April 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Add a counter utility to the tool shed.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/080242921d9f/ changeset: 080242921d9f user: greg date: 2012-04-02 22:13:08 summary: Add a counter utility to the tool shed. affected #: 7 files diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,6 +1,6 @@ import os, tempfile, shutil, subprocess, logging, string from datetime import date, datetime, timedelta -from time import strftime +from time import strftime, gmtime from galaxy import util from galaxy.datatypes.checkers import * from galaxy.util.json import * @@ -21,6 +21,37 @@ '\'' : ''' } VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) +class ShedCounter( object ): + def __init__( self, model ): + self.model = model + self.count_time = strftime( "%b %d, %Y", gmtime() ) + self.valid_tools = self.count_valid_tools() + @property + def sa_session( self ): + """Returns a SQLAlchemy session""" + return self.model.context + def count_valid_tools( self ): + valid_tools = 0 + processed_repository_ids = [] + for repository_metadata in self.sa_session.query( self.model.RepositoryMetadata ) \ + .filter( and_( self.model.RepositoryMetadata.table.c.malicious == False, + self.model.RepositoryMetadata.table.c.metadata is not None, + self.model.RepositoryMetadata.table.c.tool_versions is not None ) ): + processed_guids = [] + repository = repository_metadata.repository + if repository.id not in processed_repository_ids: + for revision_metadata in repository.downloadable_revisions: + metadata = revision_metadata.metadata + if 'tools' in metadata: + tool_dicts = metadata[ 'tools' ] + for tool_dict in tool_dicts: + guid = tool_dict[ 'guid' ] + if guid not in processed_guids: + valid_tools += 1 + processed_guids.append( guid ) + processed_repository_ids.append( repository.id ) + return valid_tools + def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ): # A tool shed repository is being installed so change the shed_tool_conf file. Parse the config file to generate the entire list # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -43,6 +43,8 @@ # Load security policy self.security_agent = self.model.security_agent self.quota_agent = galaxy.quota.NoQuotaAgent( self.model ) - self.openid_providers = OpenIDProviders() #TODO: Add OpenID support + # TODO: Add OpenID support + self.openid_providers = OpenIDProviders() + self.shed_counter = self.model.shed_counter def shutdown( self ): pass diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -321,7 +321,7 @@ def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository repo = hg.repository( get_configured_ui(), repository.repo_path ) - ctx = get_changectx_for_changeset( trans, repo, repository_metadata.changeset_revision ) + ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) class ToolsColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -140,7 +140,7 @@ changeset rev and the changeset revision string. """ repo = hg.repository( get_configured_ui(), repository.repo_path ) - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) else: @@ -425,7 +425,7 @@ repository = get_repository( trans, id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) metadata_dict = {} invalid_files = [] if ctx is not None: @@ -514,7 +514,7 @@ ancestor_metadata_dict = None for changeset in repo.changelog: current_changeset_revision = str( repo.changectx( changeset ) ) - ctx = get_changectx_for_changeset( trans, repo, current_changeset_revision ) + ctx = get_changectx_for_changeset( repo, current_changeset_revision ) if current_changeset_revision == repository.tip: current_metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, id, ctx, current_changeset_revision, repo_dir ) else: @@ -740,7 +740,7 @@ def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() -def get_changectx_for_changeset( trans, repo, changeset_revision, **kwd ): +def get_changectx_for_changeset( repo, changeset_revision, **kwd ): """Retrieve a specified changectx from a repository""" for changeset in repo.changelog: ctx = repo.changectx( changeset ) @@ -963,7 +963,7 @@ # Get the tool config file name from the hgweb url, something like: # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml old_tool_config_file_name = tool_config.split( '/' )[ -1 ] - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) fctx = None for filename in ctx: filename_head, filename_tail = os.path.split( filename ) @@ -1001,7 +1001,7 @@ refresh_on_change_values = [] for repository_metadata in repository.downloadable_revisions: changeset_revision = repository_metadata.changeset_revision - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: rev = '%04d' % ctx.rev() label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -854,7 +854,7 @@ repo = hg.repository( get_configured_ui(), repo_dir ) # Load each tool in the repository's changeset_revision to generate a list of # tool guids, since guids differentiate tools by id and version. - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx is not None: tool_guids = [] for filename in ctx: @@ -1579,7 +1579,7 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) - ctx = get_changectx_for_changeset( trans, repo, ctx_str ) + ctx = get_changectx_for_changeset( repo, ctx_str ) if ctx is None: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -13,6 +13,7 @@ from galaxy.model.orm.ext.assignmapper import * from galaxy.model.custom_types import * from galaxy.util.bunch import Bunch +from galaxy.util.shed_util import ShedCounter from galaxy.webapps.community.security import CommunityRBACAgent metadata = MetaData() @@ -247,4 +248,5 @@ result.create_tables = create_tables #load local galaxy security policy result.security_agent = CommunityRBACAgent( result ) + result.shed_counter = ShedCounter( result ) return result diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -39,7 +39,7 @@ <%def name="left_panel()"><div class="unified-panel-header" unselectable="on"> - <div class='unified-panel-header-inner'>Galaxy Tool Shed</div> + <div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools} valid tools on ${trans.app.shed_counter.count_time}</div></div><div class="page-container" style="padding: 10px;"><div class="toolMenu"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: I missed a call to a renamed method in the job manager.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/babda116a4c0/ changeset: babda116a4c0 user: natefoo date: 2012-04-02 21:38:02 summary: I missed a call to a renamed method in the job manager. affected #: 1 file diff -r 07eb5affb4c0c74f1bf95d2fb850f926d4defaf2 -r babda116a4c0193c2ee4941d09ac78940098fece lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -89,7 +89,7 @@ log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) ) JobWrapper( job, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator.' ) else: - job.handler = self.__select_handler( job ) # handler's recovery method will take it from here + job.handler = self.__get_handler( job ) # handler's recovery method will take it from here log.info( "(%d) Job in '%s' state had no handler at job manager startup, assigned '%s' handler" % ( job.id, job.state, job.handler ) ) if self.sa_session.dirty: self.sa_session.flush() 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: richard_burhans: changes to aaChanges interface
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/07eb5affb4c0/ changeset: 07eb5affb4c0 user: richard_burhans date: 2012-04-02 20:28:08 summary: changes to aaChanges interface affected #: 1 file diff -r 758f425498670dbe992701df81d277dbc7cd6de7 -r 07eb5affb4c0c74f1bf95d2fb850f926d4defaf2 tools/evolution/codingSnps.xml --- a/tools/evolution/codingSnps.xml +++ b/tools/evolution/codingSnps.xml @@ -2,7 +2,7 @@ <description>amino-acid changes caused by a set of SNPs</description><command interpreter="perl"> - codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep strand=${strand_source.strand_col} > $out_file1 + codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep strand=${strand_source.strand_col} unique=$uniqpos > $out_file1 </command><inputs> @@ -17,6 +17,10 @@ <option value="0" selected="true">No</option><option value="1">Yes</option></param> + <param name="uniqpos" type="select" label="Only report each SNP position once"> + <option value="1" selected="true">Yes</option> + <option value="0">No</option> + </param><conditional name="strand_source"><param name="strand_choice" type="select" label="Strand info"><option value="data_column">a column in the dataset</option> @@ -54,6 +58,7 @@ <param name="input2" ftype="interval" value="codingSnps_inputGenes1.bed" dbkey="hg18" /><param name="strand_choice" value="all_pos" /><param name="strand_col" value="+" /> + <param name="uniqpos" value="0" /><output name="output" file="codingSnps_output1.interval" /></test><test> @@ -62,6 +67,7 @@ <param name="col1" value="4" /><param name="strand_choice" value="all_pos" /><param name="strand_col" value="+" /> + <param name="uniqpos" value="0" /><output name="output" file="codingSnps_output2.interval" /></test><test> 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: dannon: Update cloud launch config name.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/758f42549867/ changeset: 758f42549867 user: dannon date: 2012-04-02 20:14:24 summary: Update cloud launch config name. affected #: 1 file diff -r 5ea04ccb61e8373369c41370dd3ee216a7dc6d14 -r 758f425498670dbe992701df81d277dbc7cd6de7 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -110,7 +110,7 @@ %endif ## Cloud menu. - %if app.config.get_bool( 'enable_cloud_control', False ): + %if app.config.get_bool( 'enable_cloud_launch', False ): <% menu_options = [ [_('New Cloud Cluster'), h.url_for( controller='/cloud', action='index' ) ], 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: greg: Make sure repository files displayed during installation are restricted to a max file size and contents are viewable in a browser.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5ea04ccb61e8/ changeset: 5ea04ccb61e8 user: greg date: 2012-04-02 19:27:31 summary: Make sure repository files displayed during installation are restricted to a max file size and contents are viewable in a browser. affected #: 4 files diff -r 319c7ee6873c53e57aa6b37271cb7c6afb067612 -r 5ea04ccb61e8373369c41370dd3ee216a7dc6d14 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,4 +1,4 @@ -import os, tempfile, shutil, subprocess, logging +import os, tempfile, shutil, subprocess, logging, string from datetime import date, datetime, timedelta from time import strftime from galaxy import util @@ -13,6 +13,14 @@ log = logging.getLogger( __name__ ) +# Characters that must be html escaped +MAPPED_CHARS = { '>' :'>', + '<' :'<', + '"' : '"', + '&' : '&', + '\'' : ''' } +VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) + def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ): # A tool shed repository is being installed so change the shed_tool_conf file. Parse the config file to generate the entire list # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have @@ -1096,6 +1104,34 @@ if uninstall: # Write the current in-memory version of the integrated_tool_panel.xml file to disk. trans.app.toolbox.write_integrated_tool_panel_config_file() +def to_html_escaped( text ): + """Translates the characters in text to html values""" + translated = [] + for c in text: + if c in [ '\r\n', '\n', ' ', '\t' ] or c in VALID_CHARS: + translated.append( c ) + elif c in MAPPED_CHARS: + translated.append( MAPPED_CHARS[ c ] ) + else: + translated.append( 'X' ) + return ''.join( translated ) +def to_html_str( text ): + """Translates the characters in text to sn html string""" + translated = [] + for c in text: + if c in VALID_CHARS: + translated.append( c ) + elif c in MAPPED_CHARS: + translated.append( MAPPED_CHARS[ c ] ) + elif c == ' ': + translated.append( ' ' ) + elif c == '\t': + translated.append( '    ' ) + elif c == '\n': + translated.append( '<br/>' ) + elif c not in [ '\r' ]: + translated.append( 'X' ) + return ''.join( translated ) def update_repository( current_working_dir, repo_files_dir, changeset_revision ): # Update the cloned repository to changeset_revision. It is imperative that the # installed repository is updated to the desired changeset_revision before metadata diff -r 319c7ee6873c53e57aa6b37271cb7c6afb067612 -r 5ea04ccb61e8373369c41370dd3ee216a7dc6d14 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -6,6 +6,8 @@ log = logging.getLogger( __name__ ) +MAX_CONTENT_SIZE = 32768 + class RepositoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool_shed_repository ): @@ -377,8 +379,15 @@ owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) ) url = '%s/repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( tool_shed_url, name, owner, changeset_revision ) response = urllib2.urlopen( url ) - readme_text = response.read() + raw_text = response.read() response.close() + readme_text = '' + for i, line in enumerate( raw_text ): + readme_text = '%s%s' % ( readme_text, to_html_str( line ) ) + if len( readme_text ) > MAX_CONTENT_SIZE: + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) + readme_text = '%s%s' % ( readme_text, to_html_str( large_str ) ) + break else: readme_text = '' else: diff -r 319c7ee6873c53e57aa6b37271cb7c6afb067612 -r 5ea04ccb61e8373369c41370dd3ee216a7dc6d14 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -6,7 +6,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * from galaxy.util.shed_util import copy_sample_loc_file, generate_datatypes_metadata, generate_tool_metadata, generate_workflow_metadata -from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file +from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file, to_html_escaped, to_html_str from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * diff -r 319c7ee6873c53e57aa6b37271cb7c6afb067612 -r 5ea04ccb61e8373369c41370dd3ee216a7dc6d14 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -15,14 +15,7 @@ log = logging.getLogger( __name__ ) -# Characters that must be html escaped -MAPPED_CHARS = { '>' :'>', - '<' :'<', - '"' : '"', - '&' : '&', - '\'' : ''' } MAX_CONTENT_SIZE = 32768 -VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) class CategoryListGrid( grids.Grid ): @@ -785,7 +778,7 @@ repo = hg.repository( get_configured_ui(), repo_dir ) for root, dirs, files in os.walk( repo_dir ): for name in files: - if name.lower() in [ 'readme', 'read_me' ]: + if name.lower() in [ 'readme', 'readme.txt', 'read_me', 'read_me.txt' ]: f = open( os.path.join( root, name ), 'r' ) text = f.read() f.close() @@ -1600,7 +1593,7 @@ anchors = modified + added + removed + deleted + unknown + ignored + clean diffs = [] for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ): - diffs.append( self.to_html_escaped( diff ) ) + diffs.append( to_html_escaped( diff ) ) is_malicious = change_set_is_malicious( trans, id, repository.tip ) return trans.fill_template( '/webapps/community/repository/view_changeset.mako', repository=repository, @@ -1938,20 +1931,20 @@ trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' if is_gzip( file_path ): - to_html = self.to_html_str( '\ngzip compressed file\n' ) + to_html = to_html_str( '\ngzip compressed file\n' ) elif is_bz2( file_path ): - to_html = self.to_html_str( '\nbz2 compressed file\n' ) + to_html = to_html_str( '\nbz2 compressed file\n' ) elif check_zip( file_path ): - to_html = self.to_html_str( '\nzip compressed file\n' ) + to_html = to_html_str( '\nzip compressed file\n' ) elif check_binary( file_path ): - to_html = self.to_html_str( '\nBinary file\n' ) + to_html = to_html_str( '\nBinary file\n' ) else: to_html = '' for i, line in enumerate( open( file_path ) ): - to_html = '%s%s' % ( to_html, self.to_html_str( line ) ) + to_html = '%s%s' % ( to_html, to_html_str( line ) ) if len( to_html ) > MAX_CONTENT_SIZE: large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) - to_html = '%s%s' % ( to_html, self.to_html_str( large_str ) ) + to_html = '%s%s' % ( to_html, to_html_str( large_str ) ) break return to_html @web.expose @@ -1960,34 +1953,6 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) return trans.fill_template( '/webapps/community/repository/help.mako', message=message, status=status, **kwd ) - def to_html_escaped( self, text ): - """Translates the characters in text to html values""" - translated = [] - for c in text: - if c in [ '\r\n', '\n', ' ', '\t' ] or c in VALID_CHARS: - translated.append( c ) - elif c in MAPPED_CHARS: - translated.append( MAPPED_CHARS[ c ] ) - else: - translated.append( 'X' ) - return ''.join( translated ) - def to_html_str( self, text ): - """Translates the characters in text to sn html string""" - translated = [] - for c in text: - if c in VALID_CHARS: - translated.append( c ) - elif c in MAPPED_CHARS: - translated.append( MAPPED_CHARS[ c ] ) - elif c == ' ': - translated.append( ' ' ) - elif c == '\t': - translated.append( '    ' ) - elif c == '\n': - translated.append( '<br/>' ) - elif c not in [ '\r' ]: - translated.append( 'X' ) - return ''.join( translated ) def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ): options = [] for user in trans.sa_session.query( trans.model.User ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 11 new changesets
by Bitbucket 02 Apr '12

02 Apr '12

