- galaxy-commits - lists.galaxyproject.org

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

10 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bd450366fc9d/ Changeset: bd450366fc9d User: jmchilton Date: 2014-09-09 22:41:34 Summary: Pull separate missing tools template out of run.mako. If you look at the conflicting sets of parameters these templates require I think it makes more sense to separate them this way - think result is simpler. Likewise, no need to for instance show collapse/expand all buttons on page with no actual rows for steps for instance. Most important thing here though is that now one can assume that step.module and step.state are available for all steps throughout run.mako (this will lead to further simplications). Affected #: 3 files diff -r 74b2495de918c95730f1f2fd2ac1bf502018a99f -r bd450366fc9da736c46358e6a827496c5c58d174 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1351,10 +1351,8 @@ if missing_tools: stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) return trans.fill_template( - "workflow/run.mako", - steps=[], + "workflow/missing_tools.mako", workflow=stored, - hide_fixed_params=hide_fixed_params, missing_tools=missing_tools ) # Render the form diff -r 74b2495de918c95730f1f2fd2ac1bf502018a99f -r bd450366fc9da736c46358e6a827496c5c58d174 templates/webapps/galaxy/workflow/missing_tools.mako --- /dev/null +++ b/templates/webapps/galaxy/workflow/missing_tools.mako @@ -0,0 +1,17 @@ +<%inherit file="/base.mako"/> + +<h2>Cannot run workflow "${h.to_unicode( workflow.name )}"</h2> + +%if workflow.annotation: + <div class="workflow-annotation">${workflow.annotation}</div> + <hr/> +%endif + +<div class='errormessage'> + <strong>This workflow utilizes tools which are unavailable, and cannot be run. Enable the tools listed below, or <a href="${h.url_for(controller='workflow', action='editor', id=trans.security.encode_id(workflow.id) )}" target="_parent">edit the workflow</a> to correct these errors.</strong><br/> + <ul> + %for i, tool in enumerate( missing_tools ): + <li>${tool}</li> + %endfor + </ul> +</div> \ No newline at end of file diff -r 74b2495de918c95730f1f2fd2ac1bf502018a99f -r bd450366fc9da736c46358e6a827496c5c58d174 templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -605,21 +605,11 @@ </div> %endif %endfor -%if missing_tools: - <div class='errormessage'> - <strong>This workflow utilizes tools which are unavailable, and cannot be run. Enable the tools listed below, or <a href="${h.url_for(controller='workflow', action='editor', id=trans.security.encode_id(workflow.id) )}" target="_parent">edit the workflow</a> to correct these errors.</strong><br/> - <ul> - %for i, tool in enumerate( missing_tools ): - <li>${tool}</li> - %endfor - </ul> -%else: - %if history_id is None: -<p id='new_history_p'> - <input type="checkbox" name='new_history' value="true" id='new_history_cbx'/><label for='new_history_cbx'>Send results to a new history </label> - <span id="new_history_input">named: <input type='text' name='new_history_name' value='${ h.to_unicode( workflow.name ) | h }'/></span> -</p> - %endif +%if history_id is None: + <p id='new_history_p'> + <input type="checkbox" name='new_history' value="true" id='new_history_cbx'/><label for='new_history_cbx'>Send results to a new history </label> + <span id="new_history_input">named: <input type='text' name='new_history_name' value='${ h.to_unicode( workflow.name ) | h }'/></span> + </p> +%endif <input type="submit" class="btn btn-primary" name="run_workflow" value="Run workflow" /></form> -%endif https://bitbucket.org/galaxy/galaxy-central/commits/89ab3ca6171d/ Changeset: 89ab3ca6171d User: jmchilton Date: 2014-09-09 22:41:34 Summary: Unify API for encoding runtime state across tool and input modules. Add some documentation. Affected #: 2 files diff -r bd450366fc9da736c46358e6a827496c5c58d174 -r 89ab3ca6171d10d37d26fb7c50242bd6dcde45d9 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -114,6 +114,14 @@ raise TypeError( "Abstract method" ) def encode_runtime_state( self, trans, state ): + """ Encode the runtime state (loaded from the stored step and + populated via the WorkflowModuleInjector below) for use in a hidden + parameter on the webpage. + + This will combined with runtime parameters supplied by user running + the workflow to create the final state to pass along to execute during + workflow invocation. + """ raise TypeError( "Abstract method" ) def decode_runtime_state( self, trans, string ): @@ -460,6 +468,9 @@ return self.trans.fill_template( "workflow/editor_tool_form.mako", tool=self.tool, values=self.state.inputs, errors=( self.errors or {} ) ) + def encode_runtime_state( self, trans, state ): + return state.encode( self.tool, self.trans.app ) + def update_state( self, incoming ): # Build a callback that handles setting an input to be required at # runtime. We still process all other parameters the user might have diff -r bd450366fc9da736c46358e6a827496c5c58d174 -r 89ab3ca6171d10d37d26fb7c50242bd6dcde45d9 templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -542,11 +542,15 @@ </script> %endif %for i, step in enumerate( steps ): +  + <% module = step.module %> + <input type="hidden" name="${step.id}|tool_state" value="${module.encode_runtime_state( t, step.state )}"> %if step.type == 'tool' or step.type is None: <% tool = trans.app.toolbox.get_tool( step.tool_id ) %> - <input type="hidden" name="${step.id}|tool_state" value="${step.state.encode( tool, app )}"><div class="toolForm"><div class="toolFormTitle"><span class='title_ul_text'>Step ${int(step.order_index)+1}: ${tool.name}</span> @@ -580,8 +584,6 @@ </div></div> %else: - <% module = step.module %> - <input type="hidden" name="${step.id}|tool_state" value="${module.encode_runtime_state( t, step.state )}"><div class="toolForm"><div class="toolFormTitle"><span class='title_ul_text'>Step ${int(step.order_index)+1}: ${module.name}</span> 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: 8 new changesets
by commits-noreply＠bitbucket.org 10 Sep '14

10 Sep '14

8 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce088c6f1fd4/ Changeset: ce088c6f1fd4 User: dannon Date: 2014-09-08 22:41:53 Summary: First pass removing to_json_string/from_json_string. Affected #: 107 files diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py --- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py +++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py @@ -52,4 +52,4 @@ FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) ) if __name__ == "__main__": - main() \ No newline at end of file + main() diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/datatypes/converters/fasta_to_len.py --- a/lib/galaxy/datatypes/converters/fasta_to_len.py +++ b/lib/galaxy/datatypes/converters/fasta_to_len.py @@ -49,4 +49,4 @@ out.close() if __name__ == "__main__" : - compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True ) \ No newline at end of file + compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py --- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py +++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py @@ -40,4 +40,4 @@ print >> out, "%s\t%s" %( fasta_title, sequence ) out.close() -if __name__ == "__main__" : __main__() \ No newline at end of file +if __name__ == "__main__" : __main__() diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py --- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py +++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py @@ -52,4 +52,4 @@ outfile.close() -if __name__ == "__main__": __main__() \ No newline at end of file +if __name__ == "__main__": __main__() diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/datatypes/converters/interval_to_coverage.py --- a/lib/galaxy/datatypes/converters/interval_to_coverage.py +++ b/lib/galaxy/datatypes/converters/interval_to_coverage.py @@ -149,4 +149,4 @@ fix_strand=True ) main( interval, coverage ) temp_file.close() - coverage.close() \ No newline at end of file + coverage.close() diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py --- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py @@ -26,4 +26,4 @@ FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) ) if __name__ == "__main__": - main() \ No newline at end of file + main() diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -14,7 +14,7 @@ from galaxy.datatypes.checkers import is_gzip from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes.sniff import get_headers, get_test_fname -from galaxy.util.json import to_json_string +from galaxy.util.json import dumps import dataproviders log = logging.getLogger(__name__) @@ -272,7 +272,7 @@ while cursor and ck_data[-1] != '\n': ck_data += cursor cursor = f.read(1) - return to_json_string( { 'ck_data': util.unicodify( ck_data ), 'ck_index': ck_index + 1 } ) + return dumps( { 'ck_data': util.unicodify( ck_data ), 'ck_index': ck_index + 1 } ) def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd): preview = util.string_as_bool( preview ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/datatypes/util/__init__.py --- a/lib/galaxy/datatypes/util/__init__.py +++ b/lib/galaxy/datatypes/util/__init__.py @@ -1,3 +1,3 @@ """ Utilities for Galaxy datatypes. -""" \ No newline at end of file +""" diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/external_services/result_handlers/basic.py --- a/lib/galaxy/external_services/result_handlers/basic.py +++ b/lib/galaxy/external_services/result_handlers/basic.py @@ -1,4 +1,4 @@ -from galaxy.util.json import to_json_string, from_json_string +from galaxy.util.json import dumps, loads from galaxy.util.template import fill_template import logging @@ -44,7 +44,7 @@ type = 'json_display' def handle_result( self, result, param_dict, trans ): - rval = from_json_string( result.content ) + rval = loads( result.content ) return trans.fill_template( '/external_services/generic_json.mako', result = rval, param_dict = param_dict, action=self.parent ) class ExternalServiceActionJQueryGridResultHandler( ExternalServiceActionResultHandler ): @@ -53,7 +53,7 @@ type = 'jquery_grid' def handle_result( self, result, param_dict, trans ): - rval = from_json_string( result.content ) + rval = loads( result.content ) return trans.fill_template( '/external_services/generic_jquery_grid.mako', result = rval, param_dict = param_dict, action=self.parent ) result_type_to_class = {} diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -25,7 +25,7 @@ from galaxy.jobs.runners import BaseJobRunner, JobState from galaxy.util.bunch import Bunch from galaxy.util.expressions import ExpressionContext -from galaxy.util.json import from_json_string +from galaxy.util.json import loads from galaxy.util import unicodify from .output_checker import check_output @@ -723,7 +723,7 @@ self.job_runner_mapper = JobRunnerMapper( self, queue.dispatcher.url_to_destination, self.app.job_config ) self.params = None if job.params: - self.params = from_json_string( job.params ) + self.params = loads( job.params ) if use_persisted_destination: self.job_runner_mapper.cached_job_destination = JobDestination( from_job=job ) @@ -1390,7 +1390,7 @@ if os.path.exists( meta_file ): for line in open( meta_file, 'r' ): try: - line = from_json_string( line ) + line = loads( line ) assert 'type' in line except: log.exception( '(%s) Got JSON data from tool, but data is improperly formatted or no "type" key in data' % self.job_id ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/jobs/actions/__init__.py --- a/lib/galaxy/jobs/actions/__init__.py +++ b/lib/galaxy/jobs/actions/__init__.py @@ -1,4 +1,4 @@ """ This package contains job action classes. -""" \ No newline at end of file +""" diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -5,7 +5,7 @@ import datetime import logging from galaxy.util import send_mail -from galaxy.util.json import to_json_string +from galaxy.util.json import dumps log = logging.getLogger( __name__ ) @@ -461,7 +461,7 @@ else: # Not pja stuff. pass - return to_json_string(npd) + return dumps(npd) @classmethod def get_add_list(cls): diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py --- a/lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py +++ b/lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py @@ -83,7 +83,7 @@ return self.job_states.INVALID url = 'http://' + job.params[ 'smrt_host' ] + self.api_path + '/Jobs/' + job.params[ 'smrt_job_id' ] + '/Status' r = urllib2.urlopen( url ) - status = json.from_json_string( r.read() ) + status = json.loads( r.read() ) # TODO: error handling: unexpected json or bad response, bad url, etc. if status[ 'Code' ] == 'Completed': log.debug( "SMRT Portal job '%s' is Completed. Initiating transfer." % job.params[ 'smrt_job_id' ] ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/jobs/transfer_manager.py --- a/lib/galaxy/jobs/transfer_manager.py +++ b/lib/galaxy/jobs/transfer_manager.py @@ -82,7 +82,7 @@ sock = socket.socket( socket.AF_INET, socket.SOCK_STREAM ) sock.settimeout( 5 ) sock.connect( ( 'localhost', tj.socket ) ) - sock.send( json.to_json_string( request ) ) + sock.send( json.dumps( request ) ) response = sock.recv( 8192 ) valid, response = json.validate_jsonrpc_response( response, id=request['id'] ) if not valid: diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/managers/context.py --- a/lib/galaxy/managers/context.py +++ b/lib/galaxy/managers/context.py @@ -4,7 +4,7 @@ import os -from galaxy.util.json import to_json_string +from galaxy.util.json import dumps from galaxy.util import bunch class ProvidesAppContext( object ): @@ -19,7 +19,7 @@ Application-level logging of user actions. """ if self.app.config.log_actions: - action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) ) + action = self.app.model.UserAction(action=action, context=context, params=unicode( dumps( params ) ) ) try: if user: action.user = user diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py --- a/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py +++ b/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py @@ -10,7 +10,7 @@ from sqlalchemy.exc import * from galaxy.model.custom_types import * -from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.json import loads, dumps import datetime now = datetime.datetime.utcnow @@ -62,7 +62,7 @@ for r in result: sample_id = r[0] if r[1]: - dataset_files = from_json_string(r[1]) + dataset_files = loads(r[1]) for df in dataset_files: if type(df) == type(dict()): cmd = "INSERT INTO sample_dataset VALUES (%s, %s, %s, %s, '%s', '%s', '%s', '%s', '%s')" diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py --- a/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py +++ b/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py @@ -6,7 +6,7 @@ from sqlalchemy.orm import * from migrate import * from migrate.changeset import * -from galaxy.util.json import from_json_string +from galaxy.util.json import loads import logging log = logging.getLogger( __name__ ) @@ -41,7 +41,7 @@ viz_id = viz['viz_id'] viz_rev_id = viz['viz_rev_id'] if viz[Visualization_revision_table.c.config]: - dbkey = from_json_string(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'") + dbkey = loads(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'") migrate_engine.execute("UPDATE visualization_revision SET dbkey='%s' WHERE id=%s" % (dbkey, viz_rev_id)) migrate_engine.execute("UPDATE visualization SET dbkey='%s' WHERE id=%s" % (dbkey, viz_id)) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/migrate/versions/0057_request_notify.py --- a/lib/galaxy/model/migrate/versions/0057_request_notify.py +++ b/lib/galaxy/model/migrate/versions/0057_request_notify.py @@ -10,7 +10,7 @@ from sqlalchemy.exc import * from galaxy.model.custom_types import * -from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.json import loads, dumps import datetime now = datetime.datetime.utcnow @@ -46,13 +46,13 @@ id = int(r[0]) notify_old = r[1] notify_new = dict(email=[], sample_states=[], body='', subject='') - cmd = "update request set notification='%s' where id=%i" % (to_json_string(notify_new), id) + cmd = "update request set notification='%s' where id=%i" % (dumps(notify_new), id) migrate_engine.execute( cmd ) cmd = "SELECT id, notification FROM request" result = migrate_engine.execute( cmd ) for r in result: - rr = from_json_string(str(r[1])) + rr = loads(str(r[1])) # remove the 'notify' column for non-sqlite databases. if migrate_engine.name != 'sqlite': diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py --- a/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py +++ b/lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py @@ -10,7 +10,7 @@ from sqlalchemy.exc import * from galaxy.model.custom_types import * -from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.json import loads, dumps import datetime now = datetime.datetime.utcnow diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py --- a/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py +++ b/lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py @@ -9,7 +9,7 @@ from migrate import * from migrate.changeset import * from sqlalchemy.exc import * -from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.json import loads, dumps from galaxy.model.custom_types import _sniffnfix_pg9_hex import datetime @@ -53,13 +53,13 @@ fields = str( row[1] ) if not fields.strip(): continue - fields_list = from_json_string( _sniffnfix_pg9_hex( fields ) ) + fields_list = loads( _sniffnfix_pg9_hex( fields ) ) if len( fields_list ): for index, field in enumerate( fields_list ): field[ 'name' ] = 'field_%i' % index field[ 'helptext' ] = field[ 'helptext' ].replace("'", "''").replace('"', "") field[ 'label' ] = field[ 'label' ].replace("'", "''") - fields_json = to_json_string( fields_list ) + fields_json = dumps( fields_list ) if migrate_engine.name == 'mysql': cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" %( fields_json, form_definition_id ) else: @@ -76,16 +76,16 @@ if not str( row[1] ).strip(): continue row1 = str(row[1]).replace('\n', '').replace('\r', '') - values_list = from_json_string( str( row1 ).strip() ) + values_list = loads( str( row1 ).strip() ) if not str( row[2] ).strip(): continue - fields_list = from_json_string( str( row[2] ).strip() ) + fields_list = loads( str( row[2] ).strip() ) if fields_list and type(values_list) == type(list()): values_dict = {} for field_index, field in enumerate( fields_list ): field_name = field[ 'name' ] values_dict[ field_name ] = get_value(values_list, field_index ) - cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( to_json_string( values_dict ), form_values_id ) + cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( dumps( values_dict ), form_values_id ) migrate_engine.execute( cmd ) def downgrade(migrate_engine): @@ -110,17 +110,17 @@ form_values_id = int( row[0] ) if not str( row[1] ).strip(): continue - values_dict = from_json_string( str( row[1] ) ) + values_dict = loads( str( row[1] ) ) if not str( row[2] ).strip(): continue - fields_list = from_json_string( str( row[2] ) ) + fields_list = loads( str( row[2] ) ) if fields_list: values_list = [] for field_index, field in enumerate( fields_list ): field_name = field[ 'name' ] field_value = values_dict[ field_name ] values_list.append( field_value ) - cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( to_json_string( values_list ), form_values_id ) + cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( dumps( values_list ), form_values_id ) migrate_engine.execute( cmd ) # remove name attribute from the field column of the form_definition table cmd = "SELECT f.id, f.fields FROM form_definition AS f" @@ -130,13 +130,13 @@ fields = str( row[1] ) if not fields.strip(): continue - fields_list = from_json_string( _sniffnfix_pg9_hex( fields ) ) + fields_list = loads( _sniffnfix_pg9_hex( fields ) ) if len( fields_list ): for index, field in enumerate( fields_list ): if field.has_key( 'name' ): del field[ 'name' ] if migrate_engine.name == 'mysql': - cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" %( to_json_string( fields_list ), form_definition_id ) + cmd = "UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i" %( dumps( fields_list ), form_definition_id ) else: - cmd = "UPDATE form_definition SET fields='%s' WHERE id=%i" %( to_json_string( fields_list ), form_definition_id ) + cmd = "UPDATE form_definition SET fields='%s' WHERE id=%i" %( dumps( fields_list ), form_definition_id ) migrate_engine.execute( cmd ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py --- a/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py +++ b/lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py @@ -13,7 +13,7 @@ from galaxy.model.custom_types import * -from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.json import loads, dumps import datetime now = datetime.datetime.utcnow @@ -104,7 +104,7 @@ 'layout': 'none', 'default': '' } ) form_definition_type = 'Sequencer Information Form' - form_definition_layout = to_json_string('[]') + form_definition_layout = dumps('[]') cmd = "INSERT INTO form_definition VALUES ( %s, %s, %s, '%s', '%s', %s, '%s', '%s', '%s' )" cmd = cmd % ( nextval( 'form_definition' ), localtimestamp(), @@ -112,7 +112,7 @@ form_definition_name, form_definition_desc, form_definition_current_id, - to_json_string( form_definition_fields ), + dumps( form_definition_fields ), form_definition_type, form_definition_layout ) migrate_engine.execute( cmd ) @@ -134,7 +134,7 @@ values = str( row[1] ) if not values.strip(): continue - values = from_json_string( values ) + values = loads( values ) # proceed only if sequencer_info is a valid list if values and type( values ) == type( dict() ): if sequencer_info.get( 'host', '' ) == values.get( 'field_0', '' ) \ @@ -148,7 +148,7 @@ def add_sequencer( sequencer_index, sequencer_form_definition_id, sequencer_info ): '''Adds a new sequencer to the sequencer table along with its form values.''' # Create a new form values record with the supplied sequencer information - values = to_json_string( { 'field_0': sequencer_info.get( 'host', '' ), + values = dumps( { 'field_0': sequencer_info.get( 'host', '' ), 'field_1': sequencer_info.get( 'username', '' ), 'field_2': sequencer_info.get( 'password', '' ), 'field_3': sequencer_info.get( 'data_dir', '' ), @@ -233,7 +233,7 @@ # skip if sequencer_info is empty if not sequencer_info.strip() or sequencer_info in ['None', 'null']: continue - sequencer_info = from_json_string( sequencer_info.strip() ) + sequencer_info = loads( sequencer_info.strip() ) # proceed only if sequencer_info is a valid dict if sequencer_info and type( sequencer_info ) == type( dict() ): # check if this sequencer has already been added to the sequencer table @@ -277,9 +277,9 @@ result = migrate_engine.execute( cmd ) for row in result: request_type_id = row[0] - seq_values = from_json_string( str( row[1] ) ) + seq_values = loads( str( row[1] ) ) # create the datatx_info json dict - datatx_info = to_json_string( dict( host = seq_values.get( 'field_0', '' ), + datatx_info = dumps( dict( host = seq_values.get( 'field_0', '' ), username = seq_values.get( 'field_1', '' ), password = seq_values.get( 'field_2', '' ), data_dir = seq_values.get( 'field_3', '' ), diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py --- a/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py +++ b/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py @@ -15,7 +15,7 @@ from galaxy.model.custom_types import * -from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.json import loads, dumps import datetime now = datetime.datetime.utcnow diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py --- a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py +++ b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py @@ -9,7 +9,7 @@ from sqlalchemy.exc import * import binascii -from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.json import loads, dumps import logging log = logging.getLogger( __name__ ) @@ -42,11 +42,11 @@ # first check if loading the dict from the json succeeds # if that fails, it means that the content field is corrupted. try: - field_values_dict = from_json_string( _sniffnfix_pg9_hex( str( row['field_values'] ) ) ) + field_values_dict = loads( _sniffnfix_pg9_hex( str( row['field_values'] ) ) ) except Exception, e: corrupted_rows = corrupted_rows + 1 # content field is corrupted - fields_list = from_json_string( _sniffnfix_pg9_hex( str( row['fdfields'] ) ) ) + fields_list = loads( _sniffnfix_pg9_hex( str( row['fdfields'] ) ) ) field_values_str = _sniffnfix_pg9_hex( str( row['field_values'] ) ) try: #Encoding errors? Just to be safe. @@ -85,7 +85,7 @@ # add to the new values dict field_values_dict[ field['name'] ] = value # update the db - json_values = to_json_string(field_values_dict) + json_values = dumps(field_values_dict) cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( json_values, int( row['id'] ) ) migrate_engine.execute( cmd ) try: diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py --- a/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py +++ b/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py @@ -12,7 +12,7 @@ # Need our custom types, but don't import anything else from model from galaxy.model.custom_types import * from galaxy.model.custom_types import _sniffnfix_pg9_hex -from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.json import loads, dumps import sys, logging log = logging.getLogger( __name__ ) @@ -77,7 +77,7 @@ for row in result: if row[1]: tool_shed_repository_id = row[0] - repository_metadata = from_json_string( _sniffnfix_pg9_hex( str( row[1] ) ) ) + repository_metadata = loads( _sniffnfix_pg9_hex( str( row[1] ) ) ) # Create a new row in the tool table for each tool included in repository. We will NOT # handle tool_version_associaions because we do not have the information we need to do so. tools = repository_metadata.get( 'tools', [] ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py --- a/lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py +++ b/lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py @@ -22,4 +22,4 @@ try: user.c.password.alter(type=String(40)) except: - log.exception( "Altering password column failed" ) \ No newline at end of file + log.exception( "Altering password column failed" ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/migrate/versions/0117_add_user_activation.py --- a/lib/galaxy/model/migrate/versions/0117_add_user_activation.py +++ b/lib/galaxy/model/migrate/versions/0117_add_user_activation.py @@ -54,4 +54,4 @@ user_active.drop() user_activation_token.drop() except Exception, e: - log.debug( "Dropping 'active' and 'activation_token' columns from galaxy_user table failed: %s" % ( str( e ) ) ) \ No newline at end of file + log.debug( "Dropping 'active' and 'activation_token' columns from galaxy_user table failed: %s" % ( str( e ) ) ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/orm/logging_connection_proxy.py --- a/lib/galaxy/model/orm/logging_connection_proxy.py +++ b/lib/galaxy/model/orm/logging_connection_proxy.py @@ -45,4 +45,4 @@ self.trace_logger.log( "sqlalchemy_query", message="Query executed", statement=statement, parameters=parameters, executemany=executemany, duration=duration ) - return rval \ No newline at end of file + return rval diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/search.py --- a/lib/galaxy/model/search.py +++ b/lib/galaxy/model/search.py @@ -39,7 +39,7 @@ Page, PageRevision) from galaxy.model.tool_shed_install import ToolVersion -from galaxy.util.json import to_json_string +from galaxy.util.json import dumps from sqlalchemy import and_ from sqlalchemy.orm import aliased @@ -429,7 +429,7 @@ and_( Job.id == alias.job_id, alias.name == param_name, - alias.value == to_json_string(right) + alias.value == dumps(right) ) ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0001_add_tool_shed_repository_table.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0001_add_tool_shed_repository_table.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0001_add_tool_shed_repository_table.py @@ -1,1 +1,51 @@ -../../../migrate/versions/0082_add_tool_shed_repository_table.py \ No newline at end of file +""" +Migration script to add the tool_shed_repository table. +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +import sys, logging +from galaxy.model.custom_types import * +from sqlalchemy.exc import * +import datetime +now = datetime.datetime.utcnow + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +# New table to store information about cloned tool shed repositories. +ToolShedRepository_table = Table( "tool_shed_repository", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_shed", TrimmedString( 255 ), index=True ), + Column( "name", TrimmedString( 255 ), index=True ), + Column( "description" , TEXT ), + Column( "owner", TrimmedString( 255 ), index=True ), + Column( "changeset_revision", TrimmedString( 255 ), index=True ), + Column( "deleted", Boolean, index=True, default=False ) ) + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + try: + ToolShedRepository_table.create() + except Exception, e: + log.debug( "Creating tool_shed_repository table failed: %s" % str( e ) ) + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + try: + ToolShedRepository_table.drop() + except Exception, e: + log.debug( "Dropping tool_shed_repository table failed: %s" % str( e ) ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0002_add_tool_shed_repository_table_columns.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0002_add_tool_shed_repository_table_columns.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0002_add_tool_shed_repository_table_columns.py @@ -1,1 +1,79 @@ -../../../migrate/versions/0086_add_tool_shed_repository_table_columns.py \ No newline at end of file +""" +Migration script to add the metadata, update_available and includes_datatypes columns to the tool_shed_repository table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def get_default_false(migrate_engine): + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + return "0" + elif migrate_engine.name in ['postgresql', 'postgres']: + return "false" + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + c = Column( "metadata", JSONType(), nullable=True ) + try: + c.create( ToolShedRepository_table ) + assert c is ToolShedRepository_table.c.metadata + except Exception, e: + print "Adding metadata column to the tool_shed_repository table failed: %s" % str( e ) + log.debug( "Adding metadata column to the tool_shed_repository table failed: %s" % str( e ) ) + c = Column( "includes_datatypes", Boolean, index=True, default=False ) + try: + c.create( ToolShedRepository_table, index_name="ix_tool_shed_repository_includes_datatypes") + assert c is ToolShedRepository_table.c.includes_datatypes + migrate_engine.execute( "UPDATE tool_shed_repository SET includes_datatypes=%s" % get_default_false(migrate_engine)) + except Exception, e: + print "Adding includes_datatypes column to the tool_shed_repository table failed: %s" % str( e ) + log.debug( "Adding includes_datatypes column to the tool_shed_repository table failed: %s" % str( e ) ) + c = Column( "update_available", Boolean, default=False ) + try: + c.create( ToolShedRepository_table ) + assert c is ToolShedRepository_table.c.update_available + migrate_engine.execute( "UPDATE tool_shed_repository SET update_available=%s" % get_default_false(migrate_engine)) + except Exception, e: + print "Adding update_available column to the tool_shed_repository table failed: %s" % str( e ) + log.debug( "Adding update_available column to the tool_shed_repository table failed: %s" % str( e ) ) + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + try: + ToolShedRepository_table.c.metadata.drop() + except Exception, e: + print "Dropping column metadata from the tool_shed_repository table failed: %s" % str( e ) + log.debug( "Dropping column metadata from the tool_shed_repository table failed: %s" % str( e ) ) + try: + ToolShedRepository_table.c.includes_datatypes.drop() + except Exception, e: + print "Dropping column includes_datatypes from the tool_shed_repository table failed: %s" % str( e ) + log.debug( "Dropping column includes_datatypes from the tool_shed_repository table failed: %s" % str( e ) ) + try: + ToolShedRepository_table.c.update_available.drop() + except Exception, e: + print "Dropping column update_available from the tool_shed_repository table failed: %s" % str( e ) + log.debug( "Dropping column update_available from the tool_shed_repository table failed: %s" % str( e ) ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0003_tool_id_guid_map_table.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0003_tool_id_guid_map_table.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0003_tool_id_guid_map_table.py @@ -1,1 +1,52 @@ -../../../migrate/versions/0087_tool_id_guid_map_table.py \ No newline at end of file +""" +Migration script to create the tool_id_guid_map table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +ToolIdGuidMap_table = Table( "tool_id_guid_map", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_id", String( 255 ) ), + Column( "tool_version", TEXT ), + Column( "tool_shed", TrimmedString( 255 ) ), + Column( "repository_owner", TrimmedString( 255 ) ), + Column( "repository_name", TrimmedString( 255 ) ), + Column( "guid", TEXT, index=True, unique=True ) ) + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + try: + ToolIdGuidMap_table.create() + except Exception, e: + log.debug( "Creating tool_id_guid_map table failed: %s" % str( e ) ) + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + try: + ToolIdGuidMap_table.drop() + except Exception, e: + log.debug( "Dropping tool_id_guid_map table failed: %s" % str( e ) ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0004_add_installed_changeset_revison_column.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0004_add_installed_changeset_revison_column.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0004_add_installed_changeset_revison_column.py @@ -1,1 +1,64 @@ -../../../migrate/versions/0088_add_installed_changeset_revison_column.py \ No newline at end of file +""" +Migration script to add the installed_changeset_revision column to the tool_shed_repository table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + col = Column( "installed_changeset_revision", TrimmedString( 255 ) ) + try: + col.create( ToolShedRepository_table ) + assert col is ToolShedRepository_table.c.installed_changeset_revision + except Exception, e: + print "Adding installed_changeset_revision column to the tool_shed_repository table failed: %s" % str( e ) + log.debug( "Adding installed_changeset_revision column to the tool_shed_repository table failed: %s" % str( e ) ) + # Update each row by setting the value of installed_changeset_revison to be the value of changeset_revision. + # This will be problematic if the value of changeset_revision was updated to something other than the value + # that it was when the repository was installed (because the install path determined in real time will attempt to + # find the repository using the updated changeset_revison instead of the required installed_changeset_revision), + # but at the time this script was written, this scenario is extremely unlikely. + cmd = "SELECT id AS id, " \ + + "installed_changeset_revision AS installed_changeset_revision, " \ + + "changeset_revision AS changeset_revision " \ + + "FROM tool_shed_repository;" + tool_shed_repositories = migrate_engine.execute( cmd ).fetchall() + update_count = 0 + for row in tool_shed_repositories: + cmd = "UPDATE tool_shed_repository " \ + + "SET installed_changeset_revision = '%s' " % row.changeset_revision \ + + "WHERE changeset_revision = '%s';" % row.changeset_revision + migrate_engine.execute( cmd ) + update_count += 1 + print "Updated the installed_changeset_revision column for ", update_count, " rows in the tool_shed_repository table. " +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + try: + ToolShedRepository_table.c.installed_changeset_revision.drop() + except Exception, e: + print "Dropping column installed_changeset_revision from the tool_shed_repository table failed: %s" % str( e ) + log.debug( "Dropping column installed_changeset_revision from the tool_shed_repository table failed: %s" % str( e ) ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0005_add_tool_shed_repository_table_columns.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0005_add_tool_shed_repository_table_columns.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0005_add_tool_shed_repository_table_columns.py @@ -1,1 +1,63 @@ -../../../migrate/versions/0090_add_tool_shed_repository_table_columns.py \ No newline at end of file +""" +Migration script to add the uninstalled and dist_to_shed columns to the tool_shed_repository table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def default_false(migrate_engine): + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + return "0" + elif migrate_engine.name in ['postgresql', 'postgres']: + return "false" + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + c = Column( "uninstalled", Boolean, default=False ) + try: + c.create( ToolShedRepository_table ) + assert c is ToolShedRepository_table.c.uninstalled + migrate_engine.execute( "UPDATE tool_shed_repository SET uninstalled=%s" % default_false(migrate_engine) ) + except Exception, e: + print "Adding uninstalled column to the tool_shed_repository table failed: %s" % str( e ) + c = Column( "dist_to_shed", Boolean, default=False ) + try: + c.create( ToolShedRepository_table ) + assert c is ToolShedRepository_table.c.dist_to_shed + migrate_engine.execute( "UPDATE tool_shed_repository SET dist_to_shed=%s" % default_false(migrate_engine) ) + except Exception, e: + print "Adding dist_to_shed column to the tool_shed_repository table failed: %s" % str( e ) + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + try: + ToolShedRepository_table.c.uninstalled.drop() + except Exception, e: + print "Dropping column uninstalled from the tool_shed_repository table failed: %s" % str( e ) + try: + ToolShedRepository_table.c.dist_to_shed.drop() + except Exception, e: + print "Dropping column dist_to_shed from the tool_shed_repository table failed: %s" % str( e ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0006_add_tool_version_tables.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0006_add_tool_version_tables.