - processed_at_least_one_test_failed = \ - install_and_test_statistics_dict.get( 'at_least_one_test_failed', [] ) - if repository_identifier_tup not in processed_at_least_one_test_failed: - install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_tup ) - # Record the status of this repository in the tool shed. - params[ 'tools_functionally_correct' ] = False - response_dict = \ + if can_run_functional_tests: + # Execute the contained tool's functional tests only if the repository's entire dependency + # tree is successfully installed. The following checks should discover missing dependencies + # at any level of the dependency hierarchy. + missing_repository_dependencies = \ + install_and_test_base_util.get_missing_repository_dependencies( repository, + all_missing_repository_dependencies=None ) + print 'Missing repository dependencies:\n%s' % str( missing_repository_dependencies ) + missing_tool_dependencies = \ + install_and_test_base_util.get_missing_tool_dependencies( repository, + all_missing_tool_dependencies=None ) + print 'Missing tool dependencies:\n%s' % str( missing_tool_dependencies ) + if missing_repository_dependencies or missing_tool_dependencies: + print 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ + ( changeset_revision, name, owner ) + print 'because one or more dependencies has installation errors.' + # The repository was installed successfully, but one or more dependencies had installation errors. Since + # we cannot test the tools due to these errors, we'll remove tests and tools were created during the repository + # installation process so nose will not discover them and attempt to execute them. + remove_tests( app ) + else: + print 'Revision %s of repository %s owned by %s installed successfully, so running tool tests.' % \ + ( changeset_revision, name, owner ) + # Generate the shed_tools_dict that specifies the location of test data contained within this repository. + # and configure and run functional tests for this repository. This is equivalent to + # sh run_functional_tests.sh -installed + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + # Find the path to the test-data directory within the installed repository. + has_test_data, shed_tools_dict = \ + parse_tool_panel_config( galaxy_shed_tool_conf_file, + from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + # If the repository has a test-data directory we write the generated shed_tools_dict to a temporary + # file so the functional test framework can find it. + # TODO: Eliminate the need for this shed_tools_dict since it grows large over the course of each test run. + # If it cannot be eliminated altogether, reinitialize it with each new repository install so at this point + # it contains only entries for the current repository dependency hierarchy being tested. + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) + print 'Saved generated shed_tools_dict to %s\nContents: %s' % ( galaxy_shed_tools_dict, shed_tools_dict ) + try: + install_and_test_statistics_dict = test_repository_tools( app, + repository, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + install_and_test_statistics_dict ) + except Exception, e: + exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) + log.exception( exception_message ) + tool_test_results_dict[ 'failed_tests' ].append( exception_message ) + processed_at_least_one_test_failed = \ + install_and_test_statistics_dict.get( 'at_least_one_test_failed', [] ) + if repository_identifier_tup not in processed_at_least_one_test_failed: + install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_tup ) + # Record the status of this repository in the tool shed. + params[ 'tools_functionally_correct' ] = False install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params, can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' else: print 'Skipped attempt to install revision %s of repository %s owned by %s because ' % \ ( changeset_revision, name, owner ) @@ -663,16 +664,12 @@ # Call the save_test_results_for_changeset_revision() method to execute a PUT request to the # repository_revisions API controller with the status of the test. This also sets the do_not_test # and tools_functionally correct flags and updates the time_last_tested field to today's date. - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) else: # The get_failed_test_dicts() method returns a list. print 'Revision %s of repository %s owned by %s installed successfully but did not pass functional tests.' % \ @@ -695,16 +692,12 @@ params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=set_do_not_test ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) # Remove the just-executed tests so twill will not find and re-test them along with the tools # contained in the next repository. remove_tests( app ) diff -r aea2ff5acd6805ad10db0442cc159f7e4e67a541 -r f957eec387a07f5dc7acceff2124a8ef2edac6f8 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -129,16 +129,12 @@ ( changeset_revision, name, owner ) tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) else: # See if the repository was installed in a previous test. repository = install_and_test_base_util.get_repository( name, owner, changeset_revision ) @@ -157,16 +153,12 @@ tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message params = dict( test_install_error=True, do_not_test=False ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) else: # The repository was successfully installed. print 'Installation succeeded for revision %s of repository %s owned by %s.' % \ @@ -179,16 +171,12 @@ repository_identifier_tup, install_and_test_statistics_dict, tool_test_results_dict ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) # Populate the installation containers (success or error) for the repository's immediate repository # dependencies whose containers are not yet populated. install_and_test_base_util.populate_install_containers_for_repository_dependencies( app, https://bitbucket.org/galaxy/galaxy-central/commits/1c14b0cdba15/ Changeset: 1c14b0cdba15 User: greg Date: 2014-02-10 17:34:23 Summary: merged from next-stable Affected #: 3 files diff -r 7ca065784d58e7aa77e5092952eacd963853df65 -r 1c14b0cdba15d8ffc2474a82aa3ca535e728f941 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -285,15 +285,17 @@ break return version -def get_missing_repository_dependencies( repository ): +def get_missing_repository_dependencies( repository, all_missing_repository_dependencies=None ): """ Return the entire list of missing repository dependencies for the received repository. The entire dependency tree will be inspected. """ + if all_missing_repository_dependencies is None: + all_missing_repository_dependencies = [] print 'Checking revision %s of repository %s owned by %s for missing repository dependencies.' % \ ( repository.changeset_revision, repository.name, repository.owner ) - missing_repository_dependencies = repository.missing_repository_dependencies - for missing_required_repository in missing_repository_dependencies: + all_missing_repository_dependencies.extend( repository.missing_repository_dependencies ) + for missing_required_repository in repository.missing_repository_dependencies: print 'Revision %s of required repository %s owned by %s has status %s.' % \ ( missing_required_repository.changeset_revision, missing_required_repository.name, @@ -301,24 +303,28 @@ missing_required_repository.status ) for repository_dependency in repository.repository_dependencies: if repository_dependency.missing_repository_dependencies: - missing_repository_dependencies.extend( get_missing_repository_dependencies( repository_dependency ) ) - return missing_repository_dependencies + all_missing_repository_dependencies.extend( get_missing_repository_dependencies( repository_dependency, + all_missing_repository_dependencies ) ) + return all_missing_repository_dependencies -def get_missing_tool_dependencies( repository ): +def get_missing_tool_dependencies( repository, all_missing_tool_dependencies=None ): """ Return the entire list of missing tool dependencies for the received repository. The entire dependency tree will be inspected. """ + if all_missing_tool_dependencies is None: + all_missing_tool_dependencies = [] print 'Checking revision %s of repository %s owned by %s for missing tool dependencies.' % \ ( repository.changeset_revision, repository.name, repository.owner ) - missing_tool_dependencies = repository.missing_tool_dependencies - for missing_tool_dependency in missing_tool_dependencies: + all_missing_tool_dependencies.extend( repository.missing_tool_dependencies ) + for missing_tool_dependency in repository.missing_tool_dependencies: print 'Tool dependency %s version %s has status %s.' % \ ( missing_tool_dependency.name, missing_tool_dependency.version, missing_tool_dependency.status ) for repository_dependency in repository.repository_dependencies: - if repository_dependency.includes_tool_dependencies: - missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency ) ) - return missing_tool_dependencies + if repository_dependency.missing_tool_dependencies: + all_missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency, + all_missing_tool_dependencies ) ) + return all_missing_tool_dependencies def get_repositories_to_install( tool_shed_url, test_framework ): """ @@ -950,29 +956,23 @@ repository_identifier_tup, install_and_test_statistics_dict, tool_test_results_dict ) - response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dependencies_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print'\n=============================================================' + save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) else: # The required repository's installation failed. tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = str( required_repository.error_message ) params = dict( test_install_error=True, do_not_test=False ) - response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dependencies_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print'\n=============================================================' + save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) else: print 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ ( changeset_revision, name, owner ) @@ -1059,26 +1059,26 @@ changeset_revision = repository_dict.get( 'changeset_revision', None ) if name is None or owner is None or changeset_revision is None: print 'Entries for name, owner or changeset_revision missing from repository_dict %s' % repository_dict - return {} - name = str( name ) - owner = str( owner ) - changeset_revision = str( changeset_revision ) - print '\n=============================================================' - print 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( tool_test_results_dict ) ) - print 'Updating tool_test_results for repository_metadata id %s.' % metadata_revision_id - tool_test_results_dicts.insert( 0, tool_test_results_dict ) - params[ 'tool_test_results' ] = tool_test_results_dicts - # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. - params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' - url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) - print 'url: ', url - print 'params: ', params - try: - return update( tool_shed_api_key, url, params, return_formatted=False ) - except Exception, e: - log.exception( 'Error updating tool_test_results for repository_metadata id %s:\n%s' % \ - ( str( metadata_revision_id ), str( e ) ) ) - return {} - else: - return {} + else: + name = str( name ) + owner = str( owner ) + changeset_revision = str( changeset_revision ) + print '\n=============================================================\n' + print 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( tool_test_results_dict ) ) + print 'Updating tool_test_results for repository_metadata id %s.' % metadata_revision_id + tool_test_results_dicts.insert( 0, tool_test_results_dict ) + params[ 'tool_test_results' ] = tool_test_results_dicts + # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. + params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' + url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) + print 'url: ', url + print 'params: ', params + try: + response_from_update = update( tool_shed_api_key, url, params, return_formatted=False ) + print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_from_update ) ) + print '\n=============================================================\n' + except Exception, e: + log.exception( 'Error updating tool_test_results for repository_metadata id %s:\n%s' % \ + ( str( metadata_revision_id ), str( e ) ) ) diff -r 7ca065784d58e7aa77e5092952eacd963853df65 -r 1c14b0cdba15d8ffc2474a82aa3ca535e728f941 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -195,16 +195,12 @@ # If this repository is being skipped, register the reason. tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) else: # See if the repository was installed in a previous test. repository = install_and_test_base_util.get_repository( name, owner, changeset_revision ) @@ -223,16 +219,12 @@ tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message params = dict( test_install_error=True, do_not_test=False ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) else: # The repository was successfully installed. print 'Installation succeeded for revision %s of repository %s owned by %s.' % \ @@ -243,6 +235,9 @@ # missing test components. if 'missing_test_components' not in tool_test_results_dict: tool_test_results_dict[ 'missing_test_components' ] = [] + # Hopefully we'll be able to run functional tests defined for tools contained in the repository - we'll + # assume so as the default. + can_run_functional_tests = True # Populate the installation containers (success and error) for the repository's immediate dependencies # (the entire dependency tree is not handled here). params, install_and_test_statistics_dict, tool_test_results_dict = \ @@ -254,16 +249,18 @@ if params.get( 'test_install_error', False ): # The repository was successfully installed, but one or more dependencies had installation errors, # so we'll populate the test result containers since we cannot execute any tests. - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print'\n=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) + # We cannot run functional tests for contained tools due to dependency installation errors. + print 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ + ( changeset_revision, name, owner ) + print 'because one or more dependencies has installation errors.' + can_run_functional_tests = False + remove_tests( app ) # Populate the installation containers (success or error) for the repository's immediate repository # dependencies whose