11 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/15e75fe2efae/ changeset: 15e75fe2efae user: jgoecks date: 2012-03-30 17:30:49 summary: Remove full handlebars library and replace with runtime. affected #: 2 files diff -r de2946aca8877087d761684a72ff955f46e4f5a6 -r 15e75fe2efae761ac7182a496d5c79ef3bc3a43a static/scripts/libs/handlebars-1.0.0.beta.6.js --- a/static/scripts/libs/handlebars-1.0.0.beta.6.js +++ /dev/null @@ -1,1550 +0,0 @@ -// lib/handlebars/base.js -var Handlebars = {}; - -Handlebars.VERSION = "1.0.beta.6"; - -Handlebars.helpers = {}; -Handlebars.partials = {}; - -Handlebars.registerHelper = function(name, fn, inverse) { - if(inverse) { fn.not = inverse; } - this.helpers[name] = fn; -}; - -Handlebars.registerPartial = function(name, str) { - this.partials[name] = str; -}; - -Handlebars.registerHelper('helperMissing', function(arg) { - if(arguments.length === 2) { - return undefined; - } else { - throw new Error("Could not find property '" + arg + "'"); - } -}); - -var toString = Object.prototype.toString, functionType = "[object Function]"; - -Handlebars.registerHelper('blockHelperMissing', function(context, options) { - var inverse = options.inverse || function() {}, fn = options.fn; - - - var ret = ""; - var type = toString.call(context); - - if(type === functionType) { context = context.call(this); } - - if(context === true) { - return fn(this); - } else if(context === false || context == null) { - return inverse(this); - } else if(type === "[object Array]") { - if(context.length > 0) { - for(var i=0, j=context.length; i<j; i++) { - ret = ret + fn(context[i]); - } - } else { - ret = inverse(this); - } - return ret; - } else { - return fn(context); - } -}); - -Handlebars.registerHelper('each', function(context, options) { - var fn = options.fn, inverse = options.inverse; - var ret = ""; - - if(context && context.length > 0) { - for(var i=0, j=context.length; i<j; i++) { - ret = ret + fn(context[i]); - } - } else { - ret = inverse(this); - } - return ret; -}); - -Handlebars.registerHelper('if', function(context, options) { - var type = toString.call(context); - if(type === functionType) { context = context.call(this); } - - if(!context || Handlebars.Utils.isEmpty(context)) { - return options.inverse(this); - } else { - return options.fn(this); - } -}); - -Handlebars.registerHelper('unless', function(context, options) { - var fn = options.fn, inverse = options.inverse; - options.fn = inverse; - options.inverse = fn; - - return Handlebars.helpers['if'].call(this, context, options); -}); - -Handlebars.registerHelper('with', function(context, options) { - return options.fn(context); -}); - -Handlebars.registerHelper('log', function(context) { - Handlebars.log(context); -}); -; -// lib/handlebars/compiler/parser.js -/* Jison generated parser */ -var handlebars = (function(){ - -var parser = {trace: function trace() { }, -yy: {}, -symbols_: {"error":2,"root":3,"program":4,"EOF":5,"statements":6,"simpleInverse":7,"statement":8,"openInverse":9,"closeBlock":10,"openBlock":11,"mustache":12,"partial":13,"CONTENT":14,"COMMENT":15,"OPEN_BLOCK":16,"inMustache":17,"CLOSE":18,"OPEN_INVERSE":19,"OPEN_ENDBLOCK":20,"path":21,"OPEN":22,"OPEN_UNESCAPED":23,"OPEN_PARTIAL":24,"params":25,"hash":26,"param":27,"STRING":28,"INTEGER":29,"BOOLEAN":30,"hashSegments":31,"hashSegment":32,"ID":33,"EQUALS":34,"pathSegments":35,"SEP":36,"$accept":0,"$end":1}, -terminals_: {2:"error",5:"EOF",14:"CONTENT",15:"COMMENT",16:"OPEN_BLOCK",18:"CLOSE",19:"OPEN_INVERSE",20:"OPEN_ENDBLOCK",22:"OPEN",23:"OPEN_UNESCAPED",24:"OPEN_PARTIAL",28:"STRING",29:"INTEGER",30:"BOOLEAN",33:"ID",34:"EQUALS",36:"SEP"}, -productions_: [0,[3,2],[4,3],[4,1],[4,0],[6,1],[6,2],[8,3],[8,3],[8,1],[8,1],[8,1],[8,1],[11,3],[9,3],[10,3],[12,3],[12,3],[13,3],[13,4],[7,2],[17,3],[17,2],[17,2],[17,1],[25,2],[25,1],[27,1],[27,1],[27,1],[27,1],[26,1],[31,2],[31,1],[32,3],[32,3],[32,3],[32,3],[21,1],[35,3],[35,1]], -performAction: function anonymous(yytext,yyleng,yylineno,yy,yystate,$$,_$) { - -var $0 = $$.length - 1; -switch (yystate) { -case 1: return $$[$0-1] -break; -case 2: this.$ = new yy.ProgramNode($$[$0-2], $$[$0]) -break; -case 3: this.$ = new yy.ProgramNode($$[$0]) -break; -case 4: this.$ = new yy.ProgramNode([]) -break; -case 5: this.$ = [$$[$0]] -break; -case 6: $$[$0-1].push($$[$0]); this.$ = $$[$0-1] -break; -case 7: this.$ = new yy.InverseNode($$[$0-2], $$[$0-1], $$[$0]) -break; -case 8: this.$ = new yy.BlockNode($$[$0-2], $$[$0-1], $$[$0]) -break; -case 9: this.$ = $$[$0] -break; -case 10: this.$ = $$[$0] -break; -case 11: this.$ = new yy.ContentNode($$[$0]) -break; -case 12: this.$ = new yy.CommentNode($$[$0]) -break; -case 13: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) -break; -case 14: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) -break; -case 15: this.$ = $$[$0-1] -break; -case 16: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) -break; -case 17: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1], true) -break; -case 18: this.$ = new yy.PartialNode($$[$0-1]) -break; -case 19: this.$ = new yy.PartialNode($$[$0-2], $$[$0-1]) -break; -case 20: -break; -case 21: this.$ = [[$$[$0-2]].concat($$[$0-1]), $$[$0]] -break; -case 22: this.$ = [[$$[$0-1]].concat($$[$0]), null] -break; -case 23: this.$ = [[$$[$0-1]], $$[$0]] -break; -case 24: this.$ = [[$$[$0]], null] -break; -case 25: $$[$0-1].push($$[$0]); this.$ = $$[$0-1]; -break; -case 26: this.$ = [$$[$0]] -break; -case 27: this.$ = $$[$0] -break; -case 28: this.$ = new yy.StringNode($$[$0]) -break; -case 29: this.$ = new yy.IntegerNode($$[$0]) -break; -case 30: this.$ = new yy.BooleanNode($$[$0]) -break; -case 31: this.$ = new yy.HashNode($$[$0]) -break; -case 32: $$[$0-1].push($$[$0]); this.$ = $$[$0-1] -break; -case 33: this.$ = [$$[$0]] -break; -case 34: this.$ = [$$[$0-2], $$[$0]] -break; -case 35: this.$ = [$$[$0-2], new yy.StringNode($$[$0])] -break; -case 36: this.$ = [$$[$0-2], new yy.IntegerNode($$[$0])] -break; -case 37: this.$ = [$$[$0-2], new yy.BooleanNode($$[$0])] -break; -case 38: this.$ = new yy.IdNode($$[$0]) -break; -case 39: $$[$0-2].push($$[$0]); this.$ = $$[$0-2]; -break; -case 40: this.$ = [$$[$0]] -break; -} -}, -table: [{3:1,4:2,5:[2,4],6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],22:[1,13],23:[1,14],24:[1,15]},{1:[3]},{5:[1,16]},{5:[2,3],7:17,8:18,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,19],20:[2,3],22:[1,13],23:[1,14],24:[1,15]},{5:[2,5],14:[2,5],15:[2,5],16:[2,5],19:[2,5],20:[2,5],22:[2,5],23:[2,5],24:[2,5]},{4:20,6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,4],22:[1,13],23:[1,14],24:[1,15]},{4:21,6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,4],22:[1,13],23:[1,14],24:[1,15]},{5:[2,9],14:[2,9],15:[2,9],16:[2,9],19:[2,9],20:[2,9],22:[2,9],23:[2,9],24:[2,9]},{5:[2,10],14:[2,10],15:[2,10],16:[2,10],19:[2,10],20:[2,10],22:[2,10],23:[2,10],24:[2,10]},{5:[2,11],14:[2,11],15:[2,11],16:[2,11],19:[2,11],20:[2,11],22:[2,11],23:[2,11],24:[2,11]},{5:[2,12],14:[2,12],15:[2,12],16:[2,12],19:[2,12],20:[2,12],22:[2,12],23:[2,12],24:[2,12]},{17:22,21:23,33:[1,25],35:24},{17:26,21:23,33:[1,25],35:24},{17:27,21:23,33:[1,25],35:24},{17:28,21:23,33:[1,25],35:24},{21:29,33:[1,25],35:24},{1:[2,1]},{6:30,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],22:[1,13],23:[1,14],24:[1,15]},{5:[2,6],14:[2,6],15:[2,6],16:[2,6],19:[2,6],20:[2,6],22:[2,6],23:[2,6],24:[2,6]},{17:22,18:[1,31],21:23,33:[1,25],35:24},{10:32,20:[1,33]},{10:34,20:[1,33]},{18:[1,35]},{18:[2,24],21:40,25:36,26:37,27:38,28:[1,41],29:[1,42],30:[1,43],31:39,32:44,33:[1,45],35:24},{18:[2,38],28:[2,38],29:[2,38],30:[2,38],33:[2,38],36:[1,46]},{18:[2,40],28:[2,40],29:[2,40],30:[2,40],33:[2,40],36:[2,40]},{18:[1,47]},{18:[1,48]},{18:[1,49]},{18:[1,50],21:51,33:[1,25],35:24},{5:[2,2],8:18,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,2],22:[1,13],23:[1,14],24:[1,15]},{14:[2,20],15:[2,20],16:[2,20],19:[2,20],22:[2,20],23:[2,20],24:[2,20]},{5:[2,7],14:[2,7],15:[2,7],16:[2,7],19:[2,7],20:[2,7],22:[2,7],23:[2,7],24:[2,7]},{21:52,33:[1,25],35:24},{5:[2,8],14:[2,8],15:[2,8],16:[2,8],19:[2,8],20:[2,8],22:[2,8],23:[2,8],24:[2,8]},{14:[2,14],15:[2,14],16:[2,14],19:[2,14],20:[2,14],22:[2,14],23:[2,14],24:[2,14]},{18:[2,22],21:40,26:53,27:54,28:[1,41],29:[1,42],30:[1,43],31:39,32:44,33:[1,45],35:24},{18:[2,23]},{18:[2,26],28:[2,26],29:[2,26],30:[2,26],33:[2,26]},{18:[2,31],32:55,33:[1,56]},{18:[2,27],28:[2,27],29:[2,27],30:[2,27],33:[2,27]},{18:[2,28],28:[2,28],29:[2,28],30:[2,28],33:[2,28]},{18:[2,29],28:[2,29],29:[2,29],30:[2,29],33:[2,29]},{18:[2,30],28:[2,30],29:[2,30],30:[2,30],33:[2,30]},{18:[2,33],33:[2,33]},{18:[2,40],28:[2,40],29:[2,40],30:[2,40],33:[2,40],34:[1,57],36:[2,40]},{33:[1,58]},{14:[2,13],15:[2,13],16:[2,13],19:[2,13],20:[2,13],22:[2,13],23:[2,13],24:[2,13]},{5:[2,16],14:[2,16],15:[2,16],16:[2,16],19:[2,16],20:[2,16],22:[2,16],23:[2,16],24:[2,16]},{5:[2,17],14:[2,17],15:[2,17],16:[2,17],19:[2,17],20:[2,17],22:[2,17],23:[2,17],24:[2,17]},{5:[2,18],14:[2,18],15:[2,18],16:[2,18],19:[2,18],20:[2,18],22:[2,18],23:[2,18],24:[2,18]},{18:[1,59]},{18:[1,60]},{18:[2,21]},{18:[2,25],28:[2,25],29:[2,25],30:[2,25],33:[2,25]},{18:[2,32],33:[2,32]},{34:[1,57]},{21:61,28:[1,62],29:[1,63],30:[1,64],33:[1,25],35:24},{18:[2,39],28:[2,39],29:[2,39],30:[2,39],33:[2,39],36:[2,39]},{5:[2,19],14:[2,19],15:[2,19],16:[2,19],19:[2,19],20:[2,19],22:[2,19],23:[2,19],24:[2,19]},{5:[2,15],14:[2,15],15:[2,15],16:[2,15],19:[2,15],20:[2,15],22:[2,15],23:[2,15],24:[2,15]},{18:[2,34],33:[2,34]},{18:[2,35],33:[2,35]},{18:[2,36],33:[2,36]},{18:[2,37],33:[2,37]}], -defaultActions: {16:[2,1],37:[2,23],53:[2,21]}, -parseError: function parseError(str, hash) { - throw new Error(str); -}, -parse: function parse(input) { - var self = this, stack = [0], vstack = [null], lstack = [], table = this.table, yytext = "", yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1; - this.lexer.setInput(input); - this.lexer.yy = this.yy; - this.yy.lexer = this.lexer; - if (typeof this.lexer.yylloc == "undefined") - this.lexer.yylloc = {}; - var yyloc = this.lexer.yylloc; - lstack.push(yyloc); - if (typeof this.yy.parseError === "function") - this.parseError = this.yy.parseError; - function popStack(n) { - stack.length = stack.length - 2 * n; - vstack.length = vstack.length - n; - lstack.length = lstack.length - n; - } - function lex() { - var token; - token = self.lexer.lex() || 1; - if (typeof token !== "number") { - token = self.symbols_[token] || token; - } - return token; - } - var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected; - while (true) { - state = stack[stack.length - 1]; - if (this.defaultActions[state]) { - action = this.defaultActions[state]; - } else { - if (symbol == null) - symbol = lex(); - action = table[state] && table[state][symbol]; - } - if (typeof action === "undefined" || !action.length || !action[0]) { - if (!recovering) { - expected = []; - for (p in table[state]) - if (this.terminals_[p] && p > 2) { - expected.push("'" + this.terminals_[p] + "'"); - } - var errStr = ""; - if (this.lexer.showPosition) { - errStr = "Parse error on line " + (yylineno + 1) + ":\n" + this.lexer.showPosition() + "\nExpecting " + expected.join(", ") + ", got '" + this.terminals_[symbol] + "'"; - } else { - errStr = "Parse error on line " + (yylineno + 1) + ": Unexpected " + (symbol == 1?"end of input":"'" + (this.terminals_[symbol] || symbol) + "'"); - } - this.parseError(errStr, {text: this.lexer.match, token: this.terminals_[symbol] || symbol, line: this.lexer.yylineno, loc: yyloc, expected: expected}); - } - } - if (action[0] instanceof Array && action.length > 1) { - throw new Error("Parse Error: multiple actions possible at state: " + state + ", token: " + symbol); - } - switch (action[0]) { - case 1: - stack.push(symbol); - vstack.push(this.lexer.yytext); - lstack.push(this.lexer.yylloc); - stack.push(action[1]); - symbol = null; - if (!preErrorSymbol) { - yyleng = this.lexer.yyleng; - yytext = this.lexer.yytext; - yylineno = this.lexer.yylineno; - yyloc = this.lexer.yylloc; - if (recovering > 0) - recovering--; - } else { - symbol = preErrorSymbol; - preErrorSymbol = null; - } - break; - case 2: - len = this.productions_[action[1]][1]; - yyval.$ = vstack[vstack.length - len]; - yyval._$ = {first_line: lstack[lstack.length - (len || 1)].first_line, last_line: lstack[lstack.length - 1].last_line, first_column: lstack[lstack.length - (len || 1)].first_column, last_column: lstack[lstack.length - 1].last_column}; - r = this.performAction.call(yyval, yytext, yyleng, yylineno, this.yy, action[1], vstack, lstack); - if (typeof r !== "undefined") { - return r; - } - if (len) { - stack = stack.slice(0, -1 * len * 2); - vstack = vstack.slice(0, -1 * len); - lstack = lstack.slice(0, -1 * len); - } - stack.push(this.productions_[action[1]][0]); - vstack.push(yyval.$); - lstack.push(yyval._$); - newState = table[stack[stack.length - 2]][stack[stack.length - 1]]; - stack.push(newState); - break; - case 3: - return true; - } - } - return true; -} -};/* Jison generated lexer */ -var lexer = (function(){ - -var lexer = ({EOF:1, -parseError:function parseError(str, hash) { - if (this.yy.parseError) { - this.yy.parseError(str, hash); - } else { - throw new Error(str); - } - }, -setInput:function (input) { - this._input = input; - this._more = this._less = this.done = false; - this.yylineno = this.yyleng = 0; - this.yytext = this.matched = this.match = ''; - this.conditionStack = ['INITIAL']; - this.yylloc = {first_line:1,first_column:0,last_line:1,last_column:0}; - return this; - }, -input:function () { - var ch = this._input[0]; - this.yytext+=ch; - this.yyleng++; - this.match+=ch; - this.matched+=ch; - var lines = ch.match(/\n/); - if (lines) this.yylineno++; - this._input = this._input.slice(1); - return ch; - }, -unput:function (ch) { - this._input = ch + this._input; - return this; - }, -more:function () { - this._more = true; - return this; - }, -pastInput:function () { - var past = this.matched.substr(0, this.matched.length - this.match.length); - return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\n/g, ""); - }, -upcomingInput:function () { - var next = this.match; - if (next.length < 20) { - next += this._input.substr(0, 20-next.length); - } - return (next.substr(0,20)+(next.length > 20 ? '...':'')).replace(/\n/g, ""); - }, -showPosition:function () { - var pre = this.pastInput(); - var c = new Array(pre.length + 1).join("-"); - return pre + this.upcomingInput() + "\n" + c+"^"; - }, -next:function () { - if (this.done) { - return this.EOF; - } - if (!this._input) this.done = true; - - var token, - match, - col, - lines; - if (!this._more) { - this.yytext = ''; - this.match = ''; - } - var rules = this._currentRules(); - for (var i=0;i < rules.length; i++) { - match = this._input.match(this.rules[rules[i]]); - if (match) { - lines = match[0].match(/\n.*/g); - if (lines) this.yylineno += lines.length; - this.yylloc = {first_line: this.yylloc.last_line, - last_line: this.yylineno+1, - first_column: this.yylloc.last_column, - last_column: lines ? lines[lines.length-1].length-1 : this.yylloc.last_column + match[0].length} - this.yytext += match[0]; - this.match += match[0]; - this.matches = match; - this.yyleng = this.yytext.length; - this._more = false; - this._input = this._input.slice(match[0].length); - this.matched += match[0]; - token = this.performAction.call(this, this.yy, this, rules[i],this.conditionStack[this.conditionStack.length-1]); - if (token) return token; - else return; - } - } - if (this._input === "") { - return this.EOF; - } else { - this.parseError('Lexical error on line '+(this.yylineno+1)+'. Unrecognized text.\n'+this.showPosition(), - {text: "", token: null, line: this.yylineno}); - } - }, -lex:function lex() { - var r = this.next(); - if (typeof r !== 'undefined') { - return r; - } else { - return this.lex(); - } - }, -begin:function begin(condition) { - this.conditionStack.push(condition); - }, -popState:function popState() { - return this.conditionStack.pop(); - }, -_currentRules:function _currentRules() { - return this.conditions[this.conditionStack[this.conditionStack.length-1]].rules; - }, -topState:function () { - return this.conditionStack[this.conditionStack.length-2]; - }, -pushState:function begin(condition) { - this.begin(condition); - }}); -lexer.performAction = function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) { - -var YYSTATE=YY_START -switch($avoiding_name_collisions) { -case 0: - if(yy_.yytext.slice(-1) !== "\\") this.begin("mu"); - if(yy_.yytext.slice(-1) === "\\") yy_.yytext = yy_.yytext.substr(0,yy_.yyleng-1), this.begin("emu"); - if(yy_.yytext) return 14; - -break; -case 1: return 14; -break; -case 2: this.popState(); return 14; -break; -case 3: return 24; -break; -case 4: return 16; -break; -case 5: return 20; -break; -case 6: return 19; -break; -case 7: return 19; -break; -case 8: return 23; -break; -case 9: return 23; -break; -case 10: yy_.yytext = yy_.yytext.substr(3,yy_.yyleng-5); this.popState(); return 15; -break; -case 11: return 22; -break; -case 12: return 34; -break; -case 13: return 33; -break; -case 14: return 33; -break; -case 15: return 36; -break; -case 16: /*ignore whitespace*/ -break; -case 17: this.popState(); return 18; -break; -case 18: this.popState(); return 18; -break; -case 19: yy_.yytext = yy_.yytext.substr(1,yy_.yyleng-2).replace(/\\"/g,'"'); return 28; -break; -case 20: return 30; -break; -case 21: return 30; -break; -case 22: return 29; -break; -case 23: return 33; -break; -case 24: yy_.yytext = yy_.yytext.substr(1, yy_.yyleng-2); return 33; -break; -case 25: return 'INVALID'; -break; -case 26: return 5; -break; -} -}; -lexer.rules = [/^[^\x00]*?(?=(\{\{))/,/^[^\x00]+/,/^[^\x00]{2,}?(?=(\{\{))/,/^\{\{>/,/^\{\{#/,/^\{\{\//,/^\{\{\^/,/^\{\{\s*else\b/,/^\{\{\{/,/^\{\{&/,/^\{\{![\s\S]*?\}\}/,/^\{\{/,/^=/,/^\.(?=[} ])/,/^\.\./,/^[\/.]/,/^\s+/,/^\}\}\}/,/^\}\}/,/^"(\\["]|[^"])*"/,/^true(?=[}\s])/,/^false(?=[}\s])/,/^[0-9]+(?=[}\s])/,/^[a-zA-Z0-9_$-]+(?=[=}\s\/.])/,/^\[[^\]]*\]/,/^./,/^$/]; -lexer.conditions = {"mu":{"rules":[3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26],"inclusive":false},"emu":{"rules":[2],"inclusive":false},"INITIAL":{"rules":[0,1,26],"inclusive":true}};return lexer;})() -parser.lexer = lexer; -return parser; -})(); -if (typeof require !== 'undefined' && typeof exports !== 'undefined') { -exports.parser = handlebars; -exports.parse = function () { return handlebars.parse.apply(handlebars, arguments); } -exports.main = function commonjsMain(args) { - if (!args[1]) - throw new Error('Usage: '+args[0]+' FILE'); - if (typeof process !== 'undefined') { - var source = require('fs').readFileSync(require('path').join(process.cwd(), args[1]), "utf8"); - } else { - var cwd = require("file").path(require("file").cwd()); - var source = cwd.join(args[1]).read({charset: "utf-8"}); - } - return exports.parser.parse(source); -} -if (typeof module !== 'undefined' && require.main === module) { - exports.main(typeof process !== 'undefined' ? process.argv.slice(1) : require("system").args); -} -}; -; -// lib/handlebars/compiler/base.js -Handlebars.Parser = handlebars; - -Handlebars.parse = function(string) { - Handlebars.Parser.yy = Handlebars.AST; - return Handlebars.Parser.parse(string); -}; - -Handlebars.print = function(ast) { - return new Handlebars.PrintVisitor().accept(ast); -}; - -Handlebars.logger = { - DEBUG: 0, INFO: 1, WARN: 2, ERROR: 3, level: 3, - - // override in the host environment - log: function(level, str) {} -}; - -Handlebars.log = function(level, str) { Handlebars.logger.log(level, str); }; -; -// lib/handlebars/compiler/ast.js -(function() { - - Handlebars.AST = {}; - - Handlebars.AST.ProgramNode = function(statements, inverse) { - this.type = "program"; - this.statements = statements; - if(inverse) { this.inverse = new Handlebars.AST.ProgramNode(inverse); } - }; - - Handlebars.AST.MustacheNode = function(params, hash, unescaped) { - this.type = "mustache"; - this.id = params[0]; - this.params = params.slice(1); - this.hash = hash; - this.escaped = !unescaped; - }; - - Handlebars.AST.PartialNode = function(id, context) { - this.type = "partial"; - - // TODO: disallow complex IDs - - this.id = id; - this.context = context; - }; - - var verifyMatch = function(open, close) { - if(open.original !