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0006_add_tool_version_tables.py @@ -1,1 +1,122 @@ -../../../migrate/versions/0091_add_tool_version_tables.py \ No newline at end of file +""" +Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * +from galaxy.model.custom_types import _sniffnfix_pg9_hex +from galaxy.util.json import loads, dumps + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() +#migrate_engine = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def nextval( table, col='id' ): + if migrate_engine.name == 'postgres': + return "nextval('%s_%s_seq')" % ( table, col ) + elif migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + return "null" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + +def localtimestamp(): + if migrate_engine.name == 'postgres' or migrate_engine.name == 'mysql': + return "LOCALTIMESTAMP" + elif migrate_engine.name == 'sqlite': + return "current_date || ' ' || current_time" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % db ) + +ToolVersion_table = Table( "tool_version", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_id", String( 255 ) ), + Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=True ) ) + +ToolVersionAssociation_table = Table( "tool_version_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "tool_id", Integer, ForeignKey( "tool_version.id" ), index=True, nullable=False ), + Column( "parent_id", Integer, ForeignKey( "tool_version.id" ), index=True, nullable=False ) ) + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + + ToolIdGuidMap_table = Table( "tool_id_guid_map", metadata, autoload=True ) + + metadata.reflect() + # Create the tables. + try: + ToolVersion_table.create() + except Exception, e: + log.debug( "Creating tool_version table failed: %s" % str( e ) ) + try: + ToolVersionAssociation_table.create() + except Exception, e: + log.debug( "Creating tool_version_association table failed: %s" % str( e ) ) + # Populate the tool table with tools included in installed tool shed repositories. + cmd = "SELECT id, metadata FROM tool_shed_repository" + result = migrate_engine.execute( cmd ) + count = 0 + for row in result: + if row[1]: + tool_shed_repository_id = row[0] + repository_metadata = loads( _sniffnfix_pg9_hex( str( row[1] ) ) ) + # Create a new row in the tool table for each tool included in repository. We will NOT + # handle tool_version_associaions because we do not have the information we need to do so. + tools = repository_metadata.get( 'tools', [] ) + for tool_dict in tools: + cmd = "INSERT INTO tool_version VALUES (%s, %s, %s, '%s', %s)" % \ + ( nextval( 'tool_version' ), localtimestamp(), localtimestamp(), tool_dict[ 'guid' ], tool_shed_repository_id ) + migrate_engine.execute( cmd ) + count += 1 + print "Added %d rows to the new tool_version table." % count + # Drop the tool_id_guid_map table since the 2 new tables render it unnecessary. + try: + ToolIdGuidMap_table.drop() + except Exception, e: + log.debug( "Dropping tool_id_guid_map table failed: %s" % str( e ) ) + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + + ToolIdGuidMap_table = Table( "tool_id_guid_map", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_id", String( 255 ) ), + Column( "tool_version", TEXT ), + Column( "tool_shed", TrimmedString( 255 ) ), + Column( "repository_owner", TrimmedString( 255 ) ), + Column( "repository_name", TrimmedString( 255 ) ), + Column( "guid", TEXT, index=True, unique=True ) ) + + metadata.reflect() + try: + ToolVersionAssociation_table.drop() + except Exception, e: + log.debug( "Dropping tool_version_association table failed: %s" % str( e ) ) + try: + ToolVersion_table.drop() + except Exception, e: + log.debug( "Dropping tool_version table failed: %s" % str( e ) ) + try: + ToolIdGuidMap_table.create() + except Exception, e: + log.debug( "Creating tool_id_guid_map table failed: %s" % str( e ) ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0007_add_migrate_tools_table.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0007_add_migrate_tools_table.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0007_add_migrate_tools_table.py @@ -1,1 +1,50 @@ -../../../migrate/versions/0092_add_migrate_tools_table.py \ No newline at end of file +""" +Migration script to create the migrate_tools table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +MigrateTools_table = Table( "migrate_tools", metadata, + Column( "repository_id", TrimmedString( 255 ) ), + Column( "repository_path", TEXT ), + Column( "version", Integer ) ) + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + + metadata.reflect() + # Create the table. + try: + MigrateTools_table.create() + cmd = "INSERT INTO migrate_tools VALUES ('GalaxyTools', 'lib/galaxy/tool_shed/migrate', %d)" % 1 + migrate_engine.execute( cmd ) + except Exception, e: + log.debug( "Creating migrate_tools table failed: %s" % str( e ) ) + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + try: + MigrateTools_table.drop() + except Exception, e: + log.debug( "Dropping migrate_tools table failed: %s" % str( e ) ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0008_add_ctx_rev_column.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0008_add_ctx_rev_column.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0008_add_ctx_rev_column.py @@ -1,1 +1,44 @@ -../../../migrate/versions/0097_add_ctx_rev_column.py \ No newline at end of file +""" +Migration script to add the ctx_rev column to the tool_shed_repository table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + col = Column( "ctx_rev", TrimmedString( 10 ) ) + try: + col.create( ToolShedRepository_table ) + assert col is ToolShedRepository_table.c.ctx_rev + except Exception, e: + print "Adding ctx_rev column to the tool_shed_repository table failed: %s" % str( e ) +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + try: + ToolShedRepository_table.c.ctx_rev.drop() + except Exception, e: + print "Dropping column ctx_rev from the tool_shed_repository table failed: %s" % str( e ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0009_add_tool_dependency_table.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0009_add_tool_dependency_table.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0009_add_tool_dependency_table.py @@ -1,1 +1,51 @@ -../../../migrate/versions/0099_add_tool_dependency_table.py \ No newline at end of file +""" +Migration script to add the tool_dependency table. +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +import sys, logging +from galaxy.model.custom_types import * +from sqlalchemy.exc import * +import datetime +now = datetime.datetime.utcnow + +log = logging.getLogger( __name__ ) +log.setLevel( logging.DEBUG ) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +# New table to store information about cloned tool shed repositories. +ToolDependency_table = Table( "tool_dependency", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=False ), + Column( "installed_changeset_revision", TrimmedString( 255 ) ), + Column( "name", TrimmedString( 255 ) ), + Column( "version", TrimmedString( 40 ) ), + Column( "type", TrimmedString( 40 ) ), + Column( "uninstalled", Boolean, default=False ) ) + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + try: + ToolDependency_table.create() + except Exception, e: + log.debug( "Creating tool_dependency table failed: %s" % str( e ) ) + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + try: + ToolDependency_table.drop() + except Exception, e: + log.debug( "Dropping tool_dependency table failed: %s" % str( e ) ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0010_alter_tool_dependency_table_version_column.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0010_alter_tool_dependency_table_version_column.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0010_alter_tool_dependency_table_version_column.py @@ -1,1 +1,54 @@ -../../../migrate/versions/0100_alter_tool_dependency_table_version_column.py \ No newline at end of file +""" +Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + ToolDependency_table = Table( "tool_dependency", metadata, autoload=True ) + # Change the tool_dependency table's version column from TrimmedString to Text. + if migrate_engine.name in ['postgresql', 'postgres']: + cmd = "ALTER TABLE tool_dependency ALTER COLUMN version TYPE Text;" + elif migrate_engine.name == 'mysql': + cmd = "ALTER TABLE tool_dependency MODIFY COLUMN version Text;" + else: + # We don't have to do anything for sqlite tables. From the sqlite documentation at http://sqlite.org/datatype3.html: + # 1.0 Storage Classes and Datatypes + # Each value stored in an SQLite database (or manipulated by the database engine) has one of the following storage classes: + # NULL. The value is a NULL value. + # INTEGER. The value is a signed integer, stored in 1, 2, 3, 4, 6, or 8 bytes depending on the magnitude of the value. + # REAL. The value is a floating point value, stored as an 8-byte IEEE floating point number. + # TEXT. The value is a text string, stored using the database encoding (UTF-8, UTF-16BE or UTF-16LE). + # BLOB. The value is a blob of data, stored exactly as it was input. + cmd = None + if cmd: + try: + migrate_engine.execute( cmd ) + except Exception, e: + log.debug( "Altering tool_dependency.version column from TrimmedString(40) to Text failed: %s" % str( e ) ) +def downgrade(migrate_engine): + metadata.bind = migrate_engine + # Not necessary to change column type Text to TrimmedString(40). + pass diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0011_drop_installed_changeset_revision_column.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0011_drop_installed_changeset_revision_column.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0011_drop_installed_changeset_revision_column.py @@ -1,1 +1,41 @@ -../../../migrate/versions/0101_drop_installed_changeset_revision_column.py \ No newline at end of file +""" +Migration script to drop the installed_changeset_revision column from the tool_dependency table. +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +import sys, logging +from galaxy.model.custom_types import * +from sqlalchemy.exc import * +import datetime +now = datetime.datetime.utcnow + +log = logging.getLogger( __name__ ) +log.setLevel( logging.DEBUG ) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + try: + ToolDependency_table = Table( "tool_dependency", metadata, autoload=True ) + except NoSuchTableError: + ToolDependency_table = None + log.debug( "Failed loading table tool_dependency" ) + if ToolDependency_table is not None: + try: + col = ToolDependency_table.c.installed_changeset_revision + col.drop() + except Exception, e: + log.debug( "Dropping column 'installed_changeset_revision' from tool_dependency table failed: %s" % ( str( e ) ) ) +def downgrade(migrate_engine): + metadata.bind = migrate_engine + pass diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0012_add_tool_dependency_status_columns.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0012_add_tool_dependency_status_columns.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0012_add_tool_dependency_status_columns.py @@ -1,1 +1,71 @@ -../../../migrate/versions/0102_add_tool_dependency_status_columns.py \ No newline at end of file +""" +Migration script to add status and error_message columns to the tool_dependency table and drop the uninstalled column from the tool_dependency table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + ToolDependency_table = Table( "tool_dependency", metadata, autoload=True ) + if migrate_engine.name == 'sqlite': + col = Column( "status", TrimmedString( 255 )) + else: + col = Column( "status", TrimmedString( 255 ), nullable=False) + try: + col.create( ToolDependency_table ) + assert col is ToolDependency_table.c.status + except Exception, e: + print "Adding status column to the tool_dependency table failed: %s" % str( e ) + col = Column( "error_message", TEXT ) + try: + col.create( ToolDependency_table ) + assert col is ToolDependency_table.c.error_message + except Exception, e: + print "Adding error_message column to the tool_dependency table failed: %s" % str( e ) + + if migrate_engine.name != 'sqlite': + #This breaks in sqlite due to failure to drop check constraint. + # TODO move to alembic. + try: + ToolDependency_table.c.uninstalled.drop() + except Exception, e: + print "Dropping uninstalled column from the tool_dependency table failed: %s" % str( e ) +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + ToolDependency_table = Table( "tool_dependency", metadata, autoload=True ) + try: + ToolDependency_table.c.status.drop() + except Exception, e: + print "Dropping column status from the tool_dependency table failed: %s" % str( e ) + try: + ToolDependency_table.c.error_message.drop() + except Exception, e: + print "Dropping column error_message from the tool_dependency table failed: %s" % str( e ) + col = Column( "uninstalled", Boolean, default=False ) + try: + col.create( ToolDependency_table ) + assert col is ToolDependency_table.c.uninstalled + except Exception, e: + print "Adding uninstalled column to the tool_dependency table failed: %s" % str( e ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0013_add_tool_shed_repository_status_columns.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0013_add_tool_shed_repository_status_columns.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0013_add_tool_shed_repository_status_columns.py @@ -1,1 +1,69 @@ -../../../migrate/versions/0103_add_tool_shed_repository_status_columns.py \ No newline at end of file +"""Migration script to add status and error_message columns to the tool_shed_repository table.""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +metadata = MetaData() + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + # Add the status column to the tool_shed_repository table. + col = Column( "status", TrimmedString( 255 ) ) + try: + col.create( ToolShedRepository_table ) + assert col is ToolShedRepository_table.c.status + except Exception, e: + print "Adding status column to the tool_shed_repository table failed: %s" % str( e ) + # Add the error_message column to the tool_shed_repository table. + col = Column( "error_message", TEXT ) + try: + col.create( ToolShedRepository_table ) + assert col is ToolShedRepository_table.c.error_message + except Exception, e: + print "Adding error_message column to the tool_shed_repository table failed: %s" % str( e ) + # Update the status column value for tool_shed_repositories to the default value 'Installed'. + cmd = "UPDATE tool_shed_repository SET status = 'Installed';" + try: + migrate_engine.execute( cmd ) + except Exception, e: + print "Exception executing sql command: " + print cmd + print str( e ) + # Update the status column for tool_shed_repositories that have been uninstalled. + cmd = "UPDATE tool_shed_repository SET status = 'Uninstalled' WHERE uninstalled;" + try: + migrate_engine.execute( cmd ) + except Exception, e: + print "Exception executing sql command: " + print cmd + print str( e ) + # Update the status column for tool_shed_repositories that have been deactivated. + cmd = "UPDATE tool_shed_repository SET status = 'Deactivated' where deleted and not uninstalled;" + try: + migrate_engine.execute( cmd ) + except Exception, e: + print "Exception executing sql command: " + print cmd + print str( e ) +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + try: + ToolShedRepository_table.c.status.drop() + except Exception, e: + print "Dropping column status from the tool_shed_repository table failed: %s" % str( e ) + try: + ToolShedRepository_table.c.error_message.drop() + except Exception, e: + print "Dropping column error_message from the tool_shed_repository table failed: %s" % str( e ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0014_add_repository_dependency_tables.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0014_add_repository_dependency_tables.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0014_add_repository_dependency_tables.py @@ -1,1 +1,60 @@ -../../../migrate/versions/0109_add_repository_dependency_tables.py \ No newline at end of file +""" +Migration script to add the repository_dependency and repository_repository_dependency_association tables. +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +import sys, logging +from galaxy.model.custom_types import * +from sqlalchemy.exc import * +import datetime +now = datetime.datetime.utcnow + +log = logging.getLogger( __name__ ) +log.setLevel( logging.DEBUG ) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +RepositoryDependency_table = Table( "repository_dependency", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True, nullable=False ) ) + +RepositoryRepositoryDependencyAssociation_table = Table( "repository_repository_dependency_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_shed_repository_id", Integer, ForeignKey( "tool_shed_repository.id" ), index=True ), + Column( "repository_dependency_id", Integer, ForeignKey( "repository_dependency.id" ), index=True ) ) + +def upgrade(migrate_engine): + print __doc__ + metadata.bind = migrate_engine + metadata.reflect() + try: + RepositoryDependency_table.create() + except Exception, e: + log.debug( "Creating repository_dependency table failed: %s" % str( e ) ) + try: + RepositoryRepositoryDependencyAssociation_table.create() + except Exception, e: + log.debug( "Creating repository_repository_dependency_association table failed: %s" % str( e ) ) + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + try: + RepositoryRepositoryDependencyAssociation_table.drop() + except Exception, e: + log.debug( "Dropping repository_repository_dependency_association table failed: %s" % str( e ) ) + try: + RepositoryDependency_table.drop() + except Exception, e: + log.debug( "Dropping repository_dependency table failed: %s" % str( e ) ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0015_update_migrate_tools_table.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0015_update_migrate_tools_table.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0015_update_migrate_tools_table.py @@ -1,1 +1,38 @@ -../../../migrate/versions/0113_update_migrate_tools_table.py \ No newline at end of file +""" +Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +def upgrade(migrate_engine): + print __doc__ + # Create the table. + try: + cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';" + migrate_engine.execute( cmd ) + except Exception, e: + log.debug( "Updating migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate failed: %s" % str( e ) ) + +def downgrade(migrate_engine): + try: + cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';" + migrate_engine.execute( cmd ) + except Exception, e: + log.debug( "Updating migrate_tools.repository_path column to point to the old location lib/galaxy/tool_shed/migrate failed: %s" % str( e ) ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0016_update_migrate_tools_table_again.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0016_update_migrate_tools_table_again.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0016_update_migrate_tools_table_again.py @@ -1,1 +1,40 @@ -../../../migrate/versions/0114_update_migrate_tools_table_again.py \ No newline at end of file +""" +Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + + +def upgrade(migrate_engine): + print __doc__ + # Create the table. + try: + cmd = "UPDATE migrate_tools set repository_path='lib/tool_shed/galaxy_install/migrate';" + migrate_engine.execute( cmd ) + except Exception, e: + log.debug( "Updating migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate failed: %s" % str( e ) ) + +def downgrade(migrate_engine): + try: + cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';" + migrate_engine.execute( cmd ) + except Exception, e: + log.debug( "Updating migrate_tools.repository_path column to point to the old location lib/galaxy/tool_shed/migrate failed: %s" % str( e ) ) + diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/model/tool_shed_install/migrate/versions/0017_drop_update_available_col_add_tool_shed_status_col.py --- a/lib/galaxy/model/tool_shed_install/migrate/versions/0017_drop_update_available_col_add_tool_shed_status_col.py +++ b/lib/galaxy/model/tool_shed_install/migrate/versions/0017_drop_update_available_col_add_tool_shed_status_col.py @@ -1,1 +1,77 @@ -../../../migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py \ No newline at end of file +""" +Migration script to drop the update_available Boolean column and replace it with the tool_shed_status JSONType column in the tool_shed_repository table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +import sys, logging +from galaxy.model.custom_types import * +from sqlalchemy.exc import * +import datetime +now = datetime.datetime.utcnow + +log = logging.getLogger( __name__ ) +log.setLevel( logging.DEBUG ) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def default_false( migrate_engine ): + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + return "0" + elif migrate_engine.name in [ 'postgresql', 'postgres' ]: + return "false" + +def upgrade( migrate_engine ): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + try: + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + except NoSuchTableError: + ToolShedRepository_table = None + log.debug( "Failed loading table tool_shed_repository" ) + if ToolShedRepository_table is not None: + # For some unknown reason it is no longer possible to drop a column in a migration script if using the sqlite database. + if migrate_engine.name != 'sqlite': + try: + col = ToolShedRepository_table.c.update_available + col.drop() + except Exception, e: + print "Dropping column update_available from the tool_shed_repository table failed: %s" % str( e ) + c = Column( "tool_shed_status", JSONType, nullable=True ) + try: + c.create( ToolShedRepository_table ) + assert c is ToolShedRepository_table.c.tool_shed_status + except Exception, e: + print "Adding tool_shed_status column to the tool_shed_repository table failed: %s" % str( e ) + +def downgrade( migrate_engine ): + metadata.bind = migrate_engine + metadata.reflect() + try: + ToolShedRepository_table = Table( "tool_shed_repository", metadata, autoload=True ) + except NoSuchTableError: + ToolShedRepository_table = None + log.debug( "Failed loading table tool_shed_repository" ) + if ToolShedRepository_table is not None: + # For some unknown reason it is no longer possible to drop a column in a migration script if using the sqlite database. + if migrate_engine.name != 'sqlite': + try: + col = ToolShedRepository_table.c.tool_shed_status + col.drop() + except Exception, e: + print "Dropping column tool_shed_status from the tool_shed_repository table failed: %s" % str( e ) + c = Column( "update_available", Boolean, default=False ) + try: + c.create( ToolShedRepository_table ) + assert c is ToolShedRepository_table.c.update_available + migrate_engine.execute( "UPDATE tool_shed_repository SET update_available=%s" % default_false( migrate_engine ) ) + except Exception, e: + print "Adding column update_available to the tool_shed_repository table failed: %s" % str( e ) diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/openid/__init__.py --- a/lib/galaxy/openid/__init__.py +++ b/lib/galaxy/openid/__init__.py @@ -1,3 +1,3 @@ """ OpenID functionality -""" \ No newline at end of file +""" diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -4,7 +4,7 @@ from galaxy.tools.parameters import DataToolParameter from galaxy.tools.parameters import DataCollectionToolParameter from galaxy.tools.parameters.wrapped import WrappedParameters -from galaxy.util.json import to_json_string +from galaxy.util.json import dumps from galaxy.util.none_like import NoneDataset from galaxy.util.odict import odict from galaxy.util.template import fill_template @@ -324,7 +324,7 @@ job.add_output_dataset( name, dataset ) job.object_store_id = object_store_populator.object_store_id if job_params: - job.params = to_json_string( job_params ) + job.params = dumps( job_params ) job.set_handler(tool.get_job_handler(job_params)) trans.sa_session.add( job ) # Now that we have a job id, we can remap any outputs if this is a rerun and the user chose to continue dependent jobs diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py +++ b/lib/galaxy/tools/actions/metadata.py @@ -1,7 +1,7 @@ from __init__ import ToolAction from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper from galaxy.util.odict import odict -from galaxy.util.json import to_json_string +from galaxy.util.json import dumps import logging log = logging.getLogger( __name__ ) @@ -50,7 +50,7 @@ if user: job.user_id = user.id if job_params: - job.params = to_json_string( job_params ) + job.params = dumps( job_params ) start_job_state = job.state #should be job.states.NEW try: # For backward compatibility, some tools may not have versions yet. diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -7,7 +7,7 @@ from galaxy import datatypes, util from galaxy.util.odict import odict from galaxy.datatypes import sniff -from galaxy.util.json import to_json_string +from galaxy.util.json import dumps from galaxy.model.orm import eagerload_all from galaxy.exceptions import ObjectInvalid @@ -342,7 +342,7 @@ # user cannot remove it unless the parent directory is writable. if link_data_only == 'copy_files' and trans.app.config.external_chown_script: _chown( uploaded_dataset.path ) - json_file.write( to_json_string( json ) + '\n' ) + json_file.write( dumps( json ) + '\n' ) json_file.close() if trans.app.config.external_chown_script: _chown( json_file_path ) @@ -375,7 +375,7 @@ for name, value in tool.params_to_strings( params, trans.app ).iteritems(): job.add_parameter( name, value ) - job.add_parameter( 'paramfile', to_json_string( json_file_path ) ) + job.add_parameter( 'paramfile', dumps( json_file_path ) ) object_store_id = None for i, dataset in enumerate( data_list ): if folder: diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/tools/imp_exp/__init__.py --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -8,7 +8,7 @@ from galaxy.tools.parameters.basic import UnvalidatedValue from galaxy.web.framework.helpers import to_unicode from galaxy.model.item_attrs import UsesAnnotations -from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.json import loads, dumps from galaxy.web.base.controller import UsesHistoryMixin log = logging.getLogger(__name__) @@ -108,7 +108,7 @@ # history_attr_file_name = os.path.join( archive_dir, 'history_attrs.txt') history_attr_str = read_file_contents( history_attr_file_name ) - history_attrs = from_json_string( history_attr_str ) + history_attrs = loads( history_attr_str ) # Create history. new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), \ @@ -134,12 +134,12 @@ # datasets_attrs_file_name = os.path.join( archive_dir, 'datasets_attrs.txt') datasets_attr_str = read_file_contents( datasets_attrs_file_name ) - datasets_attrs = from_json_string( datasets_attr_str ) - + datasets_attrs = loads( datasets_attr_str ) + if os.path.exists( datasets_attrs_file_name + ".provenance" ): provenance_attr_str = read_file_contents( datasets_attrs_file_name + ".provenance" ) - provenance_attrs = from_json_string( provenance_attr_str ) - datasets_attrs += provenance_attrs + provenance_attrs = loads( provenance_attr_str ) + datasets_attrs += provenance_attrs # Get counts of how often each dataset file is used; a file can # be linked to multiple dataset objects (HDAs). @@ -230,7 +230,7 @@ return self.sa_session.query( model.HistoryDatasetAssociation ) \ .filter_by( history=new_history, hid=obj_dct['hid'] ).first() return obj_dct - jobs_attrs = from_json_string( jobs_attr_str, object_hook=as_hda ) + jobs_attrs = loads( jobs_attr_str, object_hook=as_hda ) # Create each job. for job_attrs in jobs_attrs: @@ -279,7 +279,7 @@ .filter_by( history=new_history, hid=value.hid ).first() value = input_hda.id #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) - imported_job.add_parameter( name, to_json_string( value, cls=HistoryDatasetAssociationIDEncoder ) ) + imported_job.add_parameter( name, dumps( value, cls=HistoryDatasetAssociationIDEncoder ) ) # TODO: Connect jobs to input datasets. @@ -292,14 +292,14 @@ imported_job.add_output_dataset( output_hda.name, output_hda ) # Connect jobs to input datasets. - if 'input_mapping' in job_attrs: + if 'input_mapping' in job_attrs: for input_name, input_hid in job_attrs[ 'input_mapping' ].items(): #print "%s job has input dataset %i" % (imported_job.id, input_hid) input_hda = self.sa_session.query( model.HistoryDatasetAssociation ) \ .filter_by( history=new_history, hid=input_hid ).first() if input_hda: imported_job.add_input_dataset( input_name, input_hda ) - + self.sa_session.flush() @@ -409,7 +409,7 @@ } history_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name history_attrs_out = open( history_attrs_filename, 'w' ) - history_attrs_out.write( to_json_string( history_attrs ) ) + history_attrs_out.write( dumps( history_attrs ) ) history_attrs_out.close() jeha.history_attrs_filename = history_attrs_filename @@ -427,12 +427,12 @@ included_datasets.append( dataset ) datasets_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name datasets_attrs_out = open( datasets_attrs_filename, 'w' ) - datasets_attrs_out.write( to_json_string( datasets_attrs, cls=HistoryDatasetAssociationEncoder ) ) + datasets_attrs_out.write( dumps( datasets_attrs, cls=HistoryDatasetAssociationEncoder ) ) datasets_attrs_out.close() jeha.datasets_attrs_filename = datasets_attrs_filename - + provenance_attrs_out = open( datasets_attrs_filename + ".provenance", 'w' ) - provenance_attrs_out.write( to_json_string( provenance_attrs, cls=HistoryDatasetAssociationEncoder ) ) + provenance_attrs_out.write( dumps( provenance_attrs, cls=HistoryDatasetAssociationEncoder ) ) provenance_attrs_out.close() # @@ -477,7 +477,7 @@ job_attrs[ 'exit_code' ] = job.exit_code job_attrs[ 'create_time' ] = job.create_time.isoformat() job_attrs[ 'update_time' ] = job.update_time.isoformat() - + # Get the job's parameters try: @@ -509,7 +509,7 @@ jobs_attrs_filename = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name jobs_attrs_out = open( jobs_attrs_filename, 'w' ) - jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) + jobs_attrs_out.write( dumps( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) jobs_attrs_out.close() jeha.jobs_attrs_filename = jobs_attrs_filename diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/tools/imp_exp/export_history.py --- a/lib/galaxy/tools/imp_exp/export_history.py +++ b/lib/galaxy/tools/imp_exp/export_history.py @@ -39,7 +39,7 @@ except OverflowError: pass datasets_attr_in.close() - datasets_attrs = from_json_string( datasets_attr_str ) + datasets_attrs = loads( datasets_attr_str ) # Add datasets to archive and update dataset attributes. # TODO: security check to ensure that files added are in Galaxy dataset directory? @@ -54,7 +54,7 @@ # Rewrite dataset attributes file. datasets_attrs_out = open( datasets_attrs_file, 'w' ) - datasets_attrs_out.write( to_json_string( datasets_attrs ) ) + datasets_attrs_out.write( dumps( datasets_attrs ) ) datasets_attrs_out.close() # Finish archive. @@ -80,4 +80,4 @@ # Create archive. status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip ) - print status \ No newline at end of file + print status diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -85,7 +85,7 @@ for key, value in param_values.iteritems(): if key in params: value = params[ key ].value_to_basic( value, app ) - rval[ key ] = str( to_json_string( value ) ) + rval[ key ] = str( dumps( value ) ) return rval @@ -98,7 +98,7 @@ """ rval = dict() for key, value in param_values.iteritems(): - value = json_fix( from_json_string( value ) ) + value = json_fix( loads( value ) ) if key in params: value = params[key].value_from_basic( value, app, ignore_errors ) rval[ key ] = value diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/tools/util/__init__.py --- a/lib/galaxy/tools/util/__init__.py +++ b/lib/galaxy/tools/util/__init__.py @@ -3,4 +3,4 @@ FIXME: These are used by tool scripts, not the framework, and should not live in this package. -""" \ No newline at end of file +""" diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -338,8 +338,8 @@ def pretty_print_json(json_data, is_json_string=False): if is_json_string: - json_data = json.from_json_string(json_data) - return json.to_json_string(json_data, sort_keys=True, indent=4) + json_data = json.loads(json_data) + return json.dumps(json_data, sort_keys=True, indent=4) # characters that are valid valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!") diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/util/backports/__init__.py --- a/lib/galaxy/util/backports/__init__.py +++ b/lib/galaxy/util/backports/__init__.py @@ -1,3 +1,3 @@ """ Modules for providing backward compatibility with future versions of Python -""" \ No newline at end of file +""" diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 lib/galaxy/util/backports/importlib/__init__.py --- a/lib/galaxy/util/backports/importlib/__init__.py +++ b/lib/galaxy/util/backports/importlib/__init__.py @@ -39,4 +39,4 @@ ## Note: this was copied from ## http://svn.python.org/projects/python/trunk/Lib/importlib/__init__.py - ## on 24 September 2012 \ No newline at end of file + ## on 24 September 2012 This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/983a1cc80be6/ Changeset: 983a1cc80be6 User: dannon Date: 2014-09-08 23:03:22 Summary: Web helpers (${h.*}) in mako used to_json_string, now dumps. Affected #: 45 files diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/admin/external_service/reload_external_service_types.mako --- a/templates/admin/external_service/reload_external_service_types.mako +++ b/templates/admin/external_service/reload_external_service_types.mako @@ -19,4 +19,4 @@ <input type="submit" name="reload_external_service_type_button" value="Reload"/></div></div> -</form> \ No newline at end of file +</form> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/admin/requests/grid.mako --- a/templates/admin/requests/grid.mako +++ b/templates/admin/requests/grid.mako @@ -1,1 +1,1 @@ -<%inherit file="/grid_base.mako"/> \ No newline at end of file +<%inherit file="/grid_base.mako"/> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/admin/requests/view_sample_dataset.mako --- a/templates/admin/requests/view_sample_dataset.mako +++ b/templates/admin/requests/view_sample_dataset.mako @@ -76,4 +76,4 @@ <div style="clear: both"></div> %endif </div> -</div> \ No newline at end of file +</div> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/galaxy_client_app.mako --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -15,7 +15,7 @@ //TODO: global... %for key in kwargs: ( window.bootstrapped = window.bootstrapped || {} )[ '${key}' ] = ( - ${ h.to_json_string( kwargs[ key ], indent=( 2 if trans.debug else 0 ) )} ); + ${ h.dumps( kwargs[ key ], indent=( 2 if trans.debug else 0 ) )} ); %endfor define( 'bootstrapped-data', function(){ return window.bootstrapped; @@ -61,7 +61,7 @@ <%def name="get_config_json()"> ## Conv. fn to write as JSON -${ h.to_json_string( get_config_dict() )} +${ h.dumps( get_config_dict() )} </%def> @@ -106,5 +106,5 @@ <%def name="get_user_json()"> ## Conv. fn to write as JSON -${ h.to_json_string( get_user_dict() )} +${ h.dumps( get_user_dict() )} </%def> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -73,7 +73,7 @@ // load grid viewer require(['mvc/grid/grid-view'], function(GridView) { $(function() { - gridView = new GridView( ${ h.to_json_string( self.get_grid_config( embedded=embedded, insert=insert ) ) } ); + gridView = new GridView( ${ h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) } ); }); }); </script> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/grid_base_async.mako --- a/templates/grid_base_async.mako +++ b/templates/grid_base_async.mako @@ -1,4 +1,4 @@ <%namespace name="grid_base" file="./grid_base.mako" import="*" /> ${init()} -${h.to_json_string( grid_base.get_grid_config() )} +${h.dumps( grid_base.get_grid_config() )} diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/rss.mako --- a/templates/rss.mako +++ b/templates/rss.mako @@ -20,4 +20,4 @@ </item> %endfor </channel> -</rss> \ No newline at end of file +</rss> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/tagging_common.mako --- a/templates/tagging_common.mako +++ b/templates/tagging_common.mako @@ -198,7 +198,7 @@ %> var options = { - tags : ${h.to_json_string(tag_names_and_values)}, + tags : ${h.dumps(tag_names_and_values)}, editable : ${iff( editable, 'true', 'false' )}, get_toggle_link_text_fn: ${get_toggle_link_text_fn}, tag_click_fn: ${tag_click_fn}, diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/user/dbkeys.mako --- a/templates/user/dbkeys.mako +++ b/templates/user/dbkeys.mako @@ -246,4 +246,4 @@ (Len Entry option).</p></div></div> -</%def> \ No newline at end of file +</%def> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/user/new_address.mako --- a/templates/user/new_address.mako +++ b/templates/user/new_address.mako @@ -94,4 +94,4 @@ </div></form></div> -</div> \ No newline at end of file +</div> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/demo_sequencer/empty.mako --- a/templates/webapps/demo_sequencer/empty.mako +++ b/templates/webapps/demo_sequencer/empty.mako @@ -1,4 +1,4 @@ <html><body></body> -</html> \ No newline at end of file +</html> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/dataset/display.mako --- a/templates/webapps/galaxy/dataset/display.mako +++ b/templates/webapps/galaxy/dataset/display.mako @@ -26,7 +26,7 @@ data.createTabularDatasetChunkedView({ // TODO: encode id. dataset_config: - _.extend( ${h.to_json_string( item.to_dict() )}, + _.extend( ${h.dumps( item.to_dict() )}, { chunk_url: "${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( item.id ))}", diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/dataset/grid.mako --- a/templates/webapps/galaxy/dataset/grid.mako +++ b/templates/webapps/galaxy/dataset/grid.mako @@ -1,1 +1,1 @@ -<%inherit file="/grid_base.mako"/> \ No newline at end of file +<%inherit file="/grid_base.mako"/> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/dataset/item_content.mako --- a/templates/webapps/galaxy/dataset/item_content.mako +++ b/templates/webapps/galaxy/dataset/item_content.mako @@ -1,3 +1,3 @@ <%namespace file="/dataset/display.mako" import="*" /> -${render_item( item, item_data )} \ No newline at end of file +${render_item( item, item_data )} diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -17,7 +17,7 @@ require(['mvc/data'], function(data) { data.createTabularDatasetChunkedView({ - dataset_config: _.extend( ${h.to_json_string( trans.security.encode_dict_ids( dataset.to_dict() ) )}, + dataset_config: _.extend( ${h.dumps( trans.security.encode_dict_ids( dataset.to_dict() ) )}, { first_data_chunk: ${chunk} } diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -87,7 +87,7 @@ ], function( mod_masthead, mod_menu, mod_modal, mod_frame, GalaxyUpload, user, quotameter ){ if( !Galaxy.currUser ){ // this doesn't need to wait for the page being readied - Galaxy.currUser = new user.User(${ h.to_json_string( get_user_json(), indent=2 ) }); + Galaxy.currUser = new user.User(${ h.dumps( get_user_json(), indent=2 ) }); } $(function() { @@ -97,7 +97,7 @@ } // get configuration - var masthead_config = ${ h.to_json_string( masthead_config ) }; + var masthead_config = ${ h.dumps( masthead_config ) }; // load global galaxy objects Galaxy.masthead = new mod_masthead.GalaxyMasthead(masthead_config); diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -100,7 +100,7 @@ "libs/backbone/backbone": { exports: "Backbone" }, } }); - var galaxy_config = ${ h.to_json_string( self.galaxy_config ) }; + var galaxy_config = ${ h.dumps( self.galaxy_config ) }; </script></%def> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/history/citations.mako --- a/templates/webapps/galaxy/history/citations.mako +++ b/templates/webapps/galaxy/history/citations.mako @@ -32,4 +32,4 @@ </script></%def><div id="citations"> -</div> \ No newline at end of file +</div> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/history/display.mako --- a/templates/webapps/galaxy/history/display.mako +++ b/templates/webapps/galaxy/history/display.mako @@ -46,8 +46,8 @@ </div><script type="text/javascript"> var debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, - historyJSON = ${h.to_json_string( history_dict )}, - hdaJSON = ${h.to_json_string( hda_dicts )}; + historyJSON = ${h.dumps( history_dict )}, + hdaJSON = ${h.dumps( hda_dicts )}; //window.historyJSON = historyJSON; //window.hdaJSON = hdaJSON; diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/history/display_structured.mako --- a/templates/webapps/galaxy/history/display_structured.mako +++ b/templates/webapps/galaxy/history/display_structured.mako @@ -144,7 +144,7 @@ <script type="text/javascript"> define( 'display-structured', function(){ require([ 'mvc/history/hda-li-edit', 'mvc/history/hda-model' ], function( hdaEdit, hdaModel ){ - var hdaJSON = ${ h.to_json_string( hda_dicts, indent=( 2 if trans.debug else 0 ) ) }; + var hdaJSON = ${ h.dumps( hda_dicts, indent=( 2 if trans.debug else 0 ) ) }; window.hdas = hdaJSON.map( function( hda ){ return new hdaEdit.HDAListItemEdit({ diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -67,8 +67,8 @@ panel = new panelMod.AnnotatedHistoryPanel({ el : $embeddedHistory.find( ".history-panel" ), model : new historyModel.History( - ${h.to_json_string( history_dict )}, - ${h.to_json_string( hda_dicts )}, + ${h.dumps( history_dict )}, + ${h.dumps( hda_dicts )}, { logger: ( debugging )?