containers are not yet populated. install_and_test_base_util.populate_install_containers_for_repository_dependencies( app, @@ -271,63 +268,67 @@ encoded_repository_metadata_id, install_and_test_statistics_dict, can_update_tool_shed ) - # Execute the contained tool's functional tests only if the repository's entire dependency - # tree is successfully installed. - missing_repository_dependencies = install_and_test_base_util.get_missing_repository_dependencies( repository ) - missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) - if missing_repository_dependencies or missing_tool_dependencies: - print 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ - ( changeset_revision, name, owner ) - print 'because one or more dependencies has installation errors.' - # The repository was installed successfully, but one or more dependencies had installation errors. Since - # we cannot test the tools due to these errors, we'll remove tests and tools were created during the repository - # installation process so nose will not discover them and attempt to execute them. - remove_tests( app ) - else: - print 'Revision %s of repository %s owned by %s installed successfully, so running tool tests.' % \ - ( changeset_revision, name, owner ) - # Generate the shed_tools_dict that specifies the location of test data contained within this repository. - # and configure and run functional tests for this repository. This is equivalent to - # sh run_functional_tests.sh -installed - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) - # Find the path to the test-data directory within the installed repository. - has_test_data, shed_tools_dict = \ - parse_tool_panel_config( galaxy_shed_tool_conf_file, - from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) - # If the repository has a test-data directory we write the generated shed_tools_dict to a temporary - # file so the functional test framework can find it. - # TODO: Eliminate the need for this shed_tools_dict since it grows large over the course of each test run. - # If it cannot be eliminated altogether, reinitialize it with each new repository install so at this point - # it contains only entries for the current repository dependency hierarchy being tested. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) - print 'Saved generated shed_tools_dict to %s\nContents: %s' % ( galaxy_shed_tools_dict, shed_tools_dict ) - try: - install_and_test_statistics_dict = test_repository_tools( app, - repository, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - install_and_test_statistics_dict ) - except Exception, e: - exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) - log.exception( exception_message ) - tool_test_results_dict[ 'failed_tests' ].append( exception_message ) - processed_at_least_one_test_failed = \ - install_and_test_statistics_dict.get( 'at_least_one_test_failed', [] ) - if repository_identifier_tup not in processed_at_least_one_test_failed: - install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_tup ) - # Record the status of this repository in the tool shed. - params[ 'tools_functionally_correct' ] = False - response_dict = \ + if can_run_functional_tests: + # Execute the contained tool's functional tests only if the repository's entire dependency + # tree is successfully installed. The following checks should discover missing dependencies + # at any level of the dependency hierarchy. + missing_repository_dependencies = \ + install_and_test_base_util.get_missing_repository_dependencies( repository, + all_missing_repository_dependencies=None ) + print 'Missing repository dependencies:\n%s' % str( missing_repository_dependencies ) + missing_tool_dependencies = \ + install_and_test_base_util.get_missing_tool_dependencies( repository, + all_missing_tool_dependencies=None ) + print 'Missing tool dependencies:\n%s' % str( missing_tool_dependencies ) + if missing_repository_dependencies or missing_tool_dependencies: + print 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ + ( changeset_revision, name, owner ) + print 'because one or more dependencies has installation errors.' + # The repository was installed successfully, but one or more dependencies had installation errors. Since + # we cannot test the tools due to these errors, we'll remove tests and tools were created during the repository + # installation process so nose will not discover them and attempt to execute them. + remove_tests( app ) + else: + print 'Revision %s of repository %s owned by %s installed successfully, so running tool tests.' % \ + ( changeset_revision, name, owner ) + # Generate the shed_tools_dict that specifies the location of test data contained within this repository. + # and configure and run functional tests for this repository. This is equivalent to + # sh run_functional_tests.sh -installed + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + # Find the path to the test-data directory within the installed repository. + has_test_data, shed_tools_dict = \ + parse_tool_panel_config( galaxy_shed_tool_conf_file, + from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + # If the repository has a test-data directory we write the generated shed_tools_dict to a temporary + # file so the functional test framework can find it. + # TODO: Eliminate the need for this shed_tools_dict since it grows large over the course of each test run. + # If it cannot be eliminated altogether, reinitialize it with each new repository install so at this point + # it contains only entries for the current repository dependency hierarchy being tested. + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) + print 'Saved generated shed_tools_dict to %s\nContents: %s' % ( galaxy_shed_tools_dict, shed_tools_dict ) + try: + install_and_test_statistics_dict = test_repository_tools( app, + repository, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + install_and_test_statistics_dict ) + except Exception, e: + exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) + log.exception( exception_message ) + tool_test_results_dict[ 'failed_tests' ].append( exception_message ) + processed_at_least_one_test_failed = \ + install_and_test_statistics_dict.get( 'at_least_one_test_failed', [] ) + if repository_identifier_tup not in processed_at_least_one_test_failed: + install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_tup ) + # Record the status of this repository in the tool shed. + params[ 'tools_functionally_correct' ] = False install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params, can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' else: print 'Skipped attempt to install revision %s of repository %s owned by %s because ' % \ ( changeset_revision, name, owner ) @@ -663,16 +664,12 @@ # Call the save_test_results_for_changeset_revision() method to execute a PUT request to the # repository_revisions API controller with the status of the test. This also sets the do_not_test # and tools_functionally correct flags and updates the time_last_tested field to today's date. - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) else: # The get_failed_test_dicts() method returns a list. print 'Revision %s of repository %s owned by %s installed successfully but did not pass functional tests.' % \ @@ -695,16 +692,12 @@ params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=set_do_not_test ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) # Remove the just-executed tests so twill will not find and re-test them along with the tools # contained in the next repository. remove_tests( app ) diff -r 7ca065784d58e7aa77e5092952eacd963853df65 -r 1c14b0cdba15d8ffc2474a82aa3ca535e728f941 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -129,16 +129,12 @@ ( changeset_revision, name, owner ) tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) else: # See if the repository was installed in a previous test. repository = install_and_test_base_util.get_repository( name, owner, changeset_revision ) @@ -157,16 +153,12 @@ tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message params = dict( test_install_error=True, do_not_test=False ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) else: # The repository was successfully installed. print 'Installation succeeded for revision %s of repository %s owned by %s.' % \ @@ -179,16 +171,12 @@ repository_identifier_tup, install_and_test_statistics_dict, tool_test_results_dict ) - response_dict = \ - install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - print 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) - print '=============================================================' + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) # Populate the installation containers (success or error) for the repository's immediate repository # dependencies whose containers are not yet populated. install_and_test_base_util.populate_install_containers_for_repository_dependencies( app, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History panel: enable multi-select, decrease loading indicator fade time, correct disabled icon-btn color
by commits-noreply＠bitbucket.org 10 Feb '14

10 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ca065784d58/ Changeset: 7ca065784d58 User: carlfeberhard Date: 2014-02-10 15:52:40 Summary: History panel: enable multi-select, decrease loading indicator fade time, correct disabled icon-btn color Affected #: 13 files diff -r 1dc6776635ee359f32e8c661f549d2db8c06f16d -r 7ca065784d58e7aa77e5092952eacd963853df65 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -45,12 +45,16 @@ /** is the view currently in selection mode? */ this.selectable = attributes.selectable || false; + //this.log( '\t selectable:', this.selectable ); /** is the view currently selected? */ this.selected = attributes.selected || false; + //this.log( '\t selected:', this.selected ); /** is the body of this hda view expanded/not? */ this.expanded = attributes.expanded || false; + //this.log( '\t expanded:', this.expanded ); /** is the body of this hda view expanded/not? */ this.draggable = attributes.draggable || false; + //this.log( '\t draggable:', this.draggable ); this._setUpListeners(); }, @@ -412,12 +416,13 @@ // expand the body when the title is clicked or when in focus and space or enter is pressed 'click .dataset-title-bar' : 'toggleBodyVisibility', 'keydown .dataset-title-bar' : 'toggleBodyVisibility', - // toggle selected state - 'click .dataset-selector' : 'toggleSelect', // dragging - don't work, originalEvent === null //'dragstart .dataset-title-bar' : 'dragStartHandler', //'dragend .dataset-title-bar' : 'dragEndHandler' + + // toggle selected state + 'click .dataset-selector' : 'toggleSelect' }, /** Show or hide the body/details of an HDA. @@ -489,8 +494,6 @@ * Note: this also hides the primary actions */ showSelector : function( speed ){ - // if already shown, do nothing - if( this.$el.find( '.dataset-selector' ).css( 'display' ) !== 'none' ){ return; } speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); // make sure selected state is represented properly diff -r 1dc6776635ee359f32e8c661f549d2db8c06f16d -r 7ca065784d58e7aa77e5092952eacd963853df65 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -152,11 +152,14 @@ /** filters for displaying hdas */ this.filters = []; + /** selected hda ids */ + this.selectedHdaIds = []; // states/modes the panel can be in /** is the panel currently showing the dataset selection controls? */ this.selecting = attributes.selecting || false; this.annotationEditorShown = attributes.annotationEditorShown || false; + this.tagsEditorShown = attributes.tagsEditorShown || false; this._setUpListeners(); @@ -184,11 +187,11 @@ this.on( 'loading-history', function(){ // show the loading indicator when loading a new history starts... - this.showLoadingIndicator( 'loading history...' ); + this.showLoadingIndicator( 'loading history...', 40 ); }); this.on( 'loading-done', function(){ // ...hiding it again when loading is done (or there's been an error) - this.hideLoadingIndicator(); + this.hideLoadingIndicator( 40 ); }); // throw the first render up as a diff namespace using once @@ -408,6 +411,7 @@ this.model = new historyModel.History( newHistoryJSON, newHdaJSON, attributes ); this._setUpWebStorage( attributes.initiallyExpanded, attributes.show_deleted, attributes.show_hidden ); this._setUpModelEventHandlers(); + this.selectedHdaIds = []; this.trigger( 'new-model', this ); this.render(); return this; @@ -596,8 +600,8 @@ } } // search and select available to both anon/logged-in users - //$newRender.find( '.history-secondary-actions' ).prepend( this._renderSelectButton() ); - //$newRender.find( '.history-dataset-actions' ).toggle( this.selecting ); + $newRender.find( '.history-secondary-actions' ).prepend( this._renderSelectButton() ); + $newRender.find( '.history-dataset-actions' ).toggle( this.selecting ); $newRender.find( '.history-secondary-actions' ).prepend( this._renderSearchButton() ); this._setUpBehaviours( $newRender ); @@ -687,8 +691,15 @@ $where.find( '[title]' ).tooltip({ placement: 'bottom' }); // anon users shouldn't have access to any of the following - if( ( !this.model ) - || ( !Galaxy.currUser || Galaxy.currUser.isAnonymous() ) + if( !this.model ){ + return; + } + + // set up the pupup for actions available when multi selecting + this._setUpDatasetActionsPopup( $where ); + + // anon users shouldn't have access to any of the following + if( ( !Galaxy.currUser || Galaxy.currUser.isAnonymous() ) || ( Galaxy.currUser.id !== this.model.get( 'user_id' ) ) ){ return; } @@ -710,7 +721,6 @@ } } }); - this._setUpDatasetActionsPopup( $where ); }, _setUpDatasetActionsPopup : function( $where ){ @@ -785,8 +795,10 @@ }, function createAndPrepend( next ){ panel.scrollToTop(); - var $whereTo = panel.$el.find( panel.datasetsSelector ); - panel.createHdaView( hda ).$el.hide().prependTo( $whereTo ).slideDown( panel.fxSpeed ); + var $whereTo = panel.$el.find( panel.datasetsSelector ), + hdaView = panel.createHdaView( hda ); + panel.hdaViews[ hda.id ] = hdaView; + hdaView.render().