== close.original) { - throw new Handlebars.Exception(open.original + " doesn't match " + close.original); - } - }; - - Handlebars.AST.BlockNode = function(mustache, program, close) { - verifyMatch(mustache.id, close); - this.type = "block"; - this.mustache = mustache; - this.program = program; - }; - - Handlebars.AST.InverseNode = function(mustache, program, close) { - verifyMatch(mustache.id, close); - this.type = "inverse"; - this.mustache = mustache; - this.program = program; - }; - - Handlebars.AST.ContentNode = function(string) { - this.type = "content"; - this.string = string; - }; - - Handlebars.AST.HashNode = function(pairs) { - this.type = "hash"; - this.pairs = pairs; - }; - - Handlebars.AST.IdNode = function(parts) { - this.type = "ID"; - this.original = parts.join("."); - - var dig = [], depth = 0; - - for(var i=0,l=parts.length; i<l; i++) { - var part = parts[i]; - - if(part === "..") { depth++; } - else if(part === "." || part === "this") { this.isScoped = true; } - else { dig.push(part); } - } - - this.parts = dig; - this.string = dig.join('.'); - this.depth = depth; - this.isSimple = (dig.length === 1) && (depth === 0); - }; - - Handlebars.AST.StringNode = function(string) { - this.type = "STRING"; - this.string = string; - }; - - Handlebars.AST.IntegerNode = function(integer) { - this.type = "INTEGER"; - this.integer = integer; - }; - - Handlebars.AST.BooleanNode = function(bool) { - this.type = "BOOLEAN"; - this.bool = bool; - }; - - Handlebars.AST.CommentNode = function(comment) { - this.type = "comment"; - this.comment = comment; - }; - -})();; -// lib/handlebars/utils.js -Handlebars.Exception = function(message) { - var tmp = Error.prototype.constructor.apply(this, arguments); - - for (var p in tmp) { - if (tmp.hasOwnProperty(p)) { this[p] = tmp[p]; } - } - - this.message = tmp.message; -}; -Handlebars.Exception.prototype = new Error; - -// Build out our basic SafeString type -Handlebars.SafeString = function(string) { - this.string = string; -}; -Handlebars.SafeString.prototype.toString = function() { - return this.string.toString(); -}; - -(function() { - var escape = { - "<": "<", - ">": ">", - '"': """, - "'": "'", - "`": "`" - }; - - var badChars = /&(?!\w+;)|[<>"'`]/g; - var possible = /[&<>"'`]/; - - var escapeChar = function(chr) { - return escape[chr] || "&"; - }; - - Handlebars.Utils = { - escapeExpression: function(string) { - // don't escape SafeStrings, since they're already safe - if (string instanceof Handlebars.SafeString) { - return string.toString(); - } else if (string == null || string === false) { - return ""; - } - - if(!possible.test(string)) { return string; } - return string.replace(badChars, escapeChar); - }, - - isEmpty: function(value) { - if (typeof value === "undefined") { - return true; - } else if (value === null) { - return true; - } else if (value === false) { - return true; - } else if(Object.prototype.toString.call(value) === "[object Array]" && value.length === 0) { - return true; - } else { - return false; - } - } - }; -})();; -// lib/handlebars/compiler/compiler.js -Handlebars.Compiler = function() {}; -Handlebars.JavaScriptCompiler = function() {}; - -(function(Compiler, JavaScriptCompiler) { - Compiler.OPCODE_MAP = { - appendContent: 1, - getContext: 2, - lookupWithHelpers: 3, - lookup: 4, - append: 5, - invokeMustache: 6, - appendEscaped: 7, - pushString: 8, - truthyOrFallback: 9, - functionOrFallback: 10, - invokeProgram: 11, - invokePartial: 12, - push: 13, - assignToHash: 15, - pushStringParam: 16 - }; - - Compiler.MULTI_PARAM_OPCODES = { - appendContent: 1, - getContext: 1, - lookupWithHelpers: 2, - lookup: 1, - invokeMustache: 3, - pushString: 1, - truthyOrFallback: 1, - functionOrFallback: 1, - invokeProgram: 3, - invokePartial: 1, - push: 1, - assignToHash: 1, - pushStringParam: 1 - }; - - Compiler.DISASSEMBLE_MAP = {}; - - for(var prop in Compiler.OPCODE_MAP) { - var value = Compiler.OPCODE_MAP[prop]; - Compiler.DISASSEMBLE_MAP[value] = prop; - } - - Compiler.multiParamSize = function(code) { - return Compiler.MULTI_PARAM_OPCODES[Compiler.DISASSEMBLE_MAP[code]]; - }; - - Compiler.prototype = { - compiler: Compiler, - - disassemble: function() { - var opcodes = this.opcodes, opcode, nextCode; - var out = [], str, name, value; - - for(var i=0, l=opcodes.length; i<l; i++) { - opcode = opcodes[i]; - - if(opcode === 'DECLARE') { - name = opcodes[++i]; - value = opcodes[++i]; - out.push("DECLARE " + name + " = " + value); - } else { - str = Compiler.DISASSEMBLE_MAP[opcode]; - - var extraParams = Compiler.multiParamSize(opcode); - var codes = []; - - for(var j=0; j<extraParams; j++) { - nextCode = opcodes[++i]; - - if(typeof nextCode === "string") { - nextCode = "\"" + nextCode.replace("\n", "\\n") + "\""; - } - - codes.push(nextCode); - } - - str = str + " " + codes.join(" "); - - out.push(str); - } - } - - return out.join("\n"); - }, - - guid: 0, - - compile: function(program, options) { - this.children = []; - this.depths = {list: []}; - this.options = options; - - // These changes will propagate to the other compiler components - var knownHelpers = this.options.knownHelpers; - this.options.knownHelpers = { - 'helperMissing': true, - 'blockHelperMissing': true, - 'each': true, - 'if': true, - 'unless': true, - 'with': true, - 'log': true - }; - if (knownHelpers) { - for (var name in knownHelpers) { - this.options.knownHelpers[name] = knownHelpers[name]; - } - } - - return this.program(program); - }, - - accept: function(node) { - return this[node.type](node); - }, - - program: function(program) { - var statements = program.statements, statement; - this.opcodes = []; - - for(var i=0, l=statements.length; i<l; i++) { - statement = statements[i]; - this[statement.type](statement); - } - this.isSimple = l === 1; - - this.depths.list = this.depths.list.sort(function(a, b) { - return a - b; - }); - - return this; - }, - - compileProgram: function(program) { - var result = new this.compiler().compile(program, this.options); - var guid = this.guid++; - - this.usePartial = this.usePartial || result.usePartial; - - this.children[guid] = result; - - for(var i=0, l=result.depths.list.length; i<l; i++) { - depth = result.depths.list[i]; - - if(depth < 2) { continue; } - else { this.addDepth(depth - 1); } - } - - return guid; - }, - - block: function(block) { - var mustache = block.mustache; - var depth, child, inverse, inverseGuid; - - var params = this.setupStackForMustache(mustache); - - var programGuid = this.compileProgram(block.program); - - if(block.program.inverse) { - inverseGuid = this.compileProgram(block.program.inverse); - this.declare('inverse', inverseGuid); - } - - this.opcode('invokeProgram', programGuid, params.length, !!mustache.hash); - this.declare('inverse', null); - this.opcode('append'); - }, - - inverse: function(block) { - var params = this.setupStackForMustache(block.mustache); - - var programGuid = this.compileProgram(block.program); - - this.declare('inverse', programGuid); - - this.opcode('invokeProgram', null, params.length, !!block.mustache.hash); - this.declare('inverse', null); - this.opcode('append'); - }, - - hash: function(hash) { - var pairs = hash.pairs, pair, val; - - this.opcode('push', '{}'); - - for(var i=0, l=pairs.length; i<l; i++) { - pair = pairs[i]; - val = pair[1]; - - this.accept(val); - this.opcode('assignToHash', pair[0]); - } - }, - - partial: function(partial) { - var id = partial.id; - this.usePartial = true; - - if(partial.context) { - this.ID(partial.context); - } else { - this.opcode('push', 'depth0'); - } - - this.opcode('invokePartial', id.original); - this.opcode('append'); - }, - - content: function(content) { - this.opcode('appendContent', content.string); - }, - - mustache: function(mustache) { - var params = this.setupStackForMustache(mustache); - - this.opcode('invokeMustache', params.length, mustache.id.original, !!mustache.hash); - - if(mustache.escaped && !this.options.noEscape) { - this.opcode('appendEscaped'); - } else { - this.opcode('append'); - } - }, - - ID: function(id) { - this.addDepth(id.depth); - - this.opcode('getContext', id.depth); - - this.opcode('lookupWithHelpers', id.parts[0] || null, id.isScoped || false); - - for(var i=1, l=id.parts.length; i<l; i++) { - this.opcode('lookup', id.parts[i]); - } - }, - - STRING: function(string) { - this.opcode('pushString', string.string); - }, - - INTEGER: function(integer) { - this.opcode('push', integer.integer); - }, - - BOOLEAN: function(bool) { - this.opcode('push', bool.bool); - }, - - comment: function() {}, - - // HELPERS - pushParams: function(params) { - var i = params.length, param; - - while(i--) { - param = params[i]; - - if(this.options.stringParams) { - if(param.depth) { - this.addDepth(param.depth); - } - - this.opcode('getContext', param.depth || 0); - this.opcode('pushStringParam', param.string); - } else { - this[param.type](param); - } - } - }, - - opcode: function(name, val1, val2, val3) { - this.opcodes.push(Compiler.OPCODE_MAP[name]); - if(val1 !== undefined) { this.opcodes.push(val1); } - if(val2 !== undefined) { this.opcodes.push(val2); } - if(val3 !== undefined) { this.opcodes.push(val3); } - }, - - declare: function(name, value) { - this.opcodes.push('DECLARE'); - this.opcodes.push(name); - this.opcodes.push(value); - }, - - addDepth: function(depth) { - if(depth === 0) { return; } - - if(!this.depths[depth]) { - this.depths[depth] = true; - this.depths.list.push(depth); - } - }, - - setupStackForMustache: function(mustache) { - var params = mustache.params; - - this.pushParams(params); - - if(mustache.hash) { - this.hash(mustache.hash); - } - - this.ID(mustache.id); - - return params; - } - }; - - JavaScriptCompiler.prototype = { - // PUBLIC API: You can override these methods in a subclass to provide - // alternative compiled forms for name lookup and buffering semantics - nameLookup: function(parent, name, type) { - if (/^[0-9]+$/.test(name)) { - return parent + "[" + name + "]"; - } else if (JavaScriptCompiler.isValidJavaScriptVariableName(name)) { - return parent + "." + name; - } - else { - return parent + "['" + name + "']"; - } - }, - - appendToBuffer: function(string) { - if (this.environment.isSimple) { - return "return " + string + ";"; - } else { - return "buffer += " + string + ";"; - } - }, - - initializeBuffer: function() { - return this.quotedString(""); - }, - - namespace: "Handlebars", - // END PUBLIC API - - compile: function(environment, options, context, asObject) { - this.environment = environment; - this.options = options || {}; - - this.name = this.environment.name; - this.isChild = !!context; - this.context = context || { - programs: [], - aliases: { self: 'this' }, - registers: {list: []} - }; - - this.preamble(); - - this.stackSlot = 0; - this.stackVars = []; - - this.compileChildren(environment, options); - - var opcodes = environment.opcodes, opcode; - - this.i = 0; - - for(l=opcodes.length; this.i<l; this.i++) { - opcode = this.nextOpcode(0); - - if(opcode[0] === 'DECLARE') { - this.i = this.i + 2; - this[opcode[1]] = opcode[2]; - } else { - this.i = this.i + opcode[1].length; - this[opcode[0]].apply(this, opcode[1]); - } - } - - return this.createFunctionContext(asObject); - }, - - nextOpcode: function(n) { - var opcodes = this.environment.opcodes, opcode = opcodes[this.i + n], name, val; - var extraParams, codes; - - if(opcode === 'DECLARE') { - name = opcodes[this.i + 1]; - val = opcodes[this.i + 2]; - return ['DECLARE', name, val]; - } else { - name = Compiler.DISASSEMBLE_MAP[opcode]; - - extraParams = Compiler.multiParamSize(opcode); - codes = []; - - for(var j=0; j<extraParams; j++) { - codes.push(opcodes[this.i + j + 1 + n]); - } - - return [name, codes]; - } - }, - - eat: function(opcode) { - this.i = this.i + opcode.length; - }, - - preamble: function() { - var out = []; - - // this register will disambiguate helper lookup from finding a function in - // a context. This is necessary for mustache compatibility, which requires - // that context functions in blocks are evaluated by blockHelperMissing, and - // then proceed as if the resulting value was provided to blockHelperMissing. - this.useRegister('foundHelper'); - - if (!this.isChild) { - var namespace = this.namespace; - var copies = "helpers = helpers || " + namespace + ".helpers;"; - if(this.environment.usePartial) { copies = copies + " partials = partials || " + namespace + ".partials;"; } - out.push(copies); - } else { - out.push(''); - } - - if (!this.environment.isSimple) { - out.push(", buffer = " + this.initializeBuffer()); - } else { - out.push(""); - } - - // track the last context pushed into place to allow skipping the - // getContext opcode when it would be a noop - this.lastContext = 0; - this.source = out; - }, - - createFunctionContext: function(asObject) { - var locals = this.stackVars; - if (!this.isChild) { - locals = locals.concat(this.context.registers.list); - } - - if(locals.length > 0) { - this.source[1] = this.source[1] + ", " + locals.join(", "); - } - - // Generate minimizer alias mappings - if (!this.isChild) { - var aliases = [] - for (var alias in this.context.aliases) { - this.source[1] = this.source[1] + ', ' + alias + '=' + this.context.aliases[alias]; - } - } - - if (this.source[1]) { - this.source[1] = "var " + this.source[1].substring(2) + ";"; - } - - // Merge children - if (!this.isChild) { - this.source[1] += '\n' + this.context.programs.join('\n') + '\n'; - } - - if (!this.environment.isSimple) { - this.source.push("return buffer;"); - } - - var params = this.isChild ? ["depth0", "data"] : ["Handlebars", "depth0", "helpers", "partials", "data"]; - - for(var i=0, l=this.environment.depths.list.length; i<l; i++) { - params.push("depth" + this.environment.depths.list[i]); - } - - if (asObject) { - params.push(this.source.join("\n ")); - - return Function.apply(this, params); - } else { - var functionSource = 'function ' + (this.name || '') + '(' + params.join(',') + ') {\n ' + this.source.join("\n ") + '}'; - Handlebars.log(Handlebars.logger.DEBUG, functionSource + "\n\n"); - return functionSource; - } - }, - - appendContent: function(content) { - this.source.push(this.appendToBuffer(this.quotedString(content))); - }, - - append: function() { - var local = this.popStack(); - this.source.push("if(" + local + " || " + local + " === 0) { " + this.appendToBuffer(local) + " }"); - if (this.environment.isSimple) { - this.source.push("else { " + this.appendToBuffer("''") + " }"); - } - }, - - appendEscaped: function() { - var opcode = this.nextOpcode(1), extra = ""; - this.context.aliases.escapeExpression = 'this.escapeExpression'; - - if(opcode[0] === 'appendContent') { - extra = " + " + this.quotedString(opcode[1][0]); - this.eat(opcode); - } - - this.source.push(this.appendToBuffer("escapeExpression(" + this.popStack() + ")" + extra)); - }, - - getContext: function(depth) { - if(this.lastContext !== depth) { - this.lastContext = depth; - } - }, - - lookupWithHelpers: function(name, isScoped) { - if(name) { - var topStack = this.nextStack(); - - this.usingKnownHelper = false; - - var toPush; - if (!isScoped && this.options.knownHelpers[name]) { - toPush = topStack + " = " + this.nameLookup('helpers', name, 'helper'); - this.usingKnownHelper = true; - } else if (isScoped || this.options.knownHelpersOnly) { - toPush = topStack + " = " + this.nameLookup('depth' + this.lastContext, name, 'context'); - } else { - this.register('foundHelper', this.nameLookup('helpers', name, 'helper')); - toPush = topStack + " = foundHelper || " + this.nameLookup('depth' + this.lastContext, name, 'context'); - } - - toPush += ';'; - this.source.push(toPush); - } else { - this.pushStack('depth' + this.lastContext); - } - }, - - lookup: function(name) { - var topStack = this.topStack(); - this.source.push(topStack + " = (" + topStack + " === null || " + topStack + " === undefined || " + topStack + " === false ? " + - topStack + " : " + this.nameLookup(topStack, name, 'context') + ");"); - }, - - pushStringParam: function(string) { - this.pushStack('depth' + this.lastContext); - this.pushString(string); - }, - - pushString: function(string) { - this.pushStack(this.quotedString(string)); - }, - - push: function(name) { - this.pushStack(name); - }, - - invokeMustache: function(paramSize, original, hasHash) { - this.populateParams(paramSize, this.quotedString(original), "{}", null, hasHash, function(nextStack, helperMissingString, id) { - if (!this.usingKnownHelper) { - this.context.aliases.helperMissing = 'helpers.helperMissing'; - this.context.aliases.undef = 'void 0'; - this.source.push("else if(" + id + "=== undef) { " + nextStack + " = helperMissing.call(" + helperMissingString + "); }"); - if (nextStack !== id) { - this.source.push("else { " + nextStack + " = " + id + "; }"); - } - } - }); - }, - - invokeProgram: function(guid, paramSize, hasHash) { - var inverse = this.programExpression(this.inverse); - var mainProgram = this.programExpression(guid); - - this.populateParams(paramSize, null, mainProgram, inverse, hasHash, function(nextStack, helperMissingString, id) { - if (!this.usingKnownHelper) { - this.context.aliases.blockHelperMissing = 'helpers.blockHelperMissing'; - this.source.push("else { " + nextStack + " = blockHelperMissing.call(" + helperMissingString + "); }"); - } - }); - }, - - populateParams: function(paramSize, helperId, program, inverse, hasHash, fn) { - var needsRegister = hasHash || this.options.stringParams || inverse || this.options.data; - var id = this.popStack(), nextStack; - var params = [], param, stringParam, stringOptions; - - if (needsRegister) { - this.register('tmp1', program); - stringOptions = 'tmp1'; - } else { - stringOptions = '{ hash: {} }'; - } - - if (needsRegister) { - var hash = (hasHash ? this.popStack() : '{}'); - this.source.push('tmp1.hash = ' + hash + ';'); - } - - if(this.options.stringParams) { - this.source.push('tmp1.contexts = [];'); - } - - for(var i=0; i<paramSize; i++) { - param = this.popStack(); - params.push(param); - - if(this.options.stringParams) { - this.source.push('tmp1.contexts.push(' + this.popStack() + ');'); - } - } - - if(inverse) { - this.source.push('tmp1.fn = tmp1;'); - this.source.push('tmp1.inverse = ' + inverse + ';'); - } - - if(this.options.data) { - this.source.push('tmp1.data = data;'); - } - - params.push(stringOptions); - - this.populateCall(params, id, helperId || id, fn, program !