galaxy-commits November 2014

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 07 Nov '14

07 Nov '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a8f45564f23f/ Changeset: a8f45564f23f Branch: workflow-input-fix User: kell...(a)gmail.com Date: 2014-11-05 22:39:08+00:00 Summary: Fixing workflow import to correctly set the uuid Affected #: 1 file diff -r f9e8de1c84b2d60cc727ec5b64da6fe67616b7ed -r a8f45564f23fdacc27bec05364be7d99176bdec2 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -85,7 +85,7 @@ Convenience method to get a model object with the specified checks. """ return managers_base.get_object( trans, id, class_name, check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) - + # this should be here - but catching errors from sharable item controllers that *should* have SharableItemMixin # but *don't* then becomes difficult #def security_check( self, trans, item, check_ownership=False, check_accessible=False ): @@ -1596,6 +1596,8 @@ else: name = data['name'] workflow.name = name + if 'uuid' in data: + workflow.uuid = data['uuid'] # Assume no errors until we find a step that has some workflow.has_errors = False # Create each step @@ -1703,7 +1705,7 @@ data['name'] = workflow.name data['annotation'] = annotation_str if workflow.uuid is not None: - data['uuid'] = str(workflow.uuid) + data['uuid'] = str(workflow.uuid) data['steps'] = {} # For each step, rebuild the form and encode the state for step in workflow.steps: https://bitbucket.org/galaxy/galaxy-central/commits/f1172da99fb5/ Changeset: f1172da99fb5 Branch: workflow-input-fix User: kellrott Date: 2014-11-06 22:18:03+00:00 Summary: Removing whitespace fixes to avoid merge conflict Affected #: 1 file diff -r a8f45564f23fdacc27bec05364be7d99176bdec2 -r f1172da99fb5501f2fce6cdac5646bbda442cac7 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -85,7 +85,7 @@ Convenience method to get a model object with the specified checks. """ return managers_base.get_object( trans, id, class_name, check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) - + # this should be here - but catching errors from sharable item controllers that *should* have SharableItemMixin # but *don't* then becomes difficult #def security_check( self, trans, item, check_ownership=False, check_accessible=False ): @@ -1705,7 +1705,7 @@ data['name'] = workflow.name data['annotation'] = annotation_str if workflow.uuid is not None: - data['uuid'] = str(workflow.uuid) + data['uuid'] = str(workflow.uuid) data['steps'] = {} # For each step, rebuild the form and encode the state for step in workflow.steps: https://bitbucket.org/galaxy/galaxy-central/commits/93723d1cf699/ Changeset: 93723d1cf699 User: dannon Date: 2014-11-08 00:48:15+00:00 Summary: Merged in kellrott/galaxy-farm/workflow-input-fix (pull request #552) Fixing workflow import to correctly set the uuid Affected #: 1 file diff -r 04644e64c498ca4eacbfa1c6df26cb546705b96c -r 93723d1cf699eab771ccde086d34bec1fd1c22e6 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1596,6 +1596,8 @@ else: name = data['name'] workflow.name = name + if 'uuid' in data: + workflow.uuid = data['uuid'] # Assume no errors until we find a step that has some workflow.has_errors = False # Create each step Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: Integrate and optimize state population for tools api
by commits-noreply＠bitbucket.org 07 Nov '14

07 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/04644e64c498/ Changeset: 04644e64c498 User: guerler Date: 2014-11-07 18:24:22+00:00 Summary: ToolForm: Integrate and optimize state population for tools api Affected #: 1 file diff -r 1a465f5f15ec782c01926056c125fc4769d7fc06 -r 04644e64c498ca4eacbfa1c6df26cb546705b96c lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -10,7 +10,7 @@ from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import dumps from galaxy.visualization.data_providers.genome import * -from galaxy.tools.parameters import params_to_incoming +from galaxy.tools.parameters import params_to_incoming, check_param from galaxy.tools.parameters import visit_input_values from galaxy.tools.parameters.meta import expand_meta_parameters from galaxy.managers.collections_util import dictify_dataset_collection_instance @@ -574,7 +574,62 @@ # update and return dict['value'] = value return dict - + + # populate state + def initialize_state(trans, inputs, state, context=None): + context = ExpressionContext(state, context) + for input in inputs.itervalues(): + state[input.name] = input.get_initial_value(trans, context) + def populate_state(trans, inputs, state, incoming, prefix="", context=None ): + errors = dict() + context = ExpressionContext(state, context) + for input in inputs.itervalues(): + key = prefix + input.name + if input.type == 'repeat': + group_state = state[input.name] + group_errors = [] + rep_index = 0 + del group_state[:] + while True: + rep_name = "%s_%d" % (key, rep_index) + if not any([incoming_key.startswith(rep_name) for incoming_key in incoming.keys()]): + break + if rep_index < input.max: + new_state = {} + new_state['__index__'] = rep_index + initialize_state(trans, input.inputs, new_state, context) + group_state.append(new_state) + group_errors.append({}) + rep_errors = populate_state(trans, input.inputs, new_state, incoming, prefix=rep_name + "|", context=context) + if rep_errors: + group_errors[rep_index].update( rep_errors ) + else: + group_errors[-1] = { '__index__': 'Cannot add repeat (max size=%i).' % input.max } + rep_index += 1 + elif input.type == 'conditional': + group_state = state[input.name] + group_prefix = "%s|" % ( key ) + test_param_key = group_prefix + input.test_param.name + default_value = incoming.get(test_param_key, group_state.get(input.test_param.name, None)) + value, test_param_error = check_param( trans, input.test_param, default_value, context) + if test_param_error: + errors[input.name] = [test_param_error] + else: + current_case = input.get_current_case(value, trans) + group_state = state[input.name] = {} + initialize_state(trans, input.cases[current_case].inputs, group_state, context) + group_errors = populate_state( trans, input.cases[current_case].inputs, group_state, incoming, prefix=group_prefix, context=context) + if group_errors: + errors[input.name] = group_errors + group_state['__current_case__'] = current_case + group_state[ input.test_param.name ] = value + else: + value, error = check_param(trans, input, incoming.get(key, state.get(input.name, None)), context) + if error: + errors[input.name] = error + state[input.name] = value + return errors + # build model def iterate(group_inputs, inputs, tool_state, errors, other_values=None): other_values = ExpressionContext( tool_state, other_values ) @@ -593,7 +648,6 @@ group_errors = errors[input.name][i] if input.name in errors else dict() iterate( group_cache[i], input.inputs, group_state[i], group_errors, other_values ) elif input.type == 'conditional': - # TODO: loop over all cases try: test_param = group_inputs[input_index]['test_param'] test_param['value'] = convert(group_state[test_param['name']]) @@ -622,17 +676,18 @@ # do param translation here, used by datasource tools if tool.input_translator: tool.input_translator.translate( params ) - + # create tool state - state = tool.new_state(trans, all_pages=True) - errors = tool.populate_state( trans, tool.inputs, state.inputs, params.__dict__ ) + state_inputs = {} + initialize_state(trans, tool.inputs, state_inputs) + errors = populate_state(trans, tool.inputs, state_inputs, params.__dict__) # create basic tool model tool_model = tool.to_dict(trans) tool_model['inputs'] = {} # build tool model - iterate(tool_model['inputs'], tool.inputs, state.inputs, errors, '') + iterate(tool_model['inputs'], tool.inputs, state_inputs, errors, '') # load tool help tool_help = '' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: Fix boolean handling
by commits-noreply＠bitbucket.org 07 Nov '14

07 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1a465f5f15ec/ Changeset: 1a465f5f15ec User: guerler Date: 2014-11-07 15:39:19+00:00 Summary: ToolForm: Fix boolean handling Affected #: 2 files diff -r 0ac62bde7db38954702c0acba648cc8efa76a214 -r 1a465f5f15ec782c01926056c125fc4769d7fc06 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -126,6 +126,9 @@ def is_checked( value ): if value == True: return True + if isinstance( value, basestring ): + if value.lower() in [ "yes", "true", "on" ]: + return True # This may look strange upon initial inspection, but see the comments in the get_html() method # above for clarification. Basically, if value is not True, then it will always be a list with # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not diff -r 0ac62bde7db38954702c0acba648cc8efa76a214 -r 1a465f5f15ec782c01926056c125fc4769d7fc06 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -541,6 +541,11 @@ 'id' : trans.security.encode_id(v.id), 'src' : 'hda' } + elif isinstance(v, bool): + if v is True: + return 'true' + else: + return 'false' elif isinstance(v, basestring) or isnumber: return v else: @@ -591,7 +596,7 @@ # TODO: loop over all cases try: test_param = group_inputs[input_index]['test_param'] - test_param['value'] = group_state[test_param['name']] + test_param['value'] = convert(group_state[test_param['name']]) except Exception: pass i = group_state['__current_case__'] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: Merged in martenson/galaxy-central-marten (pull request #554)
by commits-noreply＠bitbucket.org 07 Nov '14