$el.hide().prependTo( $whereTo ).slideDown( panel.fxSpeed ); } ]); }, @@ -796,21 +808,19 @@ */ createHdaView : function( hda ){ var hdaId = hda.get( 'id' ), - expanded = this.storage.get( 'expandedHdas' )[ hdaId ], hdaView = new this.HDAViewClass({ - model : hda, - linkTarget : this.linkTarget, - expanded : expanded, - //draggable : true, - tagsEditorShown : this.preferences.get( 'tagsEditorShown' ), - annotationEditorShown : this.preferences.get( 'annotationEditorShown' ), - selectable : this.selecting, - hasUser : this.model.ownedByCurrUser(), - logger : this.logger - }); + model : hda, + linkTarget : this.linkTarget, + expanded : this.storage.get( 'expandedHdas' )[ hdaId ], + //draggable : true, + selectable : this.selecting, + hasUser : this.model.ownedByCurrUser(), + logger : this.logger, + tagsEditorShown : this.preferences.get( 'tagsEditorShown' ), + annotationEditorShown : this.preferences.get( 'annotationEditorShown' ) + }); this._setUpHdaListeners( hdaView ); - this.hdaViews[ hdaId ] = hdaView; - return hdaView.render(); + return hdaView; }, /** Set up HistoryPanel listeners for HDAView events. Currently binds: @@ -826,6 +836,17 @@ hdaView.on( 'body-collapsed', function( id ){ historyView.storage.removeExpandedHda( id ); }); + // maintain a list of hdas that are selected + hdaView.on( 'selected', function( hdaView ){ + var id = hdaView.model.get( 'id' ); + historyView.selectedHdaIds = _.union( historyView.selectedHdaIds, [ id ] ); + //console.debug( 'selected', historyView.selectedHdaIds ); + }); + hdaView.on( 'de-selected', function( hdaView ){ + var id = hdaView.model.get( 'id' ); + historyView.selectedHdaIds = _.without( historyView.selectedHdaIds, id ); + //console.debug( 'de-selected', historyView.selectedHdaIds ); + }); //TODO: remove? hdaView.on( 'error', function( model, xhr, options, msg ){ historyView.errorHandler( model, xhr, options, msg ); @@ -876,8 +897,8 @@ */ renderHdas : function( $whereTo ){ $whereTo = $whereTo || this.$el; - this.hdaViews = {}; var historyView = this, + newHdaViews = {}, $datasetsList = $whereTo.find( this.datasetsSelector ), // only render the shown hdas //TODO: switch to more general filtered pattern @@ -892,7 +913,13 @@ if( visibleHdas.length ){ visibleHdas.each( function( hda ){ // render it (NOTE: reverse order, newest on top (prepend)) - $datasetsList.prepend( historyView.createHdaView( hda ).$el ); + var hdaId = hda.get( 'id' ), + hdaView = historyView.createHdaView( hda ); + newHdaViews[ hdaId ] = hdaView; + if( _.contains( historyView.selectedHdaIds, hdaId ) ){ + hdaView.selected = true; + } + $datasetsList.prepend( hdaView.render().$el ); }); $whereTo.find( this.emptyMsgSelector ).hide(); @@ -900,6 +927,7 @@ //console.debug( 'emptyMsg:', $whereTo.find( this.emptyMsgSelector ) ) $whereTo.find( this.emptyMsgSelector ).show(); } + this.hdaViews = newHdaViews; return this.hdaViews; }, @@ -932,7 +960,9 @@ 'click .history-search-btn' : 'toggleSearchControls', 'click .history-select-btn' : function( e ){ this.toggleSelectors( this.fxSpeed ); }, - 'click .history-select-all-datasets-btn' : 'selectAllDatasets' + + 'click .history-select-all-datasets-btn' : 'selectAllDatasets', + 'click .history-deselect-all-datasets-btn' : 'deselectAllDatasets' }, /** Update the history size display (curr. upper right of panel). @@ -1070,6 +1100,7 @@ _.each( this.hdaViews, function( view ){ view.showSelector( speed ); }); + this.selectedHdaIds = []; }, hideSelectors : function( speed ){ @@ -1078,6 +1109,7 @@ _.each( this.hdaViews, function( view ){ view.hideSelector( speed ); }); + this.selectedHdaIds = []; }, toggleSelectors : function( speed ){ @@ -1089,22 +1121,15 @@ }, selectAllDatasets : function( event ){ - var $selectBtn = this.$el.find( '.history-select-all-datasets-btn' ); - currMode = $selectBtn.data( 'mode' ); - if( currMode === 'select' ){ - _.each( this.hdaViews, function( view ){ - view.select( event ); - }); - $selectBtn.data( 'mode', 'deselect' ); - $selectBtn.text( _l( 'De-select all' ) ); + _.each( this.hdaViews, function( view ){ + view.select( event ); + }); + }, - } else if( currMode === 'deselect' ){ - _.each( this.hdaViews, function( view ){ - view.deselect( event ); - }); - $selectBtn.data( 'mode', 'select' ); - $selectBtn.text( _l( 'Select all' ) ); - } + deselectAllDatasets : function( event ){ + _.each( this.hdaViews, function( view ){ + view.deselect( event ); + }); }, getSelectedHdaViews : function(){ diff -r 1dc6776635ee359f32e8c661f549d2db8c06f16d -r 7ca065784d58e7aa77e5092952eacd963853df65 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file diff -r 1dc6776635ee359f32e8c661f549d2db8c06f16d -r 7ca065784d58e7aa77e5092952eacd963853df65 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(c,f,a,i){var g=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});g.storageKey=function h(){return("history-panel")};var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(j){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([j],[true])))},removeExpandedHda:function(j){this.save("expandedHdas",_.omit(this.get("expandedHdas"),j))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function b(j){if(!j){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+j)}return("history:"+j)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:i.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(j){j=j||{};if(j.logger){this.logger=j.logger}this.log(this+".initialize:",j);this.HDAViewClass=j.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=j.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.preferences=new g(_.extend({id:g.storageKey()},_.pick(j,_.keys(g.prototype.defaults))));this.filters=[];this.selecting=j.selecting||false;this.annotationEditorShown=j.annotationEditorShown||false;this._setUpListeners();if(this.model){this._setUpWebStorage(j.initiallyExpanded,j.show_deleted,j.show_hidden);this._setUpModelEventHandlers()}if(j.onready){j.onready.call(this)}},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(j){this.log(this+"",arguments)},this)}},errorHandler:function(l,o,k,n,m){var j=this._parseErrorMessage(l,o,k,n,m);if(o&&o.status===0&&o.readyState===0){}else{if(o&&o.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",j.message,j.details)})}else{this.displayMessage("error",j.message,j.details)}}}},_parseErrorMessage:function(m,q,l,p,o){var k=Galaxy.currUser,j={message:this._bePolite(p),details:{user:(k instanceof User)?(k.toJSON()):(k+""),source:(m instanceof Backbone.Model)?(m.toJSON()):(m+""),xhr:q,options:(q)?(_.omit(l,"xhr")):(l)}};_.extend(j.details,o||{});if(q&&_.isFunction(q.getAllResponseHeaders)){var n=q.getAllResponseHeaders();n=_.compact(n.split("\n"));n=_.map(n,function(r){return r.split(": ")});j.details.xhr.responseHeaders=_.object(n)}return j},_bePolite:function(j){j=j||_l("An error occurred while getting updates from the server");return j+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(k){var j=this;return this.loadHistoryWithHDADetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories/"+m+"/set_as_current")};return this.loadHistoryWithHDADetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},loadHistoryWithHDADetails:function(m,l,k,o){var j=this,n=function(p){return j.getExpandedHdaIds(p.id)};return this.loadHistory(m,l,k,o,n)},loadHistory:function(m,l,k,p,n){this.trigger("loading-history",this);l=l||{};var j=this;var o=c.History.getHistoryData(m,{historyFn:k,hdaFn:p,hdaDetailIds:l.initiallyExpanded||n});return this._loadHistoryFromXHR(o,l).fail(function(s,q,r){j.trigger("error",j,s,l,_l("An error was encountered while "+q),{historyId:m,history:r||{}})}).always(function(){j.trigger("loading-done",j)})},_loadHistoryFromXHR:function(l,k){var j=this;l.then(function(m,n){j.setModel(m,n,k)});l.fail(function(n,m){j.render()});return l},setModel:function(l,j,k){k=k||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){l.user=Galaxy.currUser.toJSON()}this.model=new c.History(l,j,k);this._setUpWebStorage(k.initiallyExpanded,k.show_deleted,k.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(k,j,l){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(k)){this.storage.set("exandedHdas",k)}if(_.isBoolean(j)){this.storage.set("show_deleted",j)}if(_.isBoolean(l)){this.storage.set("show_hidden",l)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var j in sessionStorage){if(j.indexOf("history:")===0){sessionStorage.removeItem(j)}}},getStoredOptions:function(k){if(!k||k==="current"){return(this.storage)?(this.storage.get()):({})}var j=sessionStorage.getItem(d.historyStorageKey(k));return(j===null)?({}):(JSON.parse(j))},getExpandedHdaIds:function(j){var k=this.getStoredOptions(j).expandedHdas;return((_.isEmpty(k))?([]):(_.keys(k)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(k,m,j,l){this.errorHandler(k,m,j,l)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(j){this.model.fetch()},this);this.model.hdas.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[k.id])}},this)},render:function(l,m){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k;if(this.model){k=this.renderModel()}else{k=this.renderWithoutModel()}$(j).queue("fx",[function(n){if(l&&j.$el.is(":visible")){j.$el.fadeOut(l,n)}else{n()}},function(n){j.$el.empty();if(k){j.$el.append(k.children());j.renderBasedOnPrefs()}n()},function(n){if(l&&!j.$el.is(":visible")){j.$el.fadeIn(l,n)}else{n()}},function(n){if(m){m.call(this)}j.trigger("rendered",this);n()}]);return this},renderWithoutModel:function(){var j=$("<div/>"),k=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return j.append(k)},renderModel:function(){var j=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){j.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{j.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(j);this._renderAnnotation(j)}}j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},_renderTags:function(j){var k=this;this.tagsEditor=new TagsEditor({model:this.model,el:j.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("tagsEditorShown",true);k.toggleHDATagEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("tagsEditorShown",false);k.toggleHDATagEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}},_renderAnnotation:function(j){var k=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:j.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("annotationEditorShown",true);k.toggleHDAAnnotationEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("annotationEditorShown",false);k.toggleHDAAnnotationEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}},_renderSearchButton:function(j){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(j){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(j){j=j||this.$el;j.find("[title]").tooltip({placement:"bottom"});if((!this.model)||(!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var k=this;j.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(l){var m=k.model.get("name");if(l&&l!==m){k.$el.find(".history-name").text(l);k.model.save({name:l}).fail(function(){k.$el.find(".history-name").text(k.model.previous("name"))})}else{k.$el.find(".history-name").text(m)}}});this._setUpDatasetActionsPopup(j)},_setUpDatasetActionsPopup:function(j){var k=this;(new PopupMenu(j.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;k.getSelectedHdaCollection().ajaxQueue(l)}}}]))},refreshHdas:function(k,j){if(this.model){return this.model.refresh(k,j)}return $.when()},addHdaView:function(m){this.log("add."+this,m);var k=this;if(!m.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function l(o){var n=k.$el.find(k.emptyMsgSelector);if(n.is(":visible")){n.fadeOut(k.fxSpeed,o)}else{o()}},function j(o){k.scrollToTop();var n=k.$el.find(k.datasetsSelector);k.createHdaView(m).$el.hide().prependTo(n).slideDown(k.fxSpeed)}])},createHdaView:function(l){var k=l.get("id"),j=this.storage.get("expandedHdas")[k],m=new this.HDAViewClass({model:l,linkTarget:this.linkTarget,expanded:j,tagsEditorShown:this.preferences.get("tagsEditorShown"),annotationEditorShown:this.preferences.get("annotationEditorShown"),selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(m);this.hdaViews[k]=m;return m.render()},_setUpHdaListeners:function(k){var j=this;k.on("body-expanded",function(l){j.storage.addExpandedHda(l)});k.on("body-collapsed",function(l){j.storage.removeExpandedHda(l)});k.on("error",function(m,o,l,n){j.errorHandler(m,o,l,n)})},handleHdaDeletionChange:function(j){if(j.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[j.id])}},handleHdaVisibleChange:function(j){if(j.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[j.id])}},removeHdaView:function(k){if(!k){return}var j=this;k.$el.fadeOut(j.fxSpeed,function(){k.off();k.remove();delete j.hdaViews[k.model.id];if(_.isEmpty(j.hdaViews)){j.$el.find(j.emptyMsgSelector).fadeIn(j.fxSpeed,function(){j.trigger("empty-history",j)})}})},renderHdas:function(l){l=l||this.$el;this.hdaViews={};var k=this,j=l.find(this.datasetsSelector),m=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);j.empty();if(m.length){m.each(function(n){j.prepend(k.createHdaView(n).$el)});l.find(this.emptyMsgSelector).hide()}else{l.find(this.emptyMsgSelector).show()}return this.hdaViews},toggleHDATagEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.tagsEditor){l.tagsEditor.toggle.apply(l.tagsEditor,k)}})},toggleHDAAnnotationEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.annotationEditor){l.annotationEditor.toggle.apply(l.annotationEditor,k)}})},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(j){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(j){j.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},setUpSearchInput:function(k){var l=this,o=".history-search-input";function n(p){l.searchFor=p;l.filters=[function(q){return q.matchesAll(l.searchFor)}];l.trigger("search:searching",p,l);l.renderHdas()}function j(p){if(l.model.hdas.haveDetails()){n(p);return}l.$el.find(o).searchInput("toggle-loading");l.model.hdas.fetchAllDetails({silent:true}).always(function(){l.$el.find(o).searchInput("toggle-loading")}).done(function(){n(p)})}function m(){l.searchFor="";l.filters=[];l.trigger("search:clear",l);l.renderHdas()}k.searchInput({initialVal:l.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:j,onsearch:n,onclear:m});return k},showSearchControls:function(l){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k=this.$el.find(".history-search-controls"),m=k.find(".history-search-input");if(!m.children().size()){this.setUpSearchInput(m)}k.slideDown(l,function(){$(this).find("input").focus();j.preferences.set("searching",true)})},hideSearchControls:function(){speed=(speed===undefined)?(this.fxSpeed):(speed);var j=this;this.$el.find(".history-search-controls").slideUp(speed,function(){j.preferences.set("searching",false)})},toggleSearchControls:function(j){speed=(jQuery.type(j)==="number")?(j):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showSelectors:function(j){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(j);_.each(this.hdaViews,function(k){k.showSelector(j)})},hideSelectors:function(j){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(j);_.each(this.hdaViews,function(k){k.hideSelector(j)})},toggleSelectors:function(j){if(!this.selecting){this.showSelectors(j)}else{this.hideSelectors(j)}},selectAllDatasets:function(k){var j=this.