== '{}'); - }, - - populateCall: function(params, id, helperId, fn, program) { - var paramString = ["depth0"].concat(params).join(", "); - var helperMissingString = ["depth0"].concat(helperId).concat(params).join(", "); - - var nextStack = this.nextStack(); - - if (this.usingKnownHelper) { - this.source.push(nextStack + " = " + id + ".call(" + paramString + ");"); - } else { - this.context.aliases.functionType = '"function"'; - var condition = program ? "foundHelper && " : "" - this.source.push("if(" + condition + "typeof " + id + " === functionType) { " + nextStack + " = " + id + ".call(" + paramString + "); }"); - } - fn.call(this, nextStack, helperMissingString, id); - this.usingKnownHelper = false; - }, - - invokePartial: function(context) { - params = [this.nameLookup('partials', context, 'partial'), "'" + context + "'", this.popStack(), "helpers", "partials"]; - - if (this.options.data) { - params.push("data"); - } - - this.pushStack("self.invokePartial(" + params.join(", ") + ");"); - }, - - assignToHash: function(key) { - var value = this.popStack(); - var hash = this.topStack(); - - this.source.push(hash + "['" + key + "'] = " + value + ";"); - }, - - // HELPERS - - compiler: JavaScriptCompiler, - - compileChildren: function(environment, options) { - var children = environment.children, child, compiler; - - for(var i=0, l=children.length; i<l; i++) { - child = children[i]; - compiler = new this.compiler(); - - this.context.programs.push(''); // Placeholder to prevent name conflicts for nested children - var index = this.context.programs.length; - child.index = index; - child.name = 'program' + index; - this.context.programs[index] = compiler.compile(child, options, this.context); - } - }, - - programExpression: function(guid) { - if(guid == null) { return "self.noop"; } - - var child = this.environment.children[guid], - depths = child.depths.list; - var programParams = [child.index, child.name, "data"]; - - for(var i=0, l = depths.length; i<l; i++) { - depth = depths[i]; - - if(depth === 1) { programParams.push("depth0"); } - else { programParams.push("depth" + (depth - 1)); } - } - - if(depths.length === 0) { - return "self.program(" + programParams.join(", ") + ")"; - } else { - programParams.shift(); - return "self.programWithDepth(" + programParams.join(", ") + ")"; - } - }, - - register: function(name, val) { - this.useRegister(name); - this.source.push(name + " = " + val + ";"); - }, - - useRegister: function(name) { - if(!this.context.registers[name]) { - this.context.registers[name] = true; - this.context.registers.list.push(name); - } - }, - - pushStack: function(item) { - this.source.push(this.nextStack() + " = " + item + ";"); - return "stack" + this.stackSlot; - }, - - nextStack: function() { - this.stackSlot++; - if(this.stackSlot > this.stackVars.length) { this.stackVars.push("stack" + this.stackSlot); } - return "stack" + this.stackSlot; - }, - - popStack: function() { - return "stack" + this.stackSlot--; - }, - - topStack: function() { - return "stack" + this.stackSlot; - }, - - quotedString: function(str) { - return '"' + str - .replace(/\\/g, '\\\\') - .replace(/"/g, '\\"') - .replace(/\n/g, '\\n') - .replace(/\r/g, '\\r') + '"'; - } - }; - - var reservedWords = ( - "break else new var" + - " case finally return void" + - " catch for switch while" + - " continue function this with" + - " default if throw" + - " delete in try" + - " do instanceof typeof" + - " abstract enum int short" + - " boolean export interface static" + - " byte extends long super" + - " char final native synchronized" + - " class float package throws" + - " const goto private transient" + - " debugger implements protected volatile" + - " double import public let yield" - ).split(" "); - - var compilerWords = JavaScriptCompiler.RESERVED_WORDS = {}; - - for(var i=0, l=reservedWords.length; i<l; i++) { - compilerWords[reservedWords[i]] = true; - } - - JavaScriptCompiler.isValidJavaScriptVariableName = function(name) { - if(!JavaScriptCompiler.RESERVED_WORDS[name] && /^[a-zA-Z_$][0-9a-zA-Z_$]+$/.test(name)) { - return true; - } - return false; - } - -})(Handlebars.Compiler, Handlebars.JavaScriptCompiler); - -Handlebars.precompile = function(string, options) { - options = options || {}; - - var ast = Handlebars.parse(string); - var environment = new Handlebars.Compiler().compile(ast, options); - return new Handlebars.JavaScriptCompiler().compile(environment, options); -}; - -Handlebars.compile = function(string, options) { - options = options || {}; - - var compiled; - function compile() { - var ast = Handlebars.parse(string); - var environment = new Handlebars.Compiler().compile(ast, options); - var templateSpec = new Handlebars.JavaScriptCompiler().compile(environment, options, undefined, true); - return Handlebars.template(templateSpec); - } - - // Template is only compiled on first use and cached after that point. - return function(context, options) { - if (!compiled) { - compiled = compile(); - } - return compiled.call(this, context, options); - }; -}; -; -// lib/handlebars/runtime.js -Handlebars.VM = { - template: function(templateSpec) { - // Just add water - var container = { - escapeExpression: Handlebars.Utils.escapeExpression, - invokePartial: Handlebars.VM.invokePartial, - programs: [], - program: function(i, fn, data) { - var programWrapper = this.programs[i]; - if(data) { - return Handlebars.VM.program(fn, data); - } else if(programWrapper) { - return programWrapper; - } else { - programWrapper = this.programs[i] = Handlebars.VM.program(fn); - return programWrapper; - } - }, - programWithDepth: Handlebars.VM.programWithDepth, - noop: Handlebars.VM.noop - }; - - return function(context, options) { - options = options || {}; - return templateSpec.call(container, Handlebars, context, options.helpers, options.partials, options.data); - }; - }, - - programWithDepth: function(fn, data, $depth) { - var args = Array.prototype.slice.call(arguments, 2); - - return function(context, options) { - options = options || {}; - - return fn.apply(this, [context, options.data || data].concat(args)); - }; - }, - program: function(fn, data) { - return function(context, options) { - options = options || {}; - - return fn(context, options.data || data); - }; - }, - noop: function() { return ""; }, - invokePartial: function(partial, name, context, helpers, partials, data) { - options = { helpers: helpers, partials: partials, data: data }; - - if(partial === undefined) { - throw new Handlebars.Exception("The partial " + name + " could not be found"); - } else if(partial instanceof Function) { - return partial(context, options); - } else if (!Handlebars.compile) { - throw new Handlebars.Exception("The partial " + name + " could not be compiled when running in runtime-only mode"); - } else { - partials[name] = Handlebars.compile(partial); - return partials[name](context, options); - } - } -}; - -Handlebars.template = Handlebars.VM.template; -; diff -r de2946aca8877087d761684a72ff955f46e4f5a6 -r 15e75fe2efae761ac7182a496d5c79ef3bc3a43a static/scripts/libs/handlebars.runtime.js --- /dev/null +++ b/static/scripts/libs/handlebars.runtime.js @@ -0,0 +1,223 @@ +// lib/handlebars/base.js +var Handlebars = {}; + +Handlebars.VERSION = "1.0.beta.6"; + +Handlebars.helpers = {}; +Handlebars.partials = {}; + +Handlebars.registerHelper = function(name, fn, inverse) { + if(inverse) { fn.not = inverse; } + this.helpers[name] = fn; +}; + +Handlebars.registerPartial = function(name, str) { + this.partials[name] = str; +}; + +Handlebars.registerHelper('helperMissing', function(arg) { + if(arguments.length === 2) { + return undefined; + } else { + throw new Error("Could not find property '" + arg + "'"); + } +}); + +var toString = Object.prototype.toString, functionType = "[object Function]"; + +Handlebars.registerHelper('blockHelperMissing', function(context, options) { + var inverse = options.inverse || function() {}, fn = options.fn; + + + var ret = ""; + var type = toString.call(context); + + if(type === functionType) { context = context.call(this); } + + if(context === true) { + return fn(this); + } else if(context === false || context == null) { + return inverse(this); + } else if(type === "[object Array]") { + if(context.length > 0) { + for(var i=0, j=context.length; i<j; i++) { + ret = ret + fn(context[i]); + } + } else { + ret = inverse(this); + } + return ret; + } else { + return fn(context); + } +}); + +Handlebars.registerHelper('each', function(context, options) { + var fn = options.fn, inverse = options.inverse; + var ret = ""; + + if(context && context.length > 0) { + for(var i=0, j=context.length; i<j; i++) { + ret = ret + fn(context[i]); + } + } else { + ret = inverse(this); + } + return ret; +}); + +Handlebars.registerHelper('if', function(context, options) { + var type = toString.call(context); + if(type === functionType) { context = context.call(this); } + + if(!context || Handlebars.Utils.isEmpty(context)) { + return options.inverse(this); + } else { + return options.fn(this); + } +}); + +Handlebars.registerHelper('unless', function(context, options) { + var fn = options.fn, inverse = options.inverse; + options.fn = inverse; + options.inverse = fn; + + return Handlebars.helpers['if'].call(this, context, options); +}); + +Handlebars.registerHelper('with', function(context, options) { + return options.fn(context); +}); + +Handlebars.registerHelper('log', function(context) { + Handlebars.log(context); +}); +; +// lib/handlebars/utils.js +Handlebars.Exception = function(message) { + var tmp = Error.prototype.constructor.apply(this, arguments); + + for (var p in tmp) { + if (tmp.hasOwnProperty(p)) { this[p] = tmp[p]; } + } + + this.message = tmp.message; +}; +Handlebars.Exception.prototype = new Error; + +// Build out our basic SafeString type +Handlebars.SafeString = function(string) { + this.string = string; +}; +Handlebars.SafeString.prototype.toString = function() { + return this.string.toString(); +}; + +(function() { + var escape = { + "<": "<", + ">": ">", + '"': """, + "'": "'", + "`": "`" + }; + + var badChars = /&(?!\w+;)|[<>"'`]/g; + var possible = /[&<>"'`]/; + + var escapeChar = function(chr) { + return escape[chr] || "&"; + }; + + Handlebars.Utils = { + escapeExpression: function(string) { + // don't escape SafeStrings, since they're already safe + if (string instanceof Handlebars.SafeString) { + return string.toString(); + } else if (string == null || string === false) { + return ""; + } + + if(!possible.test(string)) { return string; } + return string.replace(badChars, escapeChar); + }, + + isEmpty: function(value) { + if (typeof value === "undefined") { + return true; + } else if (value === null) { + return true; + } else if (value === false) { + return true; + } else if(Object.prototype.toString.call(value) === "[object Array]" && value.length === 0) { + return true; + } else { + return false; + } + } + }; +})();; +// lib/handlebars/runtime.js +Handlebars.VM = { + template: function(templateSpec) { + // Just add water + var container = { + escapeExpression: Handlebars.Utils.escapeExpression, + invokePartial: Handlebars.VM.invokePartial, + programs: [], + program: function(i, fn, data) { + var programWrapper = this.programs[i]; + if(data) { + return Handlebars.VM.program(fn, data); + } else if(programWrapper) { + return programWrapper; + } else { + programWrapper = this.programs[i] = Handlebars.VM.program(fn); + return programWrapper; + } + }, + programWithDepth: Handlebars.VM.programWithDepth, + noop: Handlebars.VM.noop + }; + + return function(context, options) { + options = options || {}; + return templateSpec.call(container, Handlebars, context, options.helpers, options.partials, options.data); + }; + }, + + programWithDepth: function(fn, data, $depth) { + var args = Array.prototype.slice.call(arguments, 2); + + return function(context, options) { + options = options || {}; + + return fn.apply(this, [context, options.data || data].concat(args)); + }; + }, + program: function(fn, data) { + return function(context, options) { + options = options || {}; + + return fn(context, options.data || data); + }; + }, + noop: function() { return ""; }, + invokePartial: function(partial, name, context, helpers, partials, data) { + options = { helpers: helpers, partials: partials, data: data }; + + if(partial === undefined) { + throw new Handlebars.Exception("The partial " + name + " could not be found"); + } else if(partial instanceof Function) { + return partial(context, options); + } else if (!Handlebars.compile) { + throw new Handlebars.Exception("The partial " + name + " could not be compiled when running in runtime-only mode"); + } else { + partials[name] = Handlebars.compile(partial); + return partials[name](context, options); + } + } +}; + +Handlebars.template = Handlebars.VM.template; +; https://bitbucket.org/galaxy/galaxy-central/changeset/657c1295db78/ changeset: 657c1295db78 user: jgoecks date: 2012-03-30 17:46:02 summary: Enable handlebars precompilation and template insertion. affected #: 8 files diff -r 15e75fe2efae761ac7182a496d5c79ef3bc3a43a -r 657c1295db78085a845ecf68075008710eba5ed5 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -45,14 +45,28 @@ """ return "\n".join( [ stylesheet_link_tag( "/static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] ) -def js( *args ): +def js_helper( prefix, *args ): """ - Take a list of javascript names (no extension) and return appropriate + Take a prefix and list of javascript names and return appropriate string of script tags. Cache-bust with time that server started running on """ - return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=%s" % server_starttime ) for name in args ] ) + return "\n".join( [ javascript_include_tag( prefix + name + ".js?v=%s" % server_starttime ) for name in args ] ) + +def js( *args ): + """ + Take a prefix and list of javascript names and return appropriate + string of script tags. + """ + return js_helper( '/static/scripts/', *args ) + +def handlebars( *args ): + """ + Take a list of template names (no extension) and return appropriate + string of script tags. + """ + return js_helper( '/static/scripts/handlebars/compiled/', *args ) # Hashes diff -r 15e75fe2efae761ac7182a496d5c79ef3bc3a43a -r 657c1295db78085a845ecf68075008710eba5ed5 static/scripts/handlebars/compile_templates.py --- /dev/null +++ b/static/scripts/handlebars/compile_templates.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python + +# Script requires handlebars compiler be installed; use node package manager +# to install handlebars. + +import sys + +from glob import glob +from subprocess import call +from shutil import copyfile +from os import path + +cmd = "handlebars %s -f compiled/%s.js" + +# If specific scripts specified on command line, just pack them, otherwise pack +# all. + +if len( sys.argv ) > 1: + to_pack = sys.argv[1:] +else: + to_pack = glob( "*.handlebars" ) + +for fname in to_pack: + fname_base = path.splitext( path.split( fname )[1] )[0] + print fname_base + print "%s --> compiled/%s.js" % ( fname, fname_base ) + out = call( cmd % ( fname, fname_base ), shell=True ) diff -r 15e75fe2efae761ac7182a496d5c79ef3bc3a43a -r 657c1295db78085a845ecf68075008710eba5ed5 static/scripts/handlebars/compiled/panel_label.js --- /dev/null +++ b/static/scripts/handlebars/compiled/panel_label.js @@ -0,0 +1,15 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['panel_label'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; + + + buffer += "<span>"; + foundHelper = helpers.name; + stack1 = foundHelper || depth0.name; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } + buffer += escapeExpression(stack1) + "</span>"; + return buffer;}); +})(); \ No newline at end of file diff -r 15e75fe2efae761ac7182a496d5c79ef3bc3a43a -r 657c1295db78085a845ecf68075008710eba5ed5 static/scripts/handlebars/compiled/panel_section.js --- /dev/null +++ b/static/scripts/handlebars/compiled/panel_section.js @@ -0,0 +1,25 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['panel_section'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; + + + buffer += "<div class=\"toolSectionTitle\" id=\"title_"; + foundHelper = helpers.id; + stack1 = foundHelper || depth0.id; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "id", { hash: {} }); } + buffer += escapeExpression(stack1) + "\">\n <a href=\"#\"><span>"; + foundHelper = helpers.name; + stack1 = foundHelper || depth0.name; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } + buffer += escapeExpression(stack1) + "</span></a>\n</div>\n<div id=\""; + foundHelper = helpers.id; + stack1 = foundHelper || depth0.id; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "id", { hash: {} }); } + buffer += escapeExpression(stack1) + "\" class=\"toolSectionBody\" style=\"display: none; \">\n <div class=\"toolSectionBg\"></div>\n<div>"; + return buffer;}); +})(); \ No newline at end of file diff -r 15e75fe2efae761ac7182a496d5c79ef3bc3a43a -r 657c1295db78085a845ecf68075008710eba5ed5 static/scripts/handlebars/compiled/tool_link.js --- /dev/null +++ b/static/scripts/handlebars/compiled/tool_link.js @@ -0,0 +1,40 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['tool_link'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; + + + buffer += "<a class=\""; + foundHelper = helpers.id; + stack1 = foundHelper || depth0.id; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "id", { hash: {} }); } + buffer += escapeExpression(stack1) + " tool-link\" href=\""; + foundHelper = helpers.link; + stack1 = foundHelper || depth0.link; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "link", { hash: {} }); } + buffer += escapeExpression(stack1) + "\" target=\""; + foundHelper = helpers.target; + stack1 = foundHelper || depth0.target; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "target", { hash: {} }); } + buffer += escapeExpression(stack1) + "\" minsizehint=\""; + foundHelper = helpers.min_width; + stack1 = foundHelper || depth0.min_width; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "min_width", { hash: {} }); } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.name; + stack1 = foundHelper || depth0.name; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "name", { hash: {} }); } + buffer += escapeExpression(stack1) + "</a> "; + foundHelper = helpers.description; + stack1 = foundHelper || depth0.description; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "description", { hash: {} }); } + buffer += escapeExpression(stack1); + return buffer;}); +})(); \ No newline at end of file diff -r 15e75fe2efae761ac7182a496d5c79ef3bc3a43a -r 657c1295db78085a845ecf68075008710eba5ed5 static/scripts/handlebars/panel_label.handlebars --- /dev/null +++ b/static/scripts/handlebars/panel_label.handlebars @@ -0,0 +1,1 @@ +<span>{{name}}</span> \ No newline at end of file diff -r 15e75fe2efae761ac7182a496d5c79ef3bc3a43a -r 657c1295db78085a845ecf68075008710eba5ed5 static/scripts/handlebars/panel_section.handlebars --- /dev/null +++ b/static/scripts/handlebars/panel_section.handlebars @@ -0,0 +1,6 @@ +<div class="toolSectionTitle" id="title_{{id}}"> + <a href="#"><span>{{name}}</span></a> +</div> +<div id="{{id}}" class="toolSectionBody" style="display: none; "> + <div class="toolSectionBg"></div> +<div> \ No newline at end of file diff -r 15e75fe2efae761ac7182a496d5c79ef3bc3a43a -r 657c1295db78085a845ecf68075008710eba5ed5 static/scripts/handlebars/tool_link.handlebars --- /dev/null +++ b/static/scripts/handlebars/tool_link.handlebars @@ -0,0 +1,1 @@ +<a class="{{id}} tool-link" href="{{link}}" target="{{target}}" minsizehint="{{min_width}}">{{name}}</a> {{description}} \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/833332b039fb/ changeset: 833332b039fb user: jgoecks date: 