07 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0ac62bde7db3/ Changeset: 0ac62bde7db3 User: martenson Date: 2014-11-07 15:29:06+00:00 Summary: Merged in martenson/galaxy-central-marten (pull request #554) fix for password rese Affected #: 1 file diff -r 37fb229769f4a1cc02d7df26790c5c6f13e913d6 -r 0ac62bde7db38954702c0acba648cc8efa76a214 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -448,14 +448,18 @@ @web.expose def login( self, trans, refresh_frames=[], **kwd ): - '''Handle Galaxy Log in''' + """Handle Galaxy login""" redirect = kwd.get( 'redirect', trans.request.referer ).strip() root_url = url_for( '/', qualified=True ) - redirect_url = '' # always start with redirect_url being empty - # compare urls, to prevent a redirect from pointing (directly) outside of galaxy - # or to enter a logout/login loop + # Always start with redirect_url being empty. + redirect_url = '' + # Compare urls, to prevent a redirect from pointing (directly) + # outside of galaxy or to enter a logout/login loop. if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): redirect = root_url + if kwd.get( 'noredirect', False ): + # The referrer is explicitly asking not to redirect. + redirect = '' use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -463,7 +467,7 @@ user = trans.user email = kwd.get( 'email', '' ) if user: - # already logged in + # Already logged in. redirect_url = redirect message = 'You are already logged in.' status = 'info' @@ -503,9 +507,7 @@ active_view="user" ) def __validate_login( self, trans, **kwd ): - """ - Function validates numerous cases that might happen during the login time. - """ + """Validates numerous cases that might happen during the login time.""" message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'error' ) email = kwd.get( 'email', '' ) @@ -1114,12 +1116,10 @@ @web.expose def reset_password( self, trans, email=None, **kwd ): - """ - Reset the user's password. Send him/her an email with the new password. - """ + """Reset the user's password. Send an email with the new password.""" if trans.app.config.smtp_server is None: - return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) - message = util.sanitize_text(util.restore_text( kwd.get( 'message', '' ) )) + return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) + message = util.sanitize_text( util.restore_text( kwd.get( 'message', '' ) ) ) status = 'done' if kwd.get( 'reset_password_button', False ): reset_user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() @@ -1138,23 +1138,18 @@ if host == 'localhost': host = socket.getfqdn() body = 'Your password on %s has been reset to:\n\n %s\n' % ( host, new_pass ) - to = email frm = 'galaxy-no-reply@' + host subject = 'Galaxy Password Reset' try: - util.send_mail( frm, to, subject, body, trans.app.config ) + util.send_mail( frm, email, subject, body, trans.app.config ) reset_user.set_password_cleartext( new_pass ) trans.sa_session.add( reset_user ) trans.sa_session.flush() trans.log_event( "User reset password: %s" % email ) - message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login' ) ) + message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login', noredirect='true' ) ) except Exception, e: message = 'Failed to reset password: %s' % str( e ) status = 'error' - return trans.response.send_redirect( web.url_for( controller='user', - action='reset_password', - message=message, - status=status ) ) elif email is not None: message = "The specified user does not exist" status = 'error' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 07 Nov '14

07 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/db435e18d69d/ Changeset: db435e18d69d User: martenson Date: 2014-11-06 18:44:56+00:00 Summary: fix for https://trello.com/c/pML6OsMl/249-html-escaping-error-in-toolshed-password-… also removed bug with inproper redirecting when resetting password Affected #: 1 file diff -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff -r db435e18d69df4e7243e34b291d28dea457f3599 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -448,14 +448,18 @@ @web.expose def login( self, trans, refresh_frames=[], **kwd ): - '''Handle Galaxy Log in''' + """Handle Galaxy login""" redirect = kwd.get( 'redirect', trans.request.referer ).strip() root_url = url_for( '/', qualified=True ) - redirect_url = '' # always start with redirect_url being empty - # compare urls, to prevent a redirect from pointing (directly) outside of galaxy - # or to enter a logout/login loop + # Always start with redirect_url being empty. + redirect_url = '' + # Compare urls, to prevent a redirect from pointing (directly) + # outside of galaxy or to enter a logout/login loop. if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): redirect = root_url + if kwd.get( 'noredirect', False ): + # The referrer is explicitly asking not to redirect. + redirect = '' use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -463,7 +467,7 @@ user = trans.user email = kwd.get( 'email', '' ) if user: - # already logged in + # Already logged in. redirect_url = redirect message = 'You are already logged in.' status = 'info' @@ -503,9 +507,7 @@ active_view="user" ) def __validate_login( self, trans, **kwd ): - """ - Function validates numerous cases that might happen during the login time. - """ + """Validates numerous cases that might happen during the login time.""" message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'error' ) email = kwd.get( 'email', '' ) @@ -1114,12 +1116,10 @@ @web.expose def reset_password( self, trans, email=None, **kwd ): - """ - Reset the user's password. Send him/her an email with the new password. - """ + """Reset the user's password. Send an email with the new password.""" if trans.app.config.smtp_server is None: - return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) - message = util.sanitize_text(util.restore_text( kwd.get( 'message', '' ) )) + return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) + message = util.sanitize_text( util.restore_text( kwd.get( 'message', '' ) ) ) status = 'done' if kwd.get( 'reset_password_button', False ): reset_user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() @@ -1138,23 +1138,18 @@ if host == 'localhost': host = socket.getfqdn() body = 'Your password on %s has been reset to:\n\n %s\n' % ( host, new_pass ) - to = email frm = 'galaxy-no-reply@' + host subject = 'Galaxy Password Reset' try: - util.send_mail( frm, to, subject, body, trans.app.config ) + util.send_mail( frm, email, subject, body, trans.app.config ) reset_user.set_password_cleartext( new_pass ) trans.sa_session.add( reset_user ) trans.sa_session.flush() trans.log_event( "User reset password: %s" % email ) - message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login' ) ) + message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login', noredirect='true' ) ) except Exception, e: message = 'Failed to reset password: %s' % str( e ) status = 'error' - return trans.response.send_redirect( web.url_for( controller='user', - action='reset_password', - message=message, - status=status ) ) elif email is not None: message = "The specified user does not exist" status = 'error' https://bitbucket.org/galaxy/galaxy-central/commits/0ac62bde7db3/ Changeset: 0ac62bde7db3 User: martenson Date: 2014-11-07 15:29:06+00:00 Summary: Merged in martenson/galaxy-central-marten (pull request #554) fix for password rese Affected #: 1 file diff -r 37fb229769f4a1cc02d7df26790c5c6f13e913d6 -r 0ac62bde7db38954702c0acba648cc8efa76a214 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -448,14 +448,18 @@ @web.expose def login( self, trans, refresh_frames=[], **kwd ): - '''Handle Galaxy Log in''' + """Handle Galaxy login""" redirect = kwd.get( 'redirect', trans.request.referer ).strip() root_url = url_for( '/', qualified=True ) - redirect_url = '' # always start with redirect_url being empty - # compare urls, to prevent a redirect from pointing (directly) outside of galaxy - # or to enter a logout/login loop + # Always start with redirect_url being empty. + redirect_url = '' + # Compare urls, to prevent a redirect from pointing (directly) + # outside of galaxy or to enter a logout/login loop. if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): redirect = root_url + if kwd.get( 'noredirect', False ): + # The referrer is explicitly asking not to redirect. + redirect = '' use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -463,7 +467,7 @@ user = trans.user email = kwd.get( 'email', '' ) if user: - # already logged in + # Already logged in. redirect_url = redirect message = 'You are already logged in.' status = 'info' @@ -503,9 +507,7 @@ active_view="user" ) def __validate_login( self, trans, **kwd ): - """ - Function validates numerous cases that might happen during the login time. - """ + """Validates numerous cases that might happen during the login time.""" message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'error' ) email = kwd.get( 'email', '' ) @@ -1114,12 +1116,10 @@ @web.expose def reset_password( self, trans, email=None, **kwd ): - """ - Reset the user's password. Send him/her an email with the new password. - """ + """Reset the user's password. Send an email with the new password.""" if trans.app.config.smtp_server is None: - return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) - message = util.sanitize_text(util.restore_text( kwd.get( 'message', '' ) )) + return trans.show_error_message( "Mail is not configured for this Galaxy instance. Please contact your local Galaxy administrator." ) + message = util.sanitize_text( util.restore_text( kwd.get( 'message', '' ) ) ) status = 'done' if kwd.get( 'reset_password_button', False ): reset_user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).first() @@ -1138,23 +1138,18 @@ if host == 'localhost': host = socket.getfqdn() body = 'Your password on %s has been reset to:\n\n %s\n' % ( host, new_pass ) - to = email frm = 'galaxy-no-reply@' + host subject = 'Galaxy Password Reset' try: - util.send_mail( frm, to, subject, body, trans.app.config ) + util.send_mail( frm, email, subject, body, trans.app.config ) reset_user.set_password_cleartext( new_pass ) trans.sa_session.add( reset_user ) trans.sa_session.flush() trans.log_event( "User reset password: %s" % email ) - message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login' ) ) + message = "Password has been reset and emailed to: %s. <a href='%s'>Click here</a> to return to the login form." % ( email, web.url_for( controller='user', action='login', noredirect='true' ) ) except Exception, e: message = 'Failed to reset password: %s' % str( e ) status = 'error' - return trans.response.send_redirect( web.url_for( controller='user', - action='reset_password', - message=message, - status=status ) ) elif email is not None: message = "The specified user does not exist" status = 'error' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Refactoring, generalize conditional parameters
by commits-noreply＠bitbucket.org 06 Nov '14

06 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/37fb229769f4/ Changeset: 37fb229769f4 User: guerler Date: 2014-11-06 20:11:23+00:00 Summary: ToolForm: Refactoring, generalize conditional parameters Affected #: 6 files diff -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff -r 37fb229769f4a1cc02d7df26790c5c6f13e913d6 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -1,5 +1,5 @@ /** - This class creates a tool form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections. New input elements can be plugged in by adding cases to the switch block defined in the _addRow() function. + This class creates a tool form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections. New input elements can be plugged in by adding cases to the switch block defined in the _createField() function. */ define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content', 'mvc/tools/tools-input'], function(Utils, Table, Ui, Repeat, SelectContent, InputElement) { @@ -68,23 +68,61 @@ break; // default single element row default: - this._addRow(type, input_def); + this._addRow(input_def); } }, /** Add a conditional block */ _addConditional: function(input_def) { - // add label to input definition root - input_def.label = input_def.test_param.label; - - // add value to input definition root - input_def.value = input_def.test_param.value; - - // build options field - var field = this._addRow('conditional', input_def); + // link this + var self = this; - // add fields + // copy identifier + input_def.test_param.id = input_def.id; + + // build test parameter + var field = this._addRow(input_def.test_param); + + // set onchange event for test parameter + field.options.onchange = function(value) { + // identify the selected case + var selectedCase = self.app.tree.matchCase(input_def, value); + + // check value in order to hide/show options + for (var i in input_def.cases) { + // get case + var case_def = input_def.cases[i]; + + // identify subsection name + var section_id = input_def.id + '-section-' + i; + + // identify row + var section_row = self.table.get(section_id); + + // check if non-hidden elements exist + var nonhidden = false; + for (var j in case_def.inputs) { + var type = case_def.inputs[j].type; + if (type && type !