$el.find(".history-select-all-datasets-btn");currMode=j.data("mode");if(currMode==="select"){_.each(this.hdaViews,function(l){l.select(k)});j.data("mode","deselect");j.text(_l("De-select all"))}else{if(currMode==="deselect"){_.each(this.hdaViews,function(l){l.deselect(k)});j.data("mode","select");j.text(_l("Select all"))}}},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(j){return j.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(j){return j.model}),{historyId:this.model.id})},showLoadingIndicator:function(k,j,l){j=(j!==undefined)?(j):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,l)}else{this.$el.fadeOut(j);this.indicator.show(k,j,l)}},hideLoadingIndicator:function(j,k){j=(j!==undefined)?(j):(this.fxSpeed);if(this.indicator){this.indicator.hide(j,k)}},displayMessage:function(o,p,n){var l=this;this.scrollToTop();var m=this.$el.find(this.msgsSelector),j=$("<div/>").addClass(o+"message").html(p);if(!_.isEmpty(n)){var k=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(l.messageToModalOptions(o,p,n));return false});j.append(" ",k)}return m.html(j)},messageToModalOptions:function(n,p,m){var j=this,o=$("<div/>"),l={title:"Details"};function k(q){q=_.omit(q,_.functions(q));return["<table>",_.map(q,function(s,r){s=(_.isObject(s))?(k(s)):(s);return'<tr><td style="vertical-align: top; color: grey">'+r+'</td><td style="padding-left: 8px">'+s+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(m)){l.body=o.append(k(m))}else{l.body=o.html(m)}l.buttons={Ok:function(){Galaxy.modal.hide();j.clearMessages()}};return l},clearMessages:function(){var j=this.$el.find(this.msgsSelector);j.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(j){this.$el.parent().scrollTop(j)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(k,l){if(!l){this.$el.parent().parent().scrollTop(k);return this}var j=window,m=this.$el.parent().parent(),o=$(j).innerHeight(),n=(o/2)-(l/2);$(m).scrollTop(k-n);return this},scrollToId:function(k){if((!k)||(!this.hdaViews[k])){return this}var j=this.hdaViews[k].$el;this.scrollIntoView(j.offset().top,j.outerHeight());return this},scrollToHid:function(j){var k=this.model.hdas.getByHid(j);if(!k){return this}return this.scrollToId(k.id)},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(_l("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(_l("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(c,f,a,i){var g=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});g.storageKey=function h(){return("history-panel")};var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(j){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([j],[true])))},removeExpandedHda:function(j){this.save("expandedHdas",_.omit(this.get("expandedHdas"),j))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function b(j){if(!j){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+j)}return("history:"+j)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:i.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(j){j=j||{};if(j.logger){this.logger=j.logger}this.log(this+".initialize:",j);this.HDAViewClass=j.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=j.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.preferences=new g(_.extend({id:g.storageKey()},_.pick(j,_.keys(g.prototype.defaults))));this.filters=[];this.selectedHdaIds=[];this.selecting=j.selecting||false;this.annotationEditorShown=j.annotationEditorShown||false;this.tagsEditorShown=j.tagsEditorShown||false;this._setUpListeners();if(this.model){this._setUpWebStorage(j.initiallyExpanded,j.show_deleted,j.show_hidden);this._setUpModelEventHandlers()}if(j.onready){j.onready.call(this)}},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this.hideLoadingIndicator(40)});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(j){this.log(this+"",arguments)},this)}},errorHandler:function(l,o,k,n,m){var j=this._parseErrorMessage(l,o,k,n,m);if(o&&o.status===0&&o.readyState===0){}else{if(o&&o.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",j.message,j.details)})}else{this.displayMessage("error",j.message,j.details)}}}},_parseErrorMessage:function(m,q,l,p,o){var k=Galaxy.currUser,j={message:this._bePolite(p),details:{user:(k instanceof User)?(k.toJSON()):(k+""),source:(m instanceof Backbone.Model)?(m.toJSON()):(m+""),xhr:q,options:(q)?(_.omit(l,"xhr")):(l)}};_.extend(j.details,o||{});if(q&&_.isFunction(q.getAllResponseHeaders)){var n=q.getAllResponseHeaders();n=_.compact(n.split("\n"));n=_.map(n,function(r){return r.split(": ")});j.details.xhr.responseHeaders=_.object(n)}return j},_bePolite:function(j){j=j||_l("An error occurred while getting updates from the server");return j+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(k){var j=this;return this.loadHistoryWithHDADetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories/"+m+"/set_as_current")};return this.loadHistoryWithHDADetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},loadHistoryWithHDADetails:function(m,l,k,o){var j=this,n=function(p){return j.getExpandedHdaIds(p.id)};return this.loadHistory(m,l,k,o,n)},loadHistory:function(m,l,k,p,n){this.trigger("loading-history",this);l=l||{};var j=this;var o=c.History.getHistoryData(m,{historyFn:k,hdaFn:p,hdaDetailIds:l.initiallyExpanded||n});return this._loadHistoryFromXHR(o,l).fail(function(s,q,r){j.trigger("error",j,s,l,_l("An error was encountered while "+q),{historyId:m,history:r||{}})}).always(function(){j.trigger("loading-done",j)})},_loadHistoryFromXHR:function(l,k){var j=this;l.then(function(m,n){j.setModel(m,n,k)});l.fail(function(n,m){j.render()});return l},setModel:function(l,j,k){k=k||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){l.user=Galaxy.currUser.toJSON()}this.model=new c.History(l,j,k);this._setUpWebStorage(k.initiallyExpanded,k.show_deleted,k.show_hidden);this._setUpModelEventHandlers();this.selectedHdaIds=[];this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(k,j,l){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(k)){this.storage.set("exandedHdas",k)}if(_.isBoolean(j)){this.storage.set("show_deleted",j)}if(_.isBoolean(l)){this.storage.set("show_hidden",l)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var j in sessionStorage){if(j.indexOf("history:")===0){sessionStorage.removeItem(j)}}},getStoredOptions:function(k){if(!k||k==="current"){return(this.storage)?(this.storage.get()):({})}var j=sessionStorage.getItem(d.historyStorageKey(k));return(j===null)?({}):(JSON.parse(j))},getExpandedHdaIds:function(j){var k=this.getStoredOptions(j).expandedHdas;return((_.isEmpty(k))?([]):(_.keys(k)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(k,m,j,l){this.errorHandler(k,m,j,l)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(j){this.model.fetch()},this);this.model.hdas.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[k.id])}},this)},render:function(l,m){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k;if(this.model){k=this.renderModel()}else{k=this.renderWithoutModel()}$(j).queue("fx",[function(n){if(l&&j.$el.is(":visible")){j.$el.fadeOut(l,n)}else{n()}},function(n){j.$el.empty();if(k){j.$el.append(k.children());j.renderBasedOnPrefs()}n()},function(n){if(l&&!j.$el.is(":visible")){j.$el.fadeIn(l,n)}else{n()}},function(n){if(m){m.call(this)}j.trigger("rendered",this);n()}]);return this},renderWithoutModel:function(){var j=$("<div/>"),k=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return j.append(k)},renderModel:function(){var j=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){j.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{j.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(j);this._renderAnnotation(j)}}j.find(".history-secondary-actions").prepend(this._renderSelectButton());j.find(".history-dataset-actions").toggle(this.selecting);j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},_renderTags:function(j){var k=this;this.tagsEditor=new TagsEditor({model:this.model,el:j.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("tagsEditorShown",true);k.toggleHDATagEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("tagsEditorShown",false);k.toggleHDATagEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}},_renderAnnotation:function(j){var k=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:j.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("annotationEditorShown",true);k.toggleHDAAnnotationEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("annotationEditorShown",false);k.toggleHDAAnnotationEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}},_renderSearchButton:function(j){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(j){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(j){j=j||this.$el;j.find("[title]").tooltip({placement:"bottom"});if(!this.model){return}this._setUpDatasetActionsPopup(j);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var k=this;j.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(l){var m=k.model.get("name");if(l&&l!==m){k.$el.find(".history-name").text(l);k.model.save({name:l}).fail(function(){k.$el.find(".history-name").text(k.model.previous("name"))})}else{k.$el.find(".history-name").text(m)}}})},_setUpDatasetActionsPopup:function(j){var k=this;(new PopupMenu(j.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;k.getSelectedHdaCollection().ajaxQueue(l)}}}]))},refreshHdas:function(k,j){if(this.model){return this.model.refresh(k,j)}return $.when()},addHdaView:function(m){this.log("add."+this,m);var k=this;if(!m.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function l(o){var n=k.$el.find(k.emptyMsgSelector);if(n.is(":visible")){n.fadeOut(k.fxSpeed,o)}else{o()}},function j(o){k.scrollToTop();var n=k.$el.find(k.datasetsSelector),p=k.createHdaView(m);k.hdaViews[m.id]=p;p.render().$el.hide().prependTo(n).slideDown(k.fxSpeed)}])},createHdaView:function(k){var j=k.get("id"),l=new this.HDAViewClass({model:k,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[j],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:this.preferences.get("tagsEditorShown"),annotationEditorShown:this.preferences.get("annotationEditorShown")});this._setUpHdaListeners(l);return l},_setUpHdaListeners:function(k){var j=this;k.on("body-expanded",function(l){j.storage.addExpandedHda(l)});k.on("body-collapsed",function(l){j.storage.removeExpandedHda(l)});k.on("selected",function(l){var m=l.model.get("id");j.selectedHdaIds=_.union(j.selectedHdaIds,[m])});k.on("de-selected",function(l){var m=l.model.get("id");j.selectedHdaIds=_.without(j.selectedHdaIds,m)});k.on("error",function(m,o,l,n){j.errorHandler(m,o,l,n)})},handleHdaDeletionChange:function(j){if(j.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[j.id])}},handleHdaVisibleChange:function(j){if(j.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[j.id])}},removeHdaView:function(k){if(!k){return}var j=this;k.$el.fadeOut(j.fxSpeed,function(){k.off();k.remove();delete j.hdaViews[k.model.id];if(_.isEmpty(j.hdaViews)){j.$el.find(j.emptyMsgSelector).fadeIn(j.fxSpeed,function(){j.trigger("empty-history",j)})}})},renderHdas:function(l){l=l||this.$el;var k=this,n={},j=l.find(this.datasetsSelector),m=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);j.empty();if(m.length){m.each(function(p){var o=p.get("id"),q=k.createHdaView(p);n[o]=q;if(_.contains(k.selectedHdaIds,o)){q.selected=true}j.prepend(q.render().$el)});l.find(this.emptyMsgSelector).hide()}else{l.find(this.emptyMsgSelector).show()}this.hdaViews=n;return this.hdaViews},toggleHDATagEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.tagsEditor){l.tagsEditor.toggle.apply(l.tagsEditor,k)}})},toggleHDAAnnotationEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.annotationEditor){l.annotationEditor.toggle.apply(l.annotationEditor,k)}})},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(j){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(j){j.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},setUpSearchInput:function(k){var l=this,o=".history-search-input";function n(p){l.searchFor=p;l.filters=[function(q){return q.matchesAll(l.searchFor)}];l.trigger("search:searching",p,l);l.renderHdas()}function j(p){if(l.model.hdas.haveDetails()){n(p);return}l.$el.find(o).searchInput("toggle-loading");l.model.hdas.fetchAllDetails({silent:true}).always(function(){l.$el.find(o).searchInput("toggle-loading")}).done(function(){n(p)})}function m(){l.searchFor="";l.filters=[];l.trigger("search:clear",l);l.renderHdas()}k.searchInput({initialVal:l.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:j,onsearch:n,onclear:m});return k},showSearchControls:function(l){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k=this.$el.find(".history-search-controls"),m=k.find(".history-search-input");if(!m.children().size()){this.setUpSearchInput(m)}k.slideDown(l,function(){$(this).find("input").focus();j.preferences.set("searching",true)})},hideSearchControls:function(){speed=(speed===undefined)?(this.fxSpeed):(speed);var j=this;this.$el.find(".history-search-controls").slideUp(speed,function(){j.preferences.set("searching",false)})},toggleSearchControls:function(j){speed=(jQuery.type(j)==="number")?(j):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showSelectors:function(j){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(j);_.each(this.hdaViews,function(k){k.showSelector(j)});this.selectedHdaIds=[]},hideSelectors:function(j){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(j);_.each(this.hdaViews,function(k){k.hideSelector(j)});this.selectedHdaIds=[]},toggleSelectors:function(j){if(!this.selecting){this.showSelectors(j)}else{this.hideSelectors(j)}},selectAllDatasets:function(j){_.each(this.hdaViews,function(k){k.select(j)})},deselectAllDatasets:function(j){_.each(this.hdaViews,function(k){k.deselect(j)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(j){return j.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(j){return j.model}),{historyId:this.model.id})},showLoadingIndicator:function(k,j,l){j=(j!==undefined)?(j):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,l)}else{this.$el.fadeOut(j);this.indicator.show(k,j,l)}},hideLoadingIndicator:function(j,k){j=(j!==undefined)?(j):(this.fxSpeed);if(this.indicator){this.indicator.hide(j,k)}},displayMessage:function(o,p,n){var l=this;this.scrollToTop();var m=this.$el.find(this.msgsSelector),j=$("<div/>").addClass(o+"message").html(p);if(!_.isEmpty(n)){var k=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(l.messageToModalOptions(o,p,n));return false});j.append(" ",k)}return m.html(j)},messageToModalOptions:function(n,p,m){var j=this,o=$("<div/>"),l={title:"Details"};function k(q){q=_.omit(q,_.functions(q));return["<table>",_.map(q,function(s,r){s=(_.isObject(s))?(k(s)):(s);return'<tr><td style="vertical-align: top; color: grey">'+r+'</td><td style="padding-left: 8px">'+s+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(m)){l.body=o.append(k(m))}else{l.body=o.html(m)}l.buttons={Ok:function(){Galaxy.modal.hide();j.clearMessages()}};return l},clearMessages:function(){var j=this.