2012-04-02 00:19:11 summary: New tool menu generation using a JavaScript Backbone-based MVC framework. Framework principals are (a) event-based communication from model to view and (b) Backbone views act more as controllers with the HTML as the view itself. Tool menu generation and search are completely functional; recently used tools and tool tags are not yet implemented. affected #: 11 files diff -r 657c1295db78085a845ecf68075008710eba5ed5 -r 833332b039fb6f00fb148ddbae03721783216347 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -31,6 +31,7 @@ from galaxy.util.hash_util import * from galaxy.util import listify from galaxy.util.shed_util import * +from galaxy.web import url_for from galaxy.visualization.tracks.visual_analytics import TracksterConfig @@ -486,11 +487,11 @@ self.version = elem.get( "version" ) or '' self.elems = odict() - def to_dict( self ): + def to_dict( self, trans ): """ Return a dict that includes section's attributes. """ section_elts = [] for key, val in self.elems.items(): - section_elts.append( val.to_dict() ) + section_elts.append( val.to_dict( trans ) ) return { 'type': 'section', 'id': self.id, 'name': self.name, 'version': self.version, 'elems': section_elts } class ToolSectionLabel( object ): @@ -503,7 +504,7 @@ self.id = elem.get( "id" ) self.version = elem.get( "version" ) or '' - def to_dict( self ): + def to_dict( self, trans ): """ Return a dict that includes label's attributes. """ return { 'type': 'label', 'id': self.id, 'name': self.text, 'version': self.version } @@ -2260,10 +2261,19 @@ self.sa_session.flush() return primary_datasets - def to_dict( self, **kwds ): - """ Return dict that includes tool's attributes. """ - return { 'type': 'tool', 'id': self.id, 'name': self.name, - 'version': self.version, 'description': self.description } + def to_dict( self, trans ): + """ Return dict of tool attributes. """ + + # Create tool link. + if not self.tool_type.startswith( 'data_source' ): + link = url_for( controller='tool_runner', tool_id=self.id ) + else: + link = url_for( self.action, **self.get_static_param_values( trans ) ) + + return { 'type': 'tool', 'id': self.id, 'name': self.name, 'link': link, + 'version': self.version, 'description': self.description, + 'min_width': self.uihints.get( 'minwidth', -1 ), + 'target': self.target } class DataSourceTool( Tool ): """ diff -r 657c1295db78085a845ecf68075008710eba5ed5 -r 833332b039fb6f00fb148ddbae03721783216347 lib/galaxy/web/controllers/tools.py --- a/lib/galaxy/web/controllers/tools.py +++ b/lib/galaxy/web/controllers/tools.py @@ -20,12 +20,12 @@ panel_elts = [] # Taken from tool_menu.mako: for key, val in self.app.toolbox.tool_panel.items(): - panel_elts.append( val.to_dict() ) + panel_elts.append( val.to_dict( trans ) ) rval = panel_elts else: tools = [] for id, tool in self.app.toolbox.tools_by_id.items(): - tools.append( tool.to_dict() ) + tools.append( tool.to_dict( trans ) ) rval = tools return rval diff -r 657c1295db78085a845ecf68075008710eba5ed5 -r 833332b039fb6f00fb148ddbae03721783216347 static/june_2007_style/blue/tool_menu.css --- a/static/june_2007_style/blue/tool_menu.css +++ b/static/june_2007_style/blue/tool_menu.css @@ -0,0 +1,2 @@ +#tool-search{padding-top:5px;padding-bottom:10px;position:relative;} +div.toolSectionWrapper{margin-bottom:5px;} diff -r 657c1295db78085a845ecf68075008710eba5ed5 -r 833332b039fb6f00fb148ddbae03721783216347 static/june_2007_style/tool_menu.css.tmpl --- a/static/june_2007_style/tool_menu.css.tmpl +++ b/static/june_2007_style/tool_menu.css.tmpl @@ -0,0 +1,8 @@ +#tool-search { + padding-top: 5px; + padding-bottom: 10px; + position: relative; +} +div.toolSectionWrapper { + margin-bottom: 5px; +} \ No newline at end of file diff -r 657c1295db78085a845ecf68075008710eba5ed5 -r 833332b039fb6f00fb148ddbae03721783216347 static/scripts/backbone/tools.js --- /dev/null +++ b/static/scripts/backbone/tools.js @@ -0,0 +1,383 @@ +/** + * Model classes for Galaxy tools and tool panel. Models have no references to views, + * instead using events to indicate state changes; this is advantageous because + * multiple views can use the same object and models can be used without views. + */ + +/** + * Simple base model for any visible element. Includes useful attributes and ability + * to set and track visibility. + */ +var BaseModel = Backbone.Model.extend({ + defaults: { + id: null, + name: null, + hidden: false + }, + + show: function() { + this.set("hidden", false); + }, + + hide: function() { + this.set("hidden", true); + }, + + is_visible: function() { + return !this.attributes.hidden; + } +}); + +/** + * A Galaxy tool. + */ +var Tool = BaseModel.extend({ + // Default attributes. + defaults: { + description: null, + target: null, + params: [] + }, + + apply_search_results: function(results) { + ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() ); + return this.is_visible(); + } +}); + +/** + * Label or section header in tool panel. + */ +var ToolPanelLabel = BaseModel.extend({}); + +/** + * Section of tool panel with elements (labels and tools). + */ +var ToolPanelSection = BaseModel.extend({ + defaults: { + elems: [], + open: false + }, + + clear_search_results: function() { + _.each(this.attributes.elems, function(elt) { + elt.show(); + }); + + this.show(); + this.set("open", false); + }, + + apply_search_results: function(results) { + var all_hidden = true, + cur_label; + _.each(this.attributes.elems, function(elt) { + if (elt instanceof ToolPanelLabel) { + cur_label = elt; + cur_label.hide(); + } + else if (elt instanceof Tool) { + if (elt.apply_search_results(results)) { + all_hidden = false; + if (cur_label) { + cur_label.show(); + } + } + } + }); + + if (all_hidden) { + this.hide(); + } + else { + this.show(); + this.set("open", true); + } + } +}); + +/** + * Tool search that updates results when query is changed. Result value of null + * indicates that query was not run; if not null, results are from search using + * query. + */ +var ToolSearch = Backbone.Model.extend({ + defaults: { + spinner_url: "", + search_url: "", + visible: true, + query: "", + results: null + }, + + initialize: function() { + this.on("change:query", this.do_search); + }, + + /** + * Do the search and update the results. + */ + do_search: function() { + var query = this.attributes.query; + + // If query is too short, do not search. + if (query.length < 3) { + this.set("results", null); + return; + } + + // Do search via AJAX. + var q = query + '*'; + // Stop previous ajax-request + if (this.timer) { + clearTimeout(this.timer); + } + // Start a new ajax-request in X ms + $("#search-spinner").show(); + var self = this; + this.timer = setTimeout(function () { + $.get(self.attributes.search_url, { query: q }, function (data) { + self.set("results", data); + $("#search-spinner").hide(); + }, "json" ); + }, 200 ); + } +}); + +/** + * A collection of ToolPanelSections, Tools, and ToolPanelLabels. Collection + * applies search results as they become available. + */ +var ToolPanel = Backbone.Collection.extend({ + url: "/tools", + parse: function(response) { + // Recursive function to parse tool panel elements. + var parse_elt = function(elt_dict) { + var type = elt_dict.type; + if (type === 'tool') { + return new Tool(elt_dict); + } + else if (type === 'section') { + // Parse elements. + var elems = _.map(elt_dict.elems, parse_elt); + elt_dict.elems = elems; + return new ToolPanelSection(elt_dict); + } + else if (type === 'label') { + return new ToolPanelLabel(elt_dict); + } + }; + + return _.map(response, parse_elt); + }, + + initialize: function(options) { + this.tool_search = options.tool_search; + this.tool_search.on("change:results", this.apply_search_results, this); + }, + + clear_search_results: function() { + this.each(function(panel_elt) { + panel_elt.clear_search_results(); + }); + }, + + apply_search_results: function() { + var results = this.tool_search.attributes.results; + if (results === null) { + this.clear_search_results(); + return; + } + + this.each(function(panel_elt) { + panel_elt.apply_search_results(results); + }); + } +}); + +/** + * View classes for Galaxy tools and tool panel. + * + * Views use precompiled Handlebars templates for rendering. Views update as needed + * based on (a) model/collection events and (b) user interactions; in this sense, + * they are controllers are well and the HTML is the real view in the MVC architecture. + */ + +// TODO: implement a BaseModelView for handling model visibility. + +/** + * Link to a tool. + */ +var ToolLinkView = Backbone.View.extend({ + tagName: 'div', + template: Handlebars.templates.tool_link, + initialize: function() { + this.model.on("change:hidden", this.update_visible, this); + }, + render: function() { + this.$el.append( this.template(this.model.toJSON()) ); + return this; + }, + update_visible: function() { + ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); + } +}); + +/** + * Panel label/section header. + */ +var ToolPanelLabelView = Backbone.View.extend({ + tagName: 'div', + className: 'toolPanelLabel', + template: Handlebars.templates.panel_label, + initialize: function() { + this.model.on("change:hidden", this.update_visible, this); + }, + render: function() { + this.$el.append( this.template(this.model.toJSON()) ); + return this; + }, + update_visible: function() { + ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); + } +}); + +/** + * Panel section. + */ +var ToolPanelSectionView = Backbone.View.extend({ + tagName: 'div', + className: 'toolSectionWrapper', + template: Handlebars.templates.panel_section, + initialize: function() { + this.model.on("change:hidden", this.update_visible, this); + this.model.on("change:open", this.update_open, this); + }, + render: function() { + // Build using template. + this.$el.append( this.template(this.model.toJSON()) ); + + // Add tools to section. + var section_body = this.$el.find(".toolSectionBody"); + _.each(this.model.attributes.elems, function(elt) { + if (elt instanceof Tool) { + var tool_view = new ToolLinkView({model: elt, className: "toolTitle"}); + tool_view.render(); + section_body.append(tool_view.$el); + } + else if (elt instanceof ToolPanelLabel) { + var label_view = new ToolPanelLabelView({model: elt}); + label_view.render(); + section_body.append(label_view.$el); + } + else { + // TODO: handle nested section bodies? + } + }); + return this; + }, + + events: { + 'click .toolSectionTitle > a': 'toggle' + }, + + /** + * Toggle visibility of tool section. + */ + toggle: function() { + this.$el.children(".toolSectionBody").toggle("fast"); + this.model.set("open", !this.model.attributes.open); + }, + + /** + * Update whether section is open or close. + */ + update_open: function() { + (this.model.attributes.open ? + this.$el.children(".toolSectionBody").show("fast") : + this.$el.children(".toolSectionBody").hide("fast") + ); + }, + + /** + * Update section and section elements visibility after search. + */ + update_visible: function() { + ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); + } +}); + +var ToolSearchView = Backbone.View.extend({ + tagName: 'div', + id: 'tool-search', + className: 'bar', + template: Handlebars.templates.tool_search, + + events: { + 'click': 'focus_and_select', + 'keyup :input': 'query_changed' + }, + + render: function() { + this.$el.append( this.template(this.model.toJSON()) ); + return this; + }, + + focus_and_select: function() { + this.$el.find(":input").focus().select(); + }, + + query_changed: function() { + this.model.set("query", this.$el.find(":input").val()); + } +}); + +var ToolPanelView = Backbone.View.extend({ + tagName: 'div', + className: 'toolMenu', + + /** + * Waits for collection to load and then renders. + */ + initialize: function(options) { + this.collection.tool_search.on("change:results", this.handle_search_results, this); + + var self = this; + // Wait for collection to load before rendering. + this.collection.bind("reset", function() { self.render(); }); + }, + + render: function() { + var this_el = this.$el; + + // Render search. + var search_view = new ToolSearchView( {model: this.collection.tool_search} ); + search_view.render(); + this_el.append(search_view.$el); + + // Render panel. + this.collection.each(function(panel_elt) { + if (panel_elt instanceof ToolPanelSection) { + var section_title_view = new ToolPanelSectionView({model: panel_elt}); + section_title_view.render(); + this_el.append(section_title_view.$el); + } + else if (panel_elt instanceof Tool) { + var tool_view = new ToolLinkView({model: elt, className: "toolTitleNoSection"}); + tool_view.render(); + this_el.append(tool_view.$el); + } + }); + return this; + }, + + handle_search_results: function() { + var results = this.collection.tool_search.attributes.results; + if (results && results.length === 0) { + $("#search-no-results").show(); + } + else { + $("#search-no-results").hide(); + } + } +}); diff -r 657c1295db78085a845ecf68075008710eba5ed5 -r 833332b039fb6f00fb148ddbae03721783216347 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -623,7 +623,6 @@ if (initValue) { var search_input = tool_menu_frame.find("#tool-search-query"); search_input.val("search tools"); - search_input.css("font-style", "italic"); } } diff -r 657c1295db78085a845ecf68075008710eba5ed5 -r 833332b039fb6f00fb148ddbae03721783216347 static/scripts/handlebars/compile_templates.py --- a/static/scripts/handlebars/compile_templates.py +++ b/static/scripts/handlebars/compile_templates.py @@ -22,6 +22,5 @@ for fname in to_pack: fname_base = path.splitext( path.split( fname )[1] )[0] - print fname_base print "%s --> compiled/%s.js" % ( fname, fname_base ) out = call( cmd % ( fname, fname_base ), shell=True ) diff -r 657c1295db78085a845ecf68075008710eba5ed5 -r 833332b039fb6f00fb148ddbae03721783216347 static/scripts/handlebars/compiled/tool_search.js --- /dev/null +++ b/static/scripts/handlebars/compiled/tool_search.js @@ -0,0 +1,15 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['tool_search'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; + + + buffer += "<input type=\"text\" name=\"query\" value=\"search tools\" id=\"tool-search-query\" autocomplete=\"off\" class=\"search-query parent-width\" />\n<img src=\""; + foundHelper = helpers.spinner_url; + stack1 = foundHelper || depth0.spinner_url; + if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } + else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "spinner_url", { hash: {} }); } + buffer += escapeExpression(stack1) + "\" id=\"search-spinner\" class=\"search-spinner\"/>\n"; + return buffer;}); +})(); \ No newline at end of file diff -r 657c1295db78085a845ecf68075008710eba5ed5 -r 833332b039fb6f00fb148ddbae03721783216347 static/scripts/handlebars/tool_search.handlebars --- /dev/null +++ b/static/scripts/handlebars/tool_search.handlebars @@ -0,0 +1,2 @@ +<input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> +<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> diff -r 657c1295db78085a845ecf68075008710eba5ed5 -r 833332b039fb6f00fb148ddbae03721783216347 templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -26,7 +26,7 @@ ##  - ${h.js( "jquery", "galaxy.base" )} + ${h.js( "jquery", "galaxy.base", "libs/underscore", "libs/backbone", "libs/handlebars.runtime" )} </%def> ## Additional metas can be defined by templates inheriting from this one. diff -r 657c1295db78085a845ecf68075008710eba5ed5 -r 833332b039fb6f00fb148ddbae03721783216347 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -1,36 +1,7 @@ -<%! - import re -%> +<%inherit file="/base.mako"/><%namespace file="/tagging_common.mako" import="render_tool_tagging_elements" /> -## Render a tool -<%def name="render_tool( tool, section )"> - %if not tool.hidden: - %if section: - <div class="toolTitle"> - %else: - <div class="toolTitleNoSection"> - %endif - <% - if not tool.tool_type.startswith( 'data_source' ): - link = h.url_for( controller='tool_runner', tool_id=tool.id ) - else: - link = h.url_for( tool.action, ** tool.get_static_param_values( t ) ) - %> - ## FIXME: This doesn't look right - ## %if "[[" in tool.description and "]]" in tool.description: - ## ${tool.description.replace( '[[', '<a href="link" target="galaxy_main">' % $tool.id ).replace( "]]", "</a>" ) - <% tool_id = re.sub( '[^a-z0-9_]', '_', tool.id.lower() ) %> - %if tool.name: - <a class="link-${tool_id} tool-link" href="${link}" target=${tool.target} minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${_(tool.name)}</a> ${tool.description} - %else: - <a class="link-${tool_id} tool-link" href="${link}" target=${tool.target} minsizehint="${tool.uihints.get( 'minwidth', -1 )}">${tool.description}</a> - %endif - </div> - %endif -</%def> - ## Render a workflow <%def name="render_workflow( key, workflow, section )"> %if section: @@ -43,385 +14,109 @@ </div></%def> -## Render a label -<%def name="render_label( label )"> - <div class="toolPanelLabel" id="title_${label.id}"> - <span>${label.text}</span> - </div> +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.handlebars( "tool_link", "panel_label", "panel_section", "tool_search" )} + ${h.js( "galaxy.base", "json2", "autocomplete_tagging", "backbone/tools" )} + + <% + show_tool_search = "true" + if trans.user and trans.user.preferences.get( "show_tool_search", "False" ) == "False": + show_tool_search = "false" + %> + + <script type="text/javascript"> + // Init. on document load. + var tool_panel, tool_panel_view, tool_search; + $(function() { + // Set up search. + tool_search = new ToolSearch( {spinner_url: "${h.url_for('/static/images/loading_small_white_bg.gif')}", + search_url: "${h.url_for( controller='root', action='tool_search' )}", + visible: ${show_tool_search} } ); + + // Set up tool panel. + tool_panel = new ToolPanel( { tool_search: tool_search } ); + tool_panel.fetch(); + + + // Set up tool panel view and initialize. + tool_panel_view = new ToolPanelView( {collection: tool_panel} ); + $('body').prepend(tool_panel_view.$el); + + // Minsize init hint. + $( "a[minsizehint]" ).click( function() { + if ( parent.handle_minwidth_hint ) { + parent.handle_minwidth_hint( $(this).attr( "minsizehint" ) ); + } + }); + + // Log clicks on tools. + /* + $("div.toolTitle > a").click( function() { + var tool_title = $(this).attr('id').split("-")[1]; + var section_title = $.trim( $(this).parents("div.toolSectionWrapper").find("div.toolSectionTitle").text() ); + var search_active = $(this).parents("div.toolTitle").hasClass("search_match"); + + // Log action. + galaxy_async.log_user_action("tool_menu_click." + tool_title, section_title, + JSON.stringify({"search_active" : search_active})); + }); + */ + + // TODO: is this necessary? + $( "a[minsizehint]" ).click( function() { + if ( parent.handle_minwidth_hint ) { + parent.handle_minwidth_hint( $(this).attr( "minsizehint" ) ); + } + }); + }); + </script></%def> -<!DOCTYPE HTML> -<html> - <head> - <title>${_('Galaxy Tools')}</title> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> - <link href="${h.url_for('/static/style/tool_menu.css')}" rel="stylesheet" type="text/css" /> - <link href="${h.url_for('/static/style/autocomplete_tagging.css')}" rel="stylesheet" type="text/css" /> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css("tool_menu")} +</%def> - ${h.js( "jquery", "galaxy.base", "json2", "autocomplete_tagging" )} - <script type="text/javascript"> - // Set up GalaxyAsync object. - var galaxy_async = new GalaxyAsync(${str(trans.app.config.log_actions).lower()}); - galaxy_async.set_func_url(galaxy_async.log_user_action, "${h.url_for( controller='user', action='log_user_action_async' )}"); +<%def name="title()"> + ${_('Galaxy Tools')} +</%def> + +## Default body +<body class="toolMenuPage"> + + <div class="toolMenu"> + ## Feedback when search returns no results. + <div id="search-no-results" style="display: none; padding-top: 5px"> + <em><strong>Search did not match any tools.