( console ):( null ) } ) }).render(); diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/history/grid.mako --- a/templates/webapps/galaxy/history/grid.mako +++ b/templates/webapps/galaxy/history/grid.mako @@ -1,1 +1,1 @@ -<%inherit file="../grid_base.mako"/> \ No newline at end of file +<%inherit file="../grid_base.mako"/> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/history/item_content.mako --- a/templates/webapps/galaxy/history/item_content.mako +++ b/templates/webapps/galaxy/history/item_content.mako @@ -1,3 +1,3 @@ <%namespace file="/history/display.mako" import="*" /> -${render_item( item, item_data )} \ No newline at end of file +${render_item( item, item_data )} diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -83,8 +83,8 @@ show_hidden = context.get( 'show_hidden', None ) user_is_owner_json = 'true' if user_is_owner else 'false' - show_deleted_json = h.to_json_string( show_deleted ) - show_hidden_json = h.to_json_string( show_hidden ) + show_deleted_json = h.dumps( show_deleted ) + show_hidden_json = h.dumps( show_hidden ) %><div id="header" class="clear"> @@ -164,8 +164,8 @@ } var userIsOwner = ${'true' if user_is_owner else 'false'}, - historyJSON = ${h.to_json_string( history )}, - hdaJSON = ${h.to_json_string( hdas )}; + historyJSON = ${h.dumps( history )}, + hdaJSON = ${h.dumps( hdas )}; panelToUse = ( userIsOwner )? //TODO: change class names ({ location: 'mvc/history/history-panel-edit', className: 'HistoryPanel' }): diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/library/index.mako --- a/templates/webapps/galaxy/library/index.mako +++ b/templates/webapps/galaxy/library/index.mako @@ -12,4 +12,4 @@ <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="library", action="browse_libraries", default_action=default_action )}"></iframe> -</%def> \ No newline at end of file +</%def> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/page/create.mako --- a/templates/webapps/galaxy/page/create.mako +++ b/templates/webapps/galaxy/page/create.mako @@ -11,4 +11,4 @@ }); }) </script> -</%def> \ No newline at end of file +</%def> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/page/select_items_grid.mako --- a/templates/webapps/galaxy/page/select_items_grid.mako +++ b/templates/webapps/galaxy/page/select_items_grid.mako @@ -1,3 +1,3 @@ ## Template generates a grid that enables user to select items. <%namespace file="../grid_base.mako" import="*" /> -${load(True)} \ No newline at end of file +${load(True)} diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako --- a/templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako +++ b/templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako @@ -2,4 +2,4 @@ ${sample_dataset.status} </%def> -${render_sample_dataset_transfer_status( sample_dataset )} \ No newline at end of file +${render_sample_dataset_transfer_status( sample_dataset )} diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/requests/grid.mako --- a/templates/webapps/galaxy/requests/grid.mako +++ b/templates/webapps/galaxy/requests/grid.mako @@ -1,1 +1,1 @@ -<%inherit file="/grid_base.mako"/> \ No newline at end of file +<%inherit file="/grid_base.mako"/> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/root/redirect.mako --- a/templates/webapps/galaxy/root/redirect.mako +++ b/templates/webapps/galaxy/root/redirect.mako @@ -2,4 +2,4 @@ <script type="text/javascript"> top.location.href = '${redirect_url}'; -</script> \ No newline at end of file +</script> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -25,12 +25,12 @@ hidden: false }), tools = new tools_mod.ToolCollection( - ${ h.to_json_string( trans.app.toolbox.to_dict( trans, in_panel=False ) ) } + ${ h.dumps( trans.app.toolbox.to_dict( trans, in_panel=False ) ) } ), tool_panel = new tools_mod.ToolPanel({ tool_search: tool_search, tools: tools, - layout: ${h.to_json_string( trans.app.toolbox.to_dict( trans ) )} + layout: ${h.dumps( trans.app.toolbox.to_dict( trans ) )} }), tool_panel_view = new tools_mod.ToolPanelView({ model: tool_panel }); diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/tool_form.api.mako --- a/templates/webapps/galaxy/tool_form.api.mako +++ b/templates/webapps/galaxy/tool_form.api.mako @@ -36,7 +36,7 @@ <script> require(['mvc/tools/tools-form'], function(ToolsForm){ $(function(){ - var form = new ToolsForm.View(${ h.to_json_string(self.form_config) }); + var form = new ToolsForm.View(${ h.dumps(self.form_config) }); }); }); </script> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/tracks/add_tracks.mako --- a/templates/webapps/galaxy/tracks/add_tracks.mako +++ b/templates/webapps/galaxy/tracks/add_tracks.mako @@ -1,3 +1,3 @@ ## Template generates a grid that enables user to add tracks <%namespace file="../grid_base.mako" import="*" /> -${load(True)} \ No newline at end of file +${load(True)} diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/tracks/history_datasets_select_grid.mako --- a/templates/webapps/galaxy/tracks/history_datasets_select_grid.mako +++ b/templates/webapps/galaxy/tracks/history_datasets_select_grid.mako @@ -2,4 +2,4 @@ <%def name="title()"><h2>History '${grid.get_current_item( trans, **kwargs ).name}'</h2> -</%def> \ No newline at end of file +</%def> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/tracks/library_datasets_select_grid.mako --- a/templates/webapps/galaxy/tracks/library_datasets_select_grid.mako +++ b/templates/webapps/galaxy/tracks/library_datasets_select_grid.mako @@ -10,4 +10,4 @@ ${render_content(simple=True)} <script type="text/javascript"> make_popup_menus(); -</script> \ No newline at end of file +</script> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/visualization/create.mako --- a/templates/webapps/galaxy/visualization/create.mako +++ b/templates/webapps/galaxy/visualization/create.mako @@ -11,4 +11,4 @@ }); }) </script> -</%def> \ No newline at end of file +</%def> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/visualization/display.mako --- a/templates/webapps/galaxy/visualization/display.mako +++ b/templates/webapps/galaxy/visualization/display.mako @@ -89,9 +89,9 @@ vis_id: "${config.get('vis_id')}", dbkey: "${config.get('dbkey')}" }, - ${ h.to_json_string( config.get( 'viewport', dict() ) ) }, - ${ h.to_json_string( config['tracks'] ) }, - ${ h.to_json_string( config.get('bookmarks') ) } + ${ h.dumps( config.get( 'viewport', dict() ) ) }, + ${ h.dumps( config['tracks'] ) }, + ${ h.dumps( config.get('bookmarks') ) } ); // Set up keyboard navigation. @@ -105,4 +105,4 @@ }); </script> -</%def> \ No newline at end of file +</%def> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/visualization/item_content.mako --- a/templates/webapps/galaxy/visualization/item_content.mako +++ b/templates/webapps/galaxy/visualization/item_content.mako @@ -1,3 +1,3 @@ <%namespace file="/visualization/display.mako" import="*" /> -${render_item( item, item_data )} \ No newline at end of file +${render_item( item, item_data )} diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/visualization/phyloviz.mako --- a/templates/webapps/galaxy/visualization/phyloviz.mako +++ b/templates/webapps/galaxy/visualization/phyloviz.mako @@ -168,8 +168,8 @@ }; $(function firstVizLoad(){ // calls when viz is loaded for the first time - var config = ${ h.to_json_string( config )}; - var data = ${h.to_json_string(data['data'])}; + var config = ${ h.dumps( config )}; + var data = ${h.dumps(data['data'])}; initPhyloViz(data, config); }); }); diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/visualization/sweepster.mako --- a/templates/webapps/galaxy/visualization/sweepster.mako +++ b/templates/webapps/galaxy/visualization/sweepster.mako @@ -125,7 +125,7 @@ $(function() { // -- Viz set up. -- var viz = new sweepster.SweepsterVisualization( - ${ h.to_json_string( config )} + ${ h.dumps( config )} ); var viz_view = new sweepster.SweepsterVisualizationView({ model: viz }); viz_view.render(); @@ -145,4 +145,4 @@ <div class="unified-panel-header-inner"></div></div> -</%def> \ No newline at end of file +</%def> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/workflow/configure_menu.mako --- a/templates/webapps/galaxy/workflow/configure_menu.mako +++ b/templates/webapps/galaxy/workflow/configure_menu.mako @@ -95,4 +95,4 @@ </form></div></div> -</%def> \ No newline at end of file +</%def> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/workflow/item_content.mako --- a/templates/webapps/galaxy/workflow/item_content.mako +++ b/templates/webapps/galaxy/workflow/item_content.mako @@ -1,3 +1,3 @@ <%namespace file="/workflow/display.mako" import="*" /> -${render_item( item, item_data )} \ No newline at end of file +${render_item( item, item_data )} diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/galaxy/workflow/myexp_export_content.mako --- a/templates/webapps/galaxy/workflow/myexp_export_content.mako +++ b/templates/webapps/galaxy/workflow/myexp_export_content.mako @@ -45,4 +45,4 @@ </connection> %endfor %endfor -</connections> \ No newline at end of file +</connections> diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/tool_shed/category/valid_grid.mako --- a/templates/webapps/tool_shed/category/valid_grid.mako +++ b/templates/webapps/tool_shed/category/valid_grid.mako @@ -10,4 +10,4 @@ %></%def> -${grid_base.load(False, capture(self.insert))} \ No newline at end of file +${grid_base.load(False, capture(self.insert))} diff -r ce088c6f1fd47ba4628cf6cbf0c84dd7ac010086 -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 templates/webapps/tool_shed/common/grid_common.mako --- a/templates/webapps/tool_shed/common/grid_common.mako +++ b/templates/webapps/tool_shed/common/grid_common.mako @@ -24,7 +24,7 @@ %if value != "All": <% if isinstance( temp_column, TextColumn ): - value = h.to_json_string( value ) + value = h.dumps( value ) %><input type="hidden" id="${temp_column.key}" name="f-${temp_column.key}" value='${value}'/> %endif @@ -51,7 +51,7 @@ <% new_filter = list( column_filter ) del new_filter[ i ] - new_column_filter = GridColumnFilter( "", { column.key : h.to_json_string( new_filter ) } ) + new_column_filter = GridColumnFilter( "", { column.key : h.dumps( new_filter ) } ) %><a href="${url(new_column_filter.get_url_args())}"><span class="delete-search-icon" /></a></span> https://bitbucket.org/galaxy/galaxy-central/commits/25396cf39fef/ Changeset: 25396cf39fef User: dannon Date: 2014-09-08 23:11:18 Summary: Charts to_json_string/dumps swap. Affected #: 3 files diff -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -86,8 +86,8 @@ require(['plugin/app'], function(App) { // load options var options = { - id : ${h.to_json_string( visualization_id )} || undefined, - config : ${h.to_json_string( config )} + id : ${h.dumps( visualization_id )} || undefined, + config : ${h.dumps( config )} } // create application diff -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 config/plugins/visualizations/common/templates/config_utils.mako --- a/config/plugins/visualizations/common/templates/config_utils.mako +++ b/config/plugins/visualizations/common/templates/config_utils.mako @@ -36,7 +36,7 @@ 'action' : 'saved', 'type' : visualization_name, 'title' : title, - 'config' : h.to_json_string( config ) + 'config' : h.dumps( config ) } # save to existing visualization if visualization_id: diff -r 983a1cc80be61c3ccdd3c10d06737381aacb9b05 -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 config/plugins/visualizations/scatterplot/templates/scatterplot.mako --- a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako +++ b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako @@ -50,11 +50,11 @@ <script type="text/javascript"> $(function(){ var model = new ScatterplotModel({ - id : ${h.to_json_string( visualization_id )} || undefined, + id : ${h.dumps( visualization_id )} || undefined, title : "${title}", - config : ${h.to_json_string( config, indent=2 )} + config : ${h.dumps( config, indent=2 )} }); - hdaJson = ${h.to_json_string( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )}, + hdaJson = ${h.dumps( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )}, display = new ScatterplotDisplay({ el : $( '.scatterplot-display' ).attr( 'id', 'scatterplot-display-' + '${visualization_id}' ), model : model, @@ -78,11 +78,11 @@ <script type="text/javascript"> $(function(){ var model = new ScatterplotModel({ - id : ${h.to_json_string( visualization_id )} || undefined, + id : ${h.dumps( visualization_id )} || undefined, title : "${title or default_title}", - config : ${h.to_json_string( config, indent=2 )} + config : ${h.dumps( config, indent=2 )} }), - hdaJson = ${h.to_json_string( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )}, + hdaJson = ${h.dumps( trans.security.encode_dict_ids( hda.to_dict() ), indent=2 )}, editor = new ScatterplotConfigEditor({ el : $( '.scatterplot-editor' ).attr( 'id', 'scatterplot-editor-hda-' + hdaJson.id ), model : model, https://bitbucket.org/galaxy/galaxy-central/commits/23f0f1e9477f/ Changeset: 23f0f1e9477f User: dannon Date: 2014-09-09 16:04:28 Summary: Switch to_json_string/from_json_string in galaxy/scripts. Affected #: 11 files diff -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 scripts/cleanup_datasets/populate_uuid.py --- a/scripts/cleanup_datasets/populate_uuid.py +++ b/scripts/cleanup_datasets/populate_uuid.py @@ -42,4 +42,4 @@ if __name__ == "__main__": - main() \ No newline at end of file + main() diff -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py --- a/scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py +++ b/scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py @@ -28,4 +28,4 @@ print >> out, "# Removed " + str( removed_files ) + " files" if __name__ == "__main__": - main() \ No newline at end of file + main() diff -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 scripts/cleanup_datasets/rename_purged_datasets.py --- a/scripts/cleanup_datasets/rename_purged_datasets.py +++ b/scripts/cleanup_datasets/rename_purged_datasets.py @@ -29,4 +29,4 @@ print >> out, "# Renamed " + str( renamed_files ) + " files" if __name__ == "__main__": - main() \ No newline at end of file + main() diff -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 scripts/cleanup_datasets/update_dataset_size.py --- a/scripts/cleanup_datasets/update_dataset_size.py +++ b/scripts/cleanup_datasets/update_dataset_size.py @@ -31,4 +31,4 @@ sys.exit(0) if __name__ == "__main__": - main() \ No newline at end of file + main() diff -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 scripts/cleanup_datasets/update_metadata.py --- a/scripts/cleanup_datasets/update_metadata.py +++ b/scripts/cleanup_datasets/update_metadata.py @@ -73,4 +73,4 @@ sys.exit(0) if __name__ == "__main__": - main() \ No newline at end of file + main() diff -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -48,7 +48,7 @@ from galaxy import tools from galaxy.util import bunch from galaxy import util -from galaxy.util.json import to_json_string +from galaxy.util.json import dumps from functional import database_contexts from base.api_util import get_master_api_key @@ -520,7 +520,7 @@ has_test_data, shed_tools_dict = parse_tool_panel_config( shed_tool_config, shed_tools_dict ) # Persist the shed_tools_dict to the galaxy_tool_shed_test_file. shed_tools_file = open( galaxy_tool_shed_test_file, 'w' ) - shed_tools_file.write( to_json_string( shed_tools_dict ) ) + shed_tools_file.write( dumps( shed_tools_dict ) ) shed_tools_file.close() if not os.path.isabs( galaxy_tool_shed_test_file ): galaxy_tool_shed_test_file = os.path.join( os.getcwd(), galaxy_tool_shed_test_file ) diff -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 scripts/galaxy_messaging/client/scanner_interface.py --- a/scripts/galaxy_messaging/client/scanner_interface.py +++ b/scripts/galaxy_messaging/client/scanner_interface.py @@ -73,4 +73,4 @@ return - \ No newline at end of file + diff -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 scripts/galaxy_messaging/server/setup_rabbitmq.py --- a/scripts/galaxy_messaging/server/setup_rabbitmq.py +++ b/scripts/galaxy_messaging/server/setup_rabbitmq.py @@ -35,4 +35,4 @@ sys.exit(1) if __name__ == '__main__': - main( sys.argv[1] ) \ No newline at end of file + main( sys.argv[1] ) diff -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 scripts/galaxy_messaging/server/xml_helper.py --- a/scripts/galaxy_messaging/server/xml_helper.py +++ b/scripts/galaxy_messaging/server/xml_helper.py @@ -25,4 +25,4 @@ for node in nodelist: if node.nodeType == node.TEXT_NODE: rc = rc + node.data - return rc \ No newline at end of file + return rc diff -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 scripts/metagenomics/convert_title.py --- a/scripts/metagenomics/convert_title.py +++ b/scripts/metagenomics/convert_title.py @@ -36,4 +36,4 @@ print "\n".join(seq) print >> sys.stderr, "Unable to find gi number for %d sequences, the title is replaced as giunknown" %(invalid_lines) - \ No newline at end of file + diff -r 25396cf39fef9f77fbb802ed8ad5b8c2affb6cd6 -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 scripts/transfer.py --- a/scripts/transfer.py +++ b/scripts/transfer.py @@ -122,7 +122,7 @@ response = {} valid, request, response = json.validate_jsonrpc_request( request, ( 'get_state', ), () ) if valid: - self.request.send( json.to_json_string( json.jsonrpc_response( request=request, result=self.server.state_result.result ) ) ) + self.request.send( json.dumps( json.jsonrpc_response( request=request, result=self.server.state_result.result ) ) ) else: error_msg = 'Unable to serve request: %s' % response['error']['message'] if 'data' in response['error']: https://bitbucket.org/galaxy/galaxy-central/commits/a3450635b1d6/ Changeset: a3450635b1d6 User: dannon Date: 2014-09-09 16:06:35 Summary: Switch to_json_string/from_json_string in galaxy/tools. Affected #: 3 files diff -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 tools/data_source/data_source.py --- a/tools/data_source/data_source.py +++ b/tools/data_source/data_source.py @@ -3,7 +3,7 @@ # Data source application parameters are temporarily stored in the dataset file. import socket, urllib, sys, os from galaxy import eggs #eggs needs to be imported so that galaxy.util can find docutils egg... -from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.json import loads, dumps from galaxy.util import get_charset_from_http_headers import galaxy.model # need to import model before sniff to resolve a circular import dependency from galaxy.datatypes import sniff @@ -23,7 +23,7 @@ def load_input_parameters( filename, erase_file = True ): datasource_params = {} try: - json_params = from_json_string( open( filename, 'r' ).read() ) + json_params = loads( open( filename, 'r' ).read() ) datasource_params = json_params.get( 'param_dict' ) except: json_params = None @@ -44,7 +44,7 @@ max_file_size = int( sys.argv[2] ) except: max_file_size = 0 - + job_params, params = load_input_parameters( filename ) if job_params is None: #using an older tabular file enhanced_handling = False @@ -57,13 +57,13 @@ else: enhanced_handling = True json_file = open( job_params[ 'job_config' ][ 'TOOL_PROVIDED_JOB_METADATA_FILE' ], 'w' ) #specially named file for output junk to pass onto set metadata - + datatypes_registry = Registry() datatypes_registry.load_datatypes( root_dir = job_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = job_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] ) - + URL = params.get( 'URL', None ) #using exactly URL indicates that only one dataset is being downloaded URL_method = params.get( 'URL_method', None ) - + # The Python support for fetching resources from the web is layered. urllib uses the httplib # library, which in turn uses the socket library. As of Python 2.3 you can specify how long # a socket should wait for a response before timing out. By default the socket module has no @@ -71,14 +71,14 @@ # levels. However, you can set the default timeout ( in seconds ) globally for all sockets by # doing the following. socket.setdefaulttimeout( 600 ) - + for data_dict in job_params[ 'output_data' ]: cur_filename = data_dict.get( 'file_name', filename ) cur_URL = params.get( '%s|%s|URL' % ( GALAXY_PARAM_PREFIX, data_dict[ 'out_data_name' ] ), URL ) if not cur_URL: open( cur_filename, 'w' ).write( "" ) stop_err( 'The remote data source application has not sent back a URL parameter in the request.' ) - + # The following calls to urllib.urlopen() will use the above default timeout try: if not URL_method or URL_method == 'get': @@ -96,7 +96,7 @@ cur_filename, is_multi_byte = sniff.stream_to_open_named_file( page, os.open( cur_filename, os.O_WRONLY | os.O_CREAT ), cur_filename, source_encoding=get_charset_from_http_headers( page.headers ) ) except Exception, e: stop_err( 'Unable to fetch %s:\n%s' % ( cur_URL, e ) ) - + #here import checks that upload tool performs if enhanced_handling: try: @@ -106,7 +106,7 @@ info = dict( type = 'dataset', dataset_id = data_dict[ 'dataset_id' ], ext = ext) - - json_file.write( "%s\n" % to_json_string( info ) ) - + + json_file.write( "%s\n" % dumps( info ) ) + if __name__ == "__main__": __main__() diff -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -36,7 +36,7 @@ sys.stderr.write( msg ) sys.exit( ret ) def file_err( msg, dataset, json_file ): - json_file.write( to_json_string( dict( type = 'dataset', + json_file.write( dumps( dict( type = 'dataset', ext = 'data', dataset_id = dataset.dataset_id, stderr = msg ) ) + "\n" ) @@ -319,7 +319,7 @@ line_count = line_count ) if dataset.get('uuid', None) is not None: info['uuid'] = dataset.get('uuid') - json_file.write( to_json_string( info ) + "\n" ) + json_file.write( dumps( info ) + "\n" ) if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): # Groom the dataset content if necessary @@ -358,7 +358,7 @@ info = dict( type = 'dataset', dataset_id = dataset.dataset_id, stdout = 'uploaded %s file' % dataset.file_type ) - json_file.write( to_json_string( info ) + "\n" ) + json_file.write( dumps( info ) + "\n" ) def output_adjacent_tmpdir( output_path ): @@ -382,7 +382,7 @@ registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] ) for line in open( sys.argv[3], 'r' ): - dataset = from_json_string( line ) + dataset = loads( line ) dataset = util.bunch.Bunch( **safe_dict( dataset ) ) try: output_path = output_paths[int( dataset.dataset_id )][0] diff -r 23f0f1e9477f6c14abbe9f08a4b9d12f5c122631 -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 tools/filters/gff/gff_filter_by_attribute.py --- a/tools/filters/gff/gff_filter_by_attribute.py +++ b/tools/filters/gff/gff_filter_by_attribute.py @@ -1,13 +1,13 @@ #!/usr/bin/env python # This tool takes a gff file as input and creates filters on attributes based on certain properties. # The tool will skip over invalid lines within the file, informing the user about the number of lines skipped. -# TODO: much of this code is copied from the Filter1 tool (filtering.py in tools/stats/). The commonalities should be +# TODO: much of this code is copied from the Filter1 tool (filtering.py in tools/stats/). The commonalities should be # abstracted and leveraged in each filtering tool. from __future__ import division import sys from galaxy import eggs -from galaxy.util.json import to_json_string, from_json_string +from galaxy.util.json import dumps, loads # Older py compatibility try: @@ -44,7 +44,7 @@ except: if operand in secured: stop_err( "Illegal value '%s' in %s '%s'" % ( operand, description, text ) ) - + # # Process inputs. # @@ -52,13 +52,13 @@ in_fname = sys.argv[1] out_fname = sys.argv[2] cond_text = sys.argv[3] -attribute_types = from_json_string( sys.argv[4] ) +attribute_types = loads( sys.argv[4] ) # Convert types from str to type objects. for name, a_type in attribute_types.items(): check_for_executable(a_type) attribute_types[ name ] = eval( a_type ) - + # Unescape if input has been escaped mapped_str = { '__lt__': '<', @@ -72,23 +72,23 @@ } for key, value in mapped_str.items(): cond_text = cond_text.replace( key, value ) - + # Attempt to determine if the condition includes executable stuff and, if so, exit. check_for_executable( cond_text, 'condition') -# Prepare the column variable names and wrappers for column data types. Only +# Prepare the column variable names and wrappers for column data types. Only # prepare columns up to largest column in condition. attrs, type_casts = [], [] for name, attr_type in attribute_types.items(): attrs.append( name ) type_cast = "get_value('%(name)s', attribute_types['%(name)s'], attribute_values)" % ( {'name': name} ) type_casts.append( type_cast ) - + attr_str = ', '.join( attrs ) # 'c1, c2, c3, c4' type_cast_str = ', '.join( type_casts ) # 'str(c1), int(c2), int(c3), str(c4)' wrap = "%s = %s" % ( attr_str, type_cast_str ) - -# Stats + +# Stats skipped_lines = 0 first_invalid_line = 0 invalid_line = None @@ -102,7 +102,7 @@ return (a_type)(values_dict[ name ]) else: return None - + # Read and filter input file, skipping invalid lines code = ''' for i, line in enumerate( file( in_fname ) ): https://bitbucket.org/galaxy/galaxy-central/commits/c2a961719f38/ Changeset: c2a961719f38 User: dannon Date: 2014-09-09 16:12:40 Summary: Final to_json_string/from_json_string elimination in tests. Affected #: 20 files diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -16,7 +16,7 @@ from base.asserts import verify_assertions from galaxy.util import asbool -from galaxy.util.json import from_json_string +from galaxy.util.json import loads from galaxy.web import security from galaxy.web.framework.helpers import iff from urlparse import urlparse @@ -56,7 +56,7 @@ f = open( self.tool_shed_test_file, 'r' ) text = f.read() f.close() - self.shed_tools_dict = from_json_string( text ) + self.shed_tools_dict = loads( text ) else: self.shed_tools_dict = {} self.keepOutdir = os.environ.get( 'GALAXY_TEST_SAVE', '' ) @@ -1293,12 +1293,12 @@ def get_running_datasets( self ): self.visit_url( '/api/histories' ) - history_id = from_json_string( self.last_page() )[0][ 'id' ] + history_id = loads( self.last_page() )[0][ 'id' ] self.visit_url( '/api/histories/%s/contents' % history_id ) - jsondata = from_json_string( self.last_page() ) + jsondata = loads( self.last_page() ) for history_item in jsondata: self.visit_url( history_item[ 'url' ] ) - item_json = from_json_string( self.last_page() ) + item_json = loads( self.last_page() ) if item_json[ 'state' ] in [ 'queued', 'running', 'paused' ]: return True return False @@ -1394,7 +1394,7 @@ def json_from_url( self, url, params={} ): self.visit_url( url, params ) - return from_json_string( self.last_page() ) + return loads( self.last_page() ) def last_page( self ): return tc.browser.get_html() @@ -2510,4 +2510,4 @@ self.visit_url( page_url ) data = self.last_page() return data - return fetcher \ No newline at end of file + return fetcher diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/casperjs/server_env.py --- a/test/casperjs/server_env.py +++ b/test/casperjs/server_env.py @@ -100,7 +100,7 @@ f = open( self.tool_shed_test_file, 'r' ) text = f.read() f.close() - shed_tools_dict = from_json_string( text ) + shed_tools_dict = loads( text ) except Exception, exc: log.error( 'Error reading tool shed test file "%s": %s', self.tool_shed_test_file, exc, exc_info=True ) diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/functional/test_ucsc_table_browser.py --- a/test/functional/test_ucsc_table_browser.py +++ b/test/functional/test_ucsc_table_browser.py @@ -32,4 +32,4 @@ ) self.run_ucsc_main( track_params, output_params ) self.wait() - self.verify_dataset_correctness( 'GRCm38mm10_chr5_34761740-34912521.fa' ) \ No newline at end of file + self.verify_dataset_correctness( 'GRCm38mm10_chr5_34761740-34912521.fa' ) diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/install_and_test_tool_shed_repositories/__init__.py --- a/test/install_and_test_tool_shed_repositories/__init__.py +++ b/test/install_and_test_tool_shed_repositories/__init__.py @@ -1,1 +1,1 @@ -"""Install and test tool shed repositories.""" \ No newline at end of file +"""Install and test tool shed repositories.""" diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/install_and_test_tool_shed_repositories/functional/__init__.py --- a/test/install_and_test_tool_shed_repositories/functional/__init__.py +++ b/test/install_and_test_tool_shed_repositories/functional/__init__.py @@ -1,1 +1,1 @@ -'''Tests''' \ No newline at end of file +'''Tests''' diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py @@ -1,1 +1,1 @@ -"""Install and test tool shed repositories that contain tools and tool test components.""" \ No newline at end of file +"""Install and test tool shed repositories that contain tools and tool test components.""" diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc 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 @@ -42,7 +42,7 @@ from base.tool_shed_util import parse_tool_panel_config from galaxy.app import UniverseApplication -from galaxy.util.json import from_json_string +from galaxy.util.json import loads from galaxy.util import asbool from galaxy.util import unicodify from galaxy.web import buildapp @@ -312,7 +312,7 @@ # 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_file, 'r' ).read() ) ) + loads( file( galaxy_shed_tools_dict_file, '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. install_and_test_base_util.populate_galaxy_shed_tools_dict_file( galaxy_shed_tools_dict_file, diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py @@ -1,1 +1,1 @@ -"""Install and test tool shed repositories of type tool_dependency_definition.""" \ No newline at end of file +"""Install and test tool shed repositories of type tool_dependency_definition.""" diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/__init__.py --- a/test/tool_shed/__init__.py +++ b/test/tool_shed/__init__.py @@ -1,1 +1,1 @@ -"""Tool shed functional Tests""" \ No newline at end of file +"""Tool shed functional Tests""" diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -15,7 +15,7 @@ from base.tool_shed_util import repository_installation_timeout from base.twilltestcase import TwillTestCase -from galaxy.util.json import from_json_string +from galaxy.util.json import loads from galaxy.web import security from tool_shed.util.encoding_util import tool_shed_encode from tool_shed.util import shed_util_common as suc @@ -637,7 +637,7 @@ url = '/api/datatypes?upload_only=false' self.visit_galaxy_url( url ) html = self.last_page() - datatypes = from_json_string( html ) + datatypes = loads( html ) return len( datatypes ) def get_env_sh_path( self, tool_dependency_name, tool_dependency_version, repository ): @@ -714,7 +714,7 @@ # Get the current folder's contents. url = '/repository/open_folder?folder_path=%s' % request_param_path self.visit_url( url ) - file_list = from_json_string( self.last_page() ) + file_list = loads( self.last_page() ) returned_file_list = [] if current_path is not None: returned_file_list.append( current_path ) @@ -753,7 +753,7 @@ url = '/api/datatypes/sniffers' self.visit_galaxy_url( url ) html = self.last_page() - sniffers = from_json_string( html ) + sniffers = loads( html ) return len( sniffers ) def get_tools_from_repository_metadata( self, repository, include_invalid=False ): @@ -772,7 +772,7 @@ tool_guid = urllib.quote_plus( tool_metadata[ 0 ][ 'guid' ], safe='' ) api_url = '/%s' % '/'.join( [ 'api', 'tools', tool_guid ] ) self.visit_galaxy_url( api_url ) - tool_dict = from_json_string( self.last_page() ) + tool_dict = loads( self.last_page() ) tool_panel_section = tool_dict[ 'panel_section_name' ] return tool_panel_section diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/functional/test_0170_complex_prior_installation_required.py --- a/test/tool_shed/functional/test_0170_complex_prior_installation_required.py +++ b/test/tool_shed/functional/test_0170_complex_prior_installation_required.py @@ -131,4 +131,4 @@ self.check_repository_dependency( matplotlib_repository, depends_on_repository=numpy_repository ) self.display_manage_repository_page( matplotlib_repository, strings_displayed=[ 'numpy', '1.7', 'package', changeset_revision ] ) - \ No newline at end of file + diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/functional/test_0310_hg_push_from_api.py --- a/test/tool_shed/functional/test_0310_hg_push_from_api.py +++ b/test/tool_shed/functional/test_0310_hg_push_from_api.py @@ -166,4 +166,4 @@ 'Added another line to filtering.py.' ] strings_not_displayed = [ 'Added a line to filtering.py' ] self.check_repository_changelog( repository, strings_displayed=strings_displayed, strings_not_displayed=[] ) - \ No newline at end of file + diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/functional/test_0410_repository_component_review_access_control.py --- a/test/tool_shed/functional/test_0410_repository_component_review_access_control.py +++ b/test/tool_shed/functional/test_0410_repository_component_review_access_control.py @@ -192,4 +192,4 @@ changeset_revision = self.get_repository_tip( repository ) review = self.test_db_util.get_repository_review_by_user_id_changeset_revision( user.id, repository.id, changeset_revision ) self.browse_component_review( review, strings_displayed=strings_displayed ) - \ No newline at end of file + diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/functional/test_0420_citable_urls_for_repositories.py --- a/test/tool_shed/functional/test_0420_citable_urls_for_repositories.py +++ b/test/tool_shed/functional/test_0420_citable_urls_for_repositories.py @@ -227,4 +227,4 @@ encoded_user_id=None, encoded_repository_id=None, strings_displayed=strings_displayed ) - \ No newline at end of file + diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/functional/test_0460_upload_to_repository.py --- a/test/tool_shed/functional/test_0460_upload_to_repository.py +++ b/test/tool_shed/functional/test_0460_upload_to_repository.py @@ -482,4 +482,4 @@ self.display_repository_file_contents( repository, filename='repository_dependencies.xml', filepath='subfolder', - strings_displayed=[ changeset_revision ] ) \ No newline at end of file + strings_displayed=[ changeset_revision ] ) diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py --- a/test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py +++ b/test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py @@ -72,4 +72,4 @@ repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) assert self.repository_is_new( repository ), 'Uploading an incorrectly defined tool_dependencies.xml resulted in a changeset being generated.' - \ No newline at end of file + diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py --- a/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py +++ b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py @@ -116,4 +116,4 @@ self.visit_galaxy_url( url, params ) self.check_for_strings( strings_displayed ) strings_not_displayed = [ 'column_maker_1087' ] - self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) \ No newline at end of file + self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/functional/test_1170_complex_prior_installation_required.py --- a/test/tool_shed/functional/test_1170_complex_prior_installation_required.py +++ b/test/tool_shed/functional/test_1170_complex_prior_installation_required.py @@ -175,4 +175,4 @@ numpy_repository = self.test_db_util.get_installed_repository_by_name_owner( numpy_repository_name, common.test_user_1_name ) assert matplotlib_repository.update_time > numpy_repository.update_time, \ 'Error: package_numpy_1_7_0170 shows a later update time than package_matplotlib_1_2_0170' - \ No newline at end of file + diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/functional/test_1300_reset_all_metadata.py --- a/test/tool_shed/functional/test_1300_reset_all_metadata.py +++ b/test/tool_shed/functional/test_1300_reset_all_metadata.py @@ -463,4 +463,4 @@ del old_metadata[ 'tool_panel_section' ] assert repository.metadata == old_metadata, 'Metadata for %s repository %s changed after reset. \nOld: %s\nNew: %s' % \ ( repository.status, repository.name, old_metadata, repository.metadata ) - \ No newline at end of file + diff -r a3450635b1d6a4fd9a796adf72f63c4f12623ec5 -r c2a961719f380f5acf89fdc68964e40c225879bc test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -57,7 +57,7 @@ from galaxy.app import UniverseApplication as GalaxyUniverseApplication from galaxy.web import buildapp as galaxybuildapp from galaxy.util import asbool -from galaxy.util.json import to_json_string +from galaxy.util.json import dumps import nose.core import nose.config @@ -182,7 +182,7 @@ galaxy_test_proxy_port = None if 'TOOL_SHED_TEST_DBPATH' in os.environ: shed_db_path = os.environ[ 'TOOL_SHED_TEST_DBPATH' ] - else: + else: tempdir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) shed_db_path = os.path.join( tempdir, 'database' ) shed_tool_data_table_conf_file = os.environ.get( 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF', os.path.join( tool_shed_test_tmp_dir, 