$el.find(this.msgsSelector);j.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(j){this.$el.parent().scrollTop(j)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(k,l){if(!l){this.$el.parent().parent().scrollTop(k);return this}var j=window,m=this.$el.parent().parent(),o=$(j).innerHeight(),n=(o/2)-(l/2);$(m).scrollTop(k-n);return this},scrollToId:function(k){if((!k)||(!this.hdaViews[k])){return this}var j=this.hdaViews[k].$el;this.scrollIntoView(j.offset().top,j.outerHeight());return this},scrollToHid:function(j){var k=this.model.hdas.getByHid(j);if(!k){return this}return this.scrollToId(k.id)},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(_l("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(_l("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ No newline at end of file diff -r 1dc6776635ee359f32e8c661f549d2db8c06f16d -r 7ca065784d58e7aa77e5092952eacd963853df65 static/scripts/packed/templates/compiled/history-templates.js --- a/static/scripts/packed/templates/compiled/history-templates.js +++ b/static/scripts/packed/templates/compiled/history-templates.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-body"]=b(function(g,r,p,k,z){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);z=z||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(D,C){var A="",B;A+='\n <div class="dataset-summary">\n ';if(B=p.body){B=B.call(D,{hash:{},data:C})}else{B=D.body;B=typeof B===e?B.apply(D):B}if(B||B===0){A+=B}A+='\n </div>\n <div class="dataset-actions clear">\n <div class="left"></div>\n <div class="right"></div>\n </div>\n\n ';return A}function m(D,C){var A="",B;A+='\n <div class="dataset-summary">\n ';B=p["if"].call(D,D.misc_blurb,{hash:{},inverse:o.noop,fn:o.program(4,l,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.data_type,{hash:{},inverse:o.noop,fn:o.program(6,j,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.metadata_dbkey,{hash:{},inverse:o.noop,fn:o.program(9,f,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.misc_info,{hash:{},inverse:o.noop,fn:o.program(12,x,C),data:C});if(B||B===0){A+=B}A+='\n </div>\n\n <div class="dataset-actions clear">\n <div class="left"></div>\n <div class="right"></div>\n </div>\n\n ';B=p.unless.call(D,D.deleted,{hash:{},inverse:o.noop,fn:o.program(14,w,C),data:C});if(B||B===0){A+=B}A+="\n\n ";return A}function l(D,C){var A="",B;A+='\n <div class="dataset-blurb">\n <span class="value">';if(B=p.misc_blurb){B=B.call(D,{hash:{},data:C})}else{B=D.misc_blurb;B=typeof B===e?B.apply(D):B}A+=d(B)+"</span>\n </div>\n ";return A}function j(E,D){var A="",C,B;A+='\n <div class="dataset-datatype">\n <label class="prompt">';B={hash:{},inverse:o.noop,fn:o.program(7,i,D),data:D};if(C=p.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!p.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+='</label>\n <span class="value">';if(C=p.data_type){C=C.call(E,{hash:{},data:D})}else{C=E.data_type;C=typeof C===e?C.apply(E):C}A+=d(C)+"</span>\n </div>\n ";return A}function i(B,A){return"format"}function f(E,D){var A="",C,B;A+='\n <div class="dataset-dbkey">\n <label class="prompt">';B={hash:{},inverse:o.noop,fn:o.program(10,y,D),data:D};if(C=p.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!p.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+='</label>\n <span class="value">\n ';if(C=p.metadata_dbkey){C=C.call(E,{hash:{},data:D})}else{C=E.metadata_dbkey;C=typeof C===e?C.apply(E):C}A+=d(C)+"\n </span>\n </div>\n ";return A}function y(B,A){return"database"}function x(D,C){var A="",B;A+='\n <div class="dataset-info">\n <span class="value">';if(B=p.misc_info){B=B.call(D,{hash:{},data:C})}else{B=D.misc_info;B=typeof B===e?B.apply(D):B}A+=d(B)+"</span>\n </div>\n ";return A}function w(D,C){var A="",B;A+='\n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n <div class="dataset-display-applications">\n ';B=p.each.call(D,D.display_apps,{hash:{},inverse:o.noop,fn:o.program(15,v,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p.each.call(D,D.display_types,{hash:{},inverse:o.noop,fn:o.program(15,v,C),data:C});if(B||B===0){A+=B}A+='\n </div>\n\n <div class="dataset-peek">\n ';B=p["if"].call(D,D.peek,{hash:{},inverse:o.noop,fn:o.program(19,s,C),data:C});if(B||B===0){A+=B}A+="\n </div>\n\n ";return A}function v(D,C){var A="",B;A+='\n <div class="display-application">\n <span class="display-application-location">';if(B=p.label){B=B.call(D,{hash:{},data:C})}else{B=D.label;B=typeof B===e?B.apply(D):B}A+=d(B)+'</span>\n <span class="display-application-links">\n ';B=p.each.call(D,D.links,{hash:{},inverse:o.noop,fn:o.program(16,u,C),data:C});if(B||B===0){A+=B}A+="\n </span>\n </div>\n ";return A}function u(E,D){var A="",C,B;A+='\n <a target="';if(C=p.target){C=C.call(E,{hash:{},data:D})}else{C=E.target;C=typeof C===e?C.apply(E):C}A+=d(C)+'" href="';if(C=p.href){C=C.call(E,{hash:{},data:D})}else{C=E.href;C=typeof C===e?C.apply(E):C}A+=d(C)+'">';B={hash:{},inverse:o.noop,fn:o.program(17,t,D),data:D};if(C=p.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!p.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+="</a>\n ";return A}function t(C,B){var A;if(A=p.text){A=A.call(C,{hash:{},data:B})}else{A=C.text;A=typeof A===e?A.apply(C):A}return d(A)}function s(D,C){var A="",B;A+='\n <pre 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Click 'Get Data' on the left pane to start"}q+='<div class="history-controls">\n <div class="history-search-controls">\n <div class="history-search-input"></div>\n </div>\n\n <div class="history-title">\n \n ';i=p["if"].call(r,r.name,{hash:{},inverse:o.noop,fn:o.program(1,n,t),data:t});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=p["if"].call(r,r.nice_size,{hash:{},inverse:o.noop,fn:o.program(3,m,t),data:t});if(i||i===0){q+=i}q+='\n\n <div class="history-secondary-actions"></div>\n </div>\n\n <div class="message-container">\n ';i=p["if"].call(r,r.message,{hash:{},inverse:o.noop,fn:o.program(5,k,t),data:t});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:o.noop,fn:o.program(7,j,t),data:t};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+=".\n ";f={hash:{},inverse:o.noop,fn:o.program(9,g,t),data:t};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='.\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:o.noop,fn:o.program(11,s,t),data:t};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+="\n </div>";return q})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel-anon"]=b(function(h,r,p,l,w){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,h.helpers);w=w||{};var q="",i,f,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(A,z){var x="",y;x+='\n <div class="history-name">\n ';if(y=p.name){y=y.call(A,{hash:{},data:z})}else{y=A.name;y=typeof y===e?y.apply(A):y}x+=d(y)+"\n </div>\n ";return x}function m(A,z){var x="",y;x+='\n <div class="history-size">';if(y=p.nice_size){y=y.call(A,{hash:{},data:z})}else{y=A.nice_size;y=typeof y===e?y.apply(A):y}x+=d(y)+"</div>\n ";return x}function k(A,z){var x="",y;x+='\n \n <div class="';if(y=p.status){y=y.call(A,{hash:{},data:z})}else{y=A.status;y=typeof y===e?y.apply(A):y}x+=d(y)+'message">';if(y=p.message){y=y.call(A,{hash:{},data:z})}else{y=A.message;y=typeof y===e?y.apply(A):y}x+=d(y)+"</div>\n ";return x}function j(y,x){return"You are over your disk quota"}function g(y,x){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function v(y,x){return"All"}function u(y,x){return"None"}function t(y,x){return"For all selected"}function s(y,x){return"Your history is empty. 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Click 'Get Data' on the left pane to start"}q+='<div class="history-controls">\n <div class="history-search-controls">\n <div class="history-search-input"></div>\n </div>\n\n <div class="history-title">\n ';i=p["if"].call(r,r.name,{hash:{},inverse:o.noop,fn:o.program(1,n,x),data:x});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=p["if"].call(r,r.nice_size,{hash:{},inverse:o.noop,fn:o.program(3,m,x),data:x});if(i||i===0){q+=i}q+='\n\n <div class="history-secondary-actions"></div>\n </div>\n\n ';i=p["if"].call(r,r.deleted,{hash:{},inverse:o.noop,fn:o.program(5,k,x),data:x});if(i||i===0){q+=i}q+='\n\n <div class="message-container">\n ';i=p["if"].call(r,r.message,{hash:{},inverse:o.noop,fn:o.program(8,h,x),data:x});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:o.noop,fn:o.program(10,w,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+=".\n ";f={hash:{},inverse:o.noop,fn:o.program(12,v,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='.\n </div>\n \n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n <div class="history-dataset-actions">\n <button class="history-select-all-datasets-btn btn btn-default"\n data-mode="select">';f={hash:{},inverse:o.noop,fn:o.program(14,u,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='</button>\n <button class="history-dataset-action-popup-btn btn btn-default"\n >';f={hash:{},inverse:o.noop,fn:o.program(16,t,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='...</button>\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:o.noop,fn:o.program(18,s,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+="\n </div>";return q})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(g,s,q,m,y){this.compilerInfo=[4,">= 1.0.0"];q=this.merge(q,g.helpers);y=y||{};var r="",i,f,e="function",d=this.escapeExpression,p=this,c=q.blockHelperMissing;function o(C,B){var z="",A;z+='\n <div class="history-name">\n ';if(A=q.name){A=A.call(C,{hash:{},data:B})}else{A=C.name;A=typeof A===e?A.apply(C):A}z+=d(A)+"\n </div>\n ";return z}function n(C,B){var z="",A;z+='\n <div class="history-size">';if(A=q.nice_size){A=A.call(C,{hash:{},data:B})}else{A=C.nice_size;A=typeof A===e?A.apply(C):A}z+=d(A)+"</div>\n ";return z}function l(D,C){var z="",B,A;z+='\n <div class="warningmessagesmall"><strong>\n ';A={hash:{},inverse:p.noop,fn:p.program(6,k,C),data:C};if(B=q.local){B=B.call(D,A)}else{B=D.local;B=typeof B===e?B.apply(D):B}if(!q.local){B=c.call(D,B,A)}if(B||B===0){z+=B}z+="\n </strong></div>\n ";return z}function k(A,z){return"You are currently viewing a deleted history!"}function h(C,B){var z="",A;z+='\n \n <div class="';if(A=q.status){A=A.call(C,{hash:{},data:B})}else{A=C.status;A=typeof A===e?A.apply(C):A}z+=d(A)+'message">';if(A=q.message){A=A.call(C,{hash:{},data:B})}else{A=C.message;A=typeof A===e?A.apply(C):A}z+=d(A)+"</div>\n ";return z}function x(A,z){return"You are over your disk quota"}function w(A,z){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function v(A,z){return"All"}function u(A,z){return"None"}function t(A,z){return"For all selected"}function j(A,z){return"Your history is empty. Click 'Get Data' on the left pane to start"}r+='<div class="history-controls">\n <div class="history-search-controls">\n <div class="history-search-input"></div>\n </div>\n\n <div class="history-title">\n ';i=q["if"].call(s,s.name,{hash:{},inverse:p.noop,fn:p.program(1,o,y),data:y});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=q["if"].call(s,s.nice_size,{hash:{},inverse:p.noop,fn:p.program(3,n,y),data:y});if(i||i===0){r+=i}r+='\n\n <div class="history-secondary-actions btn-group"></div>\n </div>\n\n ';i=q["if"].call(s,s.deleted,{hash:{},inverse:p.noop,fn:p.program(5,l,y),data:y});if(i||i===0){r+=i}r+='\n\n <div class="message-container">\n ';i=q["if"].call(s,s.message,{hash:{},inverse:p.noop,fn:p.program(8,h,y),data:y});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:p.noop,fn:p.program(10,x,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+=".\n ";f={hash:{},inverse:p.noop,fn:p.program(12,w,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='.\n </div>\n \n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n <div class="history-dataset-actions">\n <div class="btn-group">\n <button class="history-select-all-datasets-btn btn btn-default"\n data-mode="select">';f={hash:{},inverse:p.noop,fn:p.program(14,v,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='</button>\n <button class="history-deselect-all-datasets-btn btn btn-default"\n data-mode="select">';f={hash:{},inverse:p.noop,fn:p.program(16,u,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='</button>\n </div>\n <button class="history-dataset-action-popup-btn btn btn-default"\n >';f={hash:{},inverse:p.noop,fn:p.program(18,t,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='...</button>\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:p.noop,fn:p.program(20,j,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+="\n </div>";return r})})(); \ No newline at end of file diff -r 1dc6776635ee359f32e8c661f549d2db8c06f16d -r 7ca065784d58e7aa77e5092952eacd963853df65 static/scripts/templates/compiled/history-templates.js --- a/static/scripts/templates/compiled/history-templates.js +++ b/static/scripts/templates/compiled/history-templates.js @@ -302,98 +302,125 @@ }); })();(function() { var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-historyPanel-anon'] = template(function (Handlebars,depth0,helpers,partials,data) { +templates['template-hda-skeleton'] = template(function (Handlebars,depth0,helpers,partials,data) { this.compilerInfo = [4,'>= 1.0.0']; helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; + var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; function program1(depth0,data) { - var buffer = "", stack1; - buffer += "\n <div class=\"history-name\">\n "; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n </div>\n "; - return buffer; - } - -function program3(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-size\">"; - if (stack1 = helpers.nice_size) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program5(depth0,data) { - - var buffer = "", stack1; - buffer += "\n " - + "\n <div class=\""; - if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "message\">"; - if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program7(depth0,data) { - - - return "You are over your disk quota"; - } - -function program9(depth0,data) { - - - return "Tool execution is on hold until your disk usage drops below your allocated quota"; - } - -function program11(depth0,data) { - - - return "Your history is empty. Click 'Get Data' on the left pane to start"; - } - - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n " - + "\n "; - stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; - stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n <div class=\"message-container\">\n "; - stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}; + var buffer = "", stack1, options; + buffer += "\n <div class=\"errormessagesmall\">\n "; + options = {hash:{},inverse:self.noop,fn:self.program(2, program2, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n "; - options = {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data}; + buffer += ":\n "; + options = {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n\n </div>" - + "\n\n " - + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; + buffer += "\n </div>\n "; + return buffer; + } +function program2(depth0,data) { + + + return "There was an error getting the data for this dataset"; + } + +function program4(depth0,data) { + + var stack1; + if (stack1 = helpers.error) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.error; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + return escapeExpression(stack1); + } + +function program6(depth0,data) { + + var buffer = "", stack1; + buffer += "\n "; + stack1 = helpers['if'].call(depth0, depth0.purged, {hash:{},inverse:self.program(10, program10, data),fn:self.program(7, program7, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + return buffer; + } +function program7(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n <div class=\"dataset-purged-msg warningmessagesmall\"><strong>\n "; + options = {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </strong></div>\n\n "; + return buffer; + } +function program8(depth0,data) { + + + return "This dataset has been deleted and removed from disk."; + } + +function program10(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n <div class=\"dataset-deleted-msg warningmessagesmall\"><strong>\n "; options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>"; + buffer += "\n </strong></div>\n "; + return buffer; + } +function program11(depth0,data) { + + + return "This dataset has been deleted."; + } + +function program13(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n <div class=\"dataset-hidden-msg warningmessagesmall\"><strong>\n "; + options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </strong></div>\n "; + return buffer; + } +function program14(depth0,data) { + + + return "This dataset has been hidden."; + } + + buffer += "<div class=\"dataset hda\">\n <div class=\"dataset-warnings\">\n "; + stack1 = helpers['if'].call(depth0, depth0.error, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n "; + stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n "; + stack1 = helpers.unless.call(depth0, depth0.visible, {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n\n <div class=\"dataset-selector\"><span class=\"fa fa-2x fa-square-o\"></span></div>\n <div class=\"dataset-primary-actions\"></div>\n " + + "\n <div class=\"dataset-title-bar clear\" tabindex=\"0\">\n <span class=\"dataset-state-icon state-icon\"></span>\n <div class=\"dataset-title\">\n <span class=\"hda-hid\">"; + if (stack1 = helpers.hid) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "</span>\n <span class=\"dataset-name\">"; + if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "</span>\n </div>\n </div>\n\n <div class=\"dataset-body\"></div>\n</div>"; return buffer; }); })();(function() { @@ -456,6 +483,24 @@ function program11(depth0,data) { + return "All"; + } + +function program13(depth0,data) { + + + return "None"; + } + +function program15(depth0,data) { + + + return "For all selected"; + } + +function program17(depth0,data) { + + return "Your history is empty. Click 'Get Data' on the left pane to start"; } @@ -466,7 +511,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n <div class=\"message-container\">\n "; + buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n <div class=\"message-container\">\n "; stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; @@ -481,10 +526,28 @@ else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n\n </div>" + buffer += ".\n </div>\n\n <div class=\"history-dataset-actions\">\n <div class=\"btn-group\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; + options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</button>\n <button class=\"history-deselect-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; + options = {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</button>\n </div>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; + options = {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "...</button>\n </div>\n\n </div>" + "\n\n " + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; + options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } @@ -570,16 +633,22 @@ function program14(depth0,data) { - return "Select all"; + return "All"; } function program16(depth0,data) { + return "None"; + } + +function program18(depth0,data) { + + return "For all selected"; } -function program18(depth0,data) { +function program20(depth0,data) { return "Your history is empty. Click 'Get Data' on the left pane to start"; @@ -591,7 +660,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; + buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n "; stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n <div class=\"message-container\">\n "; @@ -609,162 +678,28 @@ else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n \n <div class=\"tags-display\"></div>\n <div class=\"annotation-display\"></div>\n\n <div class=\"history-dataset-actions\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; + buffer += ".\n </div>\n \n <div class=\"tags-display\"></div>\n <div class=\"annotation-display\"></div>\n\n <div class=\"history-dataset-actions\">\n <div class=\"btn-group\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; + buffer += "</button>\n <button class=\"history-deselect-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; options = {hash:{},inverse:self.noop,fn:self.program(16, program16, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</button>\n </div>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; + options = {hash:{},inverse:self.noop,fn:self.program(18, program18, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "...</button>\n </div>\n\n </div>" + "\n\n " + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(18, program18, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>"; - return buffer; - }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-name\">\n "; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n </div>\n "; - return buffer; - } - -function program3(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-size\">"; - if (stack1 = helpers.nice_size) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program5(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n "; - return buffer; - } -function program6(depth0,data) { - - - return "You are currently viewing a deleted history!"; - } - -function program8(depth0,data) { - - var buffer = "", stack1; - buffer += "\n " - + "\n <div class=\""; - if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "message\">"; - if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program10(depth0,data) { - - - return "You are over your disk quota"; - } - -function program12(depth0,data) { - - - return "Tool execution is on hold until your disk usage drops below your allocated quota"; - } - -function program14(depth0,data) { - - - return "Select all"; - } - -function program16(depth0,data) { - - - return "For all selected"; - } - -function program18(depth0,data) { - - - return "Your history is empty. Click 'Get Data' on the left pane to start"; - } - - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n "; - stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; - stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; - stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"message-container\">\n "; - stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(10, program10, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n "; - options = {hash:{},inverse:self.noop,fn:self.program(12, program12, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n \n <div class=\"tags-display\"></div>\n <div class=\"annotation-display\"></div>\n\n <div class=\"history-dataset-actions\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; - options = {hash:{},inverse:self.noop,fn:self.program(16, program16, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "...</button>\n </div>\n\n </div>" - + "\n\n " - + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(18, program18, data),data:data}; + options = {hash:{},inverse:self.noop,fn:self.program(20, program20, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } diff -r 1dc6776635ee359f32e8c661f549d2db8c06f16d -r 7ca065784d58e7aa77e5092952eacd963853df65 static/scripts/templates/compiled/template-history-historyPanel-anon.js --- a/static/scripts/templates/compiled/template-history-historyPanel-anon.js +++ b/static/scripts/templates/compiled/template-history-historyPanel-anon.js @@ -58,6 +58,24 @@ function program11(depth0,data) { + return "All"; + } + +function program13(depth0,data) { + + + return "None"; + } + +function program15(depth0,data) { + + + return "For all selected"; + } + +function program17(depth0,data) { + + return "Your history is empty. Click 'Get Data' on the left pane to start"; } @@ -68,7 +86,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n <div class=\"message-container\">\n "; + buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n <div class=\"message-container\">\n "; stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; @@ -83,10 +101,28 @@ else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n\n </div>" + buffer += ".\n </div>\n\n <div class=\"history-dataset-actions\">\n <div class=\"btn-group\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; + options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</button>\n <button class=\"history-deselect-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; + options = {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</button>\n </div>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; + options = {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "...</button>\n </div>\n\n </div>" + "\n\n " + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; + options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } diff -r 1dc6776635ee359f32e8c661f549d2db8c06f16d -r 7ca065784d58e7aa77e5092952eacd963853df65 static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -76,16 +76,22 @@ function program14(depth0,data) { - return "Select all"; + return "All"; } function program16(depth0,data) { + return "None"; + } + +function program18(depth0,data) { + + return "For all selected"; } -function program18(depth0,data) { +function program20(depth0,data) { return "Your history is empty. Click 'Get Data' on the left pane to start"; @@ -97,7 +103,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; + buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n "; stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n <div class=\"message-container\">\n "; @@ -115,22 +121,28 @@ else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n \n <div class=\"tags-display\"></div>\n <div class=\"annotation-display\"></div>\n\n <div class=\"history-dataset-actions\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; + buffer += ".\n </div>\n \n <div class=\"tags-display\"></div>\n <div class=\"annotation-display\"></div>\n\n <div class=\"history-dataset-actions\">\n <div class=\"btn-group\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; + buffer += "</button>\n <button class=\"history-deselect-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; options = {hash:{},inverse:self.noop,fn:self.program(16, program16, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</button>\n </div>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; + options = {hash:{},inverse:self.noop,fn:self.program(18, program18, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "...</button>\n </div>\n\n </div>" + "\n\n " + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(18, program18, data),data:data}; + options = {hash:{},inverse:self.noop,fn:self.program(20, program20, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } diff -r 1dc6776635ee359f32e8c661f549d2db8c06f16d -r 7ca065784d58e7aa77e5092952eacd963853df65 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -44,8 +44,12 @@ <div class="annotation-display"></div><div class="history-dataset-actions"> - <button class="history-select-all-datasets-btn btn btn-default" - data-mode="select">{{#local}}Select all{{/local}}</button> + <div class="btn-group"> + <button class="history-select-all-datasets-btn btn btn-default" + data-mode="select">{{#local}}All{{/local}}</button> + <button class="history-deselect-all-datasets-btn btn btn-default" + data-mode="select">{{#local}}None{{/local}}</button> + </div><button class="history-dataset-action-popup-btn btn btn-default" >{{#local}}For all selected{{/local}}...</button></div> @@ -98,6 +102,17 @@ {{#local}}Tool execution is on hold until your disk usage drops below your allocated quota{{/local}}. </div> + <div class="history-dataset-actions"> + <div class="btn-group"> + <button class="history-select-all-datasets-btn btn btn-default" + data-mode="select">{{#local}}All{{/local}}</button> + <button class="history-deselect-all-datasets-btn btn btn-default" + data-mode="select">{{#local}}None{{/local}}</button> + </div> + <button class="history-dataset-action-popup-btn btn btn-default" + >{{#local}}For all selected{{/local}}...</button> + </div> + </div>{{! end history-controls }} {{! where the datasets/hdas are added }} diff -r 1dc6776635ee359f32e8c661f549d2db8c06f16d -r 7ca065784d58e7aa77e5092952eacd963853df65 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1577,7 +1577,7 @@ .workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px} .icon-btn{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;border-radius:3px;border:1px solid #bfbfbf;background-color:#f2f2f2;color:#333;cursor:pointer} .icon-btn:hover{background-color:white;color:maroon} -.icon-btn.disabled{background-color:transparent;color:#f2f2f2} +.icon-btn.disabled{background-color:transparent;color:#bfbfbf} .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:#303030} @@ -1594,7 +1594,7 @@ .history-panel .dataset .dataset-primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} .history-panel .dataset .dataset-primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} .history-panel .dataset .dataset-primary-actions .icon-btn{margin-left:2px} -.history-panel .dataset .dataset-body{display:none;padding:6px 10px 6px 8px}.history-panel .dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} +.history-panel .dataset .dataset-body{display:none;padding:0 10px 6px 8px}.history-panel .dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} .history-panel .dataset .dataset-body label{margin:0px;padding:0px;font-weight:normal} .history-panel .dataset .dataset-body .prompt{font-weight:normal;color:#555} .history-panel .dataset .dataset-body .prompt:after{content:':'} diff -r 1dc6776635ee359f32e8c661f549d2db8c06f16d -r 7ca065784d58e7aa77e5092952eacd963853df65 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -57,9 +57,10 @@ } .icon-btn.disabled { background-color: transparent; - color: @icon-btn-bg; + color: @icon-btn-border; } +// ---------------------------------------------------------------------------- search bar .search-input { .search-query { width : 100%; @@ -84,6 +85,7 @@ color : @link-color; } } + // ---------------------------------------------------------------------------- panel header buttons #history-refresh-button, #history-options-button { @@ -177,7 +179,8 @@ .dataset-body { display: none; // background-color: fadeout( white, 70% ); - .dataset-padding; + //.dataset-padding; + padding: 0px @spacing-right @spacing-bottom @spacing-left; [class$=messagesmall] { margin: 0px 0px 8px 0px; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Upload: Fixes for FF