</strong></em> + </div> - $(document).ready(function() { - // Init showing/hiding of tool sections. - $( "div.toolSectionBody" ).hide(); - $( "div.toolSectionTitle > span" ).wrap( "<a href='#'></a>" ) - var last_expanded = null; - $( "div.toolSectionTitle" ).each( function() { - var body = $(this).next( "div.toolSectionBody" ); - $(this).click( function() { - if ( body.is( ":hidden" ) ) { - if ( last_expanded ) { - last_expanded.slideUp( "fast" ); - } - last_expanded = body; - body.slideDown( "fast" ); - } else { - body.slideUp( "fast" ); - last_expanded = null; - } - return false; - }); - }); - - // Log clicks on tools. - $("div.toolTitle > a").click( function() { - var tool_title = $(this).attr('id').split("-")[1]; - var section_title = $.trim( $(this).parents("div.toolSectionWrapper").find("div.toolSectionTitle").text() ); - var search_active = $(this).parents("div.toolTitle").hasClass("search_match"); - - // Log action. - galaxy_async.log_user_action("tool_menu_click." + tool_title, section_title, - JSON.stringify({"search_active" : search_active})); - }); - - $( "a[minsizehint]" ).click( function() { - if ( parent.handle_minwidth_hint ) { - parent.handle_minwidth_hint( $(this).attr( "minsizehint" ) ); - } - }); - - // Init searching. - $("#tool-search-query").click( function () { - $(this).focus(); - $(this).select(); - }).keyup( function () { - // Remove italics. - $(this).css("font-style", "normal"); - - // Don't search if the search value is < 3 chars, but clear the search if there was a previous query - if ( this.value.length < 3 && this.lastValue && this.lastValue.length >= 3 ) { - reset_tool_search(false); - // Re-apply tags - if ( current_tags.length > 0 ) { - $.get("${h.url_for( controller='root', action='tool_search' )}", { query: "", tags: current_tags }, function (data) { - apply_search_results(data); - }, "json" ); - } - // Don't update if same value as last time - } else if ( this.value !== this.lastValue ) { - // Add class to denote that searching is active. - $(this).addClass("search_active"); - // input.addClass(config.loadingClass); - // Add '*' to facilitate partial matching. - var q = this.value + '*'; - // Stop previous ajax-request - if (this.timer) { - clearTimeout(this.timer); - } - // Start a new ajax-request in X ms - $("#search-spinner").show(); - this.timer = setTimeout(function () { - $.get("${h.url_for( controller='root', action='tool_search' )}", { query: q, tags: current_tags }, function (data) { - apply_search_results(data); - $("#search-spinner").hide(); - }, "json" ); - }, 200 ); - } - this.lastValue = this.value; - }); - - // Apply stored tags - %if trans.user and trans.user.preferences.get( 'selected_tool_tags', '' ): - current_tags = "${trans.user.preferences['selected_tool_tags']}".split(",") - $.get("${h.url_for( controller='root', action='tool_search' )}", { query: "", tags: current_tags }, function (data) { - apply_search_results(data); - }, "json" ); - $("span.tag-name").each( function() { - for ( var i in current_tags ) { - if ( $(this).text() == current_tags[i] ) { - $(this).addClass("active-tag-name"); - $(this).append("<img class='delete-tag-img' src='${h.url_for('/static/images/delete_tag_icon_gray.png')}'/>") - } - } - }); - %endif - }); - - var apply_search_results = function (data) { - // input.removeClass(config.loadingClass); - // Show live-search if results and search-term aren't empty - $("#search-no-results").hide(); - // Hide all tool sections. - $(".toolSectionWrapper").hide(); - // This hides all tools but not workflows link (which is in a .toolTitle div). - $(".toolSectionWrapper").find(".toolTitle").hide(); - if ( data.length !== 0 ) { - // Map tool ids to element ids and join them. - var s = $.map( data, function( n, i ) { return ".link-" + n.toLowerCase().replace(/[^a-z0-9_]/g,'_'); } ).join( ", " ); - - // First pass to show matching tools and their parents. - $(s).each( function() { - // Add class to denote match. - $(this).parent().addClass("search_match"); - if ($(this).parents("#recently_used_wrapper").length === 0) { - // Default behavior. - $(this).parent().show().parent().parent().show().parent().show(); - } else if ($(this).parents(".user_pref_visible").length !== 0) { - // RU menu is visible, so filter it as normal. - $(this).parent().show().parent().parent().show().parent().show(); - } else { - // RU menu is not visible, so set up classes and visibility so that if menu shown matching is - // aleady in place. - $(this).parent().show(); - } - }); - - // Hide labels that have no visible children. - $(".toolPanelLabel").each( function() { - var this_label = $(this); - var next = this_label.next(); - var no_visible_tools = true; - // Look through tools following label and, if none are visible, hide label. - while (next.length !== 0 && next.hasClass("toolTitle")) { - if (next.is(":visible")) { - no_visible_tools = false; - break; - } else { - next = next.next(); - } - } - if (no_visible_tools) { - this_label.hide(); - } - }); - } else { - $("#search-no-results").show(); - } - } - - // Update recently used tools menu. Function inserts a new item and removes the last item. - function update_recently_used() { - $.ajax({ - url: "${h.url_for( controller='/user', action='get_most_recently_used_tool_async' )}", - dataType: 'json', - error: function() { - // console.log( "Failed to update recently used list." ); - }, - success: function(new_tool_info) { - var recently_used_elts = $("#recently_used").find(".toolTitle"); - var first_elt = $(recently_used_elts.first()); - var found_in_list = false; - - // Look for new tool in current list. If found, rearrange list to move tool to top. - var new_tool_info_id = new_tool_info.id.toLowerCase().replace(/[^a-z0-9_]/, "_") - recently_used_elts.each( function(index) { - var anchor = $(this).find("a"); - if (anchor.hasClass("link-" + new_tool_info_id)) { - found_in_list = true; - - // If tool is first, do nothing. - if (index === 0) { - return; - } else { - // Tool not first; reorder. - $(this).remove(); - first_elt.before($(this)); - } - } - }); - - // If tool not in list, create new element, remove last element, and put new element first in list. - if (!found_in_list) { - new_tool_elt = $("<div class='toolTitle'> \ - <a class='link-" + new_tool_info.id + "' href='" + new_tool_info.link + "' target='" + - new_tool_info.target + "' minsizehint='" + new_tool_info.minsizehint + "'>" + - new_tool_info.name + "</a> " + new_tool_info.description + " \ - </div>"); - recently_used_elts.last().remove(); - recently_used_elts.first().before(new_tool_elt); - } - } - }); - - } - - var current_tags = new Array(); - function tool_tag_click(tag_name, tag_value) { - var add = true; - for ( var i = 0 ; i < current_tags.length ; i++ ) { - if ( current_tags[i] == tag_name ) { - current_tags.splice( i, 1 ); - add = false; - } - } - if ( add ) { - current_tags.push( tag_name ); - $("span.tag-name").each( function() { - if ( $(this).text() == tag_name ) { - $(this).addClass("active-tag-name"); - $(this).append("<img class='delete-tag-img' src='${h.url_for('/static/images/delete_tag_icon_gray.png')}'/>") - } - }); - } else { - $("span.tag-name").each( function() { - if ( $(this).text() == tag_name ) { - $(this).removeClass("active-tag-name"); - $(this).text(tag_name); - } - }); - } - if ( current_tags.length == 0 ) { - $("#search-no-results").hide(); - $(".tool-link").each( function() { - reset_tool_search(false); - }); - return; - } - var q = $("input#tool-search-query").val(); - if ( q == "search tools" ) { - q = ""; - } else if ( q.length > 0 ) { - q = q + '*'; - } - $.get("${h.url_for( controller='root', action='tool_search' )}", { query: q, tags: current_tags }, function (data) { - apply_search_results(data); - }, "json" ); - } - - </script> - </head> - - <body class="toolMenuPage"> - <div class="toolMenu"> - - ## Tool search. - <% - show_tool_search = True - if trans.user: - show_tool_search = trans.user.preferences.get( "show_tool_search", "False" ) == "True" - - if show_tool_search: - display = "block" - else: - display = "none" - %> - <div id="tool-search" class="bar" style="padding-top: 5px; padding-bottom: 10px;position: relative; display: ${display};"> - %if trans.app.config.get_bool( 'enable_tool_tags', False ): - <b>Tags:</b> - ${render_tool_tagging_elements()} + ## Link to workflow management. The location of this may change, but eventually + ## at least some workflows will appear here (the user should be able to + ## configure which of their stored workflows appear in the tools menu). + + %if t.user: + <div class="toolSectionPad"></div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle" id="title_XXinternalXXworkflow"> + <span>Workflows</span> + </div> + <div id="XXinternalXXworkflow" class="toolSectionBody"> + <div class="toolSectionBg"> + %if t.user.stored_workflow_menu_entries: + %for m in t.user.stored_workflow_menu_entries: + <div class="toolTitle"> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${m.stored_workflow.name}</a> + </div> + %endfor %endif - <input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> - <img src="${h.url_for('/static/images/loading_small_white_bg.gif')}" id="search-spinner" class="search-spinner"/> + <div class="toolTitle"> + <a href="${h.url_for( controller='workflow', action='list_for_run')}" target="galaxy_main">All workflows</a> + </div></div> - - ## Recently used tools. - %if trans.user: - <% - if trans.user.preferences.get( 'show_recently_used_menu', 'False' ) == 'True': - display = "block" - pref_class = "user_pref_visible" - else: - display = "none" - pref_class = "user_pref_hidden" - %> - <div class="toolSectionWrapper ${pref_class}" id="recently_used_wrapper" - style="display: ${display}; padding-bottom: 5px"> - <div class="toolSectionTitle"> - <span>Recently Used</span> - </div> - <div id="recently_used" class="toolSectionBody"> - <div class="toolSectionBg"> - %for tool in recent_tools: - ${render_tool( tool, True )} - %endfor - </div> - </div> - <div class="toolSectionPad"></div> - </div> - %endif - - ## Tools. - %for key, val in toolbox.tool_panel.items(): - <div class="toolSectionWrapper"> - %if key.startswith( 'tool' ): - ${render_tool( val, False )} - %elif key.startswith( 'workflow' ): - ${render_workflow( key, val, False )} - %elif key.startswith( 'section' ): - <% section = val %> - ## Render the section only if it is not empty. - %if section.elems: - <div class="toolSectionTitle" id="title_${section.id}"> - <span>${section.name}</span> - </div> - <div id="${section.id}" class="toolSectionBody"> - <div class="toolSectionBg"> - %for section_key, section_val in section.elems.items(): - %if section_key.startswith( 'tool' ): - ${render_tool( section_val, True )} - %elif section_key.startswith( 'workflow' ): - ${render_workflow( section_key, section_val, True )} - %elif section_key.startswith( 'label' ): - ${render_label( section_val )} - %endif - %endfor - </div> - </div> - %endif - %elif key.startswith( 'label' ): - ${render_label( val )} - %endif - <div class="toolSectionPad"></div> - </div> - %endfor - - ## Feedback when search returns no results. - <div id="search-no-results" style="display: none; padding-top: 5px"> - <em><strong>Search did not match any tools.</strong></em> - </div> - - ## Link to workflow management. The location of this may change, but eventually - ## at least some workflows will appear here (the user should be able to - ## configure which of their stored workflows appear in the tools menu). - - %if t.user: - <div class="toolSectionPad"></div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle" id="title_XXinternalXXworkflow"> - <span>Workflows</span> - </div> - <div id="XXinternalXXworkflow" class="toolSectionBody"> - <div class="toolSectionBg"> - %if t.user.stored_workflow_menu_entries: - %for m in t.user.stored_workflow_menu_entries: - <div class="toolTitle"> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(m.stored_workflow_id) )}" target="galaxy_main">${m.stored_workflow.name}</a> - </div> - %endfor - %endif - <div class="toolTitle"> - <a href="${h.url_for( controller='workflow', action='list_for_run')}" target="galaxy_main">All workflows</a> - </div> - </div> - </div> - %endif - </div> - </div> - </body> -</html> + %endif + + </div> +</body> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/11649eacb329/ changeset: 11649eacb329 user: jgoecks date: 2012-04-02 00:19:34 summary: Merge affected #: 10 files diff -r 833332b039fb6f00fb148ddbae03721783216347 -r 11649eacb329e0f84e64d8c07d316c26182d8be1 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -193,18 +193,33 @@ # Store advanced job management config self.job_manager = kwargs.get('job_manager', self.server_name).strip() self.job_handlers = [ x.strip() for x in kwargs.get('job_handlers', self.server_name).split(',') ] + self.default_job_handlers = [ x.strip() for x in kwargs.get('default_job_handlers', ','.join( self.job_handlers ) ).split(',') ] # Use database for IPC unless this is a standalone server (or multiple servers doing self dispatching in memory) self.track_jobs_in_database = True if ( len( self.job_handlers ) == 1 ) and ( self.job_handlers[0] == self.server_name ) and ( self.job_manager == self.server_name ): self.track_jobs_in_database = False # Store per-tool runner configs + self.tool_handlers = self.__read_tool_job_config( global_conf_parser, 'galaxy:tool_handlers', 'name' ) + self.tool_runners = self.__read_tool_job_config( global_conf_parser, 'galaxy:tool_runners', 'url' ) + self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) + # Cloud configuration options + self.enable_cloud_launch = string_as_bool( kwargs.get( 'enable_cloud_launch', False ) ) + # Galaxy messaging (AMQP) configuration options + self.amqp = {} try: - tool_runners_config = global_conf_parser.items("galaxy:tool_runners") + amqp_config = global_conf_parser.items("galaxy_amqp") + except ConfigParser.NoSectionError: + amqp_config = {} + for k, v in amqp_config: + self.amqp[k] = v + def __read_tool_job_config( self, global_conf_parser, section, key ): + try: + tool_runners_config = global_conf_parser.items( section ) # Process config to group multiple configs for the same tool. - tool_runners = {} + rval = {} for entry in tool_runners_config: - tool_config, url = entry + tool_config, val = entry tool = None runner_dict = {} if tool_config.find("[") != -1: @@ -219,29 +234,18 @@ tool = tool_config # Add runner URL. - runner_dict[ 'url' ] = url + runner_dict[ key ] = val # Create tool entry if necessary. - if tool not in tool_runners: - tool_runners[ tool ] = [] + if tool not in rval: + rval[ tool ] = [] # Add entry to runners. - tool_runners[ tool ].append( runner_dict ) + rval[ tool ].append( runner_dict ) - self.tool_runners = tool_runners + return rval except ConfigParser.NoSectionError: - self.tool_runners = [] - self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) - # Cloud configuration options - self.enable_cloud_launch = string_as_bool( kwargs.get( 'enable_cloud_launch', False ) ) - # Galaxy messaging (AMQP) configuration options - self.amqp = {} - try: - amqp_config = global_conf_parser.items("galaxy_amqp") - except ConfigParser.NoSectionError: - amqp_config = {} - for k, v in amqp_config: - self.amqp[k] = v + return [] def get( self, key, default ): return self.config_dict.get( key, default ) def get_bool( self, key, default ): diff -r 833332b039fb6f00fb148ddbae03721783216347 -r 11649eacb329e0f84e64d8c07d316c26182d8be1 lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -144,7 +144,7 @@ pass for job in jobs_to_check: - job.handler = self.__select_handler( job ) + job.handler = self.