== 'hidden') { + nonhidden = true; + break; + } + } + + // show/hide sub form + if (i == selectedCase && nonhidden) { + section_row.fadeIn('fast'); + } else { + section_row.hide(); + } + } + + // refresh form inputs + self.app.refresh(); + }; + + // add conditional sub sections for (var i in input_def.cases) { // create id tag var sub_section_id = input_def.id + '-section-' + i; @@ -208,17 +246,52 @@ this.table.append(input_def.id); }, - /** Add a single field element + /** Add a single input field element */ - _addRow: function(field_type, input_def) { + _addRow: function(input_def) { // get id var id = input_def.id; + // create input field + var field = this._createField(input_def); + + // flagging this form as dynamic will trigger api-driven refresh events + if (input_def.is_dynamic) { + this.app.is_dynamic = true; + } + + // add to field list + this.app.field_list[id] = field; + + // create input field wrapper + var input_element = new InputElement(this.app, { + label : input_def.label, + optional : input_def.optional, + help : input_def.help, + field : field + }); + + // add to element list + this.app.element_list[id] = input_element; + + // create table row + this.table.add(input_element.$el); + + // append to table + this.table.append(id); + + // return created field + return field; + }, + + /** Returns an input field for a given field type + */ + _createField: function(input_def) { // field wrapper var field = null; // identify field type - switch(field_type) { + switch(input_def.type) { // text input field case 'text' : field = this._fieldText(input_def); @@ -239,11 +312,6 @@ field = this._fieldSelect(input_def); break; - // conditional select field - case 'conditional': - field = this._fieldConditional(input_def); - break; - // hidden field case 'hidden': field = this._fieldHidden(input_def); @@ -287,97 +355,15 @@ console.debug('tools-form::_addRow() : Auto matched field type (' + field_type + ').'); } - // deactivate dynamic fields - if (input_def.is_dynamic) { - //this.app.incompatible = true; - this.app.is_dynamic = true; - } - // set field value if (input_def.value !== undefined) { field.value(input_def.value); } - // add to field list - this.app.field_list[id] = field; - - // create input field wrapper - var input_element = new InputElement(this.app, { - label : input_def.label, - optional : input_def.optional, - help : input_def.help, - field : field - }); - - // add to element list - this.app.element_list[id] = input_element; - - // create table row - this.table.add(input_element.$el); - - // append to table - this.table.append(id); - - // return created field + // return field element return field; }, - /** Conditional input field selector - */ - _fieldConditional : function(input_def) { - // link this - var self = this; - - // configure options fields - var options = []; - for (var i in input_def.test_param.options) { - var option = input_def.test_param.options[i]; - options.push({ - label: option[0], - value: option[1] - }); - } - - // select field - return new Ui.Select.View({ - id : 'field-' + input_def.id, - data : options, - onchange : function(value) { - // check value in order to hide/show options - for (var i in input_def.cases) { - // get case - var case_def = input_def.cases[i]; - - // identify subsection name - var section_id = input_def.id + '-section-' + i; - - // identify row - var section_row = self.table.get(section_id); - - // check if non-hidden elements exist - var nonhidden = false; - for (var j in case_def.inputs) { - var type = case_def.inputs[j].type; - if (type && type !== 'hidden') { - nonhidden = true; - break; - } - } - - // show/hide sub form - if (case_def.value == value && nonhidden) { - section_row.fadeIn('fast'); - } else { - section_row.hide(); - } - } - - // refresh form inputs - self.app.refresh(); - } - }); - }, - /** Data input field */ _fieldData : function(input_def) { diff -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff -r 37fb229769f4a1cc02d7df26790c5c6f13e913d6 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -104,12 +104,10 @@ // add conditional value add (job_input_id + '|' + input.test_param.name, input.id, value); - // find selected case - for (var i in input.cases) { - if (input.cases[i].value == value) { - convert(job_input_id, head[input.id + '-section-' + i]); - break; - } + // identify selected case + var selectedCase = self.matchCase(input, value); + if (selectedCase != -1) { + convert(job_input_id, head[input.id + '-section-' + selectedCase]); } break; default: @@ -146,6 +144,29 @@ return this.job_ids && this.job_ids[job_input_id]; }, + /** Match conditional values to selected cases + */ + matchCase: function(input, value) { + // format value for boolean inputs + if (input.test_param.type == 'boolean') { + if (value == 'true') { + value = input.test_param.truevalue || 'true'; + } else { + value = input.test_param.falsevalue || 'false'; + } + } + + // find selected case + for (var i in input.cases) { + if (input.cases[i].value == value) { + return i; + } + } + + // selected case not found + return -1; + }, + /** Matches identifier from api model to input elements */ matchModel: function(model, callback) { @@ -163,24 +184,24 @@ if (id != '') { index = id + '|' + index; } - if (node.type == 'repeat') { - for (var j in node.cache) { - search (index + '_' + j, node.cache[j]); - } - } else { - if (node.type == 'conditional') { + switch (node.type) { + case 'repeat': + for (var j in node.cache) { + search (index + '_' + j, node.cache[j]); + } + break; + case 'conditional': var value = node.test_param && node.test_param.value; - for (var j in node.cases) { - if (node.cases[j].value == value) { - search (index, node.cases[j].inputs); - } + var selectedCase = self.matchCase(node, value); + if (selectedCase != -1) { + search (index, node.cases[selectedCase].inputs); } - } else { + break; + default: var input_id = self.app.tree.job_ids[index]; if (input_id) { callback(input_id, node); } - } } } } diff -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff -r 37fb229769f4a1cc02d7df26790c5c6f13e913d6 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -1,5 +1,5 @@ /** - This class creates a tool form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections. New input elements can be plugged in by adding cases to the switch block defined in the _addRow() function. + This class creates a tool form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections. New input elements can be plugged in by adding cases to the switch block defined in the _createField() function. */ define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content', 'mvc/tools/tools-input'], function(Utils, Table, Ui, Repeat, SelectContent, InputElement) { @@ -68,23 +68,61 @@ break; // default single element row default: - this._addRow(type, input_def); + this._addRow(input_def); } }, /** Add a conditional block */ _addConditional: function(input_def) { - // add label to input definition root - input_def.label = input_def.test_param.label; - - // add value to input definition root - input_def.value = input_def.test_param.value; - - // build options field - var field = this._addRow('conditional', input_def); + // link this + var self = this; - // add fields + // copy identifier + input_def.test_param.id = input_def.id; + + // build test parameter + var field = this._addRow(input_def.test_param); + + // set onchange event for test parameter + field.options.onchange = function(value) { + // identify the selected case + var selectedCase = self.app.tree.matchCase(input_def, value); + + // check value in order to hide/show options + for (var i in input_def.cases) { + // get case + var case_def = input_def.cases[i]; + + // identify subsection name + var section_id = input_def.id + '-section-' + i; + + // identify row + var section_row = self.table.get(section_id); + + // check if non-hidden elements exist + var nonhidden = false; + for (var j in case_def.inputs) { + var type = case_def.inputs[j].type; + if (type && type !== 'hidden') { + nonhidden = true; + break; + } + } + + // show/hide sub form + if (i == selectedCase && nonhidden) { + section_row.fadeIn('fast'); + } else { + section_row.hide(); + } + } + + // refresh form inputs + self.app.refresh(); + }; + + // add conditional sub sections for (var i in input_def.cases) { // create id tag var sub_section_id = input_def.id + '-section-' + i; @@ -208,17 +246,52 @@ this.table.append(input_def.id); }, - /** Add a single field element + /** Add a single input field element */ - _addRow: function(field_type, input_def) { + _addRow: function(input_def) { // get id var id = input_def.id; + // create input field + var field = this._createField(input_def); + + // flagging this form as dynamic will trigger api-driven refresh events + if (input_def.is_dynamic) { + this.app.is_dynamic = true; + } + + // add to field list + this.app.field_list[id] = field; + + // create input field wrapper + var input_element = new InputElement(this.app, { + label : input_def.label, + optional : input_def.optional, + help : input_def.help, + field : field + }); + + // add to element list + this.app.element_list[id] = input_element; + + // create table row + this.table.add(input_element.$el); + + // append to table + this.table.append(id); + + // return created field + return field; + }, + + /** Returns an input field for a given field type + */ + _createField: function(input_def) { // field wrapper var field = null; // identify field type - switch(field_type) { + switch(input_def.type) { // text input field case 'text' : field = this._fieldText(input_def); @@ -239,11 +312,6 @@ field = this._fieldSelect(input_def); break; - // conditional select field - case 'conditional': - field = this._fieldConditional(input_def); - break; - // hidden field case 'hidden': field = this._fieldHidden(input_def); @@ -287,97 +355,15 @@ console.debug('tools-form::_addRow() : Auto matched field type (' + field_type + ').'); } - // deactivate dynamic fields - if (input_def.is_dynamic) { - //this.app.incompatible = true; - this.app.is_dynamic = true; - } - // set field value if (input_def.value !== undefined) { field.value(input_def.value); } - // add to field list - this.app.field_list[id] = field; - - // create input field wrapper - var input_element = new InputElement(this.app, { - label : input_def.label, - optional : input_def.optional, - help : input_def.help, - field : field - }); - - // add to element list - this.app.element_list[id] = input_element; - - // create table row - this.table.add(input_element.