'shed_tool_data_table_conf.xml' ) ) @@ -199,7 +199,7 @@ os.environ[ 'GALAXY_TEST_TOOL_DATA_PATH' ] = tool_data_path if 'GALAXY_TEST_DBPATH' in os.environ: galaxy_db_path = os.environ[ 'GALAXY_TEST_DBPATH' ] - else: + else: tempdir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) galaxy_db_path = os.path.join( tempdir, 'database' ) shed_file_path = os.path.join( shed_db_path, 'files' ) @@ -207,9 +207,9 @@ hgweb_config_file_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) new_repos_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) galaxy_tempfiles = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) - galaxy_shed_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) - galaxy_migrated_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) - galaxy_tool_dependency_dir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) + galaxy_shed_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) + galaxy_migrated_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) + galaxy_tool_dependency_dir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) os.environ[ 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ] = galaxy_tool_dependency_dir hgweb_config_dir = hgweb_config_file_path os.environ[ 'TEST_HG_WEB_CONFIG_DIR' ] = hgweb_config_dir @@ -276,8 +276,8 @@ # Generate the shed_tool_data_table_conf.xml file. file( shed_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template ) os.environ[ 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file - # ---- Build Tool Shed Application -------------------------------------------------- - toolshedapp = None + # ---- Build Tool Shed Application -------------------------------------------------- + toolshedapp = None # if not toolshed_database_connection.startswith( 'sqlite://' ): # kwargs[ 'database_engine_option_max_overflow' ] = '20' if tool_dependency_dir is not None: @@ -335,7 +335,7 @@ else: raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" ) log.info( "Embedded web server started" ) - + # ---- Optionally start up a Galaxy instance ------------------------------------------------------ if 'TOOL_SHED_TEST_OMIT_GALAXY' not in os.environ: # Generate the tool_conf.xml file. @@ -357,7 +357,7 @@ open( galaxy_shed_data_manager_conf_file, 'wb' ).write( shed_data_manager_conf_xml_template ) galaxy_global_conf = get_webapp_global_conf() galaxy_global_conf[ '__file__' ] = 'universe_wsgi.ini.sample' - + kwargs = dict( allow_user_creation = True, allow_user_deletion = True, admin_users = 'test(a)bx.psu.edu', @@ -389,15 +389,15 @@ tool_data_table_config_path = galaxy_tool_data_table_conf_file, update_integrated_tool_panel = False, use_heartbeat = False ) - - # ---- Build Galaxy Application -------------------------------------------------- + + # ---- Build Galaxy Application -------------------------------------------------- if not galaxy_database_connection.startswith( 'sqlite://' ) and not install_galaxy_database_connection.startswith( 'sqlite://' ): kwargs[ 'database_engine_option_pool_size' ] = '10' kwargs[ 'database_engine_option_max_overflow' ] = '20' galaxyapp = GalaxyUniverseApplication( **kwargs ) log.info( "Embedded Galaxy application started" ) - + # ---- Run galaxy webserver ------------------------------------------------------ galaxy_server = None galaxy_global_conf[ 'database_file' ] = galaxy_database_connection @@ -464,11 +464,11 @@ test_config = nose.config.Config( env=os.environ, ignoreFiles=ignore_files, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) # Run the tests. - result = run_tests( test_config ) + result = run_tests( test_config ) success = result.wasSuccessful() except: log.exception( "Failure running tests" ) - + log.info( "Shutting down" ) # ---- Tear down ----------------------------------------------------------- if tool_shed_server: https://bitbucket.org/galaxy/galaxy-central/commits/6f06ff96d5ca/ Changeset: 6f06ff96d5ca User: dannon Date: 2014-09-09 16:17:56 Summary: Add deprecation notice for to_json_string/from_json_string. I left these references just in case I missed something that uses them. Affected #: 1 file diff -r c2a961719f380f5acf89fdc68964e40c225879bc -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 lib/galaxy/util/json.py --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -7,8 +7,8 @@ import random import string -to_json_string = json.dumps -from_json_string = json.loads +to_json_string = json.dumps # deprecated +from_json_string = json.loads # deprecated dumps = json.dumps loads = json.loads @@ -25,9 +25,9 @@ else: return val + # Methods for handling JSON-RPC - def validate_jsonrpc_request( request, regular_methods, notification_methods ): try: request = loads( request ) https://bitbucket.org/galaxy/galaxy-central/commits/74b2495de918/ Changeset: 74b2495de918 User: dannon Date: 2014-09-09 22:31:31 Summary: Merge json changes (and some cleanup) back with central. Affected #: 62 files diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f run_functional_tests.sh --- /dev/null +++ b/run_functional_tests.sh @@ -0,0 +1,1 @@ +run_tests.sh \ No newline at end of file diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -42,6 +42,7 @@ if( this.logger ){ var log = this.logger.log; if( typeof this.logger.log === 'object' ){ +//TODO:! there has to be a way to get the lineno/file into this log = Function.prototype.bind.call( this.logger.log, this.logger ); } return log.apply( this.logger, arguments ); @@ -149,6 +150,23 @@ //============================================================================== +/** Function that allows mixing of hashs into bbone MVC while showing the mixins first + * (before the more local class overrides/hash). + * Basically, a simple reversal of param order on _.defaults() - to show mixins in top of definition. + * @example: + * var NewModel = Something.extend( mixin( MyMixinA, MyMixinB, { ... myVars : ... }) ); + * + * NOTE: this does not combine any hashes (like events, etc.) and you're expected to handle that + */ +function mixin( mixinHash1, /* mixinHash2, etc: ... variadic */ propsHash ){ + var args = Array.prototype.slice.call( arguments, 0 ), + lastArg = args.pop(); + args.unshift( lastArg ); + return _.defaults.apply( _, args ); +} + + +//============================================================================== /** A mixin for models that allow T/F/Matching to their attributes - useful when * searching or filtering collections of models. * @example: @@ -329,205 +347,6 @@ //============================================================================== -/** Function that allows mixing of hashs into bbone MVC while showing the mixins first - * (before the more local class overrides/hash). - * Basically, a simple reversal of param order on _.defaults() - to show mixins in top of definition. - * @example: - * var NewModel = Something.extend( mixin( MyMixinA, MyMixinB, { ... myVars : ... }) ); - * - * NOTE: this does not combine any hashes (like events, etc.) and you're expected to handle that - */ -function mixin( mixinHash1, /* mixinHash2, etc: ... variadic */ propsHash ){ - var args = Array.prototype.slice.call( arguments, 0 ), - lastArg = args.pop(); - args.unshift( lastArg ); - return _.defaults.apply( _, args ); -} - -//============================================================================== -/** Return an underscore template fn from an array of strings. - * @param {String[]} template the template strings to compile into the underscore template fn - * @param {String} jsonNamespace an optional namespace for the json data passed in (defaults to 'model') - * @returns {Function} the (wrapped) underscore template fn - * The function accepts: - * - * The template strings can access: - * the json/model hash using model ("<%- model.myAttr %>) using the jsonNamespace above - * _l: the localizer function - * view (if passed): ostensibly, the view using the template (handy for view instance vars) - * Because they're namespaced, undefined attributes will not throw an error. - * - * @example: - * templateBler : BASE_MVC.wrapTemplate([ - * '<div class="myclass <%- mynamespace.modelClass %>">', - * '<span><% print( _l( mynamespace.message ) ); %>:<%= view.status %></span>' - * '</div>' - * ], 'mynamespace' ) - * - * Meant to be called in a View's definition in order to compile only once. - * - */ -function wrapTemplate( template, jsonNamespace ){ - jsonNamespace = jsonNamespace || 'model'; - var templateFn = _.template( template.join( '' ) ); - return function( json, view ){ - var templateVars = { view : view || {}, _l : _l }; - templateVars[ jsonNamespace ] = json || {}; - return templateFn( templateVars ); - }; -} - -//============================================================================== -/** A view which, when first rendered, shows only summary data/attributes, but - * can be expanded to show further details (and optionally fetch those - * details from the server). - */ -var ExpandableView = Backbone.View.extend( LoggableMixin ).extend({ -//TODO: Although the reasoning behind them is different, this shares a lot with HiddenUntilActivated above: combine them - //PRECONDITION: model must have method hasDetails - //PRECONDITION: subclasses must have templates.el and templates.details - - initialize : function( attributes ){ - /** are the details of this view expanded/shown or not? */ - this.expanded = attributes.expanded || false; - //this.log( '\t expanded:', this.expanded ); - this.fxSpeed = attributes.fxSpeed || this.fxSpeed; - }, - - // ........................................................................ render main - /** jq fx speed */ - fxSpeed : 'fast', - - /** Render this content, set up ui. - * @param {Number or String} speed the speed of the render - */ - render : function( speed ){ - var $newRender = this._buildNewRender(); - this._setUpBehaviors( $newRender ); - this._queueNewRender( $newRender, speed ); - return this; - }, - - /** Build a temp div containing the new children for the view's $el. - * If the view is already expanded, build the details as well. - */ - _buildNewRender : function(){ - // create a new render using a skeleton template, render title buttons, render body, and set up events, etc. - var $newRender = $( this.templates.el( this.model.toJSON(), this ) ); - if( this.expanded ){ - this.$details( $newRender ).replaceWith( this._renderDetails().show() ); - } - return $newRender; - }, - - /** Fade out the old el, swap in the new contents, then fade in. - * @param {Number or String} speed jq speed to use for rendering effects - * @fires rendered when rendered - */ - _queueNewRender : function( $newRender, speed ) { - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - var view = this; - - $( view ).queue( 'fx', [ - function( next ){ this.$el.fadeOut( speed, next ); }, - function( next ){ - view._swapNewRender( $newRender ); - next(); - }, - function( next ){ this.$el.fadeIn( speed, next ); }, - function( next ){ - this.trigger( 'rendered', view ); - next(); - } - ]); - }, - - /** empty out the current el, move the $newRender's children in */ - _swapNewRender : function( $newRender ){ - return this.$el.empty().attr( 'class', this.className ).append( $newRender.children() ); - }, - - /** set up js behaviors, event handlers for elements within the given container - * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) - */ - _setUpBehaviors : function( $where ){ - $where = $where || this.$el; - // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) - //make_popup_menus( $where ); - $where.find( '[title]' ).tooltip({ placement : 'bottom' }); - }, - - // ......................................................................... details - /** shortcut to details DOM (as jQ) */ - $details : function( $where ){ - $where = $where || this.$el; - return $where.find( '.details' ); - }, - - /** build the DOM for the details and set up behaviors on it */ - _renderDetails : function(){ - var $newDetails = $( this.templates.details( this.model.toJSON(), this ) ); - this._setUpBehaviors( $newDetails ); - return $newDetails; - }, - - // ......................................................................... expansion/details - /** Show or hide the details - * @param {Boolean} expand if true, expand; if false, collapse - */ - toggleExpanded : function( expand ){ - expand = ( expand === undefined )?( !this.expanded ):( expand ); - if( expand ){ - this.expand(); - } else { - this.collapse(); - } - return this; - }, - - /** Render and show the full, detailed body of this view including extra data and controls. - * note: if the model does not have detailed data, fetch that data before showing the body - * @fires expanded when a body has been expanded - */ - expand : function(){ - var view = this; - return view._fetchModelDetails() - .always(function(){ - var $newDetails = view._renderDetails(); - view.$details().replaceWith( $newDetails ); - // needs to be set after the above or the slide will not show - view.expanded = true; - $newDetails.slideDown( view.fxSpeed, function(){ - view.trigger( 'expanded', view ); - }); - }); - }, - - /** Check for model details and, if none, fetch them. - * @returns {jQuery.promise} the model.fetch.xhr if details are being fetched, an empty promise if not - */ - _fetchModelDetails : function(){ - if( !this.model.hasDetails() ){ - return this.model.fetch(); - } - return jQuery.when(); - }, - - /** Hide the body/details of an HDA. - * @fires collapsed when a body has been collapsed - */ - collapse : function(){ - var view = this; - view.expanded = false; - this.$details().slideUp( view.fxSpeed, function(){ - view.trigger( 'collapsed', view ); - }); - } - -}); - - -//============================================================================== /** Mixin for views that can be dragged and dropped * Allows for the drag behavior to be turned on/off, setting/removing jQuery event * handlers each time. @@ -711,186 +530,48 @@ //============================================================================== -/** A view that is displayed in some larger list/grid/collection. - * Inherits from Expandable, Selectable, Draggable. - * The DOM contains warnings, a title bar, and a series of primary action controls. - * Primary actions are meant to be easily accessible item functions (such as delete) - * that are rendered in the title bar. +/** Return an underscore template fn from an array of strings. + * @param {String[]} template the template strings to compile into the underscore template fn + * @param {String} jsonNamespace an optional namespace for the json data passed in (defaults to 'model') + * @returns {Function} the (wrapped) underscore template fn + * The function accepts: * - * Details are rendered when the user clicks the title bar or presses enter/space when - * the title bar is in focus. + * The template strings can access: + * the json/model hash using model ("<%- model.myAttr %>) using the jsonNamespace above + * _l: the localizer function + * view (if passed): ostensibly, the view using the template (handy for view instance vars) + * Because they're namespaced, undefined attributes will not throw an error. * - * Designed as a base class for history panel contents - but usable elsewhere (I hope). + * @example: + * templateBler : BASE_MVC.wrapTemplate([ + * '<div class="myclass <%- mynamespace.modelClass %>">', + * '<span><% print( _l( mynamespace.message ) ); %>:<%= view.status %></span>' + * '</div>' + * ], 'mynamespace' ) + * + * Meant to be called in a View's definition in order to compile only once. + * */ -var ListItemView = ExpandableView.extend( mixin( SelectableViewMixin, DraggableViewMixin, { - -//TODO: that's a little contradictory - tagName : 'div', - className : 'list-item', - - /** Set up the base class and all mixins */ - initialize : function( attributes ){ - ExpandableView.prototype.initialize.call( this, attributes ); - SelectableViewMixin.initialize.call( this, attributes ); - DraggableViewMixin.initialize.call( this, attributes ); - }, - - // ........................................................................ rendering - /** In this override, call methods to build warnings, titlebar and primary actions */ - _buildNewRender : function(){ - var $newRender = ExpandableView.prototype._buildNewRender.call( this ); - $newRender.find( '.warnings' ).replaceWith( this._renderWarnings() ); - $newRender.find( '.title-bar' ).replaceWith( this._renderTitleBar() ); - $newRender.find( '.primary-actions' ).append( this._renderPrimaryActions() ); - $newRender.find( '.subtitle' ).replaceWith( this._renderSubtitle() ); - return $newRender; - }, - - /** In this override, render the selector controls and set up dragging before the swap */ - _swapNewRender : function( $newRender ){ - ExpandableView.prototype._swapNewRender.call( this, $newRender ); - if( this.selectable ){ this.showSelector( 0 ); } - if( this.draggable ){ this.draggableOn(); } - return this.$el; - }, - - /** Render any warnings the item may need to show (e.g. "I'm deleted") */ - _renderWarnings : function(){ - var view = this, - $warnings = $( '<div class="warnings"></div>' ), - json = view.model.toJSON(); -//TODO:! unordered (map) - _.each( view.templates.warnings, function( templateFn ){ - $warnings.append( $( templateFn( json, view ) ) ); - }); - return $warnings; - }, - - /** Render the title bar (the main/exposed SUMMARY dom element) */ - _renderTitleBar : function(){ - return $( this.templates.titleBar( this.model.toJSON(), this ) ); - }, - - /** Return an array of jQ objects containing common/easily-accessible item controls */ - _renderPrimaryActions : function(){ - // override this - return []; - }, - - /** Render the title bar (the main/exposed SUMMARY dom element) */ - _renderSubtitle : function(){ - return $( this.templates.subtitle( this.model.toJSON(), this ) ); - }, - - // ......................................................................... events - /** event map */ - events : { - // expand the body when the title is clicked or when in focus and space or enter is pressed - 'click .title-bar' : '_clickTitleBar', - 'keydown .title-bar' : '_keyDownTitleBar', - - // dragging - don't work, originalEvent === null - //'dragstart .dataset-title-bar' : 'dragStartHandler', - //'dragend .dataset-title-bar' : 'dragEndHandler' - - 'click .selector' : 'toggleSelect' - }, - - /** expand when the title bar is clicked */ - _clickTitleBar : function( event ){ - event.stopPropagation(); - this.toggleExpanded(); - }, - - /** expand when the title bar is in focus and enter or space is pressed */ - _keyDownTitleBar : function( event ){ - // bail (with propagation) if keydown and not space or enter - var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13; - if( event && ( event.type === 'keydown' ) - &&( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){ - this.toggleExpanded(); - event.stopPropagation(); - return false; - } - return true; - }, - - // ......................................................................... misc - /** String representation */ - toString : function(){ - var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'ListItemView(' + modelString + ')'; - } -})); - -// ............................................................................ TEMPLATES -/** underscore templates */ -ListItemView.prototype.templates = (function(){ -//TODO: move to require text! plugin - - var elTemplato = wrapTemplate([ - '<div class="list-element">', - // errors, messages, etc. - '<div class="warnings"></div>', - - // multi-select checkbox - '<div class="selector">', - '<span class="fa fa-2x fa-square-o"></span>', - '</div>', - // space for title bar buttons - gen. floated to the right - '<div class="primary-actions"></div>', - '<div class="title-bar"></div>', - - // expandable area for more details - '<div class="details"></div>', - '</div>' - ]); - - var warnings = {}; - - var titleBarTemplate = wrapTemplate([ - // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display - '<div class="title-bar clear" tabindex="0">', -//TODO: prob. belongs in dataset-list-item - '<span class="state-icon"></span>', - '<div class="title">', - '<span class="name"><%- element.name %></span>', - '</div>', - '<div class="subtitle"></div>', - '</div>' - ], 'element' ); - - var subtitleTemplate = wrapTemplate([ - // override this - '<div class="subtitle"></div>' - ]); - - var detailsTemplate = wrapTemplate([ - // override this - '<div class="details"></div>' - ]); - - return { - el : elTemplato, - warnings : warnings, - titleBar : titleBarTemplate, - subtitle : subtitleTemplate, - details : detailsTemplate +function wrapTemplate( template, jsonNamespace ){ + jsonNamespace = jsonNamespace || 'model'; + var templateFn = _.template( template.join( '' ) ); + return function( json, view ){ + var templateVars = { view : view || {}, _l : _l }; + templateVars[ jsonNamespace ] = json || {}; + return templateFn( templateVars ); }; -}()); +} //============================================================================== return { LoggableMixin : LoggableMixin, SessionStorageModel : SessionStorageModel, + mixin : mixin, SearchableModelMixin : SearchableModelMixin, HiddenUntilActivatedViewMixin : HiddenUntilActivatedViewMixin, - mixin : mixin, - wrapTemplate : wrapTemplate, - ExpandableView : ExpandableView, DraggableViewMixin : DraggableViewMixin, SelectableViewMixin : SelectableViewMixin, - ListItemView : ListItemView + wrapTemplate : wrapTemplate }; }); diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/collection/collection-li.js --- a/static/scripts/mvc/collection/collection-li.js +++ b/static/scripts/mvc/collection/collection-li.js @@ -1,11 +1,12 @@ define([ + "mvc/list/list-item", "mvc/dataset/dataset-li", "mvc/base-mvc", "utils/localization" -], function( DATASET_LI, BASE_MVC, _l ){ +], function( LIST_ITEM, DATASET_LI, BASE_MVC, _l ){ /* global Backbone, LoggableMixin */ //============================================================================== -var ListItemView = BASE_MVC.ListItemView; +var ListItemView = LIST_ITEM.ListItemView; /** @class Read only view for DatasetCollection. */ var DCListItemView = ListItemView.extend( @@ -97,8 +98,7 @@ //TODO: this might be expendable - compacted with HDAListItemView /** logger used to record this.log messages, commonly set to console */ - // comment this out to suppress log output - logger : console, + //logger : console, /** add the DCE class to the list item */ className : ListItemView.prototype.className + " dataset-collection-element", diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/collection/collection-model.js --- a/static/scripts/mvc/collection/collection-model.js +++ b/static/scripts/mvc/collection/collection-model.js @@ -270,6 +270,11 @@ return this.save( { deleted: false }, options ); }, + /** Is this collection deleted or purged? */ + isDeletedOrPurged : function(){ + return ( this.get( 'deleted' ) || this.get( 'purged' ) ); + }, + // ........................................................................ searchable /** searchable attributes for collections */ searchAttributes : [ diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/collection/collection-panel.js --- a/static/scripts/mvc/collection/collection-panel.js +++ b/static/scripts/mvc/collection/collection-panel.js @@ -1,9 +1,10 @@ define([ + "mvc/list/list-panel", "mvc/collection/collection-model", "mvc/collection/collection-li", "mvc/base-mvc", "utils/localization" -], function( DC_MODEL, DC_LI, BASE_MVC, _l ){ +], function( LIST_PANEL, DC_MODEL, DC_LI, BASE_MVC, _l ){ /* ============================================================================= TODO: @@ -11,36 +12,29 @@ // ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. */ -var CollectionPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( +var _super = LIST_PANEL.ModelListPanel; +var CollectionPanel = _super.extend( /** @lends CollectionPanel.prototype */{ //MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs) /** logger used to record this.log messages, commonly set to console */ //logger : console, - tagName : 'div', - className : 'dataset-collection-panel', - - /** (in ms) that jquery effects will use */ - fxSpeed : 'fast', + className : _super.prototype.className + ' dataset-collection-panel', /** sub view class used for datasets */ DatasetDCEViewClass : DC_LI.DatasetDCEListItemView, /** sub view class used for nested collections */ NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView, + /** key of attribute in model to assign to this.collection */ + modelCollectionKey : 'elements', // ......................................................................... SET UP /** Set up the view, set up storage, bind listeners to HistoryContents events * @param {Object} attributes optional settings for the panel */ initialize : function( attributes ){ - attributes = attributes || {}; - // set the logger if requested - if( attributes.logger ){ - this.logger = attributes.logger; - } - this.log( this + '.initialize:', attributes ); - + _super.prototype.initialize.call( this, attributes ); this.linkTarget = attributes.linkTarget || '_blank'; this.hasUser = attributes.hasUser; @@ -50,185 +44,49 @@ //window.collectionPanel = this; }, - /** create any event listeners for the panel - * @fires: rendered:initial on the first render - * @fires: empty-history when switching to a history with no HDAs or creating a new history - */ - _setUpListeners : function(){ - // debugging - //if( this.logger ){ - this.on( 'all', function( event ){ - this.log( this + '', arguments ); - }, this ); - //} - return this; + // ------------------------------------------------------------------------ sub-views + /** In this override, use model.getVisibleContents */ + _filterCollection : function(){ +//TODO: should *not* be model.getVisibleContents + return this.model.getVisibleContents(); }, - // ------------------------------------------------------------------------ history/hda event listening - /** listening for history and HDA events */ - _setUpModelEventHandlers : function(){ - return this; - }, - - // ------------------------------------------------------------------------ panel rendering - /** Render panel - * @fires: rendered when the panel is attached and fully visible - * @see Backbone.View#render - */ - render : function( speed, callback ){ - this.log( 'render:', speed, callback ); - // send a speed of 0 to have no fade in/out performed - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - //this.debug( this + '.render, fxSpeed:', speed ); - var panel = this, - $newRender; - - // handle the possibility of no model (can occur if fetching the model returns an error) - if( !this.model ){ - return this; - } - $newRender = this.renderModel(); - - // fade out existing, swap with the new, fade in, set up behaviours - $( panel ).queue( 'fx', [ - function( next ){ - if( speed && panel.$el.is( ':visible' ) ){ - panel.$el.fadeOut( speed, next ); - } else { - next(); - } - }, - function( next ){ - // swap over from temp div newRender - panel.$el.empty(); - if( $newRender ){ - panel.$el.append( $newRender.children() ); - } - next(); - }, - function( next ){ - if( speed && !panel.$el.is( ':visible' ) ){ - panel.$el.fadeIn( speed, next ); - } else { - next(); - } - }, - function( next ){ - //TODO: ideally, these would be set up before the fade in (can't because of async save text) - if( callback ){ callback.call( this ); } - panel.trigger( 'rendered', this ); - next(); - } - ]); - return this; - }, - - /** render with collection data - * @returns {jQuery} dom fragment as temporary container to be swapped out later - */ - renderModel : function( ){ - // tmp div for final swap in render -//TODO: ugh - reuse issue - refactor out - var type = this.model.get( 'collection_type' ) || this.model.object.get( 'collection_type' ), - json = _.extend( this.model.toJSON(), { - parentName : this.parentName, - type : type - }), - $newRender = $( '<div/>' ).append( this.templates.panel( json ) ); - this._setUpBehaviours( $newRender ); - this.renderContents( $newRender ); - return $newRender; - }, - - /** Set up js/widget behaviours */ - _setUpBehaviours : function( $where ){ - //TODO: these should be either sub-MVs, or handled by events - $where = $where || this.$el; - $where.find( '[title]' ).tooltip({ placement: 'bottom' }); - return this; - }, - - // ------------------------------------------------------------------------ sub-$element shortcuts - /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */ - $container : function(){ - return ( this.findContainerFn )?( this.findContainerFn.call( this ) ):( this.$el.parent() ); - }, - /** where list content views are attached */ - $datasetsList : function( $where ){ - return ( $where || this.$el ).find( '.datasets-list' ); - }, - - // ------------------------------------------------------------------------ sub-views - /** Set up/render a view for each DCE to be shown, init with model and listeners. - * DCE views are cached to the map this.contentViews (using the model.id as key). - * @param {jQuery} $whereTo what dom element to prepend the DCE views to - * @returns the number of visible DCE views - */ - renderContents : function( $whereTo ){ - //this.debug( 'renderContents, elements:', this.model.elements ); - $whereTo = $whereTo || this.$el; - - this.warn( this + '.renderContents:, model:', this.model ); - var panel = this, - contentViews = {}, - //NOTE: no filtering here - visibleContents = this.model.getVisibleContents(); - //this.debug( 'renderContents, visibleContents:', visibleContents, $whereTo ); - - this.$datasetsList( $whereTo ).empty(); - if( visibleContents && visibleContents.length ){ - visibleContents.each( function( content ){ - var contentId = content.id, - contentView = panel._createContentView( content ); - contentViews[ contentId ] = contentView; - panel._attachContentView( contentView.render(), $whereTo ); - }); - } - this.contentViews = contentViews; - return this.contentViews; - }, - - /** */ - _createContentView : function( content ){ - //this.debug( 'content json:', JSON.stringify( content, null, ' ' ) ); - var contentView = null, - ContentClass = this._getContentClass( content ); - //this.debug( 'content:', content ); - //this.debug( 'ContentClass:', ContentClass ); - contentView = new ContentClass({ - model : content, - linkTarget : this.linkTarget, - //draggable : true, - hasUser : this.hasUser, - logger : this.logger - }); - //this.debug( 'contentView:', contentView ); - this._setUpContentListeners( contentView ); - return contentView; - }, - - /** */ - _getContentClass : function( content ){ - //this.debug( this + '._getContentClass:', content ); + /** override to return proper view class based on element_type */ + _getItemViewClass : function( model ){ + //this.debug( this + '._getItemViewClass:', model ); //TODO: subclasses use DCEViewClass - but are currently unused - decide - switch( content.get( 'element_type' ) ){ + switch( model.get( 'element_type' ) ){ case 'hda': return this.DatasetDCEViewClass; case 'dataset_collection': return this.NestedDCDCEViewClass; } - throw new TypeError( 'Unknown element type:', content.get( 'element_type' ) ); + throw new TypeError( 'Unknown element type:', model.get( 'element_type' ) ); }, - /** Set up listeners for content view events. In this override, handle collection expansion. */ - _setUpContentListeners : function( contentView ){ + /** override to add link target and anon */ + _getItemViewOptions : function( model ){ + var options = _super.prototype._getItemViewOptions.call( this, model ); + return _.extend( options, { + linkTarget : this.linkTarget, + hasUser : this.hasUser + }); + }, + + /** when a sub-view is clicked in the collection panel that is itself a collection, + * hide this panel's elements and show the sub-collection in its own panel. + */ + _setUpItemViewListeners : function( view ){ var panel = this; - if( contentView.model.get( 'element_type' ) === 'dataset_collection' ){ - contentView.on( 'expanded', function( collectionView ){ + _super.prototype._setUpItemViewListeners.call( panel, view ); + //TODO:?? doesn't seem to belong here + if( view.model.get( 'element_type' ) === 'dataset_collection' ){ + view.on( 'expanded', function( collectionView ){ panel.info( 'expanded', collectionView ); panel._addCollectionPanel( collectionView ); }); } + return panel; }, /** When a sub-collection is clicked, hide the current panel and render the sub-collection in its own panel */ @@ -246,7 +104,7 @@ }); currPanel.panelStack.push( panel ); - currPanel.$( '.controls' ).add( '.datasets-list' ).hide(); + currPanel.$( '.controls' ).add( '.list-items' ).hide(); currPanel.$el.append( panel.$el ); panel.on( 'close', function(){ currPanel.render(); @@ -266,14 +124,6 @@ } }, - /** attach an contentView to the panel */ - _attachContentView : function( contentView, $whereTo ){ - $whereTo = $whereTo || this.$el; - var $datasetsList = this.$datasetsList( $whereTo ); - $datasetsList.append( contentView.$el ); - return this; - }, - // ------------------------------------------------------------------------ panel events /** event map */ events : { @@ -293,16 +143,16 @@ } }); -//----------------------------------------------------------------------------- TEMPLATES -/** underscore templates */ -CollectionPanel.templates = CollectionPanel.prototype.templates = (function(){ -// use closure to run underscore template fn only once at module load - var _panelTemplate = _.template([ + +//------------------------------------------------------------------------------ TEMPLATES +CollectionPanel.prototype.templates = (function(){ + + var controlsTemplate = BASE_MVC.wrapTemplate([ '<div class="controls">', '<div class="navigation">', '<a class="back" href="javascript:void(0)">', '<span class="fa fa-icon fa-angle-left"></span>', - _l( 'Back to ' ), '<%- collection.parentName %>', + _l( 'Back to ' ), '<%- view.parentName %>', '</a>', '</div>', @@ -310,29 +160,25 @@ '<div class="name"><%- collection.name || collection.element_identifier %></div>', '<div class="subtitle">', //TODO: remove logic from template - '<% if( collection.type === "list" ){ %>', + '<% if( collection.collection_type === "list" ){ %>', _l( 'a list of datasets' ), - '<% } else if( collection.type === "paired" ){ %>', + '<% } else if( collection.collection_type === "paired" ){ %>', _l( 'a pair of datasets' ), - '<% } else if( collection.type === "list:paired" ){ %>', + '<% } else if( collection.collection_type === "list:paired" ){ %>', _l( 'a list of paired datasets' ), '<% } %>', '</div>', '</div>', - '</div>', - // where the datasets/hdas are added - '<div class="datasets-list"></div>' - ].join( '' )); + '</div>' + ], 'collection' ); - // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within - return { - panel : function( json ){ - return _panelTemplate({ _l: _l, collection: json }); - } - }; + return _.extend( _.clone( _super.prototype.templates ), { + controls : controlsTemplate + }); }()); + // ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. */ var ListCollectionPanel = CollectionPanel.extend( diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/dataset/dataset-li.js --- a/static/scripts/mvc/dataset/dataset-li.js +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -1,8 +1,9 @@ define([ + "mvc/list/list-item", "mvc/dataset/states", "mvc/base-mvc", "utils/localization" -], function( STATES, BASE_MVC, _l ){ +], function( LIST_ITEM, STATES, BASE_MVC, _l ){ /* global Backbone */ /*============================================================================== TODO: @@ -11,7 +12,7 @@ simplify button rendering ==============================================================================*/ -var _super = BASE_MVC.ListItemView; +var _super = LIST_ITEM.ListItemView; /** @class Read only list view for either LDDAs, HDAs, or HDADCEs. * Roughly, any DatasetInstance (and not a raw Dataset). */ diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/dataset/dataset-list.js --- a/static/scripts/mvc/dataset/dataset-list.js +++ b/static/scripts/mvc/dataset/dataset-list.js @@ -1,5 +1,5 @@ define([ - "mvc/dataset/list-panel", + "mvc/list/list-panel", "mvc/dataset/dataset-li", "mvc/base-mvc", "utils/localization" diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/dataset/dataset-model.js --- a/static/scripts/mvc/dataset/dataset-model.js +++ b/static/scripts/mvc/dataset/dataset-model.js @@ -94,6 +94,9 @@ this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); } }); + this.on( 'change:urls', function(){ + console.warn( 'change:urls', arguments ); + }); // the download url (currenlty) relies on having a correct file extension this.on( 'change:id change:file_ext', function( currModel ){ this._generateUrls(); @@ -104,6 +107,8 @@ /** override to add urls */ toJSON : function(){ var json = Backbone.Model.prototype.toJSON.call( this ); + //console.warn( 'returning json?' ); + //return json; return _.extend( json, { urls : this.urls }); diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/dataset/list-panel.js --- a/static/scripts/mvc/dataset/list-panel.js +++ /dev/null @@ -1,687 +0,0 @@ -define([ - "mvc/base-mvc", - "utils/localization" -], function( BASE_MVC, _l ){ -/* ============================================================================= -TODO: - -============================================================================= */ -/** @class List that contains ListItemViews. - */ -var ListPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( -/** @lends ReadOnlyHistoryPanel.prototype */{ - - /** logger used to record this.log messages, commonly set to console */ - //logger : console, - - /** class to use for constructing the sub-views */ - viewClass : BASE_MVC.ListItemView, - - tagName : 'div', - className : 'list-panel', - - /** (in ms) that jquery effects will use */ - fxSpeed : 'fast', - - /** string to display when the model has no hdas */ - emptyMsg : _l( 'This list is empty' ), - /** string to no hdas match the search terms */ - noneFoundMsg : _l( 'No matching items found' ), - - // ......................................................................... SET UP - /** Set up the view, set up storage, bind listeners to HistoryContents events - * @param {Object} attributes optional settings for the list - */ - initialize : function( attributes, options ){ - attributes = attributes || {}; - // set the logger if requested - if( attributes.logger ){ - this.logger = attributes.logger; - } - this.log( this + '.initialize:', attributes ); - - // ---- instance vars - /** how quickly should jquery fx run? */ - this.fxSpeed = _.has( attributes, 'fxSpeed' )?( attributes.fxSpeed ):( this.fxSpeed ); - - /** filters for displaying subviews */ - this.filters = []; - /** current search terms */ - this.searchFor = attributes.searchFor || ''; - - /** loading indicator */ - this.indicator = new LoadingIndicator( this.$el ); - - /** currently showing selectors on items? */ - this.selecting = ( attributes.selecting !