by commits-noreply＠bitbucket.org 08 Feb '14

08 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1dc6776635ee/ Changeset: 1dc6776635ee User: guerler Date: 2014-02-08 07:02:50 Summary: Upload: Fixes for FF Affected #: 4 files diff -r 0c2b806274c53d16d9c9ba15501431a2103c8a54 -r 1dc6776635ee359f32e8c661f549d2db8c06f16d static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -296,27 +296,34 @@ // configure uploadbox this.uploadbox.configure({url : this.options.nginx_upload_path}); - // configure file mode - if (file_mode == 'ftp') { - this.uploadbox.configure({paramname : ''}); + // configure tool + tool_input = {}; + + // local files + if (file_mode == 'local') { + this.uploadbox.configure({paramname : 'files_0|file_data'}); } else { - this.uploadbox.configure({paramname : 'files_0|file_data'}); + this.uploadbox.configure({paramname : null}); } - // configure tool - tool_input = {}; + // new files + if (file_mode == 'new') { + tool_input['files_0|url_paste'] = url_paste; + } + + // files from ftp + if (file_mode == 'ftp') { + // add to tool configuration + tool_input['files_0|ftp_files'] = file_path; + } + + // add common configuration tool_input['dbkey'] = genome; tool_input['file_type'] = extension; tool_input['files_0|type'] = 'upload_dataset'; - tool_input['files_0|url_paste'] = url_paste; tool_input['space_to_tabs'] = space_to_tabs; tool_input['to_posix_lines'] = to_posix_lines; - // add ftp file path - if (file_mode == 'ftp') { - tool_input['files_0|ftp_files'] = file_path; - } - // setup data data = {}; data['history_id'] = this.current_history; @@ -341,8 +348,8 @@ _eventSuccess : function(index, file, message) { // update status var it = this.collection.get(index); + it.set('percentage', 100); it.set('status', 'success'); - it.set('percentage', 100); // file size var file_size = it.get('file_size'); @@ -370,9 +377,9 @@ var it = this.collection.get(index); // update status + it.set('percentage', 100); it.set('status', 'error'); it.set('info', message); - it.set('percentage', 100); // update ui button this.ui_button.set('percentage', this._upload_percentage(100, file.size)); diff -r 0c2b806274c53d16d9c9ba15501431a2103c8a54 -r 1dc6776635ee359f32e8c661f549d2db8c06f16d static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.select_extension.push([j[key],j[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){var k=h.select_genome[0];h.select_genome=[];for(key in j){if(j[key].length>1){if(j[key][1]!==k[1]){h.select_genome.push(j[key])}}}h.select_genome.sort(function(m,l){return m[0]>l[0]?1:m[0]<l[0]?-1:0});h.select_genome.unshift(k)});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="ftp"){this.uploadbox.configure({paramname:""})}else{this.uploadbox.configure({paramname:"files_0|file_data"})}tool_input={};tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=q;tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;if(h=="ftp"){tool_input["files_0|ftp_files"]=n}data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("status","success");k.set("percentage",100);var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("status","error");j.set("info",k);j.set("percentage",100);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.select_extension.push([j[key],j[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){var k=h.select_genome[0];h.select_genome=[];for(key in j){if(j[key].length>1){if(j[key][1]!==k[1]){h.select_genome.push(j[key])}}}h.select_genome.sort(function(m,l){return m[0]>l[0]?1:m[0]<l[0]?-1:0});h.select_genome.unshift(k)});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});tool_input={};if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file diff -r 0c2b806274c53d16d9c9ba15501431a2103c8a54 -r 1dc6776635ee359f32e8c661f549d2db8c06f16d static/scripts/packed/utils/uploadbox.js --- a/static/scripts/packed/utils/uploadbox.js +++ b/static/scripts/packed/utils/uploadbox.js @@ -1,1 +1,1 @@ -(function(c){jQuery.event.props.push("dataTransfer");var h={url:"",paramname:"content",maxfilesize:2048,maxfilenumber:50,dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(k,l,m){alert(m)},complete:function(){},error_filesize:"File exceeds 2GB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in.",error_missing:"No upload content available."};var a={};var e={};var f=0;var j=0;var d=false;var g=false;var b=null;var i=null;c.fn.uploadbox=function(A){a=c.extend({},h,A);b=this;b.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');b.on("drop",o);b.on("dragover",p);b.on("dragleave",x);c("#uploadbox_input").change(function(B){z(B.target.files);c(this).val("")});function o(B){if(!B.dataTransfer){return}z(B.dataTransfer.files);B.preventDefault();return false}function p(B){B.preventDefault();a.dragover.call(B)}function x(B){B.stopPropagation();a.dragleave.call(B)}function k(B){if(B.lengthComputable){a.progress(this.index,this.file,Math.round((B.loaded*100)/B.total))}}function z(D){if(d){return}var E=f;for(var C=0;C<D.length;C++){if(j>=a.maxfilenumber){break}var B=String(f++);e[B]=D[C];a.announce(B,e[B],"");j++}return E}function r(B){if(e[B]){delete e[B];j--}}function m(){if(j==0||g){g=false;d=false;a.complete();return}else{d=true}var D=-1;for(var F in e){D=F;break}var E=e[D];r(D);var C=E.size;var H=E.mode;var B=1048576*a.maxfilesize;if(C<B||E.mode=="ftp"){var G=a.initialize(D,E);if(G){q(D,E,G)}else{u(D,E,a.error_missing)}}else{u(D,E,a.error_filesize)}}function q(B,D,E){var F=new FormData();for(var C in E){F.append(C,E[C])}if(D.size>0){F.append(a.paramname,D,D.name)}i=new XMLHttpRequest();i.open("POST",a.url,true);i.setRequestHeader("Accept","application/json");i.setRequestHeader("Cache-Control","no-cache");i.setRequestHeader("X-Requested-With","XMLHttpRequest");i.onreadystatechange=function(){if(i.readyState!=i.DONE){return}var G=null;if(i.responseText){try{G=jQuery.parseJSON(i.responseText)}catch(H){G=i.responseText}}if(i.status<200||i.status>299){var I=i.statusText;if(i.status==403){I=a.error_login}else{if(i.status==0){I=a.error_server}else{if(!I){I=a.error_default}}}u(B,D,I+" ("+i.status+")")}else{y(B,D,G)}};i.upload.index=B;i.upload.file=D;i.upload.addEventListener("progress",k,false);i.send(F)}function y(B,C,D){a.success(B,C,D);m()}function u(B,C,D){a.error(B,C,D);m()}function w(){c("#uploadbox_input").trigger("click")}function t(B){for(B in e){r(B)}}function l(){if(!d){d=true;m()}}function v(){g=true}function n(B){a=c.extend({},a,B);return a}function s(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}return{select:w,add:z,remove:r,start:l,stop:v,reset:t,configure:n,compatible:s}}})(jQuery); \ No newline at end of file +(function(c){jQuery.event.props.push("dataTransfer");var h={url:"",paramname:"content",maxfilesize:2048,maxfilenumber:50,dragover:function(){},dragleave:function(){},announce:function(){},initialize:function(){},progress:function(){},success:function(){},error:function(k,l,m){alert(m)},complete:function(){},error_filesize:"File exceeds 2GB. Please use an FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in.",error_missing:"No upload content available."};var a={};var e={};var f=0;var j=0;var d=false;var g=false;var b=null;var i=null;c.fn.uploadbox=function(A){a=c.extend({},h,A);b=this;b.append('<input id="uploadbox_input" type="file" style="display: none" multiple>');b.on("drop",o);b.on("dragover",p);b.on("dragleave",x);c("#uploadbox_input").change(function(B){z(B.target.files);c(this).val("")});function o(B){if(!B.dataTransfer){return}z(B.dataTransfer.files);B.preventDefault();return false}function p(B){B.preventDefault();a.dragover.call(B)}function x(B){B.stopPropagation();a.dragleave.call(B)}function k(B){if(B.lengthComputable){a.progress(this.index,this.file,Math.round((B.loaded*100)/B.total))}}function z(D){if(d){return}var E=f;for(var C=0;C<D.length;C++){if(j>=a.maxfilenumber){break}var B=String(f++);e[B]=D[C];a.announce(B,e[B],"");j++}return E}function r(B){if(e[B]){delete e[B];j--}}function m(){if(j==0||g){g=false;d=false;a.complete();return}else{d=true}var D=-1;for(var F in e){D=F;break}var E=e[D];r(D);var C=E.size;var H=E.mode;var B=1048576*a.maxfilesize;if(C<B||E.mode=="ftp"){var G=a.initialize(D,E);if(G){q(D,E,G)}else{u(D,E,a.error_missing)}}else{u(D,E,a.error_filesize)}}function q(B,D,E){var F=new FormData();for(var C in E){F.append(C,E[C])}if(D.size>0&&a.paramname){F.append(a.paramname,D,D.name)}i=new XMLHttpRequest();i.open("POST",a.url,true);i.setRequestHeader("Accept","application/json");i.setRequestHeader("Cache-Control","no-cache");i.setRequestHeader("X-Requested-With","XMLHttpRequest");i.onreadystatechange=function(){if(i.readyState!=i.DONE){return}var G=null;if(i.responseText){try{G=jQuery.parseJSON(i.responseText)}catch(H){G=i.responseText}}if(i.status<200||i.status>299){var I=i.statusText;if(i.status==403){I=a.error_login}else{if(i.status==0){I=a.error_server}else{if(!I){I=a.error_default}}}u(B,D,I+" ("+i.status+")")}else{y(B,D,G)}};i.upload.index=B;i.upload.file=D;i.upload.addEventListener("progress",k,false);i.send(F)}function y(B,C,D){a.success(B,C,D);m()}function u(B,C,D){a.error(B,C,D);m()}function w(){c("#uploadbox_input").trigger("click")}function t(B){for(B in e){r(B)}}function l(){if(!d){d=true;m()}}function v(){g=true}function n(B){a=c.extend({},a,B);return a}function s(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}return{select:w,add:z,remove:r,start:l,stop:v,reset:t,configure:n,compatible:s}}})(jQuery); \ No newline at end of file diff -r 0c2b806274c53d16d9c9ba15501431a2103c8a54 -r 1dc6776635ee359f32e8c661f549d2db8c06f16d static/scripts/utils/uploadbox.js --- a/static/scripts/utils/uploadbox.js +++ b/static/scripts/utils/uploadbox.js @@ -219,12 +219,14 @@ { // construct form data var formData = new FormData(); - for (var key in data) + for (var key in data) { formData.append(key, data[key]); + } // check file size - if (file.size > 0) + if (file.size > 0 && opts.paramname) { formData.append(opts.paramname, file, file.name); + } // prepare request xhr = new XMLHttpRequest(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Upload: Fix progress bar in FF
by commits-noreply＠bitbucket.org 07 Feb '14

07 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0c2b806274c5/ Changeset: 0c2b806274c5 User: guerler Date: 2014-02-08 06:31:29 Summary: Upload: Fix progress bar in FF Affected #: 4 files diff -r 303f709d14276511f121c216f030400fddec2bd5 -r 0c2b806274c53d16d9c9ba15501431a2103c8a54 static/scripts/mvc/upload/upload-model.js --- a/static/scripts/mvc/upload/upload-model.js +++ b/static/scripts/mvc/upload/upload-model.js @@ -13,6 +13,7 @@ file_size : 0, file_type : null, file_path : '', + percentage : 0, // settings space_to_tabs : false, diff -r 303f709d14276511f121c216f030400fddec2bd5 -r 0c2b806274c53d16d9c9ba15501431a2103c8a54 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -342,6 +342,7 @@ // update status var it = this.collection.get(index); it.set('status', 'success'); + it.set('percentage', 100); // file size var file_size = it.get('file_size'); @@ -371,6 +372,7 @@ // update status it.set('status', 'error'); it.set('info', message); + it.set('percentage', 100); // update ui button this.ui_button.set('percentage', this._upload_percentage(100, file.size)); diff -r 303f709d14276511f121c216f030400fddec2bd5 -r 0c2b806274c53d16d9c9ba15501431a2103c8a54 static/scripts/packed/mvc/upload/upload-model.js --- a/static/scripts/packed/mvc/upload/upload-model.js +++ b/static/scripts/packed/mvc/upload/upload-model.js @@ -1,1 +1,1 @@ -define([],function(){var b=Backbone.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_mode:"local",file_size:0,file_type:null,file_path:"",space_to_tabs:false,to_posix_lines:true}});var a=Backbone.Collection.extend({model:b});return{Model:b,Collection:a}}); \ No newline at end of file +define([],function(){var b=Backbone.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_mode:"local",file_size:0,file_type:null,file_path:"",percentage:0,space_to_tabs:false,to_posix_lines:true}});var a=Backbone.Collection.extend({model:b});return{Model:b,Collection:a}}); \ No newline at end of file diff -r 303f709d14276511f121c216f030400fddec2bd5 -r 0c2b806274c53d16d9c9ba15501431a2103c8a54 static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.select_extension.push([j[key],j[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){var k=h.select_genome[0];h.select_genome=[];for(key in j){if(j[key].length>1){if(j[key][1]!==k[1]){h.select_genome.push(j[key])}}}h.select_genome.sort(function(m,l){return m[0]>l[0]?1:m[0]<l[0]?-1:0});h.select_genome.unshift(k)});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="ftp"){this.uploadbox.configure({paramname:""})}else{this.uploadbox.configure({paramname:"files_0|file_data"})}tool_input={};tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=q;tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;if(h=="ftp"){tool_input["files_0|ftp_files"]=n}data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.select_extension.push([j[key],j[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){var k=h.select_genome[0];h.select_genome=[];for(key in j){if(j[key].length>1){if(j[key][1]!==k[1]){h.select_genome.push(j[key])}}}h.select_genome.sort(function(m,l){return m[0]>l[0]?1:m[0]<l[0]?-1:0});h.select_genome.unshift(k)});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="ftp"){this.uploadbox.configure({paramname:""})}else{this.uploadbox.configure({paramname:"files_0|file_data"})}tool_input={};tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=q;tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;if(h=="ftp"){tool_input["files_0|ftp_files"]=n}data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("status","success");k.set("percentage",100);var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("status","error");j.set("info",k);j.set("percentage",100);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ 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.