$el); - - // append to table - this.table.append(id); - - // return created field + // return field element return field; }, - /** Conditional input field selector - */ - _fieldConditional : function(input_def) { - // link this - var self = this; - - // configure options fields - var options = []; - for (var i in input_def.test_param.options) { - var option = input_def.test_param.options[i]; - options.push({ - label: option[0], - value: option[1] - }); - } - - // select field - return new Ui.Select.View({ - id : 'field-' + input_def.id, - data : options, - onchange : function(value) { - // check value in order to hide/show options - for (var i in input_def.cases) { - // get case - var case_def = input_def.cases[i]; - - // identify subsection name - var section_id = input_def.id + '-section-' + i; - - // identify row - var section_row = self.table.get(section_id); - - // check if non-hidden elements exist - var nonhidden = false; - for (var j in case_def.inputs) { - var type = case_def.inputs[j].type; - if (type && type !== 'hidden') { - nonhidden = true; - break; - } - } - - // show/hide sub form - if (case_def.value == value && nonhidden) { - section_row.fadeIn('fast'); - } else { - section_row.hide(); - } - } - - // refresh form inputs - self.app.refresh(); - } - }); - }, - /** Data input field */ _fieldData : function(input_def) { diff -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff -r 37fb229769f4a1cc02d7df26790c5c6f13e913d6 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -104,12 +104,10 @@ // add conditional value add (job_input_id + '|' + input.test_param.name, input.id, value); - // find selected case - for (var i in input.cases) { - if (input.cases[i].value == value) { - convert(job_input_id, head[input.id + '-section-' + i]); - break; - } + // identify selected case + var selectedCase = self.matchCase(input, value); + if (selectedCase != -1) { + convert(job_input_id, head[input.id + '-section-' + selectedCase]); } break; default: @@ -146,6 +144,29 @@ return this.job_ids && this.job_ids[job_input_id]; }, + /** Match conditional values to selected cases + */ + matchCase: function(input, value) { + // format value for boolean inputs + if (input.test_param.type == 'boolean') { + if (value == 'true') { + value = input.test_param.truevalue || 'true'; + } else { + value = input.test_param.falsevalue || 'false'; + } + } + + // find selected case + for (var i in input.cases) { + if (input.cases[i].value == value) { + return i; + } + } + + // selected case not found + return -1; + }, + /** Matches identifier from api model to input elements */ matchModel: function(model, callback) { @@ -163,24 +184,24 @@ if (id != '') { index = id + '|' + index; } - if (node.type == 'repeat') { - for (var j in node.cache) { - search (index + '_' + j, node.cache[j]); - } - } else { - if (node.type == 'conditional') { + switch (node.type) { + case 'repeat': + for (var j in node.cache) { + search (index + '_' + j, node.cache[j]); + } + break; + case 'conditional': var value = node.test_param && node.test_param.value; - for (var j in node.cases) { - if (node.cases[j].value == value) { - search (index, node.cases[j].inputs); - } + var selectedCase = self.matchCase(node, value); + if (selectedCase != -1) { + search (index, node.cases[selectedCase].inputs); } - } else { + break; + default: var input_id = self.app.tree.job_ids[index]; if (input_id) { callback(input_id, node); } - } } } } diff -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff -r 37fb229769f4a1cc02d7df26790c5c6f13e913d6 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var l=this._addRow("conditional",h);for(var k in h.cases){var j=h.id+"-section-"+k;var m=new f(this.app,{inputs:h.cases[k].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(j)}l.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.is_dynamic=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return i},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}j.app.refresh()}})},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+field_type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,onchange:function(){j.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff -r 37fb229769f4a1cc02d7df26790c5c6f13e913d6 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(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(k,n){for(var h in n){var f=n[h];if(f.input){var p=f.input;var j=k;if(k!=""){j+="|"}j+=p.name;switch(p.type){case"repeat":var e="section-";var s=[];var m=null;for(var r in f){var l=r.indexOf(e);if(l!=-1){l+=e.length;s.push(parseInt(r.substr(l)));if(!m){m=r.substr(0,l)}}}s.sort(function(t,i){return t-i});var h=0;for(var g in s){b(j+"_"+h++,f[m+s[g]])}break;case"conditional":var q=a.app.field_list[p.id].value();c(j+"|"+p.test_param.name,p.id,q);for(var g in p.cases){if(p.cases[g].value==q){b(j,n[p.id+"-section-"+g]);break}}break;default:var o=a.app.field_list[p.id];var q=o.value();if(d[p.type]){q=d[p.type](q)}if(!o.skip){c(j,p.id,q)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchModel:function(c,e){var a={};var b=this;function d(o,l){for(var k in l){var m=l[k];var h=m.name;if(o!=""){h=o+"|"+h}if(m.type=="repeat"){for(var g in m.cache){d(h+"_"+g,m.cache[g])}}else{if(m.type=="conditional"){var n=m.test_param&&m.test_param.value;for(var g in m.cases){if(m.cases[g].value==n){d(h,m.cases[g].inputs)}}}else{var f=b.app.tree.job_ids[h];if(f){e(f,m)}}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references: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($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +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(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references: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($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History structure: incorporate tool data, refactor; HDA API: return create_time
by commits-noreply＠bitbucket.org 06 Nov '14

06 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f0d3cbd97d9/ Changeset: 5f0d3cbd97d9 User: carlfeberhard Date: 2014-11-06 17:56:13+00:00 Summary: History structure: incorporate tool data, refactor; HDA API: return create_time Affected #: 30 files diff -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff client/galaxy/scripts/mvc/history/history-panel-edit-current.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit-current.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit-current.js @@ -164,12 +164,13 @@ _setUpCollectionListeners : function(){ _super.prototype._setUpCollectionListeners.call( this ); + //TODO:?? may not be needed? see history-panel-edit, 369 // 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 ){ if( ( !model.get( 'visible' ) ) && ( !this.storage.get( 'show_hidden' ) ) ){ - this.removeItemView( this.viewFromModel( model ) ); + this.removeItemView( model ); } }, this ); }, diff -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff client/galaxy/scripts/mvc/history/history-structure-view.js --- a/client/galaxy/scripts/mvc/history/history-structure-view.js +++ b/client/galaxy/scripts/mvc/history/history-structure-view.js @@ -1,79 +1,184 @@ define([ + 'mvc/history/job-dag', 'mvc/job/job-model', 'mvc/job/job-li', 'mvc/history/history-content-model', - 'mvc/history/job-dag', + 'mvc/dataset/dataset-li', 'mvc/base-mvc', 'utils/localization', 'libs/d3' -], function( JOB, JOB_LI, HISTORY_CONTENT, JobDAG, BASE_MVC, _l ){ +], function( JobDAG, JOB, JOB_LI, HISTORY_CONTENT, DATASET_LI, BASE_MVC, _l ){ // ============================================================================ -/* TODO: -change component = this to something else +/* +TODO: + disruptive: + handle collections + retain contents to job relationships (out/input name) + + display when *only* copied datasets + need to change when/how joblessVertices are created + + components should be full height containers that scroll individually + + use history contents views for job outputCollection, not vanilla datasets + need hid + + show datasets when job not expanded + make them external to the job display + connect jobs by dataset + which datasets from job X are which inputs in job Y? + + make job data human readable (needs tool data) + show only tool.inputs with labels (w/ job.params as values) + input datasets are special + they don't appear in job.params + have to connect to datasets in the dag + connect job.inputs to any tool.inputs by tool.input.name (in params) + +API: seems like this could be handled there - duplicating the input data in the proper param space + + collections + + use cases: + operations by thread: + copy to new history + rerun + to workflow + operations by branch (all descendants): + copy to new history + rerun + to workflow + signal to noise: + collapse/expand branch + hide jobs + visually isolate branch (hide other jobs) of thread + zoom (somehow) + + layout changes: + move branch to new column in component + complicated + pyramid + circular + sources on inner radius + expansion in vertical: + obscures relations due to height + could move details to side panel + difficult to compare two+ jobs/datasets when at different points in the topo + + (other) controls: + (optionally) filter all deleted + (optionally) filter all hidden + //(optionally) filter __SET_METADATA__ + //(optionally) filter error'd jobs + help and explanation + filtering/searching of jobs + + challenges: + difficult to scale dom (for zoomout) + possible to use css transforms? + transform svg and dom elements + it is possible to use css transforms on svg nodes + use transform-origin to select origin to top left + on larger histories the svg section may become extremely large due to distance from output to input + + how-to: + descendant ids: _.keys( component.depth/breadthFirstSearchTree( start ).vertices ) + + in-panel view of anc desc + */ // ============================================================================ /** * */ +window.JobDAG = JobDAG; var HistoryStructureComponent = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ //logger : console, className : 'history-structure-component', + _INITIAL_ZOOM_LEVEL : 1.0, + _MIN_ZOOM_LEVEL : 0.25, + _LINK_ID_SEP : '-to-', + _VERTEX_NAME_DATA_KEY : 'vertex-name', + + JobItemClass : JOB_LI.JobListItemView, + ContentItemClass : DATASET_LI.DatasetListItemView, + initialize : function( attributes ){ this.log( this + '(HistoryStructureComponent).initialize:', attributes ); this.component = attributes.component; - this._jobLiMap = {}; - this._createJobModels(); + this._liMap = {}; + this._createVertexItems(); + + this.zoomLevel = attributes.zoomLevel || this._INITIAL_ZOOM_LEVEL; this.layout = this._createLayout( attributes.layoutOptions ); }, - _createJobModels : function(){ + _createVertexItems : function(){ var view = this; view.component.eachVertex( function( vertex ){ - var jobJSON = vertex.data.job, - job = new JOB.Job( jobJSON ); - - // get the models of the outputs for this job from the history - var outputModels = _.map( job.get( 'outputs' ), function( output ){ - //note: output is { src: 'hda/dataset_collection', id: <some id> } - // job output doesn't *quite* match up to normal typeId - var type = output.src === 'hda'? 