== undefined )? attributes.selecting : true; - //this.selecting = false; - - /** cached selected item.model.ids to persist btwn renders */ - this.selected = attributes.selected || []; - /** the last selected item.model.id */ - this.lastSelected = null; - - /** list item view class (when passed models) */ - this.viewClass = attributes.viewClass || this.viewClass; - - /** list item views */ - this.views = []; - /** list item models */ - this.collection = attributes.collection || ( new Backbone.Collection([]) ); - - /** filter fns run over collection items to see if they should show in the list */ - this.filters = attributes.filters || []; - -//TODO: remove - this.title = attributes.title || ''; - this.subtitle = attributes.subtitle || ''; - - this._setUpListeners(); - }, - - /** create any event listeners for the list - */ - _setUpListeners : function(){ - this.on( 'error', function( model, xhr, options, msg, details ){ - //this.errorHandler( model, xhr, options, msg, details ); - console.error( model, xhr, options, msg, details ); - }, this ); - - // show hide the loading indicator - this.on( 'loading', function(){ - this._showLoadingIndicator( 'loading...', 40 ); - }, this ); - this.on( 'loading-done', function(){ - this._hideLoadingIndicator( 40 ); - }, this ); - - // throw the first render up as a diff namespace using once (for outside consumption) - this.once( 'rendered', function(){ - this.trigger( 'rendered:initial', this ); - }, this ); - - // debugging - if( this.logger ){ - this.on( 'all', function( event ){ - this.log( this + '', arguments ); - }, this ); - } - - this._setUpCollectionListeners(); - this._setUpViewListeners(); - return this; - }, - - /** free any sub-views the list has */ - freeViews : function(){ -//TODO: stopListening? remove? - this.views = []; - return this; - }, - - // ------------------------------------------------------------------------ item listeners - /** listening for history and HDA events */ - _setUpCollectionListeners : function(){ - - this.collection.on( 'reset', function(){ - this.renderItems(); - }, this ); - - this.collection.on( 'add', this.addItemView, this ); - this.collection.on( 'remove', this.removeItemView, this ); - - // debugging - if( this.logger ){ - this.collection.on( 'all', function( event ){ - this.info( this + '(collection)', arguments ); - }, this ); - } - return this; - }, - - /** listening for history and HDA events */ - _setUpViewListeners : function(){ - - // shift to select a range - this.on( 'view:selected', function( view, ev ){ - if( ev && ev.shiftKey && this.lastSelected ){ - var lastSelectedView = _.find( this.views, function( view ){ - return view.model.id === this.lastSelected; - }); - if( lastSelectedView ){ - this.selectRange( view, lastSelectedView ); - } - } - this.selected.push( view.model.id ); - this.lastSelected = view.model.id; - }, this ); - }, - - // ------------------------------------------------------------------------ rendering - /** Render this content, set up ui. - * @param {Number or String} speed the speed of the render - */ - render : function( speed ){ - var $newRender = this._buildNewRender(); - this._setUpBehaviors( $newRender ); - this._queueNewRender( $newRender, speed ); - return this; - }, - - /** Build a temp div containing the new children for the view's $el. - */ - _buildNewRender : function(){ - // create a new render using a skeleton template, render title buttons, render body, and set up events, etc. - var json = this.model? this.model.toJSON() : {}, - $newRender = $( this.templates.el( json, this ) ); - this._renderTitle( $newRender ); - this._renderSubtitle( $newRender ); - this._renderSearch( $newRender ); - this.renderItems( $newRender ); - return $newRender; - }, - - /** - */ - _renderTitle : function( $where ){ - //$where = $where || this.$el; - //$where.find( '.title' ).replaceWith( ... ) - }, - - /** - */ - _renderSubtitle : function( $where ){ - //$where = $where || this.$el; - //$where.find( '.title' ).replaceWith( ... ) - }, - - /** Fade out the old el, swap in the new contents, then fade in. - * @param {Number or String} speed jq speed to use for rendering effects - * @fires rendered when rendered - */ - _queueNewRender : function( $newRender, speed ) { - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - var view = this; - - $( view ).queue( 'fx', [ - function( next ){ this.$el.fadeOut( speed, next ); }, - function( next ){ - view._swapNewRender( $newRender ); - next(); - }, - function( next ){ this.$el.fadeIn( speed, next ); }, - function( next ){ - view.trigger( 'rendered', view ); - next(); - } - ]); - }, - - /** empty out the current el, move the $newRender's children in */ - _swapNewRender : function( $newRender ){ - this.$el.empty().attr( 'class', this.className ).append( $newRender.children() ); - if( this.selecting ){ this.showSelectors( 0 ); } - return this; - }, - - /** */ - _setUpBehaviors : function( $where ){ - $where = $where || this.$el; - $where.find( '.controls [title]' ).tooltip({ placement: 'bottom' }); - return this; - }, - - // ------------------------------------------------------------------------ sub-$element shortcuts - /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */ - $scrollContainer : function(){ - // override - return this.$el.parent().parent(); - }, - /** */ - $list : function( $where ){ - return ( $where || this.$el ).find( '.list-items' ); - }, - /** container where list messages are attached */ - $messages : function( $where ){ - return ( $where || this.$el ).find( '.message-container' ); - }, - /** the message displayed when no views can be shown (no views, none matching search) */ - $emptyMessage : function( $where ){ - return ( $where || this.$el ).find( '.empty-message' ); - }, - - // ------------------------------------------------------------------------ hda sub-views - /** - * @param {jQuery} $whereTo what dom element to prepend the HDA views to - * @returns the visible item views - */ - renderItems : function( $whereTo ){ - $whereTo = $whereTo || this.$el; - var list = this, - newViews = []; - - var $list = this.$list( $whereTo ), - item$els = this._filterCollection().map( function( itemModel ){ -//TODO: creates views each time - not neccessarily good - var view = list._createItemView( itemModel ); - newViews.push( view ); - return view.render( 0 ).$el; - }); - this.debug( item$els ); - this.debug( newViews ); - - $list.empty(); - if( item$els.length ){ - $list.append( item$els ); - this.$emptyMessage( $whereTo ).hide(); - - } else { - this._renderEmptyMessage( $whereTo ).show(); - } - - this.views = newViews; - return newViews; - }, - - /** - */ - _filterCollection : function(){ - // override this - var list = this; - return list.collection.filter( _.bind( list._filterItem, list ) ); - }, - - /** - */ - _filterItem : function( model ){ - // override this - var list = this; - return ( _.every( list.filters.map( function( fn ){ return fn.call( model ); }) ) ) - && ( !list.searchFor || model.matchesAll( list.searchFor ) ); - }, - - /** - */ - _createItemView : function( model ){ - var ViewClass = this._getItemViewClass( model ), - options = _.extend( this._getItemViewOptions( model ), { - model : model - }), - view = new ViewClass( options ); - this._setUpItemViewListeners( view ); - return view; - }, - - _getItemViewClass : function( model ){ - // override this - return this.viewClass; - }, - - _getItemViewOptions : function( model ){ - // override this - return { - //logger : this.logger, - fxSpeed : this.fxSpeed, - expanded : false, - selectable : this.selecting, - selected : _.contains( this.selected, model.id ), - draggable : this.dragging - }; - }, - - /** - */ - _setUpItemViewListeners : function( view ){ - var list = this; - view.on( 'all', function(){ - var args = Array.prototype.slice.call( arguments, 0 ); - args[0] = 'view:' + args[0]; - list.trigger.apply( list, args ); - }); - - // debugging - //if( this.logger ){ - // view.on( 'all', function( event ){ - // this.log( this + '(view)', arguments ); - // }, this ); - //} - return this; - }, - - /** render the empty/none-found message */ - _renderEmptyMessage : function( $whereTo ){ - //this.debug( '_renderEmptyMessage', $whereTo, this.searchFor ); - var text = this.searchFor? this.noneFoundMsg : this.emptyMsg; - return this.$emptyMessage( $whereTo ).text( text ); - }, - - /** collapse all item views */ - expandAll : function(){ - _.each( this.views, function( view ){ - view.expand(); - }); - }, - - /** collapse all item views */ - collapseAll : function(){ - _.each( this.views, function( view ){ - view.collapse(); - }); - }, - - // ------------------------------------------------------------------------ collection/views syncing - /** - */ - addItemView : function( model, collection, options ){ - this.log( this + '.addItemView:', model ); - var list = this; - if( !this._filterItem( model ) ){ return undefined; } - -//TODO: sorted? position? - var view = list._createItemView( model ); - this.views.push( view ); - - $( view ).queue( 'fx', [ - function( next ){ list.$emptyMessage().fadeOut( list.fxSpeed, next ); }, - function( next ){ -//TODO: auto render? - list.$list().append( view.render().$el ); - next(); - } - ]); - return view; - }, - - /** - */ - removeItemView : function( model, collection, options ){ - this.log( this + '.removeItemView:', model ); - var list = this, - view = list.viewFromModel( model ); - if( !view ){ return undefined; } - - this.views = _.without( this.views, view ); - view.remove(); - if( !this.views.length ){ - list._renderEmptyMessage().fadeIn( list.fxSpeed ); - } - return view; - }, - - /** get views based on model - */ - viewFromModel : function( model ){ - for( var i=0; i<this.views.length; i++ ){ - var view = this.views[i]; - if( view.model === model ){ - return view; - } - } - return undefined; - }, - - /** get views based on model properties - */ - viewsWhereModel : function( properties ){ - return this.views.filter( function( view ){ - //return view.model.matches( properties ); -//TODO: replace with _.matches (underscore 1.6.0) - var json = view.model.toJSON(); - //console.debug( '\t', json, properties ); - for( var key in properties ){ - if( properties.hasOwnPropery( key ) ){ - //console.debug( '\t\t', json[ key ], view.model.properties[ key ] ); - if( json[ key ] !== view.model.properties[ key ] ){ - return false; - } - } - } - return true; - }); - }, - - /** - */ - viewRange : function( viewA, viewB ){ - if( viewA === viewB ){ return ( viewA )?( [ viewA ] ):( [] ); } - - var indexA = this.views.indexOf( viewA ), - indexB = this.views.indexOf( viewB ); - - // handle not found - if( indexA === -1 || indexB === -1 ){ - if( indexA === indexB ){ return []; } - return ( indexA === -1 )?( [ viewB ] ):( [ viewA ] ); - } - // reverse if indeces are - //note: end inclusive - return ( indexA < indexB )? - this.views.slice( indexA, indexB + 1 ) : - this.views.slice( indexB, indexA + 1 ); - }, - - // ------------------------------------------------------------------------ searching - /** render a search input for filtering datasets shown - * (see the search section in the HDA model for implementation of the actual searching) - * return will start the search - * esc will clear the search - * clicking the clear button will clear the search - * uses searchInput in ui.js - */ - _renderSearch : function( $where ){ - $where.find( '.controls .search-input' ).searchInput({ - placeholder : 'search', - initialVal : this.searchFor, - onfirstsearch : _.bind( this._firstSearch, this ), - onsearch : _.bind( this.searchItems, this ), - onclear : _.bind( this.clearSearch, this ) - }); - return $where; - }, - - _firstSearch : function( searchFor ){ - this.log( 'onFirstSearch', searchFor ); - return this.searchItems( searchFor ); - }, - - /** filter view list to those that contain the searchFor terms */ - searchItems : function( searchFor ){ - this.searchFor = searchFor; - this.trigger( 'search:searching', searchFor, this ); - this.renderItems(); - return this; - }, - - /** clear the search filters and show all views that are normally shown */ - clearSearch : function( searchFor ){ - //this.log( 'onSearchClear', this ); - this.searchFor = ''; - this.trigger( 'search:clear', this ); - this.renderItems(); - return this; - }, - - // ------------------------------------------------------------------------ selection - /** show selectors on all visible hdas and associated controls */ - showSelectors : function( speed ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - this.selecting = true; - this.$( '.list-actions' ).slideDown( speed ); - _.each( this.views, function( view ){ - view.showSelector( speed ); - }); - this.selected = []; - this.lastSelected = null; - }, - - /** hide selectors on all visible hdas and associated controls */ - hideSelectors : function( speed ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - this.selecting = false; - this.$( '.list-actions' ).slideUp( speed ); - _.each( this.views, function( view ){ - view.hideSelector( speed ); - }); - this.selected = []; - this.lastSelected = null; - }, - - /** show or hide selectors on all visible hdas and associated controls */ - toggleSelectors : function(){ - if( !this.selecting ){ - this.showSelectors(); - } else { - this.hideSelectors(); - } - }, - - /** select all visible hdas */ - selectAll : function( event ){ - _.each( this.views, function( view ){ - view.select( event ); - }); - }, - - /** deselect all visible hdas */ - deselectAll : function( event ){ - this.lastSelected = null; - _.each( this.views, function( view ){ - view.deselect( event ); - }); - }, - - /** select a range of datasets between A and B */ - selectRange : function( viewA, viewB ){ - var range = this.viewRange( viewA, viewB ); - _.each( range, function( view ){ - view.select(); - }); - return range; - }, - - /** return an array of all currently selected hdas */ - getSelectedViews : function(){ - return _.filter( this.views, function( v ){ - return v.selected; - }); - }, - - /** return an collection of the models of all currenly selected hdas */ - getSelectedModels : function(){ - return new this.collection.constructor( _.map( this.getSelectedViews(), function( view ){ - return view.model; - })); - }, - - // ------------------------------------------------------------------------ loading indicator -//TODO: questionable - /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */ - _showLoadingIndicator : function( msg, speed, callback ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - if( !this.indicator ){ - this.indicator = new LoadingIndicator( this.$el, this.$el.parent() ); - } - if( !this.$el.is( ':visible' ) ){ - this.indicator.show( 0, callback ); - } else { - this.$el.fadeOut( speed ); - this.indicator.show( msg, speed, callback ); - } - }, - - /** hide the loading indicator */ - _hideLoadingIndicator : function( speed, callback ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - if( this.indicator ){ - this.indicator.hide( speed, callback ); - } - }, - - // ------------------------------------------------------------------------ scrolling - /** get the current scroll position of the panel in its parent */ - scrollPosition : function(){ - return this.$scrollContainer().scrollTop(); - }, - - /** set the current scroll position of the panel in its parent */ - scrollTo : function( pos ){ - this.$scrollContainer().scrollTop( pos ); - return this; - }, - - /** Scrolls the panel to the top. */ - scrollToTop : function(){ - this.$scrollContainer().scrollTop( 0 ); - return this; - }, - - /** */ - scrollToItem : function( view ){ - if( !view ){ return; } - var itemTop = view.$el.offset().top; - this.$scrollContainer().scrollTop( itemTop ); - }, - - // ------------------------------------------------------------------------ panel events - /** event map */ - events : { - 'click .select-all' : 'selectAll', - 'click .deselect-all' : 'deselectAll' - }, - - // ------------------------------------------------------------------------ misc - /** Return a string rep of the history */ - toString : function(){ - return 'ListPanel(' + this.collection + ')'; - } -}); - -// ............................................................................ TEMPLATES -/** underscore templates */ -ListPanel.prototype.templates = (function(){ -//TODO: move to require text! plugin - - var elTemplate = BASE_MVC.wrapTemplate([ - // temp container - '<div>', - '<div class="controls">', - '<div class="title">', - '<div class="name"><%= model.name || view.title %></div>', - '</div>', - '<div class="subtitle"><%= view.subtitle %></div>', - '<div class="actions"></div>', - '<div class="messages"></div>', - - '<div class="search">', - '<div class="search-input"></div>', - '</div>', - - '<div class="list-actions">', - '<div class="btn-group">', - '<button class="select-all btn btn-default"', - 'data-mode="select">', _l( 'All' ), '</button>', - '<button class="deselect-all btn btn-default"', - 'data-mode="select">', _l( 'None' ), '</button>', - '</div>', - //'<button class="action-popup-btn btn btn-default">', - // _l( 'For all selected' ), '...', - //'</button>', - '</div>', - '</div>', - '<div class="list-items"></div>', - '<div class="empty-message infomessagesmall"></div>', - '</div>' - ]); - - return { - el : elTemplate - }; -}()); - - - -//============================================================================== - return { - ListPanel: ListPanel - }; -}); diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/history/hda-li.js --- a/static/scripts/mvc/history/hda-li.js +++ b/static/scripts/mvc/history/hda-li.js @@ -17,12 +17,12 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, + className : _super.prototype.className + " history-content", + initialize : function( attributes, options ){ _super.prototype.initialize.call( this, attributes, options ); }, - className : _super.prototype.className + " history-content", - // ......................................................................... misc /** String representation */ toString : function(){ diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/history/history-contents.js --- a/static/scripts/mvc/history/history-contents.js +++ b/static/scripts/mvc/history/history-contents.js @@ -53,6 +53,7 @@ */ initialize : function( models, options ){ options = options || {}; +//TODO: could probably use the contents.history_id instead this.historyId = options.historyId; //this._setUpListeners(); @@ -226,7 +227,7 @@ if( !existing ){ return model; } // merge the models _BEFORE_ calling the superclass version - var merged = existing.toJSON(); + var merged = _.clone( existing.attributes ); _.extend( merged, model ); return merged; }); @@ -303,6 +304,13 @@ return xhr; }, + /** In this override, copy the historyId to the clone */ + clone : function(){ + var clone = Backbone.Collection.prototype.clone.call( this ); + clone.historyId = this.historyId; + return clone; + }, + /** debugging */ print : function(){ var contents = this; diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -232,7 +232,7 @@ /** Get data for a history then its hdas using a sequential ajax call, return a deferred to receive both */ History.getHistoryData = function getHistoryData( historyId, options ){ options = options || {}; - var hdaDetailIds = options.hdaDetailIds || []; + var detailIdsFn = options.detailIdsFn || []; var hdcaDetailIds = options.hdcaDetailIds || []; //console.debug( 'getHistoryData:', historyId, options ); @@ -250,20 +250,20 @@ // get the number of hdas accrd. to the history return historyData && historyData.empty; } - function getHdas( historyData ){ + function getContents( historyData ){ // get the hda data // if no hdas accrd. to history: return empty immed. if( isEmpty( historyData ) ){ return []; } // if there are hdas accrd. to history: get those as well - if( _.isFunction( hdaDetailIds ) ){ - hdaDetailIds = hdaDetailIds( historyData ); + if( _.isFunction( detailIdsFn ) ){ + detailIdsFn = detailIdsFn( historyData ); } if( _.isFunction( hdcaDetailIds ) ){ hdcaDetailIds = hdcaDetailIds( historyData ); } var data = {}; - if( hdaDetailIds.length ) { - data.dataset_details = hdaDetailIds.join( ',' ); + if( detailIdsFn.length ) { + data.dataset_details = detailIdsFn.join( ',' ); } if( hdcaDetailIds.length ) { // for symmetry, not actually used by backend of consumed @@ -274,10 +274,10 @@ } // getting these concurrently is 400% slower (sqlite, local, vanilla) - so: - // chain the api calls - getting history first then hdas + // chain the api calls - getting history first then contents var historyFn = options.historyFn || getHistory, - hdaFn = options.hdaFn || getHdas; + contentsFn = options.contentsFn || getContents; // chain ajax calls: get history first, then hdas var historyXHR = historyFn( historyId ); @@ -291,15 +291,15 @@ df.reject( xhr, 'loading the history' ); }); - var hdaXHR = historyXHR.then( hdaFn ); - hdaXHR.then( function( hdaJSON ){ - df.notify({ status: 'dataset data retrieved', historyJSON: historyJSON, hdaJSON: hdaJSON }); + var contentsXHR = historyXHR.then( contentsFn ); + contentsXHR.then( function( contentsJSON ){ + df.notify({ status: 'contents data retrieved', historyJSON: historyJSON, contentsJSON: contentsJSON }); // we've got both: resolve the outer scope deferred - df.resolve( historyJSON, hdaJSON ); + df.resolve( historyJSON, contentsJSON ); }); - hdaXHR.fail( function( xhr, status, message ){ + contentsXHR.fail( function( xhr, status, message ){ // call reject on the outer deferred to allow its fail callback to run - df.reject( xhr, 'loading the datasets', { history: historyJSON } ); + df.reject( xhr, 'loading the contents', { history: historyJSON } ); }); return df; diff -r 6f06ff96d5cacd8cd73b9a7e50d43aff5322dc17 -r 74b2495de918c95730f1f2fd2ac1bf502018a99f static/scripts/mvc/history/history-panel-annotated.js --- a/static/scripts/mvc/history/history-panel-annotated.js +++ b/static/scripts/mvc/history/history-panel-annotated.js @@ -1,118 +1,97 @@ define([ "mvc/history/history-panel", "mvc/history/hda-li", + "mvc/history/hdca-li", + "mvc/base-mvc", "utils/localization" -], function( HPANEL, HDA_LI, _l ){ +], function( HPANEL, HDA_LI, HDCA_LI, BASE_MVC, _l ){ /* ============================================================================= TODO: ============================================================================= */ -var _super = HPANEL.ReadOnlyHistoryPanel; +var _super = HPANEL.HistoryPanel; // used in history/display.mako and history/embed.mako /** @class View/Controller for a tabular view of the history model. - * @name AnnotatedHistoryPanel * * As ReadOnlyHistoryPanel, but with: * history annotation always shown * datasets displayed in a table: * datasets in left cells, dataset annotations in the right - * - * @augments Backbone.View - * @borrows LoggableMixin#logger as #logger - * @borrows LoggableMixin#log as #log - * @constructs */ var AnnotatedHistoryPanel = _super.extend( /** @lends AnnotatedHistoryPanel.prototype */{ /** logger used to record this.log messages, commonly set to console */ - // comment this out to suppress log output //logger : console, - className : 'annotated-history-panel', - - //TODO:?? possibly into own annotated class - /** class to use for constructing the HDA views */ - //HDAViewClass : HDA_LI.HDAListItemView, + className : _super.prototype.className + ' annotated-history-panel', // ------------------------------------------------------------------------ panel rendering - /** render with history data - * In this override: - * replace the datasets list with a table, - * add the history annotation, - * and move the search controls - * @returns {jQuery} dom fragment as temporary container to be swapped out later + /** In this override, add the history annotation */ - renderModel : function( ){ - // why do we need this here? why isn't className being applied? - this.$el.addClass( this.className ); - var $newRender = _super.prototype.renderModel.call( this ), - // move datasets from div to table - $datasetsList = this.$datasetsList( $newRender ), - $datasetsTable = $( '<table/>' ).addClass( 'datasets-list datasets-table' ); - $datasetsTable.append( $datasetsList.children() ); - $datasetsList.replaceWith( $datasetsTable ); - //TODO: it's possible to do this with css only, right? display: table-cell, etc.? - - // add history annotation under subtitle - $newRender.find( '.history-subtitle' ).after( this.renderHistoryAnnotation() ); - - // hide search button, move search bar beneath controls (instead of above title), show, and set up - $newRender.find( '.history-search-btn' ).hide(); - $newRender.find( '.history-controls' ).after( $newRender.find( '.history-search-controls' ).show() ); - + _buildNewRender : function(){ + //TODO: shouldn't this display regardless (on all non-current panels)? + var $newRender = _super.prototype._buildNewRender.call( this ); + this.renderHistoryAnnotation( $newRender ); return $newRender; }, /** render the history's annotation as its own field */ - renderHistoryAnnotation : function(){ + renderHistoryAnnotation : function( $newRender ){ var annotation = this.model.get( 'annotation' ); - if( !annotation ){ return null; } - return $([ - '<div class="history-annotation">', annotation, '</div>' - ].join( '' )); + if( !annotation ){ return; } + $newRender.find( '.controls .annotation-display' ).text( annotation ); }, - /** Set up/render a view for each HDA to be shown, init with model and listeners. - * In this override, add table header cells to indicate the dataset, annotation columns + /** In this override, convert the list-items tag to a table + * and add table header cells to indicate the dataset, annotation columns */ - renderHdas : function( $whereTo ){ + renderItems : function( $whereTo ){ $whereTo = $whereTo || this.$el; - var hdaViews = _super.prototype.renderHdas.call( this, $whereTo ); - this.$datasetsList( $whereTo ).prepend( $( '<tr/>' ).addClass( 'headers' ).append([ - $( '<th/>' ).text( _l( 'Dataset' ) ), - $( '<th/>' ).text( _l( 'Annotation' ) ) - ])); - return hdaViews; + + // convert to table + $whereTo.find( '.list-items' ) + .replaceWith( $( '<table/>' ).addClass( 'list-items' ) ); + + // render rows/contents and prepend headers + var views = _super.prototype.renderItems.call( this, $whereTo ); + this.$list( $whereTo ) + .prepend( $( '<tr/>' ).addClass( 'headers' ).append([ + $( '<th/>' ).text( _l( 'Dataset' ) ), + $( '<th/>' ).text( _l( 'Annotation' ) ) + ])); + return views; }, - // ------------------------------------------------------------------------ hda sub-views - /** attach an hdaView to the panel - * In this override, wrap the hdaView in a table row and cell, adding a 2nd cell for the hda annotation + // ------------------------------------------------------------------------ sub-views + /** In this override, wrap the content view in a table row + * with the content in the left td and annotation/extra-info in the right */ - attachContentView : function( hdaView, $whereTo ){ - $whereTo = $whereTo || this.$el; - // build a row around the dataset with the std hdaView in the first cell and the annotation in the next - var stateClass = _.find( hdaView.el.classList, function( c ){ return ( /^state\-/ ).test( c ); }), - annotation = hdaView.model.get( 'annotation' ) || '', - $tr = $( '<tr/>' ).addClass( 'dataset-row' ).append([ - $( '<td/>' ).addClass( 'dataset-container' ).append( hdaView.$el ) - // visually match the cell bg to the dataset at runtime (prevents the empty space) - // (getting bg via jq on hidden elem doesn't work on chrome/webkit - so use states) - //.css( 'background-color', hdaView.$el.css( 'background-color' ) ), - .addClass( stateClass? stateClass.replace( '-', '-color-' ): '' ), - $( '<td/>' ).addClass( 'additional-info' ).text( annotation ) - ]); - this.$datasetsList( $whereTo ).append( $tr ); + _attachItems : function( $whereTo ){ + this.$list( $whereTo ).append( this.views.map( function( view ){ + //TODO:?? possibly make this more flexible: instead of annotation use this._additionalInfo() + // build a row around the dataset with the std itemView in the first cell and the annotation in the next + var stateClass = _.find( view.el.classList, function( c ){ return ( /^state\-/ ).test( c ); }), + annotation = view.model.get( 'annotation' ) || '', + $tr = $( '<tr/>' ).append([ + $( '<td/>' ).addClass( 'contents-container' ).append( view.$el ) + // visually match the cell bg to the dataset at runtime (prevents the empty space) + // (getting bg via jq on hidden elem doesn't work on chrome/webkit - so use states) + //.css( 'background-color', view.$el.css( 'background-color' ) ), + .addClass( stateClass? stateClass.replace( '-', '-color-' ): '' ), + $( '<td/>' ).addClass( 'additional-info' ).text( annotation ) + ]); + return $tr; + })); + return this; }, // ------------------------------------------------------------------------ panel events /** event map */ events : _.extend( _.clone( _super.prototype.events ), { + // clicking on any part of the row will expand the items 'click tr' : function( ev ){ - //if( !ev.target.hasAttribute( 'href' ) ){ - $( ev.currentTarget ).find( '.dataset-title-bar' ).click(); - //} + $( ev.currentTarget ).find( '.title-bar' ).click(); }, // prevent propagation on icon btns so they won't bubble up to tr and toggleBodyVisibility 'click .icon-btn' : function( ev ){ @@ -127,6 +106,7 @@ } }); + //============================================================================== return { AnnotatedHistoryPanel : AnnotatedHistoryPanel This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Fix to b0c8da2: fix collapse call to curr panel in options; Browser tests: fix history selectors, misc. fixes
by commits-noreply＠bitbucket.org 09 Sep '14

09 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b4e8b3080281/ Changeset: b4e8b3080281 User: carlfeberhard Date: 2014-09-09 16:09:06 Summary: Fix to b0c8da2: fix collapse call to curr panel in options; Browser tests: fix history selectors, misc. fixes Affected #: 8 files diff -r fbf45bfcdd19ce116a083a0742603234c91bc461 -r b4e8b308028162d72c4c393e1c876f1a17b2a614 templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -66,7 +66,7 @@ }, "${_("Collapse Expanded Datasets")}": function() { if( Galaxy && Galaxy.currHistoryPanel ){ - Galaxy.currHistoryPanel.collapseAllHdaBodies(); + Galaxy.currHistoryPanel.collapseAll(); } }, "${_("Include Deleted Datasets")}": function( clickEvent, thisMenuOption ) { diff -r fbf45bfcdd19ce116a083a0742603234c91bc461 -r b4e8b308028162d72c4c393e1c876f1a17b2a614 test/casperjs/anon-history-tests.js --- a/test/casperjs/anon-history-tests.js +++ b/test/casperjs/anon-history-tests.js @@ -23,7 +23,7 @@ unnamedName = spaceghost.historypanel.data.text.history.newName, nameSelector = spaceghost.historypanel.data.selectors.history.name, - subtitleSelector = spaceghost.historypanel.data.selectors.history.subtitle, + sizeSelector = spaceghost.historypanel.data.selectors.history.size, initialSizeStr = spaceghost.historypanel.data.text.history.newSize, tagIconSelector = spaceghost.historypanel.data.selectors.history.tagIcon, annoIconSelector = spaceghost.historypanel.data.selectors.history.annoIcon, @@ -47,11 +47,11 @@ this.test.assertVisible( nameSelector, 'History name is visible' ); this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); - this.test.comment( "history subtitle should display size and size should be 0 bytes" ); - this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); - this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); - this.test.assertSelectorHasText( subtitleSelector, initialSizeStr, - 'History subtitle has "' + initialSizeStr + '"' ); + this.test.comment( "history should display size and size should be 0 bytes" ); + this.test.assertExists( sizeSelector, 'Found ' + sizeSelector ); + this.test.assertVisible( sizeSelector, 'History size is visible' ); + this.test.assertSelectorHasText( sizeSelector, initialSizeStr, + 'History size has "' + initialSizeStr + '"' ); this.test.comment( "NO tags or annotations icons should be available for an anonymous user" ); this.test.assertDoesntExist( tagIconSelector, 'Tag icon button not found' ); diff -r fbf45bfcdd19ce116a083a0742603234c91bc461 -r b4e8b308028162d72c4c393e1c876f1a17b2a614 test/casperjs/api-anon-history-tests.js --- a/test/casperjs/api-anon-history-tests.js +++ b/test/casperjs/api-anon-history-tests.js @@ -8,7 +8,7 @@ spaceghost.start(); // =================================================================== TESTS -spaceghost.thenOpen( spaceghost.baseUrl ).waitForSelector( '.history-name' ); +spaceghost.thenOpen( spaceghost.baseUrl ).waitForSelector( spaceghost.historypanel.data.selectors.history.name ); spaceghost.then( function(){ // ------------------------------------------------------------------------------------------- anon allowed @@ -65,7 +65,7 @@ }); // ------------------------------------------------------------------------------------------- hdas -spaceghost.thenOpen( spaceghost.baseUrl ).waitForSelector( '.history-name' ); +spaceghost.thenOpen( spaceghost.baseUrl ).waitForSelector( spaceghost.historypanel.data.selectors.history.name ); spaceghost.then( function(){ spaceghost.tools.uploadFile( '../../test-data/1.sam', function( uploadInfo ){ this.test.assert( uploadInfo.hdaElement !== null, "Convenience function produced hda" ); diff -r fbf45bfcdd19ce116a083a0742603234c91bc461 -r b4e8b308028162d72c4c393e1c876f1a17b2a614 test/casperjs/history-panel-tests.js --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -27,6 +27,7 @@ nameSelector = spaceghost.historypanel.data.selectors.history.name, subtitleSelector = spaceghost.historypanel.data.selectors.history.subtitle, + sizeSelector = spaceghost.historypanel.data.selectors.history.size, unnamedName = spaceghost.historypanel.data.text.history.newName, initialSizeStr = spaceghost.historypanel.data.text.history.newSize, tagIconSelector = spaceghost.historypanel.data.selectors.history.tagIcon, @@ -64,11 +65,11 @@ this.test.assertVisible( nameSelector, 'History name is visible' ); this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); - this.test.comment( "history subtitle should display size and size should be: " + initialSizeStr ); - this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); - this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); - this.test.assertSelectorHasText( subtitleSelector, initialSizeStr, - 'History subtitle has "' + initialSizeStr + '"' ); + this.test.comment( "history should display size and size should be: " + initialSizeStr ); + this.test.assertExists( sizeSelector, 'Found ' + sizeSelector ); + this.test.assertVisible( sizeSelector, 'History size is visible' ); + this.test.assertSelectorHasText( sizeSelector, initialSizeStr, + 'History size has "' + initialSizeStr + '"' ); this.test.comment( "tags and annotation icons should be available" ); this.test.assertExists( tagIconSelector, 'Tag icon button found' ); @@ -157,12 +158,12 @@ this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); var onetxtFilesize = require( 'fs' ).size( filepathToUpload ), - expectedSubtitle = onetxtFilesize + ' bytes'; - this.test.comment( "history subtitle should display size and size should be " + onetxtFilesize + " bytes" ); - this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); - this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); - this.test.assertSelectorHasText( subtitleSelector, expectedSubtitle, - 'History subtitle has "' + expectedSubtitle + '": ' + this.fetchText( subtitleSelector ).trim() ); + expectedSize = onetxtFilesize + ' bytes'; + this.test.comment( "history should display size and size should be " + onetxtFilesize + " bytes" ); + this.test.assertExists( sizeSelector, 'Found ' + sizeSelector ); + this.test.assertVisible( sizeSelector, 'History size is visible' ); + this.test.assertSelectorHasText( sizeSelector, expectedSize, + 'History size has "' + expectedSize + '": ' + this.fetchText( sizeSelector ).trim() ); this.test.comment( "tags and annotation icons should be available" ); this.test.assertExists( tagIconSelector, 'Tag icon button found' ); diff -r fbf45bfcdd19ce116a083a0742603234c91bc461 -r b4e8b308028162d72c4c393e1c876f1a17b2a614 test/casperjs/login-tests.js --- a/test/casperjs/login-tests.js +++ b/test/casperjs/login-tests.js @@ -17,7 +17,8 @@ password = spaceghost.fixtureData.testUser.password; } -var userEmailSelector = '//a[contains(text(),"Logged in as")]'; +//var userEmailSelector = '//a[contains(text(),"Logged in as")]'; +var userEmailSelector = spaceghost.data.selectors.masthead.userMenu.userEmail_xpath; // =================================================================== TESTS // register a user (again...) diff -r fbf45bfcdd19ce116a083a0742603234c91bc461 -r b4e8b308028162d72c4c393e1c876f1a17b2a614 test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -356,15 +356,16 @@ }, selectors : { history : { - title : '.history-title', - name : '.history-title .history-name', - nameEditableTextInput : '.history-name input', - subtitle : '.history-subtitle', - tagIcon : '.history-secondary-actions .history-tag-btn', - tagArea : '.history-controls .tags-display', - annoIcon : '.history-secondary-actions .history-annotate-btn', - annoArea : '.history-controls .annotation-display', - emptyMsg : '.empty-history-message', + title : '.controls .title', + name : '.title .name', + nameEditableTextInput : '.name input', + subtitle : '.subtitle', + size : '.history-size', + tagIcon : '.actions .history-tag-btn', + tagArea : '.controls .tags-display', + annoIcon : '.actions .history-annotate-btn', + annoArea : '.controls .annotation-display', + emptyMsg : '.empty-message', hdaContainer: '.datasets-list' }, hda : { diff -r fbf45bfcdd19ce116a083a0742603234c91bc461 -r b4e8b308028162d72c4c393e1c876f1a17b2a614 test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -56,14 +56,14 @@ // need manual submit (not a normal html form) this.click( xpath( spaceghost.data.selectors.registrationPage.submit_xpath ) ); }); + this.waitForNavigation( 'user/create', function afterRegister(){ + // this.withMainPanel( function mainAfterRegister(){ + // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); + // spaceghost.debug( 'post registration message:\n' + spaceghost.jsonStr( messageInfo ) ); + // }); + }); }); - this.waitForNavigation( 'user/create', function afterRegister(){ - // this.withMainPanel( function mainAfterRegister(){ - // var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); - // spaceghost.debug( 'post registration message:\n' + spaceghost.jsonStr( messageInfo ) ); - // }); - }); }); }; diff -r fbf45bfcdd19ce116a083a0742603234c91bc461 -r b4e8b308028162d72c4c393e1c876f1a17b2a614 test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -638,7 +638,7 @@ } function catchNavReq( url ){ - //this.debug( 'nav.req: ' + url ); + this.debug( 'nav.req: ' + url ); for( var i=( urlsToWaitFor.length - 1 ); i>=0; i -= 1 ){ //this.debug( '\t checking: ' + urlsToWaitFor[i] ); if( urlMatches( urlsToWaitFor[i], url ) ){ 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: jmchilton: Recreate run_functional_tests.sh as symbolic link to run_tests.sh.