__get_handler( job ) log.debug( "(%s) Job assigned to handler '%s'" % ( job.id, job.handler ) ) self.sa_session.add( job ) @@ -157,9 +157,15 @@ for job in jobs_to_check: self.job_handler.job_queue.put( job.id, job.tool_id ) - def __select_handler( self, job ): - # TODO: handler selection based on params, tool, etc. - return random.choice( self.app.config.job_handlers ) + def __get_handler( self, job ): + try: + params = None + if job.params: + params = from_json_string( job.params ) + return self.app.toolbox.tools_by_id.get( job.tool_id, None ).get_job_handler( params ) + except: + log.exception( "(%s) Caught exception attempting to get tool-specific job handler for tool '%s', selecting at random from available handlers instead:" % ( job.id, job.tool_id ) ) + return random.choice( self.app.config.job_handlers ) def put( self, job_id, tool ): """Add a job to the queue (by job identifier)""" diff -r 833332b039fb6f00fb148ddbae03721783216347 -r 11649eacb329e0f84e64d8c07d316c26182d8be1 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -5,7 +5,7 @@ pkg_resources.require( "simplejson" ) -import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess +import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random import simplejson import binascii from UserDict import DictMixin @@ -115,17 +115,17 @@ tool_path = self.tool_root_dir # Only load the panel_dict under certain conditions. load_panel_dict = not self.integrated_tool_panel_config_has_contents - for elem in root: + for index, elem in enumerate( root ): if parsing_shed_tool_conf: config_elems.append( elem ) if elem.tag == 'tool': - self.load_tool_tag_set( elem, self.tool_panel, self.integrated_tool_panel, tool_path, load_panel_dict, guid=elem.get( 'guid' ) ) + self.load_tool_tag_set( elem, self.tool_panel, self.integrated_tool_panel, tool_path, load_panel_dict, guid=elem.get( 'guid' ), index=index ) elif elem.tag == 'workflow': - self.load_workflow_tag_set( elem, self.tool_panel, self.integrated_tool_panel, load_panel_dict ) + self.load_workflow_tag_set( elem, self.tool_panel, self.integrated_tool_panel, load_panel_dict, index=index ) elif elem.tag == 'section': - self.load_section_tag_set( elem, tool_path, load_panel_dict ) + self.load_section_tag_set( elem, tool_path, load_panel_dict, index=index ) elif elem.tag == 'label': - self.load_label_tag_set( elem, self.tool_panel, self.integrated_tool_panel, load_panel_dict ) + self.load_label_tag_set( elem, self.tool_panel, self.integrated_tool_panel, load_panel_dict, index=index ) if parsing_shed_tool_conf: shed_tool_conf_dict = dict( config_filename=config_filename, tool_path=tool_path, @@ -287,7 +287,7 @@ self.app.model.ToolShedRepository.table.c.owner == owner, self.app.model.ToolShedRepository.table.c.installed_changeset_revision == installed_changeset_revision ) ) \ .first() - def load_tool_tag_set( self, elem, panel_dict, integrated_panel_dict, tool_path, load_panel_dict, guid=None ): + def load_tool_tag_set( self, elem, panel_dict, integrated_panel_dict, tool_path, load_panel_dict, guid=None, index=None ): try: path = elem.get( "file" ) if guid is None: @@ -355,10 +355,13 @@ if load_panel_dict: panel_dict[ key ] = tool # Always load the tool into the integrated_panel_dict, or it will not be included in the integrated_tool_panel.xml file. - integrated_panel_dict[ key ] = tool + if key in integrated_panel_dict or index is None: + integrated_panel_dict[ key ] = tool + else: + integrated_panel_dict.insert( index, key, tool ) except: log.exception( "Error reading tool from path: %s" % path ) - def load_workflow_tag_set( self, elem, panel_dict, integrated_panel_dict, load_panel_dict ): + def load_workflow_tag_set( self, elem, panel_dict, integrated_panel_dict, load_panel_dict, index=None ): try: # TODO: should id be encoded? workflow_id = elem.get( 'id' ) @@ -368,16 +371,22 @@ if load_panel_dict: panel_dict[ key ] = workflow # Always load workflows into the integrated_panel_dict. - integrated_panel_dict[ key ] = workflow + if key in integrated_panel_dict or index is None: + integrated_panel_dict[ key ] = workflow + else: + integrated_panel_dict.insert( index, key, workflow ) except: log.exception( "Error loading workflow: %s" % workflow_id ) - def load_label_tag_set( self, elem, panel_dict, integrated_panel_dict, load_panel_dict ): + def load_label_tag_set( self, elem, panel_dict, integrated_panel_dict, load_panel_dict, index=None ): label = ToolSectionLabel( elem ) key = 'label_' + label.id if load_panel_dict: panel_dict[ key ] = label - integrated_panel_dict[ key ] = label - def load_section_tag_set( self, elem, tool_path, load_panel_dict ): + if key in integrated_panel_dict or index is None: + integrated_panel_dict[ key ] = label + else: + integrated_panel_dict.insert( index, key, label ) + def load_section_tag_set( self, elem, tool_path, load_panel_dict, index=None ): key = 'section_' + elem.get( "id" ) if key in self.tool_panel: section = self.tool_panel[ key ] @@ -391,17 +400,20 @@ else: integrated_section = ToolSection( elem ) integrated_elems = integrated_section.elems - for sub_elem in elem: + for sub_index, sub_elem in enumerate( elem ): if sub_elem.tag == 'tool': - self.load_tool_tag_set( sub_elem, elems, integrated_elems, tool_path, load_panel_dict, guid=sub_elem.get( 'guid' ) ) + self.load_tool_tag_set( sub_elem, elems, integrated_elems, tool_path, load_panel_dict, guid=sub_elem.get( 'guid' ), index=sub_index ) elif sub_elem.tag == 'workflow': - self.load_workflow_tag_set( sub_elem, elems, integrated_elems, load_panel_dict ) + self.load_workflow_tag_set( sub_elem, elems, integrated_elems, load_panel_dict, index=sub_index ) elif sub_elem.tag == 'label': - self.load_label_tag_set( sub_elem, elems, integrated_elems, load_panel_dict ) + self.load_label_tag_set( sub_elem, elems, integrated_elems, load_panel_dict, index=sub_index ) if load_panel_dict: self.tool_panel[ key ] = section # Always load sections into the integrated_tool_panel. - self.integrated_tool_panel[ key ] = integrated_section + if key in self.integrated_tool_panel or index is None: + self.integrated_tool_panel[ key ] = integrated_section + else: + self.integrated_tool_panel.insert( index, key, integrated_section ) def load_tool( self, config_file, guid=None ): """Load a single tool from the file named by `config_file` and return an instance of `Tool`.""" # Parse XML configuration file and get the root element @@ -683,31 +695,35 @@ if tool_version: return tool_version.get_version_ids( self.app ) return [] - def get_job_runner( self, job_params=None ): - # Look through runners to find one with matching parameters. - selected_runner = None - if len( self.job_runners ) == 1: - # Most tools have a single runner. - selected_runner = self.job_runners[0] + def __get_job_run_config( self, run_configs, key, job_params=None ): + # Look through runners/handlers to find one with matching parameters. + available_configs = [] + if len( run_configs ) == 1: + # Most tools have a single config. + return run_configs[0][ key ] # return to avoid random when this will be the case most of the time elif job_params is None: - # Use job runner with no params - for runner in self.job_runners: - if "params" not in runner: - selected_runner = runner + # Use job config with no params + for config in run_configs: + if "params" not in config: + available_configs.append( config ) else: - # Find runner with matching parameters. - for runner in self.job_runners: - if "params" in runner: + # Find config with matching parameters. + for config in run_configs: + if "params" in config: match = True - runner_params = runner[ "params" ] + config_params = config[ "params" ] for param, value in job_params.items(): - if param not in runner_params or \ - runner_params[ param ] != job_params[ param ]: + if param not in config_params or \ + config_params[ param ] != job_params[ param ]: match = False break if match: - selected_runner = runner - return selected_runner[ "url" ] + available_configs.append( config ) + return random.choice( available_configs )[ key ] + def get_job_runner( self, job_params=None ): + return self.__get_job_run_config( self.job_runners, key='url', job_params=job_params ) + def get_job_handler( self, job_params=None ): + return self.__get_job_run_config( self.job_handlers, key='name', job_params=job_params ) def parse( self, root, guid=None ): """ Read tool configuration from the element `root` and fill in `self`. @@ -774,6 +790,12 @@ self.parallelism = ToolParallelismInfo(parallelism) else: self.parallelism = None + # Set job handler(s). Each handler is a dict with 'url' and, optionally, 'params'. + self_id = self.id.lower() + self.job_handlers = [ { "name" : name } for name in self.app.config.default_job_handlers ] + # Set custom handler(s) if they're defined. + if self_id in self.app.config.tool_handlers: + self.job_handlers = self.app.config.tool_handlers[ self_id ] # Set job runner(s). Each runner is a dict with 'url' and, optionally, 'params'. if self.app.config.start_job_runners is None: # Jobs are always local regardless of tool config if no additional @@ -783,7 +805,6 @@ # Set job runner to the cluster default self.job_runners = [ { "url" : self.app.config.default_cluster_job_runner } ] # Set custom runner(s) if they're defined. - self_id = self.id.lower() if self_id in self.app.config.tool_runners: self.job_runners = self.app.config.tool_runners[ self_id ] # Is this a 'hidden' tool (hidden in tool menu) diff -r 833332b039fb6f00fb148ddbae03721783216347 -r 11649eacb329e0f84e64d8c07d316c26182d8be1 lib/galaxy/util/odict.py --- a/lib/galaxy/util/odict.py +++ b/lib/galaxy/util/odict.py @@ -11,23 +11,22 @@ This dictionary class extends UserDict to record the order in which items are added. Calling keys(), values(), items(), etc. will return results in this order. + """ + def __init__( self, dict = None ): + self._keys = [] + UserDict.__init__( self, dict ) - I've added iterkeys, itervalues, iteritems - """ - def __init__(self, dict = None): - self._keys = [] - UserDict.__init__(self, dict) + def __delitem__( self, key ): + UserDict.__delitem__( self, key ) + self._keys.remove( key ) - def __delitem__(self, key): - UserDict.__delitem__(self, key) - self._keys.remove(key) + def __setitem__( self, key, item ): + UserDict.__setitem__( self, key, item ) + if key not in self._keys: + self._keys.append( key ) - def __setitem__(self, key, item): - UserDict.__setitem__(self, key, item) - if key not in self._keys: self._keys.append(key) - - def clear(self): - UserDict.clear(self) + def clear( self ): + UserDict.clear( self ) self._keys = [] def copy(self): @@ -35,49 +34,43 @@ new.update( self ) return new - def items(self): - return zip(self._keys, self.values()) + def items( self ): + return zip( self._keys, self.values() ) - def keys(self): + def keys( self ): return self._keys[:] - def popitem(self): + def popitem( self ): try: key = self._keys[-1] except IndexError: - raise KeyError('dictionary is empty') + raise KeyError( 'dictionary is empty' ) + val = self[ key ] + del self[ key ] + return ( key, val ) - val = self[key] - del self[key] + def setdefault( self, key, failobj=None ): + if key not in self._keys: + self._keys.append( key ) + return UserDict.setdefault( self, key, failobj ) - return (key, val) + def update( self, dict ): + for ( key, val ) in dict.items(): + self.__setitem__( key, val ) - def setdefault(self, key, failobj = None): - if key not in self._keys: self._keys.append(key) - return UserDict.setdefault(self, key, failobj) + def values( self ): + return map( self.get, self._keys ) - def update(self, dict): - UserDict.update(self, dict) - for key in dict.keys(): - if key not in self._keys: self._keys.append(key) - - def update(self, dict): - for (key,val) in dict.items(): - self.__setitem__(key,val) - - def values(self): - return map(self.get, self._keys) - - def iterkeys(self): + def iterkeys( self ): return iter( self._keys ) - def itervalues(self): + def itervalues( self ): for key in self._keys: - yield self.get(key) + yield self.get( key ) - def iteritems(self): + def iteritems( self ): for key in self._keys: - yield key, self.get(key) + yield key, self.get( key ) def __iter__( self ): for key in self._keys: @@ -86,3 +79,7 @@ def reverse( self ): self._keys.reverse() + def insert( self, index, key, item ): + if key not in self._keys: + self._keys.insert( index, key ) + UserDict.__setitem__( self, key, item ) diff -r 833332b039fb6f00fb148ddbae03721783216347 -r 11649eacb329e0f84e64d8c07d316c26182d8be1 lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -84,6 +84,11 @@ self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False self.cloud_controller_instance = False + self.server_name = '' + self.job_manager = '' + self.job_handlers = [] + self.tool_handlers = [] + self.tool_runners = [] # Proxy features self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) diff -r 833332b039fb6f00fb148ddbae03721783216347 -r 11649eacb329e0f84e64d8c07d316c26182d8be1 run_functional_tests.sh --- a/run_functional_tests.sh +++ b/run_functional_tests.sh @@ -20,23 +20,23 @@ echo "===========================================================================================================================================" echo "'run_functional_tests.sh -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)" echo "'run_functional_tests.sh -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')" -elif [ $1 = '--migrated' ]; then +elif [ $1 = '-migrated' ]; then if [ ! $2 ]; then - python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html --migrated + python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html -migrated elif [ $2 = '-id' ]; then # TODO: This option is not tested... - python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$3 --with-nosehtml --html-report-file run_functional_tests.html --migrated + python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$3 --with-nosehtml --html-report-file run_functional_tests.html -migrated else - python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html --migrated + python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html -migrated fi -elif [ $1 = '--installed' ]; then +elif [ $1 = '-installed' ]; then if [ ! $2 ]; then - python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html --installed + python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html -installed elif [ $2 = '-id' ]; then # TODO: This option is not tested... - python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$3 --with-nosehtml --html-report-file run_functional_tests.html --installed + python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$3 --with-nosehtml --html-report-file run_functional_tests.html -installed else - python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html --installed + python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html -installed fi else python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_functional_tests.html $1 diff -r 833332b039fb6f00fb148ddbae03721783216347 -r 11649eacb329e0f84e64d8c07d316c26182d8be1 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -135,8 +135,8 @@ tool_path = os.environ.get( 'GALAXY_TEST_TOOL_PATH', 'tools' ) if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: os.environ[ 'HTTP_ACCEPT_LANGUAGE' ] = default_galaxy_locales - testing_migrated_tools = '--migrated' in sys.argv - testing_installed_tools = '--installed' in sys.argv + testing_migrated_tools = '-migrated' in sys.argv + testing_installed_tools = '-installed' in sys.argv if testing_migrated_tools or testing_installed_tools: sys.argv.pop() diff -r 833332b039fb6f00fb148ddbae03721783216347 -r 11649eacb329e0f84e64d8c07d316c26182d8be1 scripts/galaxy_messaging/server/data_transfer.py --- a/scripts/galaxy_messaging/server/data_transfer.py +++ b/scripts/galaxy_messaging/server/data_transfer.py @@ -177,7 +177,7 @@ self.update_status( SampleDataset.transfer_status.ADD_TO_LIBRARY ) try: data = {} - data[ 'folder_id' ] = api.encode_id( self.config_id_secret, '%s.%s' % ( 'folder', self.folder_id ) ) + data[ 'folder_id' ] = 'F%s' % api.encode_id( self.config_id_secret, self.folder_id ) data[ 'file_type' ] = 'auto' data[ 'server_dir' ] = self.server_dir data[ 'dbkey' ] = '' diff -r 833332b039fb6f00fb148ddbae03721783216347 -r 11649eacb329e0f84e64d8c07d316c26182d8be1 tools/genomespace/genomespace_exporter.py --- a/tools/genomespace/genomespace_exporter.py +++ b/tools/genomespace/genomespace_exporter.py @@ -49,7 +49,8 @@ def get_directory( url_opener, dm_url, path ): url = dm_url - for sub_path in path: + i = None + for i, sub_path in enumerate( path ): url = "%s/%s" % ( url, sub_path ) dir_request = urllib2.Request( url, headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' } ) dir_request.get_method = lambda: 'GET' @@ -59,10 +60,14 @@ #print "e", e, url #punting, assuming lack of permisions at this low of a level... continue break - return dir_dict + if i is not None: + path = path[i+1:] + else: + path = [] + return ( dir_dict, path ) def get_default_directory( url_opener, dm_url ): - return get_directory( url_opener, dm_url, ["defaultdirectory"] ) + return get_directory( url_opener, dm_url, ["defaultdirectory"] )[0] def create_directory( url_opener, directory_dict, new_dir, dm_url ): payload = { "isDirectory": True } @@ -142,8 +147,8 @@ dm_url = genomespace_site_dict['dmServer'] #get default directory if target_directory and target_directory[0] == '/': - directory_dict = get_directory( url_opener, dm_url, [ "%s/%s/%s" % ( GENOMESPACE_API_VERSION_STRING, 'file', target_directory[1] ) ] + target_directory[2:] )['directory'] - target_directory.pop(0) + directory_dict, target_directory = get_directory( url_opener, dm_url, [ "%s/%s/%s" % ( GENOMESPACE_API_VERSION_STRING, 'file', target_directory[1] ) ] + target_directory[2:] ) + directory_dict = directory_dict['directory'] else: directory_dict = get_default_directory( url_opener, dm_url )['directory'] #what directory to stuff this in diff -r 833332b039fb6f00fb148ddbae03721783216347 -r 11649eacb329e0f84e64d8c07d316c26182d8be1 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -562,6 +562,13 @@ # comma-separated list. #job_handlers = main +# By default, a handler from job_handlers will be selected at random if the +# tool to run does specify a handler below in [galaxy:tool_handlers]. If you +# want certain handlers to only handle jobs for tools/params explicitly +# assigned below, use default_job_handlers to specify which handlers should be +# used for jobs without explicit handlers. +#default_job_handlers = main + # This enables splitting of jobs into tasks, if specified by the particular tool config. # This is a new feature and not recommended for production servers yet. #use_tasked_jobs = False @@ -664,18 +671,30 @@ #pbs_stage_path = #pbs_dataset_server = -# ---- Tool Job Runners ----------------------------------------------------- +# ---- Per-Tool Job Management ---------------------------------------------- -# Individual per-tool job runner overrides. Parameters can be included to define -# multiple runners per tool. E.g. to run Cufflinks jobs initiated from Trackster +# Per-tool job handler and runner overrides. Parameters can be included to define multiple +# runners per tool. E.g. to run Cufflinks jobs initiated from Trackster # differently than standard Cufflinks jobs: -# cufflinks = local:/// -# cufflinks[source@trackster] = local:/// -# If not listed here, a tool will run with the runner defined with -# default_cluster_job_runner. +# +# cufflinks = local:/// +# cufflinks[source@trackster] = local:/// + +[galaxy:tool_handlers] + +# By default, Galaxy will select a handler at random from the list of +# job_handlers set above. You can override as in the following examples: +# +#upload1 = upload_handler +#cufflinks[source@trackster] = realtime_handler [galaxy:tool_runners] +# If not listed here, a tool will run with the runner defined with +# default_cluster_job_runner. These overrides for local:/// are done because +# these tools can fetch data from remote sites, which may not be suitable to +# run on a cluster (if it does not have access to the Internet, for example). + biomart = local:/// encode_db1 = local:/// hbvar = local:/// https://bitbucket.org/galaxy/galaxy-central/changeset/24501c5f17a6/ changeset: 24501c5f17a6 user: jgoecks date: 2012-04-02 16:19:10 summary: Modify pack_scripts.py to (a) pack entire directory trees and (b) only pack if necessary. Add packed versions of many scripts. affected #: 12 files diff -r 11649eacb329e0f84e64d8c07d316c26182d8be1 -r 24501c5f17a6310f39f5e3a5d55f8a00d7a67213 static/scripts/pack_scripts.py --- a/static/scripts/pack_scripts.py +++ b/static/scripts/pack_scripts.