'dataset' : 'dataset_collection', - typeId = HISTORY_CONTENT.typeIdStr( type, output.id ); - return view.model.contents.get( typeId ); - }); - // set the collection (HistoryContents) for the job to that json (setting historyId for proper ajax urls) - job.outputCollection.reset( outputModels ); - job.outputCollection.historyId = view.model.id; - //this.debug( job.outputCollection ); - - // create the bbone view for the job (to be positioned later accrd. to the layout) and cache - var li = new JOB_LI.JobListItemView({ model: job }); - //var li = new JOB_LI.JobListItemView({ model: job }); - li.render( 0 ).$el.appendTo( view.$el ); - view._jobLiMap[ job.id ] = li; - view._setUpJobListeners( li ); - +//TODO: hack + var type = vertex.data.job? 'job' : 'copy', + li; + if( type === 'job' ){ + li = view._createJobListItem( vertex ); + } else if( type === 'copy' ){ + li = view._createContentListItem( vertex ); + } + view._liMap[ vertex.name ] = li; }); - return view.jobs; + view.debug( '_liMap:', view._liMap ); }, - _setUpJobListeners : function( jobLi ){ - // update the layout during expansion and collapsing of job and output li's - jobLi.on( 'expanding expanded collapsing collapsed', this.render, this ); - jobLi.foldout.on( 'view:expanding view:expanded view:collapsing view:collapsed', this.render, this ); + _createJobListItem : function( vertex ){ + this.debug( '_createJobListItem:', vertex ); + var view = this, + jobData = vertex.data, + job = new JOB.Job( jobData.job ); + + // get the models of the outputs for this job from the history + var outputModels = _.map( job.get( 'outputs' ), function( output ){ + //note: output is { src: 'hda/dataset_collection', id: <some id> } + // job output doesn't *quite* match up to normal typeId + var type = output.src === 'hda'? 'dataset' : 'dataset_collection', + typeId = HISTORY_CONTENT.typeIdStr( type, output.id ); + return view.model.contents.get( typeId ); + }); + // set the collection (HistoryContents) for the job to that json (setting historyId for proper ajax urls) + job.outputCollection.reset( outputModels ); + job.outputCollection.historyId = view.model.id; + //this.debug( job.outputCollection ); + + // create the bbone view for the job (to be positioned later accrd. to the layout) and cache + var li = new view.JobItemClass({ model: job, tool: jobData.tool, jobData: jobData }); + li.on( 'expanding expanded collapsing collapsed', view.renderGraph, view ); + li.foldout.on( 'view:expanding view:expanded view:collapsing view:collapsed', view.renderGraph, view ); + return li; + }, + + _createContentListItem : function( vertex ){ + this.debug( '_createContentListItem:', vertex ); + var view = this, + content = vertex.data, + typeId = HISTORY_CONTENT.typeIdStr( content.history_content_type, content.id ); + content = view.model.contents.get( typeId ); + var li = new view.ContentItemClass({ model: content }); + li.on( 'expanding expanded collapsing collapsed', view.renderGraph, view ); + return li; }, layoutDefaults : { - paddingTop : 8, - paddingLeft : 20, linkSpacing : 16, - jobHeight : 308, - jobWidthSpacing : 320, + linkWidth : 0, + linkHeight : 0, + jobWidth : 300, + jobHeight : 300, + jobSpacing : 12, linkAdjX : 4, linkAdjY : 0 }, @@ -85,8 +190,7 @@ layout = _.extend( options, { nodeMap : {}, links : [], - el : { width: 0, height: 0 }, - svg : { width: 0, height: 0, top: 0, left: 0 } + svg : { width: 0, height: 0 } }); vertices.forEach( function( v, j ){ @@ -105,56 +209,50 @@ return layout; }, - _updateLayout : function(){ - var view = this, - layout = view.layout; - - layout.svg.height = layout.paddingTop + ( layout.linkSpacing * _.size( layout.nodeMap ) ); - layout.el.height = layout.svg.height + layout.jobHeight; - -//TODO:?? can't we just alter the component v and e's directly? - // layout the job views putting jobWidthSpacing btwn each - var x = layout.paddingLeft, - y = layout.svg.height; - _.each( layout.nodeMap, function( node, jobId ){ - //this.debug( node, jobId ); - node.x = x; - node.y = y; - x += layout.jobWidthSpacing; - }); - layout.el.width = layout.svg.width = Math.max( layout.el.width, x ); - - // layout the links - connecting each job by it's main coords (currently) -//TODO: somehow adjust the svg height based on the largest distance the longest connection needs - layout.links.forEach( function( link ){ - var source = layout.nodeMap[ link.source ], - target = layout.nodeMap[ link.target ]; - link.x1 = source.x + layout.linkAdjX; - link.y1 = source.y + layout.linkAdjY; - link.x2 = target.x + layout.linkAdjX; - link.y2 = target.y + layout.linkAdjY; - }); - //this.debug( JSON.stringify( layout, null, ' ' ) ); - return this.layout; - }, - render : function( options ){ this.debug( this + '.render:', options ); var view = this; + view.$el.html([ + '<header></header>', + '<nav class="controls"></nav>', + '<figure class="graph"></figure>', + '<footer></footer>' + ].join( '' ) ); + + var $graph = view.$graph(); + view.component.eachVertex( function( vertex ){ + view._liMap[ vertex.name ].render( 0 ).$el.appendTo( $graph ) + // store the name in the DOM and cache by that name + .data( view._VERTEX_NAME_DATA_KEY, vertex.name ); + }); + view.renderGraph(); + return this; + }, + + $graph : function(){ + return this.$( '.graph' ); + }, + + renderGraph : function( options ){ + this.debug( this + '.renderGraph:', options ); + var view = this; function _render(){ + view._updateLayout(); // set up the display containers - view.$el - .width( view.layout.el.width ) - .height( view.layout.el.height ); + view.$graph() + // use css3 transform to scale component graph + .css( 'transform', [ 'scale(', view.zoomLevel, ',', view.zoomLevel, ')' ].join( '' ) ) + .width( view.layout.svg.width ) + .height( view.layout.svg.height ); view.renderSVG(); // position the job views accrd. to the layout view.component.eachVertex( function( v ){ -//TODO:? liMap needed - can't we attach to vertex? - var li = view._jobLiMap[ v.name ], - position = view.layout.nodeMap[ li.model.id ]; +//TODO:?? liMap needed - can't we attach to vertex? + var li = view._liMap[ v.name ], + position = view.layout.nodeMap[ v.name ]; //this.debug( position ); li.$el.css({ top: position.y, left: position.x }); }); @@ -168,13 +266,52 @@ return this; }, - renderSVG : function(){ + _updateLayout : function(){ + this.debug( this + '._updateLayout:' ); var view = this, layout = view.layout; - var svg = d3.select( this.el ).select( 'svg' ); + layout.linkHeight = layout.linkSpacing * _.size( layout.nodeMap ); + layout.svg.height = layout.linkHeight + layout.jobHeight; + + // reset for later max comparison + layout.svg.width = 0; + +//TODO:?? can't we just alter the component v and e's directly? + // layout the job views putting jobSpacing btwn each + var x = 0, + y = layout.linkHeight; + _.each( layout.nodeMap, function( node, jobId ){ + //this.debug( node, jobId ); + node.x = x; + node.y = y; + x += layout.jobWidth + layout.jobSpacing; + }); + layout.svg.width = layout.linkWidth = Math.max( layout.svg.width, x ); + + // layout the links - connecting each job by it's main coords (currently) +//TODO: somehow adjust the svg height based on the largest distance the longest connection needs + layout.links.forEach( function( link ){ + var source = layout.nodeMap[ link.source ], + target = layout.nodeMap[ link.target ]; + link.x1 = source.x + layout.linkAdjX; + link.y1 = source.y + layout.linkAdjY; + link.x2 = target.x + layout.linkAdjX; + link.y2 = target.y + layout.linkAdjY; + }); + + this.debug( JSON.stringify( layout, null, ' ' ) ); + return this.layout; + }, + + renderSVG : function(){ + this.debug( this + '.renderSVG:' ); + var view = this, + layout = view.layout; + + var svg = d3.select( this.$graph().get(0) ).select( 'svg' ); if( svg.empty() ){ - svg = d3.select( this.el ).append( 'svg' ); + svg = d3.select( this.$graph().get(0) ).append( 'svg' ); } svg @@ -183,14 +320,14 @@ function highlightConnect( d ){ d3.select( this ).classed( 'highlighted', true ); - view._jobLiMap[ d.source ].$el.addClass( 'highlighted' ); - view._jobLiMap[ d.target ].$el.addClass( 'highlighted' ); + view._liMap[ d.source ].$el.addClass( 'highlighted' ); + view._liMap[ d.target ].$el.addClass( 'highlighted' ); } function unhighlightConnect( d ){ d3.select( this ).classed( 'highlighted', false ); - view._jobLiMap[ d.source ].$el.removeClass( 'highlighted' ); - view._jobLiMap[ d.target ].$el.removeClass( 'highlighted' ); + view._liMap[ d.source ].$el.removeClass( 'highlighted' ); + view._liMap[ d.target ].$el.removeClass( 'highlighted' ); } var connections = svg.selectAll( '.connection' ) @@ -199,21 +336,19 @@ connections .enter().append( 'path' ) .attr( 'class', 'connection' ) - .attr( 'id', function( d ){ return d.source + '-' + d.target; }) + .attr( 'id', function( d ){ return [ d.source, d.target ].join( view._LINK_ID_SEP ); }) .on( 'mouseover', highlightConnect ) .on( 'mouseout', unhighlightConnect ); connections .attr( 'd', function( d ){ return view._connectionPath( d ); }); -//TODO: ? can we use tick here to update the links? - return svg.node(); }, _connectionPath : function( d ){ var CURVE_X = 0, - controlY = ( ( d.x2 - d.x1 ) / this.layout.svg.width ) * this.layout.svg.height; + controlY = ( ( d.x2 - d.x1 ) / this.layout.svg.width ) * this.layout.linkHeight; return [ 'M', d.x1, ',', d.y1, ' ', 'C', @@ -224,11 +359,12 @@ }, events : { - 'mouseover .job.list-item' : function( ev ){ this.highlightConnected( ev.currentTarget, true ); }, - 'mouseout .job.list-item' : function( ev ){ this.highlightConnected( ev.currentTarget, false ); } + 'mouseover .graph > .list-item' : function( ev ){ this.highlightConnected( ev.currentTarget, true ); }, + 'mouseout .graph > .list-item' : function( ev ){ this.highlightConnected( ev.currentTarget, false ); } }, highlightConnected : function( jobElement, highlight ){ + this.debug( 'highlightConnected', jobElement, highlight ); highlight = highlight !== undefined? highlight : true; var view = this, @@ -237,21 +373,32 @@ connectionClass = highlight? 'connection highlighted' : 'connection'; //console.debug( 'mouseover', this ); - var $jobs = jobClassFn.call( $( jobElement ), 'highlighted' ), - id = $jobs.attr( 'id' ).replace( 'job-', '' ); + var $hoverTarget = jobClassFn.call( $( jobElement ), 'highlighted' ), + id = $hoverTarget.data( view._VERTEX_NAME_DATA_KEY ); // immed. ancestors component.edges({ target: id }).forEach( function( edge ){ - jobClassFn.call( view.$( '#job-' + edge.source ), 'highlighted' ); - view.$( '#' + edge.source + '-' + id ).attr( 'class', connectionClass ); + var ancestorId = edge.source, + ancestorLi = view._liMap[ ancestorId ]; + //view.debug( '\t ancestor:', ancestorId, ancestorLi ); + jobClassFn.call( ancestorLi.$el, 'highlighted' ); + view.$( '#' + ancestorId + view._LINK_ID_SEP + id ).attr( 'class', connectionClass ); }); // descendants component.vertices[ id ].eachEdge( function( edge ){ - jobClassFn.call( view.$( '#job-' + edge.target ), 'highlighted' ); - view.$( '#' + id + '-' + edge.target ).attr( 'class', connectionClass ); + var descendantId = edge.target, + descendantLi = view._liMap[ descendantId ]; + //view.debug( '\t descendant:', descendantId, descendantLi ); + jobClassFn.call( descendantLi.