by commits-noreply＠bitbucket.org 09 Sep '14

09 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fbf45bfcdd19/ Changeset: fbf45bfcdd19 User: jmchilton Date: 2014-09-09 14:29:45 Summary: Recreate run_functional_tests.sh as symbolic link to run_tests.sh. It is deprecated and will be removed someday - but we should mention in it more explicitly in a dev news brief and give it a few releases. See also Peter's comments on https://bitbucket.org/galaxy/galaxy-central/commits/6b26b7df6924de890ee547f…. Affected #: 1 file diff -r 45a68696164451320e07537fa6fb8872686f710d -r fbf45bfcdd19ce116a083a0742603234c91bc461 run_functional_tests.sh --- /dev/null +++ b/run_functional_tests.sh @@ -0,0 +1,1 @@ +run_tests.sh \ 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: carlfeberhard: Cleanup b0c8da2
by commits-noreply＠bitbucket.org 09 Sep '14

09 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/45a686961644/ Changeset: 45a686961644 User: carlfeberhard Date: 2014-09-08 22:56:07 Summary: Cleanup b0c8da2 Affected #: 10 files diff -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca -r 45a68696164451320e07537fa6fb8872686f710d static/scripts/mvc/collection/collection-li.js --- a/static/scripts/mvc/collection/collection-li.js +++ b/static/scripts/mvc/collection/collection-li.js @@ -98,8 +98,7 @@ //TODO: this might be expendable - compacted with HDAListItemView /** logger used to record this.log messages, commonly set to console */ - // comment this out to suppress log output - logger : console, + //logger : console, /** add the DCE class to the list item */ className : ListItemView.prototype.className + " dataset-collection-element", diff -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca -r 45a68696164451320e07537fa6fb8872686f710d static/scripts/mvc/collection/collection-panel.js --- a/static/scripts/mvc/collection/collection-panel.js +++ b/static/scripts/mvc/collection/collection-panel.js @@ -18,7 +18,7 @@ //MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs) /** logger used to record this.log messages, commonly set to console */ - logger : console, + //logger : console, className : _super.prototype.className + ' dataset-collection-panel', @@ -41,7 +41,7 @@ this.panelStack = []; this.parentName = attributes.parentName; - window.collectionPanel = this; + //window.collectionPanel = this; }, // ------------------------------------------------------------------------ sub-views diff -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca -r 45a68696164451320e07537fa6fb8872686f710d static/scripts/mvc/history/history-panel-edit-current.js --- a/static/scripts/mvc/history/history-panel-edit-current.js +++ b/static/scripts/mvc/history/history-panel-edit-current.js @@ -131,7 +131,6 @@ // if a hidden item is created (gen. by a workflow), moves thru the updater to the ready state, // then: remove it from the collection if the panel is set to NOT show hidden datasets this.collection.on( 'state:ready', function( model, newState, oldState ){ - console.debug( 'state:ready', model, newState, model.get( 'visible' ), this.storage.get( 'show_hidden' ) ); if( ( !model.get( 'visible' ) ) && ( !this.storage.get( 'show_hidden' ) ) ){ this.removeItemView( this.viewFromModel( model ) ); @@ -274,7 +273,6 @@ }); panel.panelStack.push( overlaid ); - console.debug( panel.$( '.controls' ).add( panel.$list() ) ); panel.$( '.controls' ).add( panel.$list() ).hide(); panel.$el.append( overlaid.$el ); overlaid.on( 'close', function(){ diff -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca -r 45a68696164451320e07537fa6fb8872686f710d static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -429,14 +429,11 @@ // if sentry is available, attempt to get the event id var parsed = this._parseErrorMessage( model, xhr, options, msg, details ); // it's possible to have a triggered error before the message container is rendered - wait for it to show - console.debug( this.$messages(), this.$messages().is( ':visible' ) ); if( !this.$messages().is( ':visible' ) ){ - console.debug( 'parsing error - waiting for render', model, xhr, options, msg, details ); this.once( 'rendered', function(){ this.displayMessage( 'error', parsed.message, parsed.details ); }); } else { - console.debug( 'parsing error - showing', model, xhr, options, msg, details ); this.displayMessage( 'error', parsed.message, parsed.details ); } } @@ -543,7 +540,6 @@ /** Remove all messages from the panel. */ clearMessages : function( ev ){ - console.debug( ev.currentTarget ); $( ev.currentTarget ).fadeOut( this.fxSpeed, function(){ $( this ).remove(); }); diff -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca -r 45a68696164451320e07537fa6fb8872686f710d static/scripts/mvc/list/list-panel.js --- a/static/scripts/mvc/list/list-panel.js +++ b/static/scripts/mvc/list/list-panel.js @@ -419,7 +419,6 @@ _renderEmptyMessage : function( $whereTo ){ this.debug( '_renderEmptyMessage', $whereTo, this.searchFor ); var text = this.searchFor? this.noneFoundMsg : this.emptyMsg; - console.debug( this.$emptyMessage( $whereTo ) ); return this.$emptyMessage( $whereTo ).text( text ); }, diff -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca -r 45a68696164451320e07537fa6fb8872686f710d static/scripts/packed/mvc/collection/collection-li.js --- a/static/scripts/packed/mvc/collection/collection-li.js +++ b/static/scripts/packed/mvc/collection/collection-li.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,h,i,d){var e=a.ListItemView;var c=e.extend({className:e.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},fxSpeed:"fast",initialize:function(j){if(j.logger){this.logger=this.model.logger=j.logger}this.log(this+"(DCListItemView).initialize:",j);e.prototype.initialize.call(this,j)},expand:function(){var j=this;return j._fetchModelDetails().always(function(){j.trigger("expanded",j)})},_renderSubtitle:function(){var j=$('<div class="subtitle"></div>');switch(this.model.get("collection_type")){case"list":return j.text(d("a list of datasets"));case"paired":return j.text(d("a pair of datasets"));case"list:paired":return j.text(d("a list of paired datasets"))}return j},toString:function(){var j=(this.model)?(this.model+""):("(no model)");return"DCListItemView("+j+")"}});c.prototype.templates=(function(){var j=i.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},e.prototype.templates,{titleBar:j})}());var f=e.extend({logger:console,className:e.prototype.className+" dataset-collection-element",fxSpeed:"fast",initialize:function(j){if(j.logger){this.logger=this.model.logger=j.logger}this.log("DCEListItemView.initialize:",j);e.prototype.initialize.call(this,j)},toString:function(){var j=(this.model)?(this.model+""):("(no model)");return"DCEListItemView("+j+")"}});f.prototype.templates=(function(){var j=i.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return _.extend({},e.prototype.templates,{titleBar:j})}());var b=h.DatasetListItemView.extend({className:h.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(j){if(j.logger){this.logger=this.model.logger=j.logger}this.log("DatasetDCEListItemView.initialize:",j);h.DatasetListItemView.prototype.initialize.call(this,j)},toString:function(){var j=(this.model)?(this.model+""):("(no model)");return"DatasetDCEListItemView("+j+")"}});b.prototype.templates=(function(){var j=i.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return _.extend({},h.DatasetListItemView.prototype.templates,{titleBar:j})}());var g=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(j){c.prototype._swapNewRender.call(this,j);var k=this.model.get("state")||"ok";this.$el.addClass("state-"+k);return this.$el},toString:function(){var j=(this.model)?(this.model+""):("(no model)");return"NestedDCDCEListItemView("+j+")"}});return{DCListItemView:c,DCEListItemView:f,DatasetDCEListItemView:b,NestedDCDCEListItemView:g}}); \ No newline at end of file +define(["mvc/list/list-item","mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,h,i,d){var e=a.ListItemView;var c=e.extend({className:e.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},fxSpeed:"fast",initialize:function(j){if(j.logger){this.logger=this.model.logger=j.logger}this.log(this+"(DCListItemView).initialize:",j);e.prototype.initialize.call(this,j)},expand:function(){var j=this;return j._fetchModelDetails().always(function(){j.trigger("expanded",j)})},_renderSubtitle:function(){var j=$('<div class="subtitle"></div>');switch(this.model.get("collection_type")){case"list":return j.text(d("a list of datasets"));case"paired":return j.text(d("a pair of datasets"));case"list:paired":return j.text(d("a list of paired datasets"))}return j},toString:function(){var j=(this.model)?(this.model+""):("(no model)");return"DCListItemView("+j+")"}});c.prototype.templates=(function(){var j=i.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},e.prototype.templates,{titleBar:j})}());var f=e.extend({className:e.prototype.className+" dataset-collection-element",fxSpeed:"fast",initialize:function(j){if(j.logger){this.logger=this.model.logger=j.logger}this.log("DCEListItemView.initialize:",j);e.prototype.initialize.call(this,j)},toString:function(){var j=(this.model)?(this.model+""):("(no model)");return"DCEListItemView("+j+")"}});f.prototype.templates=(function(){var j=i.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return _.extend({},e.prototype.templates,{titleBar:j})}());var b=h.DatasetListItemView.extend({className:h.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(j){if(j.logger){this.logger=this.model.logger=j.logger}this.log("DatasetDCEListItemView.initialize:",j);h.DatasetListItemView.prototype.initialize.call(this,j)},toString:function(){var j=(this.model)?(this.model+""):("(no model)");return"DatasetDCEListItemView("+j+")"}});b.prototype.templates=(function(){var j=i.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return _.extend({},h.DatasetListItemView.prototype.templates,{titleBar:j})}());var g=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(j){c.prototype._swapNewRender.call(this,j);var k=this.model.get("state")||"ok";this.$el.addClass("state-"+k);return this.$el},toString:function(){var j=(this.model)?(this.model+""):("(no model)");return"NestedDCDCEListItemView("+j+")"}});return{DCListItemView:c,DCEListItemView:f,DatasetDCEListItemView:b,NestedDCDCEListItemView:g}}); \ No newline at end of file diff -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca -r 45a68696164451320e07537fa6fb8872686f710d static/scripts/packed/mvc/collection/collection-panel.js --- a/static/scripts/packed/mvc/collection/collection-panel.js +++ b/static/scripts/packed/mvc/collection/collection-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-panel","mvc/collection/collection-model","mvc/collection/collection-li","mvc/base-mvc","utils/localization"],function(a,d,f,j,b){var h=a.ModelListPanel;var g=h.extend({logger:console,className:h.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:f.DatasetDCEListItemView,NestedDCDCEViewClass:f.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(k){h.prototype.initialize.call(this,k);this.linkTarget=k.linkTarget||"_blank";this.hasUser=k.hasUser;this.panelStack=[];this.parentName=k.parentName;window.collectionPanel=this},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(k){switch(k.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",k.get("element_type"))},_getItemViewOptions:function(l){var k=h.prototype._getItemViewOptions.call(this,l);return _.extend(k,{linkTarget:this.linkTarget,hasUser:this.hasUser})},_setUpItemViewListeners:function(l){var k=this;h.prototype._setUpItemViewListeners.call(k,l);if(l.model.get("element_type")==="dataset_collection"){l.on("expanded",function(m){k.info("expanded",m);k._addCollectionPanel(m)})}return k},_addCollectionPanel:function(m){var n=this,k=m.model;var l=new i({model:k,parentName:this.model.get("name"),linkTarget:this.linkTarget});n.panelStack.push(l);n.$(".controls").add(".list-items").hide();n.$el.append(l.$el);l.on("close",function(){n.render();m.collapse();n.panelStack.pop()});if(!l.model.hasDetails()){var o=l.model.fetch();o.done(function(){l.render()})}else{l.render()}},events:{"click .navigation .back":"close"},close:function(k){this.$el.remove();this.trigger("close")},toString:function(){return"CollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});g.prototype.templates=(function(){var k=j.wrapTemplate(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',b("Back to "),"<%- view.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.collection_type === "list" ){ %>',b("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',b("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',b("a list of paired datasets"),"<% } %>","</div>","</div>","</div>"],"collection");return _.extend(_.clone(h.prototype.templates),{controls:k})}());var e=g.extend({DatasetDCEViewClass:f.DatasetDCEListItemView,toString:function(){return"ListCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var i=e.extend({toString:function(){return"PairCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var c=g.extend({NestedDCDCEViewClass:f.NestedDCDCEListItemView,toString:function(){return"ListOfPairsCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CollectionPanel:g,ListCollectionPanel:e,PairCollectionPanel:i,ListOfPairsCollectionPanel:c}}); \ No newline at end of file +define(["mvc/list/list-panel","mvc/collection/collection-model","mvc/collection/collection-li","mvc/base-mvc","utils/localization"],function(a,d,f,j,b){var h=a.ModelListPanel;var g=h.extend({className:h.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:f.DatasetDCEListItemView,NestedDCDCEViewClass:f.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(k){h.prototype.initialize.call(this,k);this.linkTarget=k.linkTarget||"_blank";this.hasUser=k.hasUser;this.panelStack=[];this.parentName=k.parentName},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(k){switch(k.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",k.get("element_type"))},_getItemViewOptions:function(l){var k=h.prototype._getItemViewOptions.call(this,l);return _.extend(k,{linkTarget:this.linkTarget,hasUser:this.hasUser})},_setUpItemViewListeners:function(l){var k=this;h.prototype._setUpItemViewListeners.call(k,l);if(l.model.get("element_type")==="dataset_collection"){l.on("expanded",function(m){k.info("expanded",m);k._addCollectionPanel(m)})}return k},_addCollectionPanel:function(m){var n=this,k=m.model;var l=new i({model:k,parentName:this.model.get("name"),linkTarget:this.linkTarget});n.panelStack.push(l);n.$(".controls").add(".list-items").hide();n.$el.append(l.$el);l.on("close",function(){n.render();m.collapse();n.panelStack.pop()});if(!l.model.hasDetails()){var o=l.model.fetch();o.done(function(){l.render()})}else{l.render()}},events:{"click .navigation .back":"close"},close:function(k){this.$el.remove();this.trigger("close")},toString:function(){return"CollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});g.prototype.templates=(function(){var k=j.wrapTemplate(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',b("Back to "),"<%- view.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.collection_type === "list" ){ %>',b("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',b("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',b("a list of paired datasets"),"<% } %>","</div>","</div>","</div>"],"collection");return _.extend(_.clone(h.prototype.templates),{controls:k})}());var e=g.extend({DatasetDCEViewClass:f.DatasetDCEListItemView,toString:function(){return"ListCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var i=e.extend({toString:function(){return"PairCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var c=g.extend({NestedDCDCEViewClass:f.NestedDCDCEListItemView,toString:function(){return"ListOfPairsCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CollectionPanel:g,ListCollectionPanel:e,PairCollectionPanel:i,ListOfPairsCollectionPanel:c}}); \ No newline at end of file diff -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca -r 45a68696164451320e07537fa6fb8872686f710d static/scripts/packed/mvc/history/history-panel-edit-current.js --- a/static/scripts/packed/mvc/history/history-panel-edit-current.js +++ b/static/scripts/packed/mvc/history/history-panel-edit-current.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[]},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(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",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){console.debug("state:ready",k,l,k.get("visible"),this.storage.get("show_hidden"));if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_attachItems:function(j){this.$list(j).append(this.views.reverse().map(function(k){return k.$el}));return this},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);if(k instanceof j.HDCAViewClass){k.off("expanded");k.on("expanded",function(l){j.info("expanded",l);j._addCollectionPanel(l)});k.off("collapsed")}},_addCollectionPanel:function(l){var k=this,j=l.model;this.debug("history panel (stack), collectionModel:",j);var n=new (this._getCollectionPanelClass(j))({model:j,HDAViewClass:this.HDAViewClass,parentName:this.model.get("name"),linkTarget:this.linkTarget});k.panelStack.push(n);console.debug(k.$(".controls").add(k.$list()));k.$(".controls").add(k.$list()).hide();k.$el.append(n.$el);n.on("close",function(){k.render();l.collapse();k.panelStack.pop()});if(!n.model.hasDetails()){var m=n.model.fetch();m.done(function(){n.render()})}else{n.render()}},_getCollectionPanelClass:function(j){switch(j.get("collection_type")){case"list":return a.ListCollectionPanel;case"paired":return a.PairCollectionPanel;case"list:paired":return a.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+j.get("collection_type"))},addItemView:function(o,p,n){this.log(this+".addItemView:",o);if(!this._filterItem(o)){return undefined}var l=this;if(this.panelStack.length){return l}var k=l._createItemView(o);this.views.unshift(k);l.scrollToTop();$({}).queue([function m(r){var q=l.$emptyMessage();if(q.is(":visible")){q.fadeOut(l.fxSpeed,r)}else{r()}},function j(q){l.scrollToTop();l.$list().prepend(k.render(0).$el.hide());k.$el.slideDown(l.fxSpeed)}]);return k},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(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[]},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(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",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_attachItems:function(j){this.$list(j).append(this.views.reverse().map(function(k){return k.$el}));return this},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);if(k instanceof j.HDCAViewClass){k.off("expanded");k.on("expanded",function(l){j.info("expanded",l);j._addCollectionPanel(l)});k.off("collapsed")}},_addCollectionPanel:function(l){var k=this,j=l.model;this.debug("history panel (stack), collectionModel:",j);var n=new (this._getCollectionPanelClass(j))({model:j,HDAViewClass:this.HDAViewClass,parentName:this.model.get("name"),linkTarget:this.linkTarget});k.panelStack.push(n);k.$(".controls").add(k.$list()).hide();k.$el.append(n.$el);n.on("close",function(){k.render();l.collapse();k.panelStack.pop()});if(!n.model.hasDetails()){var m=n.model.fetch();m.done(function(){n.render()})}else{n.render()}},_getCollectionPanelClass:function(j){switch(j.get("collection_type")){case"list":return a.ListCollectionPanel;case"paired":return a.PairCollectionPanel;case"list:paired":return a.ListOfPairsCollectionPanel}throw new TypeError("Uknown collection_type: "+j.get("collection_type"))},addItemView:function(o,p,n){this.log(this+".addItemView:",o);if(!this._filterItem(o)){return undefined}var l=this;if(this.panelStack.length){return l}var k=l._createItemView(o);this.views.unshift(k);l.scrollToTop();$({}).queue([function m(r){var q=l.$emptyMessage();if(q.is(":visible")){q.fadeOut(l.fxSpeed,r)}else{r()}},function j(q){l.scrollToTop();l.$list().prepend(k.render(0).$el.hide());k.$el.slideDown(l.fxSpeed)}]);return k},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(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file diff -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca -r 45a68696164451320e07537fa6fb8872686f710d 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/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(d,f,l,b,a,g,n,e){var j=n.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:false,show_hidden:false},addExpandedHda:function(o){var p="expandedIds";this.save(p,_.extend(this.get(p),_.object([o.id],[o.get("id")])))},removeExpandedHda:function(o){var p="expandedIds";this.save(p,_.omit(this.get(p),o.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});j.storageKeyPrefix="history:";j.historyStorageKey=function h(o){if(!o){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+o)}return(j.storageKeyPrefix+o)};j.get=function c(o){return new j({id:j.historyStorageKey(o)})};j.clearAll=function i(p){for(var o in sessionStorage){if(o.indexOf(j.storageKeyPrefix)===0){sessionStorage.removeItem(o)}}};var m=d.ModelListPanel;var k=m.extend({HDAViewClass:b.HDAListItemView,HDCAViewClass:a.HDCAListItemView,collectionClass:l.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:m.prototype.className+" history-panel",emptyMsg:e("This history is empty"),noneFoundMsg:e("No matching datasets found"),searchPlaceholder:e("search datasets"),initialize:function(o){m.prototype.initialize.call(this,o);this.linkTarget=o.linkTarget||"_blank"},freeModel:function(){m.prototype.freeModel.call(this);if(this.model){this.model.clearUpdateTimeout()}return this},_setUpListeners:function(){m.prototype._setUpListeners.call(this);this.on("error",function(p,s,o,r,q){this.errorHandler(p,s,o,r,q)});this.on("loading-done",function(){if(!this.views.length){this.trigger("empty-history",this)}})},loadHistoryWithDetails:function(r,q,p,s){this.info("loadHistoryWithDetails:",r,q,p,s);var o=function(t){return _.values(j.get(t.id).get("expandedIds"))};return this.loadHistory(r,q,p,s,o)},loadHistory:function(s,r,q,t,o){this.info("loadHistory:",s,r,q,t,o);var p=this;r=r||{};p.trigger("loading",p);var u=f.History.getHistoryData(s,{historyFn:q,contentsFn:t,detailIdsFn:r.initiallyExpanded||o});return p._loadHistoryFromXHR(u,r).fail(function(x,v,w){p.trigger("error",p,x,r,e("An error was encountered while "+v),{historyId:s,history:w||{}})}).always(function(){p.trigger("loading-done",p)})},_loadHistoryFromXHR:function(q,p){var o=this;q.then(function(r,s){o.JSONToModel(r,s,p);o.render()});q.fail(function(s,r){o.render()});return q},JSONToModel:function(r,o,p){this.log("JSONToModel:",r,o,p);p=p||{};var q=new f.History(r,o,p);this.setModel(q);return q},setModel:function(p,o){o=o||{};m.prototype.setModel.call(this,p,o);if(this.model){this._setUpWebStorage(o.initiallyExpanded,o.show_deleted,o.show_hidden)}},_setUpWebStorage:function(p,o,q){this.storage=new j({id:j.historyStorageKey(this.model.get("id"))});if(_.isObject(p)){this.storage.set("expandedIds",p)}if(_.isBoolean(o)){this.storage.set("show_deleted",o)}if(_.isBoolean(q)){this.storage.set("show_hidden",q)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_buildNewRender:function(){var o=m.prototype._buildNewRender.call(this);if(this.multiselectActions.length){o.find(".controls .actions").prepend(this._renderSelectButton())}return o},_renderSelectButton:function(o){return faIconButton({title:e("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(o){var p=o.get("history_content_type");switch(p){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+p)},_filterItem:function(p){var o=this;return(m.prototype._filterItem.call(o,p)&&(!p.hidden()||o.storage.get("show_hidden"))&&(!p.isDeletedOrPurged()||o.storage.get("show_deleted")))},_getItemViewOptions:function(p){var o=m.prototype._getItemViewOptions.call(this,p);return _.extend(o,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[p.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(p){var o=this;m.prototype._setUpItemViewListeners.call(o,p);p.on("expanded",function(q){o.storage.addExpandedHda(q.model)});p.on("collapsed",function(q){o.storage.removeExpandedHda(q.model)});return this},refreshContents:function(p,o){if(this.model){return this.model.refresh(p,o)}return $.when()},getSelectedModels:function(){var o=m.prototype.getSelectedModels.call(this);o.historyId=this.collection.historyId;return o},events:_.extend(_.clone(m.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),toggleShowDeleted:function(o){o=(o!==undefined)?(o):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",o);this.renderItems();return this.storage.get("show_deleted")},toggleShowHidden:function(o){o=(o!==undefined)?(o):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",o);this.renderItems();return this.storage.get("show_hidden")},_firstSearch:function(o){var p=this,q=".history-search-input";this.log("onFirstSearch",o);if(p.model.contents.haveDetails()){p.searchItems(o);return}p.$el.find(q).searchInput("toggle-loading");p.model.contents.fetchAllDetails({silent:true}).always(function(){p.$el.find(q).searchInput("toggle-loading")}).done(function(){p.searchItems(o)})},errorHandler:function(q,t,p,s,r){this.error(q,t,p,s,r);if(t&&t.status===0&&t.readyState===0){}else{if(t&&t.status===502){}else{var o=this._parseErrorMessage(q,t,p,s,r);console.debug(this.$messages(),this.$messages().is(":visible"));if(!this.$messages().is(":visible")){console.debug("parsing error - waiting for render",q,t,p,s,r);this.once("rendered",function(){this.displayMessage("error",o.message,o.details)})}else{console.debug("parsing error - showing",q,t,p,s,r);this.displayMessage("error",o.message,o.details)}}}},_parseErrorMessage:function(s,v,w,q,o,t){var r=Galaxy.currUser,u={message:this._bePolite(q),details:{message:q,raven:(window.Raven&&_.isFunction(Raven.lastEventId))?(Raven.lastEventId()):(undefined),agent:navigator.userAgent,url:(window.Galaxy)?(Galaxy.lastAjax.url):(undefined),data:(window.Galaxy)?(Galaxy.lastAjax.data):(undefined),options:(v)?(_.omit(w,"xhr")):(w),xhr:v,source:(_.isFunction(s.toJSON))?(s.toJSON()):(s+""),user:(r instanceof g.User)?(r.toJSON()):(r+"")}};_.extend(u.details,o||{});if(v&&_.isFunction(v.getAllResponseHeaders)){var p=v.getAllResponseHeaders();p=_.compact(p.split("\n"));p=_.map(p,function(x){return x.split(": ")});u.details.xhr.responseHeaders=_.object(p)}return u},_bePolite:function(o){o=o||e("An error occurred while getting updates from the server");return o+". "+e("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(t,u,s){var q=this;this.scrollToTop();var r=this.$messages(),o=$("<div/>").addClass(t+"message").html(u);if(!_.isEmpty(s)){var p=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(q._messageToModalOptions(t,u,s));return false});o.append(" ",p)}return r.html(o)},_messageToModalOptions:function(r,u,q){var o=this,p={title:"Details"};if(_.isObject(q)){q=_.omit(q,_.functions(q));var t=JSON.stringify(q,null," "),s=$("<pre/>").text(t);p.body=$("<div/>").append(s)}else{p.body=$("<div/>").html(q)}p.buttons={Ok:function(){Galaxy.modal.hide();o.clearMessages()}};return p},clearMessages:function(o){console.debug(o.currentTarget);$(o.currentTarget).fadeOut(this.fxSpeed,function(){$(this).remove()});return this},scrollToHid:function(o){return this.scrollToItem(_.first(this.viewsWhereModel({hid:o})))},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});k.prototype.templates=(function(){var o=n.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= history.name %></div>',"</div>",'<div class="subtitle">',"</div>",'<div class="history-size"><%= history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',e("This history has been deleted"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',e("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',e("None"),"</button>","</div>",'<button class="list-action-popup-btn btn btn-default">',e("For all selected"),"...</button>","</div>","</div>"],"history");return _.extend(_.clone(m.prototype.templates),{controls:o})}());return{HistoryPanel:k}}); \ No newline at end of file +define(["mvc/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(d,f,l,b,a,g,n,e){var j=n.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:false,show_hidden:false},addExpandedHda:function(o){var p="expandedIds";this.save(p,_.extend(this.get(p),_.object([o.id],[o.get("id")])))},removeExpandedHda:function(o){var p="expandedIds";this.save(p,_.omit(this.get(p),o.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});j.storageKeyPrefix="history:";j.historyStorageKey=function h(o){if(!o){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+o)}return(j.storageKeyPrefix+o)};j.get=function c(o){return new j({id:j.historyStorageKey(o)})};j.clearAll=function i(p){for(var o in sessionStorage){if(o.indexOf(j.storageKeyPrefix)===0){sessionStorage.removeItem(o)}}};var m=d.ModelListPanel;var k=m.extend({HDAViewClass:b.HDAListItemView,HDCAViewClass:a.HDCAListItemView,collectionClass:l.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:m.prototype.className+" history-panel",emptyMsg:e("This history is empty"),noneFoundMsg:e("No matching datasets found"),searchPlaceholder:e("search datasets"),initialize:function(o){m.prototype.initialize.call(this,o);this.linkTarget=o.linkTarget||"_blank"},freeModel:function(){m.prototype.freeModel.call(this);if(this.model){this.model.clearUpdateTimeout()}return this},_setUpListeners:function(){m.prototype._setUpListeners.call(this);this.on("error",function(p,s,o,r,q){this.errorHandler(p,s,o,r,q)});this.on("loading-done",function(){if(!this.views.length){this.trigger("empty-history",this)}})},loadHistoryWithDetails:function(r,q,p,s){this.info("loadHistoryWithDetails:",r,q,p,s);var o=function(t){return _.values(j.get(t.id).get("expandedIds"))};return this.loadHistory(r,q,p,s,o)},loadHistory:function(s,r,q,t,o){this.info("loadHistory:",s,r,q,t,o);var p=this;r=r||{};p.trigger("loading",p);var u=f.History.getHistoryData(s,{historyFn:q,contentsFn:t,detailIdsFn:r.initiallyExpanded||o});return p._loadHistoryFromXHR(u,r).fail(function(x,v,w){p.trigger("error",p,x,r,e("An error was encountered while "+v),{historyId:s,history:w||{}})}).always(function(){p.trigger("loading-done",p)})},_loadHistoryFromXHR:function(q,p){var o=this;q.then(function(r,s){o.JSONToModel(r,s,p);o.render()});q.fail(function(s,r){o.render()});return q},JSONToModel:function(r,o,p){this.log("JSONToModel:",r,o,p);p=p||{};var q=new f.History(r,o,p);this.setModel(q);return q},setModel:function(p,o){o=o||{};m.prototype.setModel.call(this,p,o);if(this.model){this._setUpWebStorage(o.initiallyExpanded,o.show_deleted,o.show_hidden)}},_setUpWebStorage:function(p,o,q){this.storage=new j({id:j.historyStorageKey(this.model.get("id"))});if(_.isObject(p)){this.storage.set("expandedIds",p)}if(_.isBoolean(o)){this.storage.set("show_deleted",o)}if(_.isBoolean(q)){this.storage.set("show_hidden",q)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_buildNewRender:function(){var o=m.prototype._buildNewRender.call(this);if(this.multiselectActions.length){o.find(".controls .actions").prepend(this._renderSelectButton())}return o},_renderSelectButton:function(o){return faIconButton({title:e("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(o){var p=o.get("history_content_type");switch(p){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+p)},_filterItem:function(p){var o=this;return(m.prototype._filterItem.call(o,p)&&(!p.hidden()||o.storage.get("show_hidden"))&&(!p.isDeletedOrPurged()||o.storage.get("show_deleted")))},_getItemViewOptions:function(p){var o=m.prototype._getItemViewOptions.call(this,p);return _.extend(o,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[p.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(p){var o=this;m.prototype._setUpItemViewListeners.call(o,p);p.on("expanded",function(q){o.storage.addExpandedHda(q.model)});p.on("collapsed",function(q){o.storage.removeExpandedHda(q.model)});return this},refreshContents:function(p,o){if(this.model){return this.model.refresh(p,o)}return $.when()},getSelectedModels:function(){var o=m.prototype.getSelectedModels.call(this);o.historyId=this.collection.historyId;return o},events:_.extend(_.clone(m.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),toggleShowDeleted:function(o){o=(o!==undefined)?(o):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",o);this.renderItems();return this.storage.get("show_deleted")},toggleShowHidden:function(o){o=(o!==undefined)?(o):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",o);this.renderItems();return this.storage.get("show_hidden")},_firstSearch:function(o){var p=this,q=".history-search-input";this.log("onFirstSearch",o);if(p.model.contents.haveDetails()){p.searchItems(o);return}p.$el.find(q).searchInput("toggle-loading");p.model.contents.fetchAllDetails({silent:true}).always(function(){p.$el.find(q).searchInput("toggle-loading")}).done(function(){p.searchItems(o)})},errorHandler:function(q,t,p,s,r){this.error(q,t,p,s,r);if(t&&t.status===0&&t.readyState===0){}else{if(t&&t.status===502){}else{var o=this._parseErrorMessage(q,t,p,s,r);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",o.message,o.details)})}else{this.displayMessage("error",o.message,o.details)}}}},_parseErrorMessage:function(s,v,w,q,o,t){var r=Galaxy.currUser,u={message:this._bePolite(q),details:{message:q,raven:(window.Raven&&_.isFunction(Raven.lastEventId))?(Raven.lastEventId()):(undefined),agent:navigator.userAgent,url:(window.Galaxy)?(Galaxy.lastAjax.url):(undefined),data:(window.Galaxy)?(Galaxy.lastAjax.data):(undefined),options:(v)?(_.omit(w,"xhr")):(w),xhr:v,source:(_.isFunction(s.toJSON))?(s.toJSON()):(s+""),user:(r instanceof g.User)?(r.toJSON()):(r+"")}};_.extend(u.details,o||{});if(v&&_.isFunction(v.getAllResponseHeaders)){var p=v.getAllResponseHeaders();p=_.compact(p.split("\n"));p=_.map(p,function(x){return x.split(": ")});u.details.xhr.responseHeaders=_.object(p)}return u},_bePolite:function(o){o=o||e("An error occurred while getting updates from the server");return o+". "+e("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(t,u,s){var q=this;this.scrollToTop();var r=this.$messages(),o=$("<div/>").addClass(t+"message").html(u);if(!_.isEmpty(s)){var p=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(q._messageToModalOptions(t,u,s));return false});o.append(" ",p)}return r.html(o)},_messageToModalOptions:function(r,u,q){var o=this,p={title:"Details"};if(_.isObject(q)){q=_.omit(q,_.functions(q));var t=JSON.stringify(q,null," "),s=$("<pre/>").text(t);p.body=$("<div/>").append(s)}else{p.body=$("<div/>").html(q)}p.buttons={Ok:function(){Galaxy.modal.hide();o.clearMessages()}};return p},clearMessages:function(o){$(o.currentTarget).fadeOut(this.fxSpeed,function(){$(this).remove()});return this},scrollToHid:function(o){return this.scrollToItem(_.first(this.viewsWhereModel({hid:o})))},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});k.prototype.templates=(function(){var o=n.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= history.name %></div>',"</div>",'<div class="subtitle">',"</div>",'<div class="history-size"><%= history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',e("This history has been deleted"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',e("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',e("None"),"</button>","</div>",'<button class="list-action-popup-btn btn btn-default">',e("For all selected"),"...</button>","</div>","</div>"],"history");return _.extend(_.clone(m.prototype.templates),{controls:o})}());return{HistoryPanel:k}}); \ No newline at end of file diff -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca -r 45a68696164451320e07537fa6fb8872686f710d static/scripts/packed/mvc/list/list-panel.js --- a/static/scripts/packed/mvc/list/list-panel.js +++ b/static/scripts/packed/mvc/list/list-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=_.find(this.views,function(i){return i.model.id===this.lastSelected});if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find(".list-items")},$messages:function(f){return(f||this.$el).find(".messages")},$emptyMessage:function(f){return(f||this.$el).find(".empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;console.debug(this.$emptyMessage(f));return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModel:function(g){for(var h=0;h<this.views.length;h++){var f=this.views[h];if(f.model===g){return f}}return undefined},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(f){this.$scrollContainer().scrollTop(f);return this},scrollToTop:function(){this.$scrollContainer().scrollTop(0);return this},scrollToItem:function(f){if(!f){return this}var g=f.$el.offset().top;this.$scrollContainer().scrollTop(g);return this},scrollToId:function(f){return this.scrollToItem(this.viewFromModelId(f))},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();this.trigger("new-model",this)}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);this.debug("\t .controls:",this.$(".controls"));this.debug("\t $controls:",f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file +define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=_.find(this.views,function(i){return i.model.id===this.lastSelected});if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find(".list-items")},$messages:function(f){return(f||this.$el).find(".messages")},$emptyMessage:function(f){return(f||this.$el).find(".empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModel:function(g){for(var h=0;h<this.views.length;h++){var f=this.views[h];if(f.model===g){return f}}return undefined},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(f){this.$scrollContainer().scrollTop(f);return this},scrollToTop:function(){this.$scrollContainer().scrollTop(0);return this},scrollToItem:function(f){if(!f){return this}var g=f.$el.offset().top;this.$scrollContainer().scrollTop(g);return this},scrollToId:function(f){return this.scrollToItem(this.viewFromModelId(f))},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();this.trigger("new-model",this)}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);this.debug("\t .controls:",this.$(".controls"));this.debug("\t $controls:",f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ 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: ToolForm: Generate json for tools api, improve ui-tabs
by commits-noreply＠bitbucket.org 09 Sep '14