1 0

commit/galaxy-central: guerler: Charts: Adjust to viz framework change
by commits-noreply＠bitbucket.org 07 Feb '14

07 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/303f709d1427/ Changeset: 303f709d1427 User: guerler Date: 2014-02-08 06:06:46 Summary: Charts: Adjust to viz framework change Affected #: 1 file diff -r 375c04b4a7085c91c48201fc5d7376ab613874c8 -r 303f709d14276511f121c216f030400fddec2bd5 config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -61,7 +61,7 @@ require(['app'], function(App) { // load options var options = { - config : ${h.to_json_string( query_args )}, + config : ${h.to_json_string( config )}, dataset : ${h.to_json_string( trans.security.encode_dict_ids( hda.to_dict() ) )} } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Upload: Add error handler to ftp file api controller, remove timeout for extension info popup
by commits-noreply＠bitbucket.org 07 Feb '14

07 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/375c04b4a708/ Changeset: 375c04b4a708 User: guerler Date: 2014-02-08 05:15:43 Summary: Upload: Add error handler to ftp file api controller, remove timeout for extension info popup Affected #: 5 files diff -r 4228b5439785c10aaf638db4e18be65dfd6b9275 -r 375c04b4a7085c91c48201fc5d7376ab613874c8 lib/galaxy/webapps/galaxy/api/ftp_files.py --- a/lib/galaxy/webapps/galaxy/api/ftp_files.py +++ b/lib/galaxy/webapps/galaxy/api/ftp_files.py @@ -18,35 +18,43 @@ GET /api/ftp_files/ Displays local files. """ - # initialize response - response = [] - # identify ftp directory - user_ftp_base_dir = trans.app.config.ftp_upload_dir - if user_ftp_base_dir is None: - return [] - - # identify user sub directory - user_ftp_dir = None - if user_ftp_base_dir is not None and trans is not None and trans.user is not None: - identifier = trans.app.config.ftp_upload_dir_identifier - user_ftp_dir = os.path.join( user_ftp_base_dir, getattr(trans.user, identifier) ) - if user_ftp_dir is None: - return [] + # look for ftp files + try: + # initialize response + response = [] + + # identify ftp directory + user_ftp_base_dir = trans.app.config.ftp_upload_dir + if user_ftp_base_dir is None: + return [] + + # identify user sub directory + user_ftp_dir = None + if user_ftp_base_dir is not None and trans is not None and trans.user is not None: + identifier = trans.app.config.ftp_upload_dir_identifier + user_ftp_dir = os.path.join( user_ftp_base_dir, getattr(trans.user, identifier) ) + if user_ftp_dir is None: + return [] - # read directory - if os.path.exists( user_ftp_dir ): - for ( dirpath, dirnames, filenames ) in os.walk( user_ftp_dir ): - for filename in filenames: - path = os.path.relpath( os.path.join( dirpath, filename ), user_ftp_dir ) - statinfo = os.lstat( os.path.join( dirpath, filename ) ) - response.append( dict( path = path, - size = statinfo.st_size, - ctime = time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) + # read directory + if os.path.exists( user_ftp_dir ): + for ( dirpath, dirnames, filenames ) in os.walk( user_ftp_dir ): + for filename in filenames: + path = os.path.relpath( os.path.join( dirpath, filename ), user_ftp_dir ) + statinfo = os.lstat( os.path.join( dirpath, filename ) ) + response.append( dict( path = path, + size = statinfo.st_size, + ctime = time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) + + # sort by path + response = sorted(response, key=itemgetter("path")) + + # return + return response - # sort by path - response = sorted(response, key=itemgetter("path")) - - # return - return response + except Exception, exception: + log.error( 'could not get ftp files: %s', str( exception ), exc_info=True ) + trans.response.status = 500 + return { 'error': str( exception ) } diff -r 4228b5439785c10aaf638db4e18be65dfd6b9275 -r 375c04b4a7085c91c48201fc5d7376ab613874c8 static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -16,8 +16,7 @@ return Backbone.View.extend({ // options options: { - padding : 8, - timeout : 2000 + padding : 8 }, // states @@ -325,16 +324,6 @@ }, // attach file info popup - _hideExtensionInfo : function() - { - // remove popup - var self = this - this.popover_timeout = setTimeout(function() { - self._destroyExtensionInfo(); - }, this.options.timeout); - }, - - // attach file info popup _destroyExtensionInfo : function() { this.$el.find('#extension-info').popover('destroy'); diff -r 4228b5439785c10aaf638db4e18be65dfd6b9275 -r 375c04b4a7085c91c48201fc5d7376ab613874c8 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -105,7 +105,7 @@ // load extension var self = this; - Utils.jsonFromUrl(galaxy_config.root + "api/datatypes", + Utils.jsonFromUrl(galaxy_config.root + "api/datatypes?upload_only=True", function(datatypes) { for (key in datatypes) self.select_extension.push([datatypes[key], datatypes[key]]); diff -r 4228b5439785c10aaf638db4e18be65dfd6b9275 -r 375c04b4a7085c91c48201fc5d7376ab613874c8 static/scripts/packed/mvc/upload/upload-row.js --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover"],function(d,b,e,a,c){return Backbone.View.extend({options:{padding:8,timeout:2000},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,initialize:function(i,g){this.app=i;var f=this;this.model=new b.Model(g);this.setElement(this._template(g));var h=this.$el;this.settings=new c.View({title:"Upload configuration",container:h.find("#settings"),placement:"bottom"});h.find("#symbol").on("click",function(){f._removeRow()});h.find("#extension-info").on("click",function(j){f._showExtensionInfo()}).on("mousedown",function(j){j.preventDefault()});h.find("#settings").on("click",function(j){f._showSettings()}).on("mousedown",function(j){j.preventDefault()});h.find("#text-content").on("keyup",function(j){f.model.set("url_paste",$(j.target).val());f.model.set("file_size",$(j.target).val().length)});h.find("#genome").on("change",function(j){f.model.set("genome",$(j.target).val())});h.find("#extension").on("change",function(j){f.model.set("extension",$(j.target).val())});h.find("#space_to_tabs").on("change",function(j){f.model.set("space_to_tabs",$(j.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:extension",function(){f._destroyExtensionInfo()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f._destroyExtensionInfo();f.remove()});this.app.collection.on("reset",function(){f._destroyExtensionInfo();f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},_refreshGenome:function(){var f=this.model.get("genome");this.$el.find("#genome").val(f)},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){g.find("#text-content").attr("disabled",false);g.find("#genome").attr("disabled",false);g.find("#extension").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{g.find("#text-content").attr("disabled",true);g.find("#genome").attr("disabled",true);g.find("#extension").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var f=$(this.el).find("#extension-info");var h=this.model.get("extension");var g=$(this.el).find("#extension").find("option:selected").text();if(!this.extension_popup){this.extension_popup=new c.View({content:e(h),placement:"bottom",container:f})}if(!this.extension_popup.visible){this.extension_popup.title(g);this.extension_popup.empty();this.extension_popup.append(e(h));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_hideExtensionInfo:function(){var f=this;this.popover_timeout=setTimeout(function(){f._destroyExtensionInfo()},this.options.timeout)},_destroyExtensionInfo:function(){this.$el.find("#extension-info").popover("destroy")},_template:function(h){var g=this;var f='<tr id="upload-item-'+h.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';f+='<td><select id="extension" class="extension">';for(key in g.app.select_extension){f+='<option value="'+g.app.select_extension[key][1]+'">'+g.app.select_extension[key][0]+"</option>"}f+='</select>  <i id="extension-info" class="upload-icon-button fa fa-search"/></td>';f+='<td><select id="genome" class="genome">';for(key in g.app.select_genome){f+='<option value="'+g.app.select_genome[key][1]+'">'+g.app.select_genome[key][0]+"</option>"}f+="</select></td>";f+='<td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>';return f}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui.popover"],function(d,b,e,a,c){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,initialize:function(i,g){this.app=i;var f=this;this.model=new b.Model(g);this.setElement(this._template(g));var h=this.$el;this.settings=new c.View({title:"Upload configuration",container:h.find("#settings"),placement:"bottom"});h.find("#symbol").on("click",function(){f._removeRow()});h.find("#extension-info").on("click",function(j){f._showExtensionInfo()}).on("mousedown",function(j){j.preventDefault()});h.find("#settings").on("click",function(j){f._showSettings()}).on("mousedown",function(j){j.preventDefault()});h.find("#text-content").on("keyup",function(j){f.model.set("url_paste",$(j.target).val());f.model.set("file_size",$(j.target).val().length)});h.find("#genome").on("change",function(j){f.model.set("genome",$(j.target).val())});h.find("#extension").on("change",function(j){f.model.set("extension",$(j.target).val())});h.find("#space_to_tabs").on("change",function(j){f.model.set("space_to_tabs",$(j.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:extension",function(){f._destroyExtensionInfo()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f._destroyExtensionInfo();f.remove()});this.app.collection.on("reset",function(){f._destroyExtensionInfo();f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},_refreshGenome:function(){var f=this.model.get("genome");this.$el.find("#genome").val(f)},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){g.find("#text-content").attr("disabled",false);g.find("#genome").attr("disabled",false);g.find("#extension").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{g.find("#text-content").attr("disabled",true);g.find("#genome").attr("disabled",true);g.find("#extension").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var f=$(this.el).find("#extension-info");var h=this.model.get("extension");var g=$(this.el).find("#extension").find("option:selected").text();if(!this.extension_popup){this.extension_popup=new c.View({content:e(h),placement:"bottom",container:f})}if(!this.extension_popup.visible){this.extension_popup.title(g);this.extension_popup.empty();this.extension_popup.append(e(h));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_destroyExtensionInfo:function(){this.$el.find("#extension-info").popover("destroy")},_template:function(h){var g=this;var f='<tr id="upload-item-'+h.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td>';f+='<td><select id="extension" class="extension">';for(key in g.app.select_extension){f+='<option value="'+g.app.select_extension[key][1]+'">'+g.app.select_extension[key][0]+"</option>"}f+='</select>  <i id="extension-info" class="upload-icon-button fa fa-search"/></td>';f+='<td><select id="genome" class="genome">';for(key in g.app.select_genome){f+='<option value="'+g.app.select_genome[key][1]+'">'+g.app.select_genome[key][0]+"</option>"}f+="</select></td>";f+='<td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>';return f}})}); \ No newline at end of file diff -r 4228b5439785c10aaf638db4e18be65dfd6b9275 -r 375c04b4a7085c91c48201fc5d7376ab613874c8 static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(j){for(key in j){h.select_extension.push([j[key],j[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){var k=h.select_genome[0];h.select_genome=[];for(key in j){if(j[key].length>1){if(j[key][1]!==k[1]){h.select_genome.push(j[key])}}}h.select_genome.sort(function(m,l){return m[0]>l[0]?1:m[0]<l[0]?-1:0});h.select_genome.unshift(k)});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="ftp"){this.uploadbox.configure({paramname:""})}else{this.uploadbox.configure({paramname:"files_0|file_data"})}tool_input={};tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=q;tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;if(h=="ftp"){tool_input["files_0|ftp_files"]=n}data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui.popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.select_extension.push([j[key],j[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){var k=h.select_genome[0];h.select_genome=[];for(key in j){if(j[key].length>1){if(j[key][1]!==k[1]){h.select_genome.push(j[key])}}}h.select_genome.sort(function(m,l){return m[0]>l[0]?1:m[0]<l[0]?-1:0});h.select_genome.unshift(k)});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="ftp"){this.uploadbox.configure({paramname:""})}else{this.uploadbox.configure({paramname:"files_0|file_data"})}tool_input={};tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=q;tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;if(h=="ftp"){tool_input["files_0|ftp_files"]=n}data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ 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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