$el, 'highlighted' ); + view.$( '#' + id + view._LINK_ID_SEP + descendantId ).attr( 'class', connectionClass ); }); }, + zoom : function( level ){ + this.zoomLevel = Math.min( 1.0, Math.max( this._MIN_ZOOM_LEVEL, level ) ); + return this.renderGraph(); + }, + toString : function(){ return 'HistoryStructureComponent(' + this.model.id + ')'; } @@ -268,45 +415,34 @@ className : HistoryStructureComponent.prototype.className + ' vertical', - layoutDefaults : { - paddingTop : 8, - paddingLeft : 20, - linkSpacing : 16, - jobWidth : 308, - jobHeight : 308, - initialSpacing : 64, - jobSpacing : 16, + layoutDefaults : _.extend( _.clone( HistoryStructureComponent.prototype.layoutDefaults ), { linkAdjX : 0, linkAdjY : 4 - }, + }), //TODO: how can we use the dom height of the job li's - they're not visible when this is called? _updateLayout : function(){ + this.debug( this + '._updateLayout:' ); var view = this, layout = view.layout; //this.info( this.cid, '_updateLayout' ) - layout.svg.width = layout.paddingLeft + ( layout.linkSpacing * _.size( layout.nodeMap ) ); - layout.el.width = layout.svg.width + layout.jobWidth; + layout.linkWidth = layout.linkSpacing * _.size( layout.nodeMap ); + layout.svg.width = layout.linkWidth + layout.jobWidth; // reset height - we'll get the max Y below to assign to it - layout.el.height = 0; + layout.svg.height = 0; -//TODO:?? can't we just alter the component v and e's directly? - var x = layout.svg.width, - y = layout.paddingTop; - _.each( layout.nodeMap, function( node, jobId ){ - //this.debug( node, jobId ); + //TODO:?? can't we just alter the component v and e's directly? + var x = layout.linkWidth, + y = 0; + _.each( layout.nodeMap, function( node, nodeId ){ node.x = x; node.y = y; - var li = view._jobLiMap[ jobId ]; - if( li.$el.is( ':visible' ) ){ - y += li.$el.height() + layout.jobSpacing; - } else { - y += layout.initialSpacing + layout.jobSpacing; - } + var li = view._liMap[ nodeId ]; + y += li.$el.height() + layout.jobSpacing; }); - layout.el.height = layout.svg.height = Math.max( layout.el.height, y ); + layout.linkHeight = layout.svg.height = Math.max( layout.svg.height, y ); // layout the links - connecting each job by it's main coords (currently) layout.links.forEach( function( link ){ @@ -316,17 +452,16 @@ link.y1 = source.y + layout.linkAdjY; link.x2 = target.x + layout.linkAdjX; link.y2 = target.y + layout.linkAdjY; - view.debug( 'link:', link.x1, link.y1, link.x2, link.y2, link ); + //view.debug( 'link:', link.x1, link.y1, link.x2, link.y2, link ); }); - //this.debug( JSON.stringify( layout, null, ' ' ) ); - view.debug( 'el:', layout.el ); - view.debug( 'svg:', layout.svg ); + + this.debug( JSON.stringify( layout, null, ' ' ) ); return layout; }, _connectionPath : function( d ){ var CURVE_Y = 0, - controlX = ( ( d.y2 - d.y1 ) / this.layout.svg.height ) * this.layout.svg.width; + controlX = ( ( d.y2 - d.y1 ) / this.layout.svg.height ) * this.layout.linkWidth; return [ 'M', d.x1, ',', d.y1, ' ', 'C', @@ -352,40 +487,60 @@ className : 'history-structure', + _layoutToComponentClass : { + 'horizontal' : HistoryStructureComponent, + 'vertical' : VerticalHistoryStructureComponent + }, + //_DEFAULT_LAYOUT : 'horizontal', + _DEFAULT_LAYOUT : 'vertical', + initialize : function( attributes ){ + this.layout = _.contains( attributes.layout, _.keys( this._layoutToComponentClass ) )? + attributes.layout : this._DEFAULT_LAYOUT; this.log( this + '(HistoryStructureView).initialize:', attributes, this.model ); -//TODO: to model - this.jobs = attributes.jobs; + //TODO:?? to model - maybe glom jobs onto model in order to persist + // cache jobs since we need to re-create the DAG if settings change + this._processTools( attributes.tools ); + this._processJobs( attributes.jobs ); this._createDAG(); }, + _processTools : function( tools ){ + this.tools = tools || {}; + return this.tools; + }, + + _processJobs : function( jobs ){ + this.jobs = jobs || []; + return this.jobs; + }, + _createDAG : function(){ this.dag = new JobDAG({ historyContents : this.model.contents.toJSON(), + tools : this.tools, jobs : this.jobs, excludeSetMetadata : true, excludeErroredJobs : true }); -//window.dag = this.dag; - this.log( this + '.dag:', this.dag ); - + this.debug( this + '.dag:', this.dag ); this._createComponents(); }, _createComponents : function(){ this.log( this + '._createComponents' ); var structure = this; -//window.structure = structure; structure.componentViews = structure.dag.weakComponentGraphArray().map( function( componentGraph ){ return structure._createComponent( componentGraph ); }); + return structure.componentViews; }, _createComponent : function( component ){ this.log( this + '._createComponent:', component ); - //return new HistoryStructureComponent({ - return new VerticalHistoryStructureComponent({ + var ComponentClass = this._layoutToComponentClass[ this.layout ]; + return new ComponentClass({ model : this.model, component : component }); @@ -395,7 +550,7 @@ this.log( this + '.render:', options ); var structure = this; - structure.$el.html([ + structure.$el.addClass( 'clear' ).html([ '<div class="controls"></div>', '<div class="components"></div>' ].join( '' )); @@ -410,8 +565,17 @@ return this.$( '.components' ); }, + changeLayout : function( layout ){ + if( !( layout in this._layoutToComponentClass ) ){ + throw new Error( this + ': unknown layout: ' + layout ); + } + this.layout = layout; + this._createComponents(); + return this.render(); + }, + toString : function(){ - return 'HistoryStructureView(' + ')'; + return 'HistoryStructureView(' + this.model.id + ')'; } }); diff -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff client/galaxy/scripts/mvc/history/job-dag.js --- a/client/galaxy/scripts/mvc/history/job-dag.js +++ b/client/galaxy/scripts/mvc/history/job-dag.js @@ -9,15 +9,19 @@ * using the connections between job inputs and outputs. */ var JobDAG = function( options ){ + options = options || {}; var self = this; //this.logger = console; + self.filters = []; + // instance vars //TODO: needed? + self._jobsData = []; self._historyContentsMap = {}; - self.filters = []; + self._toolMap = {}; - self._idMap = {}; + self._outputIdToJobMap = {}; self.noInputJobs = []; self.noOutputJobs = []; @@ -25,7 +29,11 @@ self.filteredSetMetadata = []; self.filteredErroredJobs = []; - _super.call( self, true, null, options ); + self.dataKeys = [ 'jobs', 'historyContents', 'tools' ]; + _super.call( self, true, + _.pick( options, self.dataKeys ), + _.omit( options, self.dataKeys ) + ); }; JobDAG.prototype = new GRAPH.Graph(); JobDAG.prototype.constructor = JobDAG; @@ -33,29 +41,19 @@ // add logging ability - turn off/on using the this.logger statement above addLogging( JobDAG ); + // ---------------------------------------------------------------------------- /** process jobs, options, filters, and any history data, then create the graph */ JobDAG.prototype.init = function _init( options ){ options = options || {}; - _super.prototype.init.call( this, options ); - var self = this, - historyContentsJSON = options.historyContents || []; - jobsJSON = options.jobs || []; - - historyContentsJSON.forEach( function( content, i ){ - self._historyContentsMap[ content.id ] = _.clone( content ); - }); - - self.options = _.defaults( _.omit( options, 'historyContents', 'jobs' ), { + var self = this; + self.options = _.defaults( options, { excludeSetMetadata : false }); self.filters = self._initFilters(); -//TODO: O( 3N ) - self.preprocessJobs( _.clone( jobsJSON ) ); - self.createGraph(); - + _super.prototype.init.call( self, options ); return self; }; @@ -92,127 +90,233 @@ return filters; }; -/** sort the jobs and cache any that pass all filters into _idMap by job.id */ +/** */ +JobDAG.prototype.read = function _read( data ){ + var self = this; + if( _.has( data, 'historyContents' ) && _.has( data, 'jobs' ) && _.has( data, 'tools' ) ){ + // a job dag is composed of these three elements: + // clone the 3 data sources into the DAG, processing the jobs finally using the history and tools + self.preprocessHistoryContents( data.historyContents || [] ) + .preprocessTools( data.tools || {} ) + .preprocessJobs( data.jobs || [] ); + + // filter jobs and create the vertices and edges of the job DAG + self.createGraph( self._filterJobs() ); + return self; + } + return _super.prototype.read.call( this, data ); +}; + +/** */ +JobDAG.prototype.preprocessHistoryContents = function _preprocessHistoryContents( historyContents ){ + this.info( 'processing history' ); + var self = this; + self._historyContentsMap = {}; + + historyContents.forEach( function( content, i ){ + self._historyContentsMap[ content.id ] = _.clone( content ); + }); + return self; +}; + +/** */ +JobDAG.prototype.preprocessTools = function _preprocessTools( tools ){ + this.info( 'processing tools' ); + var self = this; + self._toolMap = {}; + + _.each( tools, function( tool, id ){ + self._toolMap[ id ] = _.clone( tool ); + }); + return self; +}; + +/** sort the cloned jobs, decorate with tool and history contents info, and store in prop array */ JobDAG.prototype.preprocessJobs = function _preprocessJobs( jobs ){ this.info( 'processing jobs' ); + var self = this; + self._outputIdToJobMap = {}; - var self = this; -//TODO:? sorting neccessary? - self.sort( jobs ).forEach( function( job, i ){ - var jobData = self.preprocessJob( job, i ); - if( jobData ){ - self._idMap[ job.id ] = jobData; - } + self._jobsData = self.sort( jobs ).map( function( job ){ + return self.preprocessJob( _.clone( job ) ); }); +//console.debug( JSON.stringify( self._jobsData, null, ' ' ) ); +//console.debug( JSON.stringify( self._outputIdToJobMap, null, ' ' ) ); return self; }; /** sort the jobs based on update time */ JobDAG.prototype.sort = function _sort( jobs ){ function cmpCreate( a, b ){ - if( a.update_time > b.update_time ){ return 1; } - if( a.update_time < b.update_time ){ return -1; } + if( a.create_time > b.create_time ){ return 1; } + if( a.create_time < b.create_time ){ return -1; } return 0; } return jobs.sort( cmpCreate ); }; -/** proces input/output, filter based on job data returning data if passing, null if not */ +/** decorate with input/output datasets and tool */ JobDAG.prototype.preprocessJob = function _preprocessJob( job, index ){ //this.info( 'preprocessJob', job, index ); var self = this, - jobData = { index: index, job: job }; + jobData = { job: job }; - jobData.inputs = self.datasetMapToIdArray( job.inputs, function( dataset, nameInJob ){ - //TODO:? store output name in self._datasets[ output.id ] from creating job? - }); - if( jobData.inputs.length === 0 ){ + jobData.inputs = self._processInputs( job ); + if( _.size( jobData.inputs ) === 0 ){ self.noInputJobs.push( job.id ); } - jobData.outputs = self.datasetMapToIdArray( job.outputs, function( dataset, nameInJob ){ - - }); - if( jobData.outputs.length === 0 ){ + jobData.outputs = self._processOutputs( job ); + if( _.size( jobData.outputs ) === 0 ){ self.noOutputJobs.push( job.id ); } - //self.debug( JSON.stringify( jobData, null, ' ' ) ); - // apply