09 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/95b3be32cac3/ Changeset: 95b3be32cac3 User: guerler Date: 2014-09-08 22:52:28 Summary: ToolForm: Generate json for tools api, improve ui-tabs Affected #: 6 files diff -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -157,6 +157,7 @@ // trigger refresh self.refresh(); + self._submit(); } }); }, @@ -177,7 +178,7 @@ // submit _submit: function() { - console.log(this.tree.jobDictionary()); + console.log(this.tree.finalize()); } }); diff -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -11,24 +11,23 @@ // creates tree structure refresh: function() { - // check if section is available - if (!this.app.section) { - return {}; - } - // create dictionary this.dict = {}; // create xml object this.xml = $('<div/>'); + // check if section is available + if (!this.app.section) { + return {}; + } + // fill dictionary this._iterate(this.app.section.$el, this.dict, this.xml); }, - // convert to job dictionary - jobDictionary: function() { + finalize: function() { // link this var self = this; @@ -38,22 +37,48 @@ // converter between raw dictionary and job dictionary function convert(identifier, head) { for (var i in head) { - if (head[i].input) { - var input = head[i].input; - var job_input_id = identifier + input.name; + var node = head[i]; + if (node.input) { + // get node + var input = node.input; - if (input.type == 'repeat') { - + // create identifier + var job_input_id = identifier; + if (identifier != '') { + job_input_id += '|'; + } + job_input_id += input.name; - } else { - //var value = self.app.field_list[input.id].value(); - switch(input.type) { - case 'repeat': - job_def[job_input_id] = value; - break; - default: - job_def[job_input_id] = value; - } + // process input type + switch (input.type) { + // handle repeats + case 'repeat': + var index = 0; + for (var j in node) { + if (j.indexOf('section') != -1) { + convert(job_input_id + '_' + index++, node[j]); + } + } + break; + // handle conditionals + case 'conditional': + // get conditional value + var value = self.app.field_list[input.id].value(); + + // find selected case + for (var j in input.cases) { + if (input.cases[j].value == value) { + convert(job_input_id, head[input.id + '-section-' + j]); + break; + } + } + + // break + break; + default: + // handle default value + var value = self.app.field_list[input.id].value(); + job_def[job_input_id] = value; } } } @@ -61,49 +86,10 @@ // start conversion convert('', this.dict); - + // return result return job_def; }, - - // iterate - _iterate: function(parent, dict, xml) { - // get child nodes - var self = this; - var children = $(parent).children(); - children.each(function() { - // get child element - var child = this; - - // get id - var id = $(child).attr('id'); - - // create new branch - if ($(child).hasClass('section-row') || $(child).hasClass('tab-pane')) { - // create sub dictionary - dict[id] = {}; - - // add input element if it exists - var input = self.app.input_list[id]; - if (input) { - dict[id] = { - input : input - } - } - - // create xml element - var $el = $('<div id="' + id + '"/>'); - - // append xml - xml.append($el); - - // fill sub dictionary - self._iterate(child, dict[id], $el); - } else { - self._iterate(child, dict, xml); - } - }); - }, // find referenced elements findReferences: function(identifier, type) { @@ -176,6 +162,45 @@ // return return referenced; + }, + + // iterate + _iterate: function(parent, dict, xml) { + // get child nodes + var self = this; + var children = $(parent).children(); + children.each(function() { + // get child element + var child = this; + + // get id + var id = $(child).attr('id'); + + // create new branch + if ($(child).hasClass('section-row') || $(child).hasClass('tab-pane')) { + // create sub dictionary + dict[id] = {}; + + // add input element if it exists + var input = self.app.input_list[id]; + if (input) { + dict[id] = { + input : input + } + } + + // create xml element + var $el = $('<div id="' + id + '"/>'); + + // append xml + xml.append($el); + + // fill sub dictionary + self._iterate(child, dict[id], $el); + } else { + self._iterate(child, dict, xml); + } + }); } }); diff -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca static/scripts/mvc/ui/ui-tabs.js --- a/static/scripts/mvc/ui/ui-tabs.js +++ b/static/scripts/mvc/ui/ui-tabs.js @@ -20,7 +20,8 @@ this.$nav = null; this.$content = null; this.first_tab = null; - + this.current_id = null; + // configure options this.options = Utils.merge(options, this.optionsDefault); @@ -139,6 +140,11 @@ self.show(id); } }); + + // initialize current id + if (!this.current_id) { + this.current_id = id; + } }, // delete tab @@ -183,10 +189,14 @@ // show selected tab if (id) { - this.$el.find('.tab-element').removeClass('active'); - this.$el.find('.tab-pane').removeClass('active'); + // reassign active class + this.$el.find('#tab-' + this.current_id).removeClass('active'); + this.$el.find('#' + this.current_id).removeClass('active'); this.$el.find('#tab-' + id).addClass('active'); this.$el.find('#' + id).addClass('active'); + + // update current id + this.current_id = id; } // change diff -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,k,i,a,f,d,h,j,c){var e=Backbone.Model.extend({initialize:function(l){this.url=galaxy_config.root+"api/tools/"+l.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(m){var l=this;this.options=m;this.model=new e({id:m.id});this.tree=new c(this);this.field_list={};this.input_list={};this.datasets=new h({history_id:this.options.history_id,success:function(){l._initializeToolForm()}})},_initializeToolForm:function(){var m=this;var n=new k.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(m.options.biostar_url+"/p/new/post/")}});var o=new k.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(m.options.biostar_url+"/t/"+m.options.id+"/")}});var l=new k.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+m.options.id)}});this.model.fetch({error:function(p){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){m.inputs=m.model.get("inputs");m.portlet=new g.View({icon:"fa-wrench",title:"<b>"+m.model.get("name")+"</b> "+m.model.get("description"),buttons:{execute:new k.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){m._submit()}})},operations:{button_question:n,button_search:o,button_share:l}});if(!m.options.biostar_url){n.$el.hide();o.$el.hide()}m.message=new k.Message();m.portlet.append(m.message.$el);$(m.main_el).append(m.portlet.$el);if(m.options.help!=""){$(m.main_el).append(d.help(m.options.help))}if(m.options.citations){$(m.main_el).append(d.citations());var p=new i.ToolCitationCollection();p.tool_id=m.options.id;var q=new a.CitationListView({collection:p});q.render();p.fetch()}m.setElement(m.portlet.content());m.section=new j.View(m,{inputs:m.model.get("inputs")});m.portlet.append(m.section.$el);m.refresh()}})},refresh:function(){this.tree.refresh();for(var l in this.field_list){this.field_list[l].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")},_submit:function(){console.log(this.tree.jobDictionary())}});return{View:b}}); \ No newline at end of file +define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,k,i,a,f,d,h,j,c){var e=Backbone.Model.extend({initialize:function(l){this.url=galaxy_config.root+"api/tools/"+l.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(m){var l=this;this.options=m;this.model=new e({id:m.id});this.tree=new c(this);this.field_list={};this.input_list={};this.datasets=new h({history_id:this.options.history_id,success:function(){l._initializeToolForm()}})},_initializeToolForm:function(){var m=this;var n=new k.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(m.options.biostar_url+"/p/new/post/")}});var o=new k.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(m.options.biostar_url+"/t/"+m.options.id+"/")}});var l=new k.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+m.options.id)}});this.model.fetch({error:function(p){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){m.inputs=m.model.get("inputs");m.portlet=new g.View({icon:"fa-wrench",title:"<b>"+m.model.get("name")+"</b> "+m.model.get("description"),buttons:{execute:new k.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){m._submit()}})},operations:{button_question:n,button_search:o,button_share:l}});if(!m.options.biostar_url){n.$el.hide();o.$el.hide()}m.message=new k.Message();m.portlet.append(m.message.$el);$(m.main_el).append(m.portlet.$el);if(m.options.help!=""){$(m.main_el).append(d.help(m.options.help))}if(m.options.citations){$(m.main_el).append(d.citations());var p=new i.ToolCitationCollection();p.tool_id=m.options.id;var q=new a.CitationListView({collection:p});q.render();p.fetch()}m.setElement(m.portlet.content());m.section=new j.View(m,{inputs:m.model.get("inputs")});m.portlet.append(m.section.$el);m.refresh();m._submit()}})},refresh:function(){this.tree.refresh();for(var l in this.field_list){this.field_list[l].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")},_submit:function(){console.log(this.tree.finalize())}});return{View:b}}); \ No newline at end of file diff -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){if(!this.app.section){return{}}this.dict={};this.xml=$("<div/>");this._iterate(this.app.section.$el,this.dict,this.xml)},jobDictionary:function(){var a=this;var b={};function c(e,g){for(var f in g){if(g[f].input){var d=g[f].input;var h=e+d.name;if(d.type=="repeat"){}else{switch(d.type){case"repeat":b[h]=value;break;default:b[h]=value}}}}}c("",this.dict);return b},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")||$(i).hasClass("tab-pane")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})},findReferences:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;var b={};function c(k,l){for(var f in l){var d=l[f];if(d.input){var m=d.input;var h=k;if(k!=""){h+="|"}h+=m.name;switch(m.type){case"repeat":var g=0;for(var e in d){if(e.indexOf("section")!=-1){c(h+"_"+g++,d[e])}}break;case"conditional":var n=a.app.field_list[m.id].value();for(var e in m.cases){if(m.cases[e].value==n){c(h,l[m.id+"-section-"+e]);break}}break;default:var n=a.app.field_list[m.id].value();b[h]=n}}}}c("",this.dict);return b},findReferences:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")||$(i).hasClass("tab-pane")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file diff -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 -r 95b3be32cac3b11937fcc8813fb27a58ce0c18ca static/scripts/packed/mvc/ui/ui-tabs.js --- a/static/scripts/packed/mvc/ui/ui-tabs.js +++ b/static/scripts/packed/mvc/ui/ui-tabs.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,min:null,max:null,onchange:null},initialize:function(e){this.visible=false;this.$nav=null;this.$content=null;this.first_tab=null;this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);this.list={};var d=this;if(this.options.operations){$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.find(".operations").append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom",container:d.$el});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(f){var e=this;var h=f.id;var g=$(this._template_tab(f));var d=$(this._template_tab_content(f));this.list[h]=f.ondel?true:false;if(this.options.onnew){this.$nav.find("#new-tab").before(g)}else{this.$nav.append(g)}d.append(f.$el);this.$content.append(d);if(this.size()==1){g.addClass("active");d.addClass("active");this.first_tab=h}if(this.options.max&&this.size()>=this.options.max){this.$el.find("#new-tab").hide()}if(f.ondel){var c=g.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom",container:e.$el});c.on("click",function(){c.tooltip("destroy");e.$el.find(".tooltip").remove();f.ondel();return false})}g.on("click",function(i){i.preventDefault();if(f.onclick){f.onclick()}else{e.show(h)}})},del:function(c){this.$el.find("#tab-"+c).remove();this.$el.find("#"+c).remove();if(this.first_tab==c){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}if(this.list[c]){delete this.list[c]}if(this.size()<this.options.max){this.$el.find("#new-tab").show()}},delRemovable:function(){for(var c in this.list){this.del(c)}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.$el.find(".tab-element").removeClass("active");this.$el.find(".tab-pane").removeClass("active");this.$el.find("#tab-"+c).addClass("active");this.$el.find("#"+c).addClass("active")}if(this.options.onchange){this.options.onchange(c)}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.$el.find("#tab-title-text-"+e);if(d){c.html(d)}return c.html()},retitle:function(d){var c=0;for(var e in this.list){this.title(e,++c+": "+d)}},_template:function(c){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(c){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="tab-'+d.id+'" class="tab-element"><a id="tab-title-link-'+d.id+'" title="" href="#'+d.id+'" data-original-title=""><span id="tab-title-text-'+d.id+'" class="tab-title-text">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="'+c.id+'" class="tab-pane"/>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,min:null,max:null,onchange:null},initialize:function(e){this.visible=false;this.$nav=null;this.$content=null;this.first_tab=null;this.current_id=null;this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);this.list={};var d=this;if(this.options.operations){$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.find(".operations").append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom",container:d.$el});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(f){var e=this;var h=f.id;var g=$(this._template_tab(f));var d=$(this._template_tab_content(f));this.list[h]=f.ondel?true:false;if(this.options.onnew){this.$nav.find("#new-tab").before(g)}else{this.$nav.append(g)}d.append(f.$el);this.$content.append(d);if(this.size()==1){g.addClass("active");d.addClass("active");this.first_tab=h}if(this.options.max&&this.size()>=this.options.max){this.$el.find("#new-tab").hide()}if(f.ondel){var c=g.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom",container:e.$el});c.on("click",function(){c.tooltip("destroy");e.$el.find(".tooltip").remove();f.ondel();return false})}g.on("click",function(i){i.preventDefault();if(f.onclick){f.onclick()}else{e.show(h)}});if(!this.current_id){this.current_id=h}},del:function(c){this.$el.find("#tab-"+c).remove();this.$el.find("#"+c).remove();if(this.first_tab==c){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}if(this.list[c]){delete this.list[c]}if(this.size()<this.options.max){this.$el.find("#new-tab").show()}},delRemovable:function(){for(var c in this.list){this.del(c)}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.$el.find("#tab-"+this.current_id).removeClass("active");this.$el.find("#"+this.current_id).removeClass("active");this.$el.find("#tab-"+c).addClass("active");this.$el.find("#"+c).addClass("active");this.current_id=c}if(this.options.onchange){this.options.onchange(c)}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.$el.find("#tab-title-text-"+e);if(d){c.html(d)}return c.html()},retitle:function(d){var c=0;for(var e in this.list){this.title(e,++c+": "+d)}},_template:function(c){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(c){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="tab-'+d.id+'" class="tab-element"><a id="tab-title-link-'+d.id+'" title="" href="#'+d.id+'" data-original-title=""><span id="tab-title-text-'+d.id+'" class="tab-title-text">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="'+c.id+'" class="tab-pane"/>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: History panel: make search input shown by default, remove toggle; List panel: make collection-panel and history-panel inherit from list-panel, move list-panel and base-mvc.list-item to mvc/list; general history and collection panel refactoring
by commits-noreply＠bitbucket.org 09 Sep '14

09 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b0c8da2b3c1e/ Changeset: b0c8da2b3c1e User: carlfeberhard Date: 2014-09-08 22:49:30 Summary: History panel: make search input shown by default, remove toggle; List panel: make collection-panel and history-panel inherit from list-panel, move list-panel and base-mvc.list-item to mvc/list; general history and collection panel refactoring Affected #: 48 files diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -42,6 +42,7 @@ if( this.logger ){ var log = this.logger.log; if( typeof this.logger.log === 'object' ){ +//TODO:! there has to be a way to get the lineno/file into this log = Function.prototype.bind.call( this.logger.log, this.logger ); } return log.apply( this.logger, arguments ); @@ -149,6 +150,23 @@ //============================================================================== +/** Function that allows mixing of hashs into bbone MVC while showing the mixins first + * (before the more local class overrides/hash). + * Basically, a simple reversal of param order on _.defaults() - to show mixins in top of definition. + * @example: + * var NewModel = Something.extend( mixin( MyMixinA, MyMixinB, { ... myVars : ... }) ); + * + * NOTE: this does not combine any hashes (like events, etc.) and you're expected to handle that + */ +function mixin( mixinHash1, /* mixinHash2, etc: ... variadic */ propsHash ){ + var args = Array.prototype.slice.call( arguments, 0 ), + lastArg = args.pop(); + args.unshift( lastArg ); + return _.defaults.apply( _, args ); +} + + +//============================================================================== /** A mixin for models that allow T/F/Matching to their attributes - useful when * searching or filtering collections of models. * @example: @@ -329,205 +347,6 @@ //============================================================================== -/** Function that allows mixing of hashs into bbone MVC while showing the mixins first - * (before the more local class overrides/hash). - * Basically, a simple reversal of param order on _.defaults() - to show mixins in top of definition. - * @example: - * var NewModel = Something.extend( mixin( MyMixinA, MyMixinB, { ... myVars : ... }) ); - * - * NOTE: this does not combine any hashes (like events, etc.) and you're expected to handle that - */ -function mixin( mixinHash1, /* mixinHash2, etc: ... variadic */ propsHash ){ - var args = Array.prototype.slice.call( arguments, 0 ), - lastArg = args.pop(); - args.unshift( lastArg ); - return _.defaults.apply( _, args ); -} - -//============================================================================== -/** Return an underscore template fn from an array of strings. - * @param {String[]} template the template strings to compile into the underscore template fn - * @param {String} jsonNamespace an optional namespace for the json data passed in (defaults to 'model') - * @returns {Function} the (wrapped) underscore template fn - * The function accepts: - * - * The template strings can access: - * the json/model hash using model ("<%- model.myAttr %>) using the jsonNamespace above - * _l: the localizer function - * view (if passed): ostensibly, the view using the template (handy for view instance vars) - * Because they're namespaced, undefined attributes will not throw an error. - * - * @example: - * templateBler : BASE_MVC.wrapTemplate([ - * '<div class="myclass <%- mynamespace.modelClass %>">', - * '<span><% print( _l( mynamespace.message ) ); %>:<%= view.status %></span>' - * '</div>' - * ], 'mynamespace' ) - * - * Meant to be called in a View's definition in order to compile only once. - * - */ -function wrapTemplate( template, jsonNamespace ){ - jsonNamespace = jsonNamespace || 'model'; - var templateFn = _.template( template.join( '' ) ); - return function( json, view ){ - var templateVars = { view : view || {}, _l : _l }; - templateVars[ jsonNamespace ] = json || {}; - return templateFn( templateVars ); - }; -} - -//============================================================================== -/** A view which, when first rendered, shows only summary data/attributes, but - * can be expanded to show further details (and optionally fetch those - * details from the server). - */ -var ExpandableView = Backbone.View.extend( LoggableMixin ).extend({ -//TODO: Although the reasoning behind them is different, this shares a lot with HiddenUntilActivated above: combine them - //PRECONDITION: model must have method hasDetails - //PRECONDITION: subclasses must have templates.el and templates.details - - initialize : function( attributes ){ - /** are the details of this view expanded/shown or not? */ - this.expanded = attributes.expanded || false; - //this.log( '\t expanded:', this.expanded ); - this.fxSpeed = attributes.fxSpeed || this.fxSpeed; - }, - - // ........................................................................ render main - /** jq fx speed */ - fxSpeed : 'fast', - - /** Render this content, set up ui. - * @param {Number or String} speed the speed of the render - */ - render : function( speed ){ - var $newRender = this._buildNewRender(); - this._setUpBehaviors( $newRender ); - this._queueNewRender( $newRender, speed ); - return this; - }, - - /** Build a temp div containing the new children for the view's $el. - * If the view is already expanded, build the details as well. - */ - _buildNewRender : function(){ - // create a new render using a skeleton template, render title buttons, render body, and set up events, etc. - var $newRender = $( this.templates.el( this.model.toJSON(), this ) ); - if( this.expanded ){ - this.$details( $newRender ).replaceWith( this._renderDetails().show() ); - } - return $newRender; - }, - - /** Fade out the old el, swap in the new contents, then fade in. - * @param {Number or String} speed jq speed to use for rendering effects - * @fires rendered when rendered - */ - _queueNewRender : function( $newRender, speed ) { - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - var view = this; - - $( view ).queue( 'fx', [ - function( next ){ this.$el.fadeOut( speed, next ); }, - function( next ){ - view._swapNewRender( $newRender ); - next(); - }, - function( next ){ this.$el.fadeIn( speed, next ); }, - function( next ){ - this.trigger( 'rendered', view ); - next(); - } - ]); - }, - - /** empty out the current el, move the $newRender's children in */ - _swapNewRender : function( $newRender ){ - return this.$el.empty().attr( 'class', this.className ).append( $newRender.children() ); - }, - - /** set up js behaviors, event handlers for elements within the given container - * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) - */ - _setUpBehaviors : function( $where ){ - $where = $where || this.$el; - // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) - //make_popup_menus( $where ); - $where.find( '[title]' ).tooltip({ placement : 'bottom' }); - }, - - // ......................................................................... details - /** shortcut to details DOM (as jQ) */ - $details : function( $where ){ - $where = $where || this.$el; - return $where.find( '.details' ); - }, - - /** build the DOM for the details and set up behaviors on it */ - _renderDetails : function(){ - var $newDetails = $( this.templates.details( this.model.toJSON(), this ) ); - this._setUpBehaviors( $newDetails ); - return $newDetails; - }, - - // ......................................................................... expansion/details - /** Show or hide the details - * @param {Boolean} expand if true, expand; if false, collapse - */ - toggleExpanded : function( expand ){ - expand = ( expand === undefined )?( !this.expanded ):( expand ); - if( expand ){ - this.expand(); - } else { - this.collapse(); - } - return this; - }, - - /** Render and show the full, detailed body of this view including extra data and controls. - * note: if the model does not have detailed data, fetch that data before showing the body - * @fires expanded when a body has been expanded - */ - expand : function(){ - var view = this; - return view._fetchModelDetails() - .always(function(){ - var $newDetails = view._renderDetails(); - view.$details().replaceWith( $newDetails ); - // needs to be set after the above or the slide will not show - view.expanded = true; - $newDetails.slideDown( view.fxSpeed, function(){ - view.trigger( 'expanded', view ); - }); - }); - }, - - /** Check for model details and, if none, fetch them. - * @returns {jQuery.promise} the model.fetch.xhr if details are being fetched, an empty promise if not - */ - _fetchModelDetails : function(){ - if( !this.model.hasDetails() ){ - return this.model.fetch(); - } - return jQuery.when(); - }, - - /** Hide the body/details of an HDA. - * @fires collapsed when a body has been collapsed - */ - collapse : function(){ - var view = this; - view.expanded = false; - this.$details().slideUp( view.fxSpeed, function(){ - view.trigger( 'collapsed', view ); - }); - } - -}); - - -//============================================================================== /** Mixin for views that can be dragged and dropped * Allows for the drag behavior to be turned on/off, setting/removing jQuery event * handlers each time. @@ -711,186 +530,48 @@ //============================================================================== -/** A view that is displayed in some larger list/grid/collection. - * Inherits from Expandable, Selectable, Draggable. - * The DOM contains warnings, a title bar, and a series of primary action controls. - * Primary actions are meant to be easily accessible item functions (such as delete) - * that are rendered in the title bar. +/** Return an underscore template fn from an array of strings. + * @param {String[]} template the template strings to compile into the underscore template fn + * @param {String} jsonNamespace an optional namespace for the json data passed in (defaults to 'model') + * @returns {Function} the (wrapped) underscore template fn + * The function accepts: * - * Details are rendered when the user clicks the title bar or presses enter/space when - * the title bar is in focus. + * The template strings can access: + * the json/model hash using model ("<%- model.myAttr %>) using the jsonNamespace above + * _l: the localizer function + * view (if passed): ostensibly, the view using the template (handy for view instance vars) + * Because they're namespaced, undefined attributes will not throw an error. * - * Designed as a base class for history panel contents - but usable elsewhere (I hope). + * @example: + * templateBler : BASE_MVC.wrapTemplate([ + * '<div class="myclass <%- mynamespace.modelClass %>">', + * '<span><% print( _l( mynamespace.message ) ); %>:<%= view.status %></span>' + * '</div>' + * ], 'mynamespace' ) + * + * Meant to be called in a View's definition in order to compile only once. + * */ -var ListItemView = ExpandableView.extend( mixin( SelectableViewMixin, DraggableViewMixin, { - -//TODO: that's a little contradictory - tagName : 'div', - className : 'list-item', - - /** Set up the base class and all mixins */ - initialize : function( attributes ){ - ExpandableView.prototype.initialize.call( this, attributes ); - SelectableViewMixin.initialize.call( this, attributes ); - DraggableViewMixin.initialize.call( this, attributes ); - }, - - // ........................................................................ rendering - /** In this override, call methods to build warnings, titlebar and primary actions */ - _buildNewRender : function(){ - var $newRender = ExpandableView.prototype._buildNewRender.call( this ); - $newRender.find( '.warnings' ).replaceWith( this._renderWarnings() ); - $newRender.find( '.title-bar' ).replaceWith( this._renderTitleBar() ); - $newRender.find( '.primary-actions' ).append( this._renderPrimaryActions() ); - $newRender.find( '.subtitle' ).replaceWith( this._renderSubtitle() ); - return $newRender; - }, - - /** In this override, render the selector controls and set up dragging before the swap */ - _swapNewRender : function( $newRender ){ - ExpandableView.prototype._swapNewRender.call( this, $newRender ); - if( this.selectable ){ this.showSelector( 0 ); } - if( this.draggable ){ this.draggableOn(); } - return this.$el; - }, - - /** Render any warnings the item may need to show (e.g. "I'm deleted") */ - _renderWarnings : function(){ - var view = this, - $warnings = $( '<div class="warnings"></div>' ), - json = view.model.toJSON(); -//TODO:! unordered (map) - _.each( view.templates.warnings, function( templateFn ){ - $warnings.append( $( templateFn( json, view ) ) ); - }); - return $warnings; - }, - - /** Render the title bar (the main/exposed SUMMARY dom element) */ - _renderTitleBar : function(){ - return $( this.templates.titleBar( this.model.toJSON(), this ) ); - }, - - /** Return an array of jQ objects containing common/easily-accessible item controls */ - _renderPrimaryActions : function(){ - // override this - return []; - }, - - /** Render the title bar (the main/exposed SUMMARY dom element) */ - _renderSubtitle : function(){ - return $( this.templates.subtitle( this.model.toJSON(), this ) ); - }, - - // ......................................................................... events - /** event map */ - events : { - // expand the body when the title is clicked or when in focus and space or enter is pressed - 'click .title-bar' : '_clickTitleBar', - 'keydown .title-bar' : '_keyDownTitleBar', - - // dragging - don't work, originalEvent === null - //'dragstart .dataset-title-bar' : 'dragStartHandler', - //'dragend .dataset-title-bar' : 'dragEndHandler' - - 'click .selector' : 'toggleSelect' - }, - - /** expand when the title bar is clicked */ - _clickTitleBar : function( event ){ - event.stopPropagation(); - this.toggleExpanded(); - }, - - /** expand when the title bar is in focus and enter or space is pressed */ - _keyDownTitleBar : function( event ){ - // bail (with propagation) if keydown and not space or enter - var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13; - if( event && ( event.type === 'keydown' ) - &&( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){ - this.toggleExpanded(); - event.stopPropagation(); - return false; - } - return true; - }, - - // ......................................................................... misc - /** String representation */ - toString : function(){ - var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'ListItemView(' + modelString + ')'; - } -})); - -// ............................................................................ TEMPLATES -/** underscore templates */ -ListItemView.prototype.templates = (function(){ -//TODO: move to require text! plugin - - var elTemplato = wrapTemplate([ - '<div class="list-element">', - // errors, messages, etc. - '<div class="warnings"></div>', - - // multi-select checkbox - '<div class="selector">', - '<span class="fa fa-2x fa-square-o"></span>', - '</div>', - // space for title bar buttons - gen. floated to the right - '<div class="primary-actions"></div>', - '<div class="title-bar"></div>', - - // expandable area for more details - '<div class="details"></div>', - '</div>' - ]); - - var warnings = {}; - - var titleBarTemplate = wrapTemplate([ - // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display - '<div class="title-bar clear" tabindex="0">', -//TODO: prob. belongs in dataset-list-item - '<span class="state-icon"></span>', - '<div class="title">', - '<span class="name"><%- element.name %></span>', - '</div>', - '<div class="subtitle"></div>', - '</div>' - ], 'element' ); - - var subtitleTemplate = wrapTemplate([ - // override this - '<div class="subtitle"></div>' - ]); - - var detailsTemplate = wrapTemplate([ - // override this - '<div class="details"></div>' - ]); - - return { - el : elTemplato, - warnings : warnings, - titleBar : titleBarTemplate, - subtitle : subtitleTemplate, - details : detailsTemplate +function wrapTemplate( template, jsonNamespace ){ + jsonNamespace = jsonNamespace || 'model'; + var templateFn = _.template( template.join( '' ) ); + return function( json, view ){ + var templateVars = { view : view || {}, _l : _l }; + templateVars[ jsonNamespace ] = json || {}; + return templateFn( templateVars ); }; -}()); +} //============================================================================== return { LoggableMixin : LoggableMixin, SessionStorageModel : SessionStorageModel, + mixin : mixin, SearchableModelMixin : SearchableModelMixin, HiddenUntilActivatedViewMixin : HiddenUntilActivatedViewMixin, - mixin : mixin, - wrapTemplate : wrapTemplate, - ExpandableView : ExpandableView, DraggableViewMixin : DraggableViewMixin, SelectableViewMixin : SelectableViewMixin, - ListItemView : ListItemView + wrapTemplate : wrapTemplate }; }); diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/collection/collection-li.js --- a/static/scripts/mvc/collection/collection-li.js +++ b/static/scripts/mvc/collection/collection-li.js @@ -1,11 +1,12 @@ define([ + "mvc/list/list-item", "mvc/dataset/dataset-li", "mvc/base-mvc", "utils/localization" -], function( DATASET_LI, BASE_MVC, _l ){ +], function( LIST_ITEM, DATASET_LI, BASE_MVC, _l ){ /* global Backbone, LoggableMixin */ //============================================================================== -var ListItemView = BASE_MVC.ListItemView; +var ListItemView = LIST_ITEM.ListItemView; /** @class Read only view for DatasetCollection. */ var DCListItemView = ListItemView.extend( diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/collection/collection-model.js --- a/static/scripts/mvc/collection/collection-model.js +++ b/static/scripts/mvc/collection/collection-model.js @@ -270,6 +270,11 @@ return this.save( { deleted: false }, options ); }, + /** Is this collection deleted or purged? */ + isDeletedOrPurged : function(){ + return ( this.get( 'deleted' ) || this.get( 'purged' ) ); + }, + // ........................................................................ searchable /** searchable attributes for collections */ searchAttributes : [ diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/collection/collection-panel.js --- a/static/scripts/mvc/collection/collection-panel.js +++ b/static/scripts/mvc/collection/collection-panel.js @@ -1,9 +1,10 @@ define([ + "mvc/list/list-panel", "mvc/collection/collection-model", "mvc/collection/collection-li", "mvc/base-mvc", "utils/localization" -], function( DC_MODEL, DC_LI, BASE_MVC, _l ){ +], function( LIST_PANEL, DC_MODEL, DC_LI, BASE_MVC, _l ){ /* ============================================================================= TODO: @@ -11,224 +12,81 @@ // ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. */ -var CollectionPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( +var _super = LIST_PANEL.ModelListPanel; +var CollectionPanel = _super.extend( /** @lends CollectionPanel.prototype */{ //MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs) /** logger used to record this.log messages, commonly set to console */ - //logger : console, + logger : console, - tagName : 'div', - className : 'dataset-collection-panel', - - /** (in ms) that jquery effects will use */ - fxSpeed : 'fast', + className : _super.prototype.className + ' dataset-collection-panel', /** sub view class used for datasets */ DatasetDCEViewClass : DC_LI.DatasetDCEListItemView, /** sub view class used for nested collections */ NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView, + /** key of attribute in model to assign to this.collection */ + modelCollectionKey : 'elements', // ......................................................................... SET UP /** Set up the view, set up storage, bind listeners to HistoryContents events * @param {Object} attributes optional settings for the panel */ initialize : function( attributes ){ - attributes = attributes || {}; - // set the logger if requested - if( attributes.logger ){ - this.logger = attributes.logger; - } - this.log( this + '.initialize:', attributes ); - + _super.prototype.initialize.call( this, attributes ); this.linkTarget = attributes.linkTarget || '_blank'; this.hasUser = attributes.hasUser; this.panelStack = []; this.parentName = attributes.parentName; - //window.collectionPanel = this; - }, - - /** create any event listeners for the panel - * @fires: rendered:initial on the first render - * @fires: empty-history when switching to a history with no HDAs or creating a new history - */ - _setUpListeners : function(){ - // debugging - //if( this.logger ){ - this.on( 'all', function( event ){ - this.log( this + '', arguments ); - }, this ); - //} - return this; - }, - - // ------------------------------------------------------------------------ history/hda event listening - /** listening for history and HDA events */ - _setUpModelEventHandlers : function(){ - return this; - }, - - // ------------------------------------------------------------------------ panel rendering - /** Render panel - * @fires: rendered when the panel is attached and fully visible - * @see Backbone.View#render - */ - render : function( speed, callback ){ - this.log( 'render:', speed, callback ); - // send a speed of 0 to have no fade in/out performed - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - //this.debug( this + '.render, fxSpeed:', speed ); - var panel = this, - $newRender; - - // handle the possibility of no model (can occur if fetching the model returns an error) - if( !this.model ){ - return this; - } - $newRender = this.renderModel(); - - // fade out existing, swap with the new, fade in, set up behaviours - $( panel ).queue( 'fx', [ - function( next ){ - if( speed && panel.$el.is( ':visible' ) ){ - panel.$el.fadeOut( speed, next ); - } else { - next(); - } - }, - function( next ){ - // swap over from temp div newRender - panel.$el.empty(); - if( $newRender ){ - panel.$el.append( $newRender.children() ); - } - next(); - }, - function( next ){ - if( speed && !panel.$el.is( ':visible' ) ){ - panel.$el.fadeIn( speed, next ); - } else { - next(); - } - }, - function( next ){ - //TODO: ideally, these would be set up before the fade in (can't because of async save text) - if( callback ){ callback.call( this ); } - panel.trigger( 'rendered', this ); - next(); - } - ]); - return this; - }, - - /** render with collection data - * @returns {jQuery} dom fragment as temporary container to be swapped out later - */ - renderModel : function( ){ - // tmp div for final swap in render -//TODO: ugh - reuse issue - refactor out - var type = this.model.get( 'collection_type' ) || this.model.object.get( 'collection_type' ), - json = _.extend( this.model.toJSON(), { - parentName : this.parentName, - type : type - }), - $newRender = $( '<div/>' ).append( this.templates.panel( json ) ); - this._setUpBehaviours( $newRender ); - this.renderContents( $newRender ); - return $newRender; - }, - - /** Set up js/widget behaviours */ - _setUpBehaviours : function( $where ){ - //TODO: these should be either sub-MVs, or handled by events - $where = $where || this.$el; - $where.find( '[title]' ).tooltip({ placement: 'bottom' }); - return this; - }, - - // ------------------------------------------------------------------------ sub-$element shortcuts - /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */ - $container : function(){ - return ( this.findContainerFn )?( this.findContainerFn.call( this ) ):( this.$el.parent() ); - }, - /** where list content views are attached */ - $datasetsList : function( $where ){ - return ( $where || this.$el ).find( '.datasets-list' ); + window.collectionPanel = this; }, // ------------------------------------------------------------------------ sub-views - /** Set up/render a view for each DCE to be shown, init with model and listeners. - * DCE views are cached to the map this.contentViews (using the model.id as key). - * @param {jQuery} $whereTo what dom element to prepend the DCE views to - * @returns the number of visible DCE views - */ - renderContents : function( $whereTo ){ - //this.debug( 'renderContents, elements:', this.model.elements ); - $whereTo = $whereTo || this.$el; - - this.warn( this + '.renderContents:, model:', this.model ); - var panel = this, - contentViews = {}, - //NOTE: no filtering here - visibleContents = this.model.getVisibleContents(); - //this.debug( 'renderContents, visibleContents:', visibleContents, $whereTo ); - - this.$datasetsList( $whereTo ).empty(); - if( visibleContents && visibleContents.length ){ - visibleContents.each( function( content ){ - var contentId = content.id, - contentView = panel._createContentView( content ); - contentViews[ contentId ] = contentView; - panel._attachContentView( contentView.render(), $whereTo ); - }); - } - this.contentViews = contentViews; - return this.contentViews; + /** In this override, use model.getVisibleContents */ + _filterCollection : function(){ +//TODO: should *not* be model.getVisibleContents + return this.model.getVisibleContents(); }, - /** */ - _createContentView : function( content ){ - //this.debug( 'content json:', JSON.stringify( content, null, ' ' ) ); - var contentView = null, - ContentClass = this._getContentClass( content ); - //this.debug( 'content:', content ); - //this.debug( 'ContentClass:', ContentClass ); - contentView = new ContentClass({ - model : content, - linkTarget : this.linkTarget, - //draggable : true, - hasUser : this.hasUser, - logger : this.logger - }); - //this.debug( 'contentView:', contentView ); - this._setUpContentListeners( contentView ); - return contentView; - }, - - /** */ - _getContentClass : function( content ){ - //this.debug( this + '._getContentClass:', content ); + /** override to return proper view class based on element_type */ + _getItemViewClass : function( model ){ + //this.debug( this + '._getItemViewClass:', model ); //TODO: subclasses use DCEViewClass - but are currently unused - decide - switch( content.get( 'element_type' ) ){ + switch( model.get( 'element_type' ) ){ case 'hda': return this.DatasetDCEViewClass; case 'dataset_collection': return this.NestedDCDCEViewClass; } - throw new TypeError( 'Unknown element type:', content.get( 'element_type' ) ); + throw new TypeError( 'Unknown element type:', model.get( 'element_type' ) ); }, - /** Set up listeners for content view events. In this override, handle collection expansion. */ - _setUpContentListeners : function( contentView ){ + /** override to add link target and anon */ + _getItemViewOptions : function( model ){ + var options = _super.prototype._getItemViewOptions.call( this, model ); + return _.extend( options, { + linkTarget : this.linkTarget, + hasUser : this.hasUser + }); + }, + + /** when a sub-view is clicked in the collection panel that is itself a collection, + * hide this panel's elements and show the sub-collection in its own panel. + */ + _setUpItemViewListeners : function( view ){ var panel = this; - if( contentView.model.get( 'element_type' ) === 'dataset_collection' ){ - contentView.on( 'expanded', function( collectionView ){ + _super.prototype._setUpItemViewListeners.call( panel, view ); + //TODO:?? doesn't seem to belong here + if( view.model.get( 'element_type' ) === 'dataset_collection' ){ + view.on( 'expanded', function( collectionView ){ panel.info( 'expanded', collectionView ); panel._addCollectionPanel( collectionView ); }); } + return panel; }, /** When a sub-collection is clicked, hide the current panel and render the sub-collection in its own panel */ @@ -246,7 +104,7 @@ }); currPanel.panelStack.push( panel ); - currPanel.$( '.controls' ).add( '.datasets-list' ).hide(); + currPanel.$( '.controls' ).add( '.list-items' ).hide(); currPanel.$el.append( panel.$el ); panel.on( 'close', function(){ currPanel.render(); @@ -266,14 +124,6 @@ } }, - /** attach an contentView to the panel */ - _attachContentView : function( contentView, $whereTo ){ - $whereTo = $whereTo || this.$el; - var $datasetsList = this.$datasetsList( $whereTo ); - $datasetsList.append( contentView.$el ); - return this; - }, - // ------------------------------------------------------------------------ panel events /** event map */ events : { @@ -293,16 +143,16 @@ } }); -//----------------------------------------------------------------------------- TEMPLATES -/** underscore templates */ -CollectionPanel.templates = CollectionPanel.prototype.templates = (function(){ -// use closure to run underscore template fn only once at module load - var _panelTemplate = _.template([ + +//------------------------------------------------------------------------------ TEMPLATES +CollectionPanel.prototype.templates = (function(){ + + var controlsTemplate = BASE_MVC.wrapTemplate([ '<div class="controls">', '<div class="navigation">', '<a class="back" href="javascript:void(0)">', '<span class="fa fa-icon fa-angle-left"></span>', - _l( 'Back to ' ), '<%- collection.parentName %>', + _l( 'Back to ' ), '<%- view.parentName %>', '</a>', '</div>', @@ -310,29 +160,25 @@ '<div class="name"><%- collection.name || collection.element_identifier %></div>', '<div class="subtitle">', //TODO: remove logic from template - '<% if( collection.type === "list" ){ %>', + '<% if( collection.collection_type === "list" ){ %>', _l( 'a list of datasets' ), - '<% } else if( collection.type === "paired" ){ %>', + '<% } else if( collection.collection_type === "paired" ){ %>', _l( 'a pair of datasets' ), - '<% } else if( collection.type === "list:paired" ){ %>', + '<% } else if( collection.collection_type === "list:paired" ){ %>', _l( 'a list of paired datasets' ), '<% } %>', '</div>', '</div>', - '</div>', - // where the datasets/hdas are added - '<div class="datasets-list"></div>' - ].join( '' )); + '</div>' + ], 'collection' ); - // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within - return { - panel : function( json ){ - return _panelTemplate({ _l: _l, collection: json }); - } - }; + return _.extend( _.clone( _super.prototype.templates ), { + controls : controlsTemplate + }); }()); + // ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. */ var ListCollectionPanel = CollectionPanel.extend( diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/dataset/dataset-li.js --- a/static/scripts/mvc/dataset/dataset-li.js +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -1,8 +1,9 @@ define([ + "mvc/list/list-item", "mvc/dataset/states", "mvc/base-mvc", "utils/localization" -], function( STATES, BASE_MVC, _l ){ +], function( LIST_ITEM, STATES, BASE_MVC, _l ){ /* global Backbone */ /*============================================================================== TODO: @@ -11,7 +12,7 @@ simplify button rendering ==============================================================================*/ -var _super = BASE_MVC.ListItemView; +var _super = LIST_ITEM.ListItemView; /** @class Read only list view for either LDDAs, HDAs, or HDADCEs. * Roughly, any DatasetInstance (and not a raw Dataset). */ diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/dataset/dataset-list.js --- a/static/scripts/mvc/dataset/dataset-list.js +++ b/static/scripts/mvc/dataset/dataset-list.js @@ -1,5 +1,5 @@ define([ - "mvc/dataset/list-panel", + "mvc/list/list-panel", "mvc/dataset/dataset-li", "mvc/base-mvc", "utils/localization" diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/dataset/dataset-model.js --- a/static/scripts/mvc/dataset/dataset-model.js +++ b/static/scripts/mvc/dataset/dataset-model.js @@ -94,6 +94,9 @@ this.trigger( 'state:ready', currModel, newState, this.previous( 'state' ) ); } }); + this.on( 'change:urls', function(){ + console.warn( 'change:urls', arguments ); + }); // the download url (currenlty) relies on having a correct file extension this.on( 'change:id change:file_ext', function( currModel ){ this._generateUrls(); @@ -104,6 +107,8 @@ /** override to add urls */ toJSON : function(){ var json = Backbone.Model.prototype.toJSON.call( this ); + //console.warn( 'returning json?' ); + //return json; return _.extend( json, { urls : this.urls }); diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/dataset/list-panel.js --- a/static/scripts/mvc/dataset/list-panel.js +++ /dev/null @@ -1,687 +0,0 @@ -define([ - "mvc/base-mvc", - "utils/localization" -], function( BASE_MVC, _l ){ -/* ============================================================================= -TODO: - -============================================================================= */ -/** @class List that contains ListItemViews. - */ -var ListPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( -/** @lends ReadOnlyHistoryPanel.prototype */{ - - /** logger used to record this.log messages, commonly set to console */ - //logger : console, - - /** class to use for constructing the sub-views */ - viewClass : BASE_MVC.ListItemView, - - tagName : 'div', - className : 'list-panel', - - /** (in ms) that jquery effects will use */ - fxSpeed : 'fast', - - /** string to display when the model has no hdas */ - emptyMsg : _l( 'This list is empty' ), - /** string to no hdas match the search terms */ - noneFoundMsg : _l( 'No matching items found' ), - - // ......................................................................... SET UP - /** Set up the view, set up storage, bind listeners to HistoryContents events - * @param {Object} attributes optional settings for the list - */ - initialize : function( attributes, options ){ - attributes = attributes || {}; - // set the logger if requested - if( attributes.logger ){ - this.logger = attributes.logger; - } - this.log( this + '.initialize:', attributes ); - - // ---- instance vars - /** how quickly should jquery fx run? */ - this.fxSpeed = _.has( attributes, 'fxSpeed' )?