filters after processing job allowing access to the additional data above in the filters - for( var i=0; i<self.filters.length; i++ ){ - if( !self.filters[i].call( self, jobData ) ){ - self.debug( 'job', job.id, ' has been filtered out by function:\n', self.filters[i] ); - return null; - } - } + jobData.tool = self._toolMap[ job.tool_id ]; - //self.info( 'preprocessJob returning', jobData ); + //self.info( '\t jobData:', jobData ); return jobData; }; -/** make verbose input/output lists more concise, sanity checking along the way - * processFn is called on each input/output and passed the dataset obj (id,src) and the input/output name. +/** */ -JobDAG.prototype.datasetMapToIdArray = function _datasetMapToIdArray( datasetMap, processFn ){ +JobDAG.prototype._processInputs = function __processInputs( job ){ + var self = this, + inputs = job.inputs, + inputMap = {}; + _.each( inputs, function( input, nameInJob ){ + input = _.clone( self._validateInputOutput( input ) ); + input.name = nameInJob; + // since this is a DAG and we're processing in order of create time, + // the inputs for this job will already be listed in _outputIdToJobMap + // TODO: we can possibly exploit this + //console.debug( 'input in _outputIdToJobMap', self._outputIdToJobMap[ input.id ] ); + input.content = self._historyContentsMap[ input.id ]; + inputMap[ input.id ] = input; + }); + return inputMap; +}; + +/** + */ +JobDAG.prototype._validateInputOutput = function __validateInputOutput( inputOutput ){ + if( !inputOutput.id ){ + throw new Error( 'No id on job input/output: ', JSON.stringify( inputOutput ) ); + } + if( !inputOutput.src || inputOutput.src !== 'hda' ){ + throw new Error( 'Bad src on job input/output: ', JSON.stringify( inputOutput ) ); + } + return inputOutput; +}; + +/** + */ +JobDAG.prototype._processOutputs = function __processOutputs( job ){ + var self = this, + outputs = job.outputs, + outputMap = {}; + _.each( outputs, function( output, nameInJob ){ + output = _.clone( self._validateInputOutput( output ) ); + output.name = nameInJob; + // add dataset content to jobData + output.content = self._historyContentsMap[ output.id ]; + outputMap[ output.id ] = output; + + self._outputIdToJobMap[ output.id ] = job.id; + }); + return outputMap; +}; + +/** */ +JobDAG.prototype._filterJobs = function __filterJobs(){ var self = this; - return _.map( datasetMap, function( dataset, nameInJob ){ - if( !dataset.id ){ - throw new Error( 'No id on datasetMap: ', JSON.stringify( dataset ) ); + return self._jobsData.filter( function( j, i ){ return self._filterJob( j, i ); }); +}; + +/** + */ +JobDAG.prototype._filterJob = function _filterJob( jobData, index ){ + // apply filters after processing job allowing access to the additional data above inside the filters + var self = this; + for( var i=0; i<self.filters.length; i++ ){ + if( !self.filters[i].call( self, jobData ) ){ + self.debug( '\t job', jobData.job.id, ' has been filtered out by function:\n', self.filters[i] ); + return false; } - if( !dataset.src || dataset.src !== 'hda' ){ - throw new Error( 'Bad src on datasetMap: ', JSON.stringify( dataset ) ); - } - processFn.call( self, dataset, nameInJob ); - return dataset.id; - }); + } + return true; }; /** Walk all the jobs (vertices), attempting to find connections * between datasets used as both inputs and outputs (edges) */ -JobDAG.prototype.createGraph = function _createGraph(){ +JobDAG.prototype.createGraph = function _createGraph( jobsData ){ var self = this; self.debug( 'connections:' ); + //console.debug( jobsData ); - _.each( self._idMap, function( sourceJobData, sourceJobId ){ - self.debug( '\t', sourceJobId, sourceJobData ); - self.createVertex( sourceJobId, sourceJobData ); - - sourceJobData.usedIn = []; - _.each( sourceJobData.outputs, function( outputDatasetId ){ -//TODO: O(n^2) - _.each( self._idMap, function( targetJobData, targetJobId ){ - if( targetJobData === sourceJobData ){ return; } - - if( targetJobData.inputs.indexOf( outputDatasetId ) !== -1 ){ - self.info( '\t\t\t found connection: ', sourceJobId, targetJobId ); - sourceJobData.usedIn.push({ job: targetJobId, output: outputDatasetId }); - - self.createVertex( targetJobId, targetJobData ); - - self.createEdge( sourceJobId, targetJobId, self.directed, { - dataset : outputDatasetId - }); - } + _.each( jobsData, function( jobData ){ + var id = jobData.job.id; + self.debug( '\t', id, jobData ); + self.createVertex( id, jobData ); + }); + _.each( jobsData, function( jobData ){ + var targetId = jobData.job.id; + _.each( jobData.inputs, function( input, inputId ){ + //console.debug( '\t\t target input:', inputId, input ); + var sourceId = self._outputIdToJobMap[ inputId ]; + //console.debug( '\t\t source job id:', sourceId ); + if( !sourceId ){ + var joblessVertex = self.createJobLessVertex( inputId ); + sourceId = joblessVertex.name; + } +//TODO:?? no checking here whether sourceId is actually in the vertex map + //console.debug( '\t\t creating edge, source:', sourceId, self.vertices[ sourceId ] ); + //console.debug( '\t\t creating edge, target:', targetId, self.vertices[ targetId ] ); + self.createEdge( sourceId, targetId, self.directed, { + dataset : inputId }); }); }); - self.debug( 'job data: ', JSON.stringify( self._idMap, null, ' ' ) ); + //console.debug( self.toVerticesAndEdges().edges ); + + self.debug( 'final graph: ', JSON.stringify( self.toVerticesAndEdges(), null, ' ' ) ); return self; }; +/** Return a 'mangled' version of history contents id to prevent contents <-> job id collision */ +JobDAG.prototype.createJobLessVertex = function _createJobLessVertex( contentId ){ + // currently, copied contents are the only history contents without jobs (that I know of) + //note: following needed to prevent id collision btwn content and jobs in vertex map + var JOBLESS_ID_MANGLER = 'copy-', + mangledId = JOBLESS_ID_MANGLER + contentId; + return this.createVertex( mangledId, this._historyContentsMap[ contentId ] ); +}; + /** Override to re-sort (ugh) jobs in each component by update time */ -Graph.prototype.weakComponentGraphArray = function(){ +JobDAG.prototype.weakComponentGraphArray = function(){ + var dag = this; return this.weakComponents().map( function( component ){ //TODO: this seems to belong above (in sort) - why isn't it preserved? + // note: using create_time (as opposed to update_time) + // since update_time for jobless/copied datasets is changes more often component.vertices.sort( function cmpCreate( a, b ){ - if( a.data.job.update_time > b.data.job.update_time ){ return 1; } - if( a.data.job.update_time < b.data.job.update_time ){ return -1; } + var aCreateTime = a.data.job? a.data.job.create_time : a.data.create_time, + bCreateTime = b.data.job? b.data.job.create_time : b.data.create_time; + if( aCreateTime > bCreateTime ){ return 1; } + if( aCreateTime < bCreateTime ){ return -1; } return 0; }); - return new Graph( this.directed, component ); + return new Graph( dag.directed, component ); }); }; +JobDAG.prototype._jobsDataMap = function(){ + var jobsDataMap = {}; + this._jobsData.forEach( function( jobData ){ + jobsDataMap[ jobData.job.id ] = jobData; + }); + return jobsDataMap; +}; + // ============================================================================ return JobDAG; diff -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff client/galaxy/scripts/mvc/job/job-li.js --- a/client/galaxy/scripts/mvc/job/job-li.js +++ b/client/galaxy/scripts/mvc/job/job-li.js @@ -14,7 +14,6 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, - className : _super.prototype.className + " job", id : function(){ return [ 'job', this.model.get( 'id' ) ].join( '-' ); @@ -28,6 +27,9 @@ this.log( this + '.initialize:', attributes ); _super.prototype.initialize.call( this, attributes ); + this.tool = attributes.tool || {}; + this.jobData = attributes.jobData || {}; + /** where should pages from links be displayed? (default to new tab/window) */ this.linkTarget = attributes.linkTarget || '_blank'; }, @@ -50,6 +52,61 @@ }); }, + // ........................................................................ template helpers + // all of these are ADAPTERs - in other words, it might be better if the API returned the final form + // or something similar in order to remove some of the complexity here + + /** Return tool.inputs that should/can be safely displayed */ + _labelParamMap : function(){ + //ADAPTER + var params = this.model.get( 'params' ), + labelParamMap = {}; + _.each( this.tool.inputs, function( i ){ + //console.debug( i.label, i.model_class ); + if( i.label && i.model_class !== 'DataToolParameter' ){ + labelParamMap[ i.label ] = params[ i.name ]; + } + }); + return labelParamMap; + }, + + _labelInputMap : function(){ + //ADAPTER + var view = this, + labelInputMap = {}; + _.each( this.jobData.inputs, function( input ){ + var toolInput = view._findToolInput( input.name ); + if( toolInput ){ + labelInputMap[ toolInput.label ] = input; + } + }); + return labelInputMap; + }, + + /** Return a tool.inputs object that matches (or partially matches) the given (job input) name */ + _findToolInput : function( name ){ + //ADAPTER + var toolInputs = this.tool.inputs, + exactMatch = _.findWhere( toolInputs, { name : name }); + if( exactMatch ){ return exactMatch; } + return this._findRepeatToolInput( name, toolInputs ); + }, + + /** Return a tool.inputs object that partially matches the given (job input) name (for repeat dataset inputs)*/ + _findRepeatToolInput : function( name, toolInputs ){ + //ADAPTER + toolInputs = toolInputs || this.tool.inputs; + var partialMatch = _.find( toolInputs, function( i ){ + return name.indexOf( i.name ) === 0; + }); + if( !partialMatch ){ return undefined; } + + var subMatch = _.find( partialMatch.inputs, function( i ){ + return name.indexOf( i.name ) !== -1; + }); + return subMatch; + }, + // ........................................................................ misc /** String representation */ toString : function(){ @@ -86,38 +143,58 @@ '<div class="title-bar clear" tabindex="0">', //'<span class="state-icon"></span>', '<div class="title">', - '<span class="name"><%- job.tool_id %></span>', + '<span class="name"><%- view.tool.name %></span>', '</div>', - '<div class="subtitle"></div>', + '<div class="subtitle">', + '<span class="description"><%- view.tool.description %></span', + '<span class="create-time">', + ' ', _l( 'Created' ), ': <%= new Date( job.create_time ).toString() %>, ', + '</span', + '</div>', '</div>' ], 'job' ); - //var subtitleTemplate = BASE_MVC.wrapTemplate([ - // // override this - // '<div class="subtitle">', - // _l( 'Created' ), ': <%= new Date( job.create_time ).toString() %>, ', - // _l( 'Updated' ), ': <%= new Date( job.update_time ).toString() %>', - // '</div>' - //], 'job' ); - // - //var detailsTemplate = BASE_MVC.wrapTemplate([ - // '<div class="details">', - // '<div class="params">', - // '<% _.each( job.params, function( param, paramName ){ %>', - // '<div class="param">', - // '<label class="prompt"><%= paramName %></label>', - // '<span class="value"><%= param %></span>', - // '</div>', - // '<% }) %>', - // '</div>', - // '</div>' - //], 'job' ); + var subtitleTemplate = BASE_MVC.wrapTemplate([ + '<div class="subtitle">', + '<span class="description"><%- view.tool.description %></span', + //'<span class="create-time">', + // ' ', _l( 'Created' ), ': <%= new Date( job.create_time ).toString() %>, ', + //'</span', + //'<span class="version">', + // ' (', _l( 'version' ), ': <%= view.tool.version %>)', + //'</span', + '</div>' + ], 'job' ); + + var detailsTemplate = BASE_MVC.wrapTemplate([ + '<div class="details">', + //'<div class="version">', + // '<label class="prompt">', _l( 'Version' ), '</label>', + // '<span class="value"><%= view.tool.version %></span>', + //'</div>', + '<div class="params">', + '<% _.each( view._labelInputMap(), function( input, label ){ %>', + '<div class="input" data-input-name="<%= input.name %>" data-input-id="<%= input.id %>">', + '<label class="prompt"><%= label %></label>', +//TODO: input dataset name + '<span class="value"><%= input.content.name %></span>', + '</div>', + '<% }) %>', + '<% _.each( view._labelParamMap(), function( param, label ){ %>', + '<div class="param" data-input-name="<%= param.name %>">', + '<label class="prompt"><%= label %></label>', + '<span class="value"><%= param %></span>', + '</div>', + '<% }) %>', + '</div>', + '</div>' + ], 'job' ); return _.extend( {}, _super.prototype.templates, { - //el : elTemplate, + //el : elTemplate, titleBar : titleBarTemplate, - //subtitle : subtitleTemplate, - //details : detailsTemplate + subtitle : subtitleTemplate, + details : detailsTemplate }); }()); diff -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff client/galaxy/scripts/mvc/job/job-model.js --- a/client/galaxy/scripts/mvc/job/job-model.js +++ b/client/galaxy/scripts/mvc/job/job-model.js @@ -19,7 +19,7 @@ defaults : { model_class : 'Job', - tool : null, + tool_id : null, exit_code : null, inputs : {}, @@ -31,9 +31,27 @@ state : STATES.NEW }, + /** override to parse params on incomming */ + parse : function( response, options ){ + response.params = this.parseParams( response.params ); + return response; + }, + + /** override to treat param values as json */ + parseParams : function( params ){ + var newParams = {}; + _.each( params, function( value, key ){ + newParams[ key ] = JSON.parse( value ); + }); + return newParams; + }, + /** instance vars and listeners */ initialize : function( attributes, options ){ this.debug( this + '(Job).initialize', attributes, options ); + + this.set( 'params', this.parseParams( this.get( 'params' ) ), { silent: true }); + this.outputCollection = attributes.outputCollection || new HISTORY_CONTENTS.HistoryContents([]); this._setUpListeners(); }, @@ -62,7 +80,7 @@ /** Does this model already contain detailed data (as opposed to just summary level data)? */ hasDetails : function(){ //?? this may not be reliable - return _.isEmpty( this.get( 'outputs' ) ); + return !_.isEmpty( this.get( 'outputs' ) ); }, // ........................................................................ ajax @@ -73,9 +91,9 @@ // ........................................................................ searching // see base-mvc, SearchableModelMixin /** what attributes of an Job will be used in a text search */ - searchAttributes : [ - 'tool' - ], + //searchAttributes : [ + // 'tool' + //], // ........................................................................ misc /** String representation */ diff -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff client/galaxy/scripts/mvc/list/list-panel.js --- a/client/galaxy/scripts/mvc/list/list-panel.js +++ b/client/galaxy/scripts/mvc/list/list-panel.js @@ -514,6 +514,7 @@ /** get views based on model */ viewFromModel : function( model ){ + if( !model ){ return undefined; } return this.viewFromModelId( model.id ); }, diff -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff client/galaxy/scripts/utils/graph.js --- a/client/galaxy/scripts/utils/graph.js +++ b/client/galaxy/scripts/utils/graph.js @@ -596,8 +596,9 @@ /** Return an array of graphs of the weakly connected components in this graph */ Graph.prototype.weakComponentGraphArray = function(){ //note: although this can often look like the original graph - edges can be lost + var graph = this; return this.weakComponents().map( function( component ){ - return new Graph( this.directed, component ); + return new Graph( graph.directed, component ); }); }; diff -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2019,6 +2019,7 @@ state = hda.state, history_content_type=hda.history_content_type, file_size = int( hda.get_size() ), + create_time = hda.create_time.isoformat(), update_time = hda.update_time.isoformat(), data_type = hda.datatype.__class__.__module__ + '.' + hda.datatype.__class__.__name__, genome_build = hda.dbkey, @@ -2034,6 +2035,10 @@ tags_str_list.append( tag_str ) rval[ 'tags' ] = tags_str_list + #if getattr( hda, 'hidden_beneath_collection_instance', False ): + # collection_id = hda.hidden_beneath_collection_instance.id + # rval['collection_id'] = collection_id + if hda.copied_from_library_dataset_dataset_association is not None: rval['copied_from_ldda_id'] = hda.copied_from_library_dataset_dataset_association.id diff -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -1,9 +1,11 @@ import logging from cgi import escape +import urllib import galaxy.util from galaxy import model from galaxy import web +from galaxy import exceptions from galaxy import managers from galaxy.datatypes.data import nice_size from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings @@ -529,7 +531,7 @@ return trans.fill_template( "history/display_structured.mako", items=items, history=history ) @web.expose - def structure( self, trans, id=None ): + def structure( self, trans, id=None, **kwargs ): """ """ if not id: @@ -543,11 +545,19 @@ jobs = ( trans.sa_session.query( trans.app.model.Job ) .filter( trans.app.model.Job.user == trans.user ) .filter( trans.app.model.Job.history_id == trans.security.decode_id( id ) ) ).all() - jobs = map( lambda j: self.encode_all_ids( trans, j.to_dict( 'element' ), True ), jobs ) + tools = {} + for tool_id in set( map( lambda j: j[ 'tool_id' ], jobs ) ): + unquoted_id = urllib.unquote_plus( tool_id ) + tool = self.app.toolbox.get_tool( unquoted_id ) + if not tool: + raise exceptions.ObjectNotFound( "Could not find tool with id '%s'" % tool_id ) + #TODO: some fallback for tool information + tools[ tool_id ] = tool.to_dict( trans, io_details=True, link_details=True ) + return trans.fill_template( "history/structure.mako", historyId=history_dictionary[ 'id' ], - history=history_dictionary, hdas=hda_dictionaries, jobs=jobs ) + history=history_dictionary, hdas=hda_dictionaries, jobs=jobs, tools=tools, **kwargs ) @web.expose def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): diff -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c -r 5f0d3cbd97d9c1472bdb8249f3df72d6683caaff 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 @@ -164,12 +164,13 @@ _setUpCollectionListeners : function(){ _super.prototype._setUpCollectionListeners.call( this ); + //TODO:?? may not be needed? see history-panel-edit, 369 // 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 ){ if( ( !model.get( 'visible' ) ) && ( !this.storage.get( 'show_hidden' ) ) ){ - this.removeItemView( this.viewFromModel( model ) ); + this.removeItemView( model ); } }, this ); }, This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Closed branch peterjc/fix-typo-nothting-sic-in-test-exception-1415290865597
by commits-noreply＠bitbucket.org 06 Nov '14

06 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/721d12962630/ Changeset: 721d12962630 Branch: peterjc/fix-typo-nothting-sic-in-test-exception-1415290865597 User: dan Date: 2014-11-06 16:32:49+00:00 Summary: Closed branch peterjc/fix-typo-nothting-sic-in-test-exception-1415290865597 Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Merged in peterjc/galaxy-central-1/peterjc/fix-typo-nothting-sic-in-test-exception-1415290865597 (pull request #553)
by commits-noreply＠bitbucket.org 06 Nov '14

06 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6fd14d9f8b09/ Changeset: 6fd14d9f8b09 User: dan Date: 2014-11-06 16:27:20+00:00 Summary: Merged in peterjc/galaxy-central-1/peterjc/fix-typo-nothting-sic-in-test-exception-1415290865597 (pull request #553) Fix typo nothting [sic] in test exception Affected #: 1 file diff -r 4f8bee770d0be3f13cb7d2283a288c588b54ad63 -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -345,7 +345,7 @@ for metadata_elem in output_elem.findall( 'metadata' ): metadata[ metadata_elem.get('name') ] = metadata_elem.get( 'value' ) if not (assert_list or file or extra_files or metadata): - raise Exception( "Test output defines nothting to check (e.g. must have a 'file' check against, assertions to check, etc...)") + raise Exception( "Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, etc...)") attributes['assert_list'] = assert_list attributes['extra_files'] = extra_files attributes['metadata'] = metadata Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 06 Nov '14

06 Nov '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/db9d27255059/ Changeset: db9d27255059 Branch: peterjc/fix-typo-nothting-sic-in-test-exception-1415290865597 User: peterjc Date: 2014-11-06 16:21:45+00:00 Summary: Fix typo nothting [sic] in test exception Affected #: 1 file diff -r 4f8bee770d0be3f13cb7d2283a288c588b54ad63 -r db9d272550593edb566ff67d2731782f0f6b78f0 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -345,7 +345,7 @@ for metadata_elem in output_elem.findall( 'metadata' ): metadata[ metadata_elem.get('name') ] = metadata_elem.get( 'value' ) if not (assert_list or file or extra_files or metadata): - raise Exception( "Test output defines nothting to check (e.g. must have a 'file' check against, assertions to check, etc...)") + raise Exception( "Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, etc...)") attributes['assert_list'] = assert_list attributes['extra_files'] = extra_files attributes['metadata'] = metadata https://bitbucket.org/galaxy/galaxy-central/commits/6fd14d9f8b09/ Changeset: 6fd14d9f8b09 User: dan Date: 2014-11-06 16:27:20+00:00 Summary: Merged in peterjc/galaxy-central-1/peterjc/fix-typo-nothting-sic-in-test-exception-1415290865597 (pull request #553) Fix typo nothting [sic] in test exception Affected #: 1 file diff -r 4f8bee770d0be3f13cb7d2283a288c588b54ad63 -r 6fd14d9f8b099e926a2b8fa462938d8955c1713c lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -345,7 +345,7 @@ for metadata_elem in output_elem.findall( 'metadata' ): metadata[ metadata_elem.get('name') ] = metadata_elem.get( 'value' ) if not (assert_list or file or extra_files or metadata): - raise Exception( "Test output defines nothting to check (e.g. must have a 'file' check against, assertions to check, etc...)") + raise Exception( "Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, etc...)") attributes['assert_list'] = assert_list attributes['extra_files'] = extra_files attributes['metadata'] = metadata Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits November 2014