( attributes.fxSpeed ):( this.fxSpeed ); - - /** filters for displaying subviews */ - this.filters = []; - /** current search terms */ - this.searchFor = attributes.searchFor || ''; - - /** loading indicator */ - this.indicator = new LoadingIndicator( this.$el ); - - /** currently showing selectors on items? */ - this.selecting = ( attributes.selecting !== undefined )? attributes.selecting : true; - //this.selecting = false; - - /** cached selected item.model.ids to persist btwn renders */ - this.selected = attributes.selected || []; - /** the last selected item.model.id */ - this.lastSelected = null; - - /** list item view class (when passed models) */ - this.viewClass = attributes.viewClass || this.viewClass; - - /** list item views */ - this.views = []; - /** list item models */ - this.collection = attributes.collection || ( new Backbone.Collection([]) ); - - /** filter fns run over collection items to see if they should show in the list */ - this.filters = attributes.filters || []; - -//TODO: remove - this.title = attributes.title || ''; - this.subtitle = attributes.subtitle || ''; - - this._setUpListeners(); - }, - - /** create any event listeners for the list - */ - _setUpListeners : function(){ - this.on( 'error', function( model, xhr, options, msg, details ){ - //this.errorHandler( model, xhr, options, msg, details ); - console.error( model, xhr, options, msg, details ); - }, this ); - - // show hide the loading indicator - this.on( 'loading', function(){ - this._showLoadingIndicator( 'loading...', 40 ); - }, this ); - this.on( 'loading-done', function(){ - this._hideLoadingIndicator( 40 ); - }, this ); - - // throw the first render up as a diff namespace using once (for outside consumption) - this.once( 'rendered', function(){ - this.trigger( 'rendered:initial', this ); - }, this ); - - // debugging - if( this.logger ){ - this.on( 'all', function( event ){ - this.log( this + '', arguments ); - }, this ); - } - - this._setUpCollectionListeners(); - this._setUpViewListeners(); - return this; - }, - - /** free any sub-views the list has */ - freeViews : function(){ -//TODO: stopListening? remove? - this.views = []; - return this; - }, - - // ------------------------------------------------------------------------ item listeners - /** listening for history and HDA events */ - _setUpCollectionListeners : function(){ - - this.collection.on( 'reset', function(){ - this.renderItems(); - }, this ); - - this.collection.on( 'add', this.addItemView, this ); - this.collection.on( 'remove', this.removeItemView, this ); - - // debugging - if( this.logger ){ - this.collection.on( 'all', function( event ){ - this.info( this + '(collection)', arguments ); - }, this ); - } - return this; - }, - - /** listening for history and HDA events */ - _setUpViewListeners : function(){ - - // shift to select a range - this.on( 'view:selected', function( view, ev ){ - if( ev && ev.shiftKey && this.lastSelected ){ - var lastSelectedView = _.find( this.views, function( view ){ - return view.model.id === this.lastSelected; - }); - if( lastSelectedView ){ - this.selectRange( view, lastSelectedView ); - } - } - this.selected.push( view.model.id ); - this.lastSelected = view.model.id; - }, this ); - }, - - // ------------------------------------------------------------------------ rendering - /** Render this content, set up ui. - * @param {Number or String} speed the speed of the render - */ - render : function( speed ){ - var $newRender = this._buildNewRender(); - this._setUpBehaviors( $newRender ); - this._queueNewRender( $newRender, speed ); - return this; - }, - - /** Build a temp div containing the new children for the view's $el. - */ - _buildNewRender : function(){ - // create a new render using a skeleton template, render title buttons, render body, and set up events, etc. - var json = this.model? this.model.toJSON() : {}, - $newRender = $( this.templates.el( json, this ) ); - this._renderTitle( $newRender ); - this._renderSubtitle( $newRender ); - this._renderSearch( $newRender ); - this.renderItems( $newRender ); - return $newRender; - }, - - /** - */ - _renderTitle : function( $where ){ - //$where = $where || this.$el; - //$where.find( '.title' ).replaceWith( ... ) - }, - - /** - */ - _renderSubtitle : function( $where ){ - //$where = $where || this.$el; - //$where.find( '.title' ).replaceWith( ... ) - }, - - /** Fade out the old el, swap in the new contents, then fade in. - * @param {Number or String} speed jq speed to use for rendering effects - * @fires rendered when rendered - */ - _queueNewRender : function( $newRender, speed ) { - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - var view = this; - - $( view ).queue( 'fx', [ - function( next ){ this.$el.fadeOut( speed, next ); }, - function( next ){ - view._swapNewRender( $newRender ); - next(); - }, - function( next ){ this.$el.fadeIn( speed, next ); }, - function( next ){ - view.trigger( 'rendered', view ); - next(); - } - ]); - }, - - /** empty out the current el, move the $newRender's children in */ - _swapNewRender : function( $newRender ){ - this.$el.empty().attr( 'class', this.className ).append( $newRender.children() ); - if( this.selecting ){ this.showSelectors( 0 ); } - return this; - }, - - /** */ - _setUpBehaviors : function( $where ){ - $where = $where || this.$el; - $where.find( '.controls [title]' ).tooltip({ placement: 'bottom' }); - return this; - }, - - // ------------------------------------------------------------------------ sub-$element shortcuts - /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */ - $scrollContainer : function(){ - // override - return this.$el.parent().parent(); - }, - /** */ - $list : function( $where ){ - return ( $where || this.$el ).find( '.list-items' ); - }, - /** container where list messages are attached */ - $messages : function( $where ){ - return ( $where || this.$el ).find( '.message-container' ); - }, - /** the message displayed when no views can be shown (no views, none matching search) */ - $emptyMessage : function( $where ){ - return ( $where || this.$el ).find( '.empty-message' ); - }, - - // ------------------------------------------------------------------------ hda sub-views - /** - * @param {jQuery} $whereTo what dom element to prepend the HDA views to - * @returns the visible item views - */ - renderItems : function( $whereTo ){ - $whereTo = $whereTo || this.$el; - var list = this, - newViews = []; - - var $list = this.$list( $whereTo ), - item$els = this._filterCollection().map( function( itemModel ){ -//TODO: creates views each time - not neccessarily good - var view = list._createItemView( itemModel ); - newViews.push( view ); - return view.render( 0 ).$el; - }); - this.debug( item$els ); - this.debug( newViews ); - - $list.empty(); - if( item$els.length ){ - $list.append( item$els ); - this.$emptyMessage( $whereTo ).hide(); - - } else { - this._renderEmptyMessage( $whereTo ).show(); - } - - this.views = newViews; - return newViews; - }, - - /** - */ - _filterCollection : function(){ - // override this - var list = this; - return list.collection.filter( _.bind( list._filterItem, list ) ); - }, - - /** - */ - _filterItem : function( model ){ - // override this - var list = this; - return ( _.every( list.filters.map( function( fn ){ return fn.call( model ); }) ) ) - && ( !list.searchFor || model.matchesAll( list.searchFor ) ); - }, - - /** - */ - _createItemView : function( model ){ - var ViewClass = this._getItemViewClass( model ), - options = _.extend( this._getItemViewOptions( model ), { - model : model - }), - view = new ViewClass( options ); - this._setUpItemViewListeners( view ); - return view; - }, - - _getItemViewClass : function( model ){ - // override this - return this.viewClass; - }, - - _getItemViewOptions : function( model ){ - // override this - return { - //logger : this.logger, - fxSpeed : this.fxSpeed, - expanded : false, - selectable : this.selecting, - selected : _.contains( this.selected, model.id ), - draggable : this.dragging - }; - }, - - /** - */ - _setUpItemViewListeners : function( view ){ - var list = this; - view.on( 'all', function(){ - var args = Array.prototype.slice.call( arguments, 0 ); - args[0] = 'view:' + args[0]; - list.trigger.apply( list, args ); - }); - - // debugging - //if( this.logger ){ - // view.on( 'all', function( event ){ - // this.log( this + '(view)', arguments ); - // }, this ); - //} - return this; - }, - - /** render the empty/none-found message */ - _renderEmptyMessage : function( $whereTo ){ - //this.debug( '_renderEmptyMessage', $whereTo, this.searchFor ); - var text = this.searchFor? this.noneFoundMsg : this.emptyMsg; - return this.$emptyMessage( $whereTo ).text( text ); - }, - - /** collapse all item views */ - expandAll : function(){ - _.each( this.views, function( view ){ - view.expand(); - }); - }, - - /** collapse all item views */ - collapseAll : function(){ - _.each( this.views, function( view ){ - view.collapse(); - }); - }, - - // ------------------------------------------------------------------------ collection/views syncing - /** - */ - addItemView : function( model, collection, options ){ - this.log( this + '.addItemView:', model ); - var list = this; - if( !this._filterItem( model ) ){ return undefined; } - -//TODO: sorted? position? - var view = list._createItemView( model ); - this.views.push( view ); - - $( view ).queue( 'fx', [ - function( next ){ list.$emptyMessage().fadeOut( list.fxSpeed, next ); }, - function( next ){ -//TODO: auto render? - list.$list().append( view.render().$el ); - next(); - } - ]); - return view; - }, - - /** - */ - removeItemView : function( model, collection, options ){ - this.log( this + '.removeItemView:', model ); - var list = this, - view = list.viewFromModel( model ); - if( !view ){ return undefined; } - - this.views = _.without( this.views, view ); - view.remove(); - if( !this.views.length ){ - list._renderEmptyMessage().fadeIn( list.fxSpeed ); - } - return view; - }, - - /** get views based on model - */ - viewFromModel : function( model ){ - for( var i=0; i<this.views.length; i++ ){ - var view = this.views[i]; - if( view.model === model ){ - return view; - } - } - return undefined; - }, - - /** get views based on model properties - */ - viewsWhereModel : function( properties ){ - return this.views.filter( function( view ){ - //return view.model.matches( properties ); -//TODO: replace with _.matches (underscore 1.6.0) - var json = view.model.toJSON(); - //console.debug( '\t', json, properties ); - for( var key in properties ){ - if( properties.hasOwnPropery( key ) ){ - //console.debug( '\t\t', json[ key ], view.model.properties[ key ] ); - if( json[ key ] !== view.model.properties[ key ] ){ - return false; - } - } - } - return true; - }); - }, - - /** - */ - viewRange : function( viewA, viewB ){ - if( viewA === viewB ){ return ( viewA )?( [ viewA ] ):( [] ); } - - var indexA = this.views.indexOf( viewA ), - indexB = this.views.indexOf( viewB ); - - // handle not found - if( indexA === -1 || indexB === -1 ){ - if( indexA === indexB ){ return []; } - return ( indexA === -1 )?( [ viewB ] ):( [ viewA ] ); - } - // reverse if indeces are - //note: end inclusive - return ( indexA < indexB )? - this.views.slice( indexA, indexB + 1 ) : - this.views.slice( indexB, indexA + 1 ); - }, - - // ------------------------------------------------------------------------ searching - /** render a search input for filtering datasets shown - * (see the search section in the HDA model for implementation of the actual searching) - * return will start the search - * esc will clear the search - * clicking the clear button will clear the search - * uses searchInput in ui.js - */ - _renderSearch : function( $where ){ - $where.find( '.controls .search-input' ).searchInput({ - placeholder : 'search', - initialVal : this.searchFor, - onfirstsearch : _.bind( this._firstSearch, this ), - onsearch : _.bind( this.searchItems, this ), - onclear : _.bind( this.clearSearch, this ) - }); - return $where; - }, - - _firstSearch : function( searchFor ){ - this.log( 'onFirstSearch', searchFor ); - return this.searchItems( searchFor ); - }, - - /** filter view list to those that contain the searchFor terms */ - searchItems : function( searchFor ){ - this.searchFor = searchFor; - this.trigger( 'search:searching', searchFor, this ); - this.renderItems(); - return this; - }, - - /** clear the search filters and show all views that are normally shown */ - clearSearch : function( searchFor ){ - //this.log( 'onSearchClear', this ); - this.searchFor = ''; - this.trigger( 'search:clear', this ); - this.renderItems(); - return this; - }, - - // ------------------------------------------------------------------------ selection - /** show selectors on all visible hdas and associated controls */ - showSelectors : function( speed ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - this.selecting = true; - this.$( '.list-actions' ).slideDown( speed ); - _.each( this.views, function( view ){ - view.showSelector( speed ); - }); - this.selected = []; - this.lastSelected = null; - }, - - /** hide selectors on all visible hdas and associated controls */ - hideSelectors : function( speed ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - this.selecting = false; - this.$( '.list-actions' ).slideUp( speed ); - _.each( this.views, function( view ){ - view.hideSelector( speed ); - }); - this.selected = []; - this.lastSelected = null; - }, - - /** show or hide selectors on all visible hdas and associated controls */ - toggleSelectors : function(){ - if( !this.selecting ){ - this.showSelectors(); - } else { - this.hideSelectors(); - } - }, - - /** select all visible hdas */ - selectAll : function( event ){ - _.each( this.views, function( view ){ - view.select( event ); - }); - }, - - /** deselect all visible hdas */ - deselectAll : function( event ){ - this.lastSelected = null; - _.each( this.views, function( view ){ - view.deselect( event ); - }); - }, - - /** select a range of datasets between A and B */ - selectRange : function( viewA, viewB ){ - var range = this.viewRange( viewA, viewB ); - _.each( range, function( view ){ - view.select(); - }); - return range; - }, - - /** return an array of all currently selected hdas */ - getSelectedViews : function(){ - return _.filter( this.views, function( v ){ - return v.selected; - }); - }, - - /** return an collection of the models of all currenly selected hdas */ - getSelectedModels : function(){ - return new this.collection.constructor( _.map( this.getSelectedViews(), function( view ){ - return view.model; - })); - }, - - // ------------------------------------------------------------------------ loading indicator -//TODO: questionable - /** hide the $el and display a loading indicator (in the $el's parent) when loading new data */ - _showLoadingIndicator : function( msg, speed, callback ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - if( !this.indicator ){ - this.indicator = new LoadingIndicator( this.$el, this.$el.parent() ); - } - if( !this.$el.is( ':visible' ) ){ - this.indicator.show( 0, callback ); - } else { - this.$el.fadeOut( speed ); - this.indicator.show( msg, speed, callback ); - } - }, - - /** hide the loading indicator */ - _hideLoadingIndicator : function( speed, callback ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - if( this.indicator ){ - this.indicator.hide( speed, callback ); - } - }, - - // ------------------------------------------------------------------------ scrolling - /** get the current scroll position of the panel in its parent */ - scrollPosition : function(){ - return this.$scrollContainer().scrollTop(); - }, - - /** set the current scroll position of the panel in its parent */ - scrollTo : function( pos ){ - this.$scrollContainer().scrollTop( pos ); - return this; - }, - - /** Scrolls the panel to the top. */ - scrollToTop : function(){ - this.$scrollContainer().scrollTop( 0 ); - return this; - }, - - /** */ - scrollToItem : function( view ){ - if( !view ){ return; } - var itemTop = view.$el.offset().top; - this.$scrollContainer().scrollTop( itemTop ); - }, - - // ------------------------------------------------------------------------ panel events - /** event map */ - events : { - 'click .select-all' : 'selectAll', - 'click .deselect-all' : 'deselectAll' - }, - - // ------------------------------------------------------------------------ misc - /** Return a string rep of the history */ - toString : function(){ - return 'ListPanel(' + this.collection + ')'; - } -}); - -// ............................................................................ TEMPLATES -/** underscore templates */ -ListPanel.prototype.templates = (function(){ -//TODO: move to require text! plugin - - var elTemplate = BASE_MVC.wrapTemplate([ - // temp container - '<div>', - '<div class="controls">', - '<div class="title">', - '<div class="name"><%= model.name || view.title %></div>', - '</div>', - '<div class="subtitle"><%= view.subtitle %></div>', - '<div class="actions"></div>', - '<div class="messages"></div>', - - '<div class="search">', - '<div class="search-input"></div>', - '</div>', - - '<div class="list-actions">', - '<div class="btn-group">', - '<button class="select-all btn btn-default"', - 'data-mode="select">', _l( 'All' ), '</button>', - '<button class="deselect-all btn btn-default"', - 'data-mode="select">', _l( 'None' ), '</button>', - '</div>', - //'<button class="action-popup-btn btn btn-default">', - // _l( 'For all selected' ), '...', - //'</button>', - '</div>', - '</div>', - '<div class="list-items"></div>', - '<div class="empty-message infomessagesmall"></div>', - '</div>' - ]); - - return { - el : elTemplate - }; -}()); - - - -//============================================================================== - return { - ListPanel: ListPanel - }; -}); diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/history/hda-li.js --- a/static/scripts/mvc/history/hda-li.js +++ b/static/scripts/mvc/history/hda-li.js @@ -17,12 +17,12 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, + className : _super.prototype.className + " history-content", + initialize : function( attributes, options ){ _super.prototype.initialize.call( this, attributes, options ); }, - className : _super.prototype.className + " history-content", - // ......................................................................... misc /** String representation */ toString : function(){ diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/history/history-contents.js --- a/static/scripts/mvc/history/history-contents.js +++ b/static/scripts/mvc/history/history-contents.js @@ -53,6 +53,7 @@ */ initialize : function( models, options ){ options = options || {}; +//TODO: could probably use the contents.history_id instead this.historyId = options.historyId; //this._setUpListeners(); @@ -226,7 +227,7 @@ if( !existing ){ return model; } // merge the models _BEFORE_ calling the superclass version - var merged = existing.toJSON(); + var merged = _.clone( existing.attributes ); _.extend( merged, model ); return merged; }); @@ -303,6 +304,13 @@ return xhr; }, + /** In this override, copy the historyId to the clone */ + clone : function(){ + var clone = Backbone.Collection.prototype.clone.call( this ); + clone.historyId = this.historyId; + return clone; + }, + /** debugging */ print : function(){ var contents = this; diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -232,7 +232,7 @@ /** Get data for a history then its hdas using a sequential ajax call, return a deferred to receive both */ History.getHistoryData = function getHistoryData( historyId, options ){ options = options || {}; - var hdaDetailIds = options.hdaDetailIds || []; + var detailIdsFn = options.detailIdsFn || []; var hdcaDetailIds = options.hdcaDetailIds || []; //console.debug( 'getHistoryData:', historyId, options ); @@ -250,20 +250,20 @@ // get the number of hdas accrd. to the history return historyData && historyData.empty; } - function getHdas( historyData ){ + function getContents( historyData ){ // get the hda data // if no hdas accrd. to history: return empty immed. if( isEmpty( historyData ) ){ return []; } // if there are hdas accrd. to history: get those as well - if( _.isFunction( hdaDetailIds ) ){ - hdaDetailIds = hdaDetailIds( historyData ); + if( _.isFunction( detailIdsFn ) ){ + detailIdsFn = detailIdsFn( historyData ); } if( _.isFunction( hdcaDetailIds ) ){ hdcaDetailIds = hdcaDetailIds( historyData ); } var data = {}; - if( hdaDetailIds.length ) { - data.dataset_details = hdaDetailIds.join( ',' ); + if( detailIdsFn.length ) { + data.dataset_details = detailIdsFn.join( ',' ); } if( hdcaDetailIds.length ) { // for symmetry, not actually used by backend of consumed @@ -274,10 +274,10 @@ } // getting these concurrently is 400% slower (sqlite, local, vanilla) - so: - // chain the api calls - getting history first then hdas + // chain the api calls - getting history first then contents var historyFn = options.historyFn || getHistory, - hdaFn = options.hdaFn || getHdas; + contentsFn = options.contentsFn || getContents; // chain ajax calls: get history first, then hdas var historyXHR = historyFn( historyId ); @@ -291,15 +291,15 @@ df.reject( xhr, 'loading the history' ); }); - var hdaXHR = historyXHR.then( hdaFn ); - hdaXHR.then( function( hdaJSON ){ - df.notify({ status: 'dataset data retrieved', historyJSON: historyJSON, hdaJSON: hdaJSON }); + var contentsXHR = historyXHR.then( contentsFn ); + contentsXHR.then( function( contentsJSON ){ + df.notify({ status: 'contents data retrieved', historyJSON: historyJSON, contentsJSON: contentsJSON }); // we've got both: resolve the outer scope deferred - df.resolve( historyJSON, hdaJSON ); + df.resolve( historyJSON, contentsJSON ); }); - hdaXHR.fail( function( xhr, status, message ){ + contentsXHR.fail( function( xhr, status, message ){ // call reject on the outer deferred to allow its fail callback to run - df.reject( xhr, 'loading the datasets', { history: historyJSON } ); + df.reject( xhr, 'loading the contents', { history: historyJSON } ); }); return df; diff -r 9d15e899516411c9b491f66f001a55136b1173b9 -r b0c8da2b3c1e37b3108bd6bc6b8ad919afef9b43 static/scripts/mvc/history/history-panel-annotated.js --- a/static/scripts/mvc/history/history-panel-annotated.js +++ b/static/scripts/mvc/history/history-panel-annotated.js @@ -1,118 +1,97 @@ define([ "mvc/history/history-panel", "mvc/history/hda-li", + "mvc/history/hdca-li", + "mvc/base-mvc", "utils/localization" -], function( HPANEL, HDA_LI, _l ){ +], function( HPANEL, HDA_LI, HDCA_LI, BASE_MVC, _l ){ /* ============================================================================= TODO: ============================================================================= */ -var _super = HPANEL.ReadOnlyHistoryPanel; +var _super = HPANEL.HistoryPanel; // used in history/display.mako and history/embed.mako /** @class View/Controller for a tabular view of the history model. - * @name AnnotatedHistoryPanel * * As ReadOnlyHistoryPanel, but with: * history annotation always shown * datasets displayed in a table: * datasets in left cells, dataset annotations in the right - * - * @augments Backbone.View - * @borrows LoggableMixin#logger as #logger - * @borrows LoggableMixin#log as #log - * @constructs */ var AnnotatedHistoryPanel = _super.extend( /** @lends AnnotatedHistoryPanel.prototype */{ /** logger used to record this.log messages, commonly set to console */ - // comment this out to suppress log output //logger : console, - className : 'annotated-history-panel', - - //TODO:?? possibly into own annotated class - /** class to use for constructing the HDA views */ - //HDAViewClass : HDA_LI.HDAListItemView, + className : _super.prototype.className + ' annotated-history-panel', // ------------------------------------------------------------------------ panel rendering - /** render with history data - * In this override: - * replace the datasets list with a table, - * add the history annotation, - * and move the search controls - * @returns {jQuery} dom fragment as temporary container to be swapped out later + /** In this override, add the history annotation */ - renderModel : function( ){ - // why do we need this here? why isn't className being applied? - this.$el.addClass( this.className ); - var $newRender = _super.prototype.renderModel.call( this ), - // move datasets from div to table - $datasetsList = this.$datasetsList( $newRender ), - $datasetsTable = $( '<table/>' ).addClass( 'datasets-list datasets-table' ); - $datasetsTable.append( $datasetsList.children() ); - $datasetsList.replaceWith( $datasetsTable ); - //TODO: it's possible to do this with css only, right? display: table-cell, etc.? - - // add history annotation under subtitle - $newRender.find( '.history-subtitle' ).after( this.renderHistoryAnnotation() ); - - // hide search button, move search bar beneath controls (instead of above title), show, and set up - $newRender.find( '.history-search-btn' ).hide(); - $newRender.find( '.history-controls' ).after( $newRender.find( '.history-search-controls' ).show() ); - + _buildNewRender : function(){ + //TODO: shouldn't this display regardless (on all non-current panels)? + var $newRender = _super.prototype._buildNewRender.call( this ); + this.renderHistoryAnnotation( $newRender ); return $newRender; }, /** render the history's annotation as its own field */ - renderHistoryAnnotation : function(){ + renderHistoryAnnotation : function( $newRender ){ var annotation = this.model.get( 'annotation' ); - if( !annotation ){ return null; } - return $([ - '<div class="history-annotation">', annotation, '</div>' - ].join( '' )); + if( !annotation ){ return; } + $newRender.find( '.controls .annotation-display' ).text( annotation ); }, - /** Set up/render a view for each HDA to be shown, init with model and listeners. - * In this override, add table header cells to indicate the dataset, annotation columns + /** In this override, convert the list-items tag to a table + * and add table header cells to indicate the dataset, annotation columns */ - renderHdas : function( $whereTo ){ + renderItems : function( $whereTo ){ $whereTo = $whereTo || this.$el; - var hdaViews = _super.prototype.renderHdas.call( this, $whereTo ); - this.$datasetsList( $whereTo ).prepend( $( '<tr/>' ).addClass( 'headers' ).append([ - $( '<th/>' ).text( _l( 'Dataset' ) ), - $( '<th/>' ).text( _l( 'Annotation' ) ) - ])); - return hdaViews; + + // convert to table + $whereTo.find( '.list-items' ) + .replaceWith( $( '<table/>' ).addClass( 'list-items' ) ); + + // render rows/contents and prepend headers + var views = _super.prototype.renderItems.call( this, $whereTo ); + this.$list( $whereTo ) + .prepend( $( '<tr/>' ).addClass( 'headers' ).append([ + $( '<th/>' ).text( _l( 'Dataset' ) ), + $( '<th/>' ).text( _l( 'Annotation' ) ) + ])); + return views; }, - // ------------------------------------------------------------------------ hda sub-views - /** attach an hdaView to the panel - * In this override, wrap the hdaView in a table row and cell, adding a 2nd cell for the hda annotation + // ------------------------------------------------------------------------ sub-views + /** In this override, wrap the content view in a table row + * with the content in the left td and annotation/extra-info in the right */ - attachContentView : function( hdaView, $whereTo ){ - $whereTo = $whereTo || this.$el; - // build a row around the dataset with the std hdaView in the first cell and the annotation in the next - var stateClass = _.find( hdaView.el.classList, function( c ){ return ( /^state\-/ ).test( c ); }), - annotation = hdaView.model.get( 'annotation' ) || '', - $tr = $( '<tr/>' ).addClass( 'dataset-row' ).append([ - $( '<td/>' ).addClass( 'dataset-container' ).append( hdaView.$el ) - // visually match the cell bg to the dataset at runtime (prevents the empty space) - // (getting bg via jq on hidden elem doesn't work on chrome/webkit - so use states) - //.css( 'background-color', hdaView.$el.css( 'background-color' ) ), - .addClass( stateClass? stateClass.replace( '-', '-color-' ): '' ), - $( '<td/>' ).addClass( 'additional-info' ).text( annotation ) - ]); - this.$datasetsList( $whereTo ).append( $tr ); + _attachItems : function( $whereTo ){ + this.$list( $whereTo ).append( this.views.map( function( view ){ + //TODO:?? possibly make this more flexible: instead of annotation use this._additionalInfo() + // build a row around the dataset with the std itemView in the first cell and the annotation in the next + var stateClass = _.find( view.el.classList, function( c ){ return ( /^state\-/ ).test( c ); }), + annotation = view.model.get( 'annotation' ) || '', + $tr = $( '<tr/>' ).append([ + $( '<td/>' ).addClass( 'contents-container' ).append( view.$el ) + // visually match the cell bg to the dataset at runtime (prevents the empty space) + // (getting bg via jq on hidden elem doesn't work on chrome/webkit - so use states) + //.css( 'background-color', view.$el.css( 'background-color' ) ), + .addClass( stateClass? stateClass.replace( '-', '-color-' ): '' ), + $( '<td/>' ).addClass( 'additional-info' ).text( annotation ) + ]); + return $tr; + })); + return this; }, // ------------------------------------------------------------------------ panel events /** event map */ events : _.extend( _.clone( _super.prototype.events ), { + // clicking on any part of the row will expand the items 'click tr' : function( ev ){ - //if( !ev.target.hasAttribute( 'href' ) ){ - $( ev.currentTarget ).find( '.dataset-title-bar' ).click(); - //} + $( ev.currentTarget ).find( '.title-bar' ).click(); }, // prevent propagation on icon btns so they won't bubble up to tr and toggleBodyVisibility 'click .icon-btn' : function( ev ){ @@ -127,6 +106,7 @@ } }); + //============================================================================== return { AnnotatedHistoryPanel : AnnotatedHistoryPanel This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Fix to 419ca68: re-add ability to re-size right and left panels using mouse events
by commits-noreply＠bitbucket.org 09 Sep '14

09 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9d15e8995164/ Changeset: 9d15e8995164 User: carlfeberhard Date: 2014-09-08 21:10:49 Summary: Fix to 419ca68: re-add ability to re-size right and left panels using mouse events Affected #: 2 files diff -r 7c19138e41ada844f5515aba40a6ec7928b11fcb -r 9d15e899516411c9b491f66f001a55136b1173b9 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -92,28 +92,32 @@ } }, init: function() { - var self = this; + var self = this, + prevX; // Pull the collapse element out to body level so it is visible when panel is hidden - this.$toggle.remove().appendTo( "body" ); - // Resizing using drag element - this.$drag.on( "dragstart", function( e, d ) { - $( '#DD-helper' ).show(); - d.width = self.$panel.width(); - }).on( "dragend", function() { - $( '#DD-helper' ).hide(); - }).on( "drag", function( e, d ) { - var x; - if ( self.left ) { - x = d.width + d.deltaX; - } else { - x = d.width - d.deltaX; - } - // Limit range - x = Math.min( MAX_PANEL_WIDTH, Math.max( MIN_PANEL_WIDTH, x ) ); - self.resize( x ); - }); + self.$toggle.remove().appendTo( "body" ); // Hide/show using toggle element self.$toggle.on( "click", function() { self.do_toggle(); } ); + + // Resizing using drag element + function move( e ){ + var delta = e.pageX - prevX; + prevX = e.pageX; + + var oldWidth = self.$panel.width(), + newWidth = ( self.left )?( oldWidth + delta ):( oldWidth - delta ); + // Limit range + newWidth = Math.min( MAX_PANEL_WIDTH, Math.max( MIN_PANEL_WIDTH, newWidth ) ); + self.resize( newWidth ); + } + this.$drag.on( "mousedown", function( e ) { + prevX = e.pageX; + $( '#DD-helper' ).show() + .on( 'mousemove', move ) + .one( 'mouseup', function( e ){ + $( this ).hide().off( 'mousemove', move ); + }); + }); } }); diff -r 7c19138e41ada844f5515aba40a6ec7928b11fcb -r 9d15e899516411c9b491f66f001a55136b1173b9 static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").appendTo("body").hide()}};var b=160,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop;this.$header.find(".close").on("click",d.proxy(this.hide,this))};d.extend(f.prototype,{setContent:function(p){this.$header.hide();if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}if(p.closeButton){this.$header.find(".close").show();this.$header.show()}else{this.$header.find(".close").hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='progress-bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$overlay.addClass("in");this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-this.$footer.outerHeight()-this.$header.outerHeight()-parseInt(this.$dialog.css("padding-top"),10)-parseInt(this.$dialog.css("padding-bottom"),10))}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#top-modal"),dialog:d("#top-modal-dialog"),backdrop:d("#top-modal-backdrop")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});m.setContent({closeButton:true,title:" ",body:d("<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>")});m.show({backdrop:true})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file +!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").appendTo("body").hide()}};var b=160,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var o=this,p;o.$toggle.remove().appendTo("body");o.$toggle.on("click",function(){o.do_toggle()});function n(s){var t=s.pageX-p;p=s.pageX;var q=o.$panel.width(),r=(o.left)?(q+t):(q-t);r=Math.min(h,Math.max(b,r));o.resize(r)}this.$drag.on("mousedown",function(q){p=q.pageX;d("#DD-helper").show().on("mousemove",n).one("mouseup",function(r){d(this).hide().off("mousemove",n)})})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop;this.$header.find(".close").on("click",d.proxy(this.hide,this))};d.extend(f.prototype,{setContent:function(p){this.$header.hide();if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}if(p.closeButton){this.$header.find(".close").show();this.$header.show()}else{this.$header.find(".close").hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='progress-bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$overlay.addClass("in");this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-this.$footer.outerHeight()-this.$header.outerHeight()-parseInt(this.$dialog.css("padding-top"),10)-parseInt(this.$dialog.css("padding-bottom"),10))}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#top-modal"),dialog:d("#top-modal-dialog"),backdrop:d("#top-modal-backdrop")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});m.setContent({closeButton:true,title:" ",body:d("<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>")});m.show({backdrop:true})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ 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: carlfeberhard: Fix for d576558: re-add url_for for webapp and decorators
by commits-noreply＠bitbucket.org 08 Sep '14

08 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7c19138e41ad/ Changeset: 7c19138e41ad User: carlfeberhard Date: 2014-09-08 20:28:52 Summary: Fix for d576558: re-add url_for for webapp and decorators Affected #: 2 files diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r 7c19138e41ada844f5515aba40a6ec7928b11fcb lib/galaxy/web/framework/decorators.py --- a/lib/galaxy/web/framework/decorators.py +++ b/lib/galaxy/web/framework/decorators.py @@ -6,6 +6,7 @@ eggs.require( "Paste" ) import paste.httpexceptions +from galaxy.web.framework import url_for from galaxy import util from galaxy.exceptions import error_codes from galaxy.exceptions import MessageException diff -r 02852a8e49e23cd1090f798e99702057fa24bc1d -r 7c19138e41ada844f5515aba40a6ec7928b11fcb lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -33,6 +33,7 @@ from galaxy.util.sanitize_html import sanitize_html from galaxy.managers import context +from galaxy.web.framework import url_for from galaxy.web.framework import base from galaxy.web.framework import helpers from galaxy.web.framework import formbuilder 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: jmchilton: Add very basic functional tests for tool param validation.
by commits-noreply＠bitbucket.org 08 Sep '14

08 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/02852a8e49e2/ Changeset: 02852a8e49e2 User: jmchilton Date: 2014-09-08 16:33:54 Summary: Add very basic functional tests for tool param validation. Including same test with workflow parameter substition - gotta admit I thought that workflow test was going to fail - so this week is looking pretty good :). Affected #: 5 files diff -r f295824b2f9eb38d3de1121b63dc8a19f54ee0e9 -r 02852a8e49e23cd1090f798e99702057fa24bc1d test/api/test_workflow_validation_1.ga --- /dev/null +++ b/test/api/test_workflow_validation_1.ga @@ -0,0 +1,33 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "test_validation_1", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [], + "name": "Validation (default)", + "outputs": [ + { + "name": "out_file1", + "type": "data" + } + ], + "position": { + "left": 10, + "top": 10 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "validation_default", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"\\\"cow\\\"\", \"chromInfo\": \"\\\"/home/john/workspace/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": null, + "type": "tool", + "user_outputs": [] + } + }, + "uuid": "d058c6a0-6d70-44f4-a177-01859fc6aa37" +} \ No newline at end of file diff -r f295824b2f9eb38d3de1121b63dc8a19f54ee0e9 -r 02852a8e49e23cd1090f798e99702057fa24bc1d test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -478,6 +478,21 @@ self.__assert_lines_hid_line_count_is( history_id, 2, 5 ) self.__assert_lines_hid_line_count_is( history_id, 3, 5 ) + @skip_without_tool( "validation_default" ) + def test_parameter_substitution_validation( self ): + workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_validation_1" ) + uploaded_workflow_id = self.workflow_populator.create_workflow( workflow ) + history_id = self.dataset_populator.new_history() + workflow_request = dict( + history="hist_id=%s" % history_id, + workflow_id=uploaded_workflow_id, + parameters=dumps( dict( validation_default=dict( input1="\" ; echo \"moo" ) ) ) + ) + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 200 ) + self.dataset_populator.wait_for_history( history_id, assert_ok=True ) + self.assertEquals("__dq__ X echo __dq__moo\n", self.dataset_populator.get_history_dataset_content( history_id ) ) + @skip_without_tool( "random_lines1" ) def test_run_replace_params_by_steps( self ): workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_step_params" ) diff -r f295824b2f9eb38d3de1121b63dc8a19f54ee0e9 -r 02852a8e49e23cd1090f798e99702057fa24bc1d test/functional/tools/for_workflows/head.xml --- a/test/functional/tools/for_workflows/head.xml +++ b/test/functional/tools/for_workflows/head.xml @@ -1,6 +1,6 @@ <tool id="head" name="Select first"><description>lines from a dataset</description> - <command>head $input $lineNum > $out_file1</command> + <command>head -n $lineNum $input > $out_file1</command><inputs><param name="lineNum" size="5" type="integer" value="10" label="Select first" help="lines"/><param format="txt" name="input" type="data" label="from"/> diff -r f295824b2f9eb38d3de1121b63dc8a19f54ee0e9 -r 02852a8e49e23cd1090f798e99702057fa24bc1d test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -21,6 +21,7 @@ <tool file="implicit_default_conds.xml" /><tool file="multi_data_param.xml" /><tool file="special_params.xml" /> + <tool file="validation_default.xml" /><tool file="collection_paired_test.xml" /><tool file="collection_nested_test.xml" /><tool file="collection_mixed_param.xml" /> diff -r f295824b2f9eb38d3de1121b63dc8a19f54ee0e9 -r 02852a8e49e23cd1090f798e99702057fa24bc1d test/functional/tools/validation_default.xml --- /dev/null +++ b/test/functional/tools/validation_default.xml @@ -0,0 +1,23 @@ +<tool id="validation_default" name="Validation (default)"> + <command> + echo "$input1" > out1; + </command> + <inputs> + <param name="input1" type="text" label="Concatenate Dataset" /> + </inputs> + <outputs> + <data name="out_file1" from_work_dir="out1" /> + </outputs> + <tests> + <test> + <param name="input1" value="" ; echo "moo" /> + <output name="out_file1"> + <assert_contents> + <has_line line="__dq__ X echo __dq__moo" /> + </assert_contents> + </output> + </test> + </tests> + <help> + </help> +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0