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -import sys +import sys, os from glob import glob from subprocess import call @@ -16,16 +16,52 @@ # If specific scripts specified on command line, just pack them, otherwise pack # all. +def recursive_glob( pattern, excluded_dirs ): + """ + Returns all items that match pattern in root and subdirectories. + """ + + a_dir, a_pattern = path.split( pattern ) + + # Skip excluded dirs. + if a_dir in excluded_dirs: + return [] + + # Search current dir. + # print a_dir, a_pattern + rval = glob( pattern ) + for item in glob( path.join( a_dir, "*" ) ): + if path.isdir( item ): + rval.extend( recursive_glob( path.join( item, a_pattern ), excluded_dirs ) ) + + return rval + +# Get files to pack. if len( sys.argv ) > 1: to_pack = sys.argv[1:] else: - to_pack = glob( "*.js" ) - to_pack.extend( glob( "libs/*.js" ) ) + to_pack = recursive_glob( "*.js", [ "packed" ] ) + for fname in to_pack: d = dict( fname=fname ) + packed_fname = path.join( 'packed', fname ) + + # Only copy if full version is newer than packed version. + if path.exists( packed_fname ) and ( path.getmtime( fname ) < path.getmtime( packed_fname ) ): + print "Packed is current: %s" % fname + continue + print "%(fname)s --> packed/%(fname)s" % d + + # Create destination dir if necessary. + dir, name = os.path.split( packed_fname ) + if not path.exists( dir ): + print "Creating needed directory %s" % dir + os.makedirs( dir ) + + # Copy/pack. if fname in do_not_pack: - copyfile( fname, path.join( 'packed', fname ) ) + copyfile( fname, path.join( packed_fname ) ) else: out = call( cmd % d, shell=True ) diff -r 11649eacb329e0f84e64d8c07d316c26182d8be1 -r 24501c5f17a6310f39f5e3a5d55f8a00d7a67213 static/scripts/packed/backbone/tools.js --- /dev/null +++ b/static/scripts/packed/backbone/tools.js @@ -0,0 +1,1 @@ +var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=Backbone.Model.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var ToolLinkView=Backbone.View.extend({tagName:"div",template:Handlebars.templates.tool_link,initialize:function(){this.model.on("change:hidden",this.update_visible,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolPanelLabelView=Backbone.View.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,initialize:function(){this.model.on("change:hidden",this.update_visible,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolPanelSectionView=Backbone.View.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.$el.children(".toolSectionBody").toggle("fast");this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").show("fast"):this.$el.children(".toolSectionBody").hide("fast"))},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(b){this.collection.tool_search.on("change:results",this.handle_search_results,this);var a=this;this.collection.bind("reset",function(){a.render()})},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:elt,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file diff -r 11649eacb329e0f84e64d8c07d316c26182d8be1 -r 24501c5f17a6310f39f5e3a5d55f8a00d7a67213 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul class='dropdown-menu' id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No Options.</li>").appendTo(g)}$.each(f,function(j,i){if(i){g.append($("<li></li>").append($("<a 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GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var 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11649eacb329e0f84e64d8c07d316c26182d8be1 -r 24501c5f17a6310f39f5e3a5d55f8a00d7a67213 static/scripts/packed/handlebars/compiled/panel_label.js --- /dev/null +++ b/static/scripts/packed/handlebars/compiled/panel_label.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.panel_label=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+="<span>";h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+"</span>";return i})})(); \ No newline at end of file diff -r 11649eacb329e0f84e64d8c07d316c26182d8be1 -r 24501c5f17a6310f39f5e3a5d55f8a00d7a67213 static/scripts/packed/handlebars/compiled/panel_section.js --- /dev/null +++ b/static/scripts/packed/handlebars/compiled/panel_section.js @@ -0,0 +1,1 @@ +(function(){var 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b/static/scripts/packed/handlebars/compiled/tool_link.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_link=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<a class="';h=d.id;c=h||n.id;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"id",{hash:{}})}}i+=j(c)+' tool-link" href="';h=d.link;c=h||n.link;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"link",{hash:{}})}}i+=j(c)+'" target="';h=d.target;c=h||n.target;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"target",{hash:{}})}}i+=j(c)+'" minsizehint="';h=d.min_width;c=h||n.min_width;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"min_width",{hash:{}})}}i+=j(c)+'">';h=d.name;c=h||n.name;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"name",{hash:{}})}}i+=j(c)+"</a> ";h=d.description;c=h||n.description;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"description",{hash:{}})}}i+=j(c);return i})})(); \ No newline at end of file diff -r 11649eacb329e0f84e64d8c07d316c26182d8be1 -r 24501c5f17a6310f39f5e3a5d55f8a00d7a67213 static/scripts/packed/handlebars/compiled/tool_search.js --- /dev/null +++ b/static/scripts/packed/handlebars/compiled/tool_search.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a.tool_search=b(function(e,n,d,l,k){d=d||e.helpers;var i="",c,h,o=this,f="function",m=d.helperMissing,g=void 0,j=this.escapeExpression;i+='<input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query parent-width" />\n<img src="';h=d.spinner_url;c=h||n.spinner_url;if(typeof c===f){c=c.call(n,{hash:{}})}else{if(c===g){c=m.call(n,"spinner_url",{hash:{}})}}i+=j(c)+'" id="search-spinner" class="search-spinner"/>\n';return i})})(); \ No newline at end of file diff -r 11649eacb329e0f84e64d8c07d316c26182d8be1 -r 24501c5f17a6310f39f5e3a5d55f8a00d7a67213 static/scripts/packed/libs/handlebars-1.0.0.beta.6.js --- a/static/scripts/packed/libs/handlebars-1.0.0.beta.6.js +++ /dev/null @@ -1,1 +0,0 @@ -var Handlebars={};Handlebars.VERSION="1.0.beta.6";Handlebars.helpers={};Handlebars.partials={};Handlebars.registerHelper=function(b,c,a){if(a){c.not=a}this.helpers[b]=c};Handlebars.registerPartial=function(a,b){this.partials[a]=b};Handlebars.registerHelper("helperMissing",function(a){if(arguments.length===2){return undefined}else{throw new Error("Could not find property '"+a+"'")}});var toString=Object.prototype.toString,functionType="[object Function]";Handlebars.registerHelper("blockHelperMissing",function(f,d){var a=d.inverse||function(){},h=d.fn;var c="";var g=toString.call(f);if(g===functionType){f=f.call(this)}if(f===true){return h(this)}else{if(f===false||f==null){return a(this)}else{if(g==="[object Array]"){if(f.length>0){for(var 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q=0;q<s.length;q++){p=this._input.match(this.rules[s[q]]);if(p){n=p[0].match(/\n.*/g);if(n){this.yylineno+=n.length}this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:n?n[n.length-1].length-1:this.yylloc.last_column+p[0].length};this.yytext+=p[0];this.match+=p[0];this.matches=p;this.yyleng=this.yytext.length;this._more=false;this._input=this._input.slice(p[0].length);this.matched+=p[0];r=this.performAction.call(this,this.yy,this,s[q],this.conditionStack[this.conditionStack.length-1]);if(r){return r}else{return}}}if(this._input===""){return this.EOF}else{this.parseError("Lexical error on line "+(this.yylineno+1)+". Unrecognized text.\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})}},lex:function g(){var n=this.next();if(typeof n!=="undefined"){return n}else{return this.lex()}},begin:function h(n){this.conditionStack.push(n)},popState:function m(){return this.conditionStack.pop()},_currentRules:function k(){return this.conditions[this.conditionStack[this.conditionStack.length-1]].rules},topState:function(){return this.conditionStack[this.conditionStack.length-2]},pushState:function h(n){this.begin(n)}});j.performAction=function i(r,o,q,n){var p=n;switch(q){case 0:if(o.yytext.slice(-1)!=="\\"){this.begin("mu")}if(o.yytext.slice(-1)==="\\"){o.yytext=o.yytext.substr(0,o.yyleng-1),this.begin("emu")}if(o.yytext){return 14}break;case 1:return 14;break;case 2:this.popState();return 14;break;case 3:return 24;break;case 4:return 16;break;case 5:return 20;break;case 6:return 19;break;case 7:return 19;break;case 8:return 23;break;case 9:return 23;break;case 10:o.yytext=o.yytext.substr(3,o.yyleng-5);this.popState();return 15;break;case 11:return 22;break;case 12:return 34;break;case 13:return 33;break;case 14:return 33;break;case 15:return 36;break;case 16:break;case 17:this.popState();return 18;break;case 18:this.popState();return 18;break;case 19:o.yytext=o.yytext.substr(1,o.yyleng-2).replace(/\\"/g,'"');return 28;break;case 20:return 30;break;case 21:return 30;break;case 22:return 29;break;case 23:return 33;break;case 24:o.yytext=o.yytext.substr(1,o.yyleng-2);return 33;break;case 25:return"INVALID";break;case 26:return 5;break}};j.rules=[/^[^\x00]*?(?=(\{\{))/,/^[^\x00]+/,/^[^\x00]{2,}?(?=(\{\{))/,/^\{\{>/,/^\{\{#/,/^\{\{\//,/^\{\{\^/,/^\{\{\s*else\b/,/^\{\{\{/,/^\{\{&/,/^\{\{![\s\S]*?\}\}/,/^\{\{/,/^=/,/^\.(?=[} ])/,/^\.\./,/^[\/.]/,/^\s+/,/^\}\}\}/,/^\}\}/,/^"(\\["]|[^"])*"/,/^true(?=[}\s])/,/^false(?=[}\s])/,/^[0-9]+(?=[}\s])/,/^[a-zA-Z0-9_$-]+(?=[=}\s\/.])/,/^\[[^\]]*\]/,/^./,/^$/];j.conditions={mu:{rules:[3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26],inclusive:false},emu:{rules:[2],inclusive:false},INITIAL:{rules:[0,1,26],inclusive:true}};return j})();f.lexer=a;return f})();if(typeof require!=="undefined"&&typeof exports!=="undefined"){exports.parser=handlebars;exports.parse=function(){return handlebars.parse.apply(handlebars,arguments)};exports.main=function commonjsMain(a){if(!a[1]){throw new Error("Usage: "+a[0]+" FILE")}if(typeof process!=="undefined"){var c=require("fs").readFileSync(require("path").join(process.cwd(),a[1]),"utf8")}else{var b=require("file").path(require("file").cwd());var c=b.join(a[1]).read({charset:"utf-8"})}return exports.parser.parse(c)};if(typeof module!=="undefined"&&require.main===module){exports.main(typeof process!=="undefined"?process.argv.slice(1):require("system").args)}}Handlebars.Parser=handlebars;Handlebars.parse=function(a){Handlebars.Parser.yy=Handlebars.AST;return Handlebars.Parser.parse(a)};Handlebars.print=function(a){return new Handlebars.PrintVisitor().accept(a)};Handlebars.logger={DEBUG:0,INFO:1,WARN:2,ERROR:3,level:3,log:function(b,a){}};Handlebars.log=function(b,a){Handlebars.logger.log(b,a)};(function(){Handlebars.AST={};Handlebars.AST.ProgramNode=function(c,b){this.type="program";this.statements=c;if(b){this.inverse=new Handlebars.AST.ProgramNode(b)}};Handlebars.AST.MustacheNode=function(d,c,b){this.type="mustache";this.id=d[0];this.params=d.slice(1);this.hash=c;this.escaped=!b};Handlebars.AST.PartialNode=function(c,b){this.type="partial";this.id=c;this.context=b};var a=function(b,c){if(b.original!==c.original){throw new Handlebars.Exception(b.original+" doesn't match "+c.original)}};Handlebars.AST.BlockNode=function(c,b,d){a(c.id,d);this.type="block";this.mustache=c;this.program=b};Handlebars.AST.InverseNode=function(c,b,d){a(c.id,d);this.type="inverse";this.mustache=c;this.program=b};Handlebars.AST.ContentNode=function(b){this.type="content";this.string=b};Handlebars.AST.HashNode=function(b){this.type="hash";this.pairs=b};Handlebars.AST.IdNode=function(f){this.type="ID";this.original=f.join(".");var d=[],g=0;for(var e=0,b=f.length;e<b;e++){var c=f[e];if(c===".."){g++}else{if(c==="."||c==="this"){this.isScoped=true}else{d.push(c)}}}this.parts=d;this.string=d.join(".");this.depth=g;this.isSimple=(d.length===1)&&(g===0)};Handlebars.AST.StringNode=function(b){this.type="STRING";this.string=b};Handlebars.AST.IntegerNode=function(b){this.type="INTEGER";this.integer=b};Handlebars.AST.BooleanNode=function(b){this.type="BOOLEAN";this.bool=b};Handlebars.AST.CommentNode=function(b){this.type="comment";this.comment=b}})();Handlebars.Exception=function(b){var a=Error.prototype.constructor.apply(this,arguments);for(var c in a){if(a.hasOwnProperty(c)){this[c]=a[c]}}this.message=a.message};Handlebars.Exception.prototype=new Error;Handlebars.SafeString=function(a){this.string=a};Handlebars.SafeString.prototype.toString=function(){return this.string.toString()};(function(){var c={"<":"<",">":">",'"':""","'":"'","`":"`"};var d=/&(?!\w+;)|[<>"'`]/g;var b=/[&<>"'`]/;var a=function(e){return c[e]||"&"};Handlebars.Utils={escapeExpression:function(e){if(e instanceof Handlebars.SafeString){return e.toString()}else{if(e==null||e===false){return""}}if(!b.test(e)){return e}return e.replace(d,a)},isEmpty:function(e){if(typeof e==="undefined"){return true}else{if(e===null){return true}else{if(e===false){return true}else{if(Object.prototype.toString.call(e)==="[object Array]"&&e.length===0){return true}else{return false}}}}}}})();Handlebars.Compiler=function(){};Handlebars.JavaScriptCompiler=function(){};(function(f,e){f.OPCODE_MAP={appendContent:1,getContext:2,lookupWithHelpers:3,lookup:4,append:5,invokeMustache:6,appendEscaped:7,pushString:8,truthyOrFallback:9,functionOrFallback:10,invokeProgram:11,invokePartial:12,push:13,assignToHash:15,pushStringParam:16};f.MULTI_PARAM_OPCODES={appendContent:1,getContext:1,lookupWithHelpers:2,lookup:1,invokeMustache:3,pushString:1,truthyOrFallback:1,functionOrFallback:1,invokeProgram:3,invokePartial:1,push:1,assignToHash:1,pushStringParam:1};f.DISASSEMBLE_MAP={};for(var h in f.OPCODE_MAP){var g=f.OPCODE_MAP[h];f.DISASSEMBLE_MAP[g]=h}f.multiParamSize=function(i){return f.MULTI_PARAM_OPCODES[f.DISASSEMBLE_MAP[i]]};f.prototype={compiler:f,disassemble:function(){var t=this.opcodes,r,n;var q=[],v,m,w;for(var s=0,o=t.length;s<o;s++){r=t[s];if(r==="DECLARE"){m=t[++s];w=t[++s];q.push("DECLARE "+m+" = "+w)}else{v=f.DISASSEMBLE_MAP[r];var u=f.multiParamSize(r);var k=[];for(var p=0;p<u;p++){n=t[++s];if(typeof n==="string"){n='"'+n.replace("\n","\\n")+'"'}k.push(n)}v=v+" "+k.join(" ");q.push(v)}}return q.join("\n")},guid:0,compile:function(i,k){this.children=[];this.depths={list:[]};this.options=k;var l=this.options.knownHelpers;this.options.knownHelpers={helperMissing:true,blockHelperMissing:true,each:true,"if":true,unless:true,"with":true,log:true};if(l){for(var j in l){this.options.knownHelpers[j]=l[j]}}return this.program(i)},accept:function(i){return this[i.type](i)},program:function(m){var k=m.statements,o;this.opcodes=[];for(var n=0,j=k.length;n<j;n++){o=k[n];this[o.type](o)}this.isSimple=j===1;this.depths.list=this.depths.list.sort(function(l,i){return l-i});return this},compileProgram:function(m){var j=new this.compiler().compile(m,this.options);var n=this.guid++;this.usePartial=this.usePartial||j.usePartial;this.children[n]=j;for(var o=0,k=j.depths.list.length;o<k;o++){depth=j.depths.list[o];if(depth<2){continue}else{this.addDepth(depth-1)}}return n},block:function(o){var l=o.mustache;var n,p,j,k;var m=this.setupStackForMustache(l);var i=this.compileProgram(o.program);if(o.program.inverse){k=this.compileProgram(o.program.inverse);this.declare("inverse",k)}this.opcode("invokeProgram",i,m.length,!!l.hash);this.declare("inverse",null);this.opcode("append")},inverse:function(k){var j=this.setupStackForMustache(k.mustache);var i=this.compileProgram(k.program);this.declare("inverse",i);this.opcode("invokeProgram",null,j.length,!!k.mustache.hash);this.declare("inverse",null);this.opcode("append")},hash:function(n){var m=n.pairs,p,o;this.opcode("push","{}");for(var k=0,j=m.length;k<j;k++){p=m[k];o=p[1];this.accept(o);this.opcode("assignToHash",p[0])}},partial:function(i){var j=i.id;this.usePartial=true;if(i.context){this.ID(i.context)}else{this.opcode("push","depth0")}this.opcode("invokePartial",j.original);this.opcode("append")},content:function(i){this.opcode("appendContent",i.string)},mustache:function(i){var j=this.setupStackForMustache(i);this.opcode("invokeMustache",j.length,i.id.original,!!i.hash);if(i.escaped&&!this.options.noEscape){this.opcode("appendEscaped")}else{this.opcode("append")}},ID:function(m){this.addDepth(m.depth);this.opcode("getContext",m.depth);this.opcode("lookupWithHelpers",m.parts[0]||null,m.isScoped||false);for(var k=1,j=m.parts.length;k<j;k++){this.opcode("lookup",m.parts[k])}},STRING:function(i){this.opcode("pushString",i.string)},INTEGER:function(i){this.opcode("push",i.integer)},BOOLEAN:function(i){this.opcode("push",i.bool)},comment:function(){},pushParams:function(l){var j=l.length,k;while(j--){k=l[j];if(this.options.stringParams){if(k.depth){this.addDepth(k.depth)}this.opcode("getContext",k.depth||0);this.opcode("pushStringParam",k.string)}else{this[k.type](k)}}},opcode:function(i,l,k,j){this.opcodes.push(f.OPCODE_MAP[i]);if(l!==undefined){this.opcodes.push(l)}if(k!==undefined){this.opcodes.push(k)}if(j!==undefined){this.opcodes.push(j)}},declare:function(i,j){this.opcodes.push("DECLARE");this.opcodes.push(i);this.opcodes.push(j)},addDepth:function(i){if(i===0){return}if(!this.depths[i]){this.depths[i]=true;this.depths.list.push(i)}},setupStackForMustache:function(i){var j=i.params;this.pushParams(j);if(i.hash){this.hash(i.hash)}this.ID(i.id);return j}};e.prototype={nameLookup:function(k,i,j){if(/^[0-9]+$/.test(i)){return k+"["+i+"]"}else{if(e.isValidJavaScriptVariableName(i)){return k+"."+i}else{return k+"['"+i+"']"}}},appendToBuffer:function(i){if(this.environment.isSimple){return"return "+i+";"}else{return"buffer += "+i+";"}},initializeBuffer:function(){return this.quotedString("")},namespace:"Handlebars",compile:function(i,j,l,k){this.environment=i;this.options=j||{};this.name=this.environment.name;this.isChild=!!l;this.context=l||{programs:[],aliases:{self:"this"},registers:{list:[]}};this.preamble();this.stackSlot=0;this.stackVars=[];this.compileChildren(i,j);var n=i.opcodes,m;this.i=0;for(b=n.length;this.i<b;this.i++){m=this.nextOpcode(0);if(m[0]==="DECLARE"){this.i=this.i+2;this[m[1]]=m[2]}else{this.i=this.i+m[1].length;this[m[0]].apply(this,m[1])}}return this.createFunctionContext(k)},nextOpcode:function(r){var o=this.environment.opcodes,m=o[this.i+r],l,p;var q,i;if(m==="DECLARE"){l=o[this.i+1];p=o[this.i+2];return["DECLARE",l,p]}else{l=f.DISASSEMBLE_MAP[m];q=f.multiParamSize(m);i=[];for(var k=0;k<q;k++){i.push(o[this.i+k+1+r])}return[l,i]}},eat:function(i){this.i=this.i+i.length},preamble:function(){var i=[];this.useRegister("foundHelper");if(!this.isChild){var j=this.namespace;var k="helpers = helpers || "+j+".helpers;";if(this.environment.usePartial){k=k+" partials = partials || "+j+".partials;"}i.push(k)}else{i.push("")}if(!this.environment.isSimple){i.push(", buffer = "+this.initializeBuffer())}else{i.push("")}this.lastContext=0;this.source=i},createFunctionContext:function(p){var q=this.stackVars;if(!this.isChild){q=q.concat(this.context.registers.list)}if(q.length>0){this.source[1]=this.source[1]+", "+q.join(", ")}if(!this.isChild){var k=[];for(var o in this.context.aliases){this.source[1]=this.source[1]+", "+o+"="+this.context.aliases[o]}}if(this.source[1]){this.source[1]="var "+this.source[1].substring(2)+";"}if(!this.isChild){this.source[1]+="\n"+this.context.programs.join("\n")+"\n"}if(!this.environment.isSimple){this.source.push("return buffer;")}var r=this.isChild?["depth0","data"]:["Handlebars","depth0","helpers","partials","data"];for(var n=0,j=this.environment.depths.list.length;n<j;n++){r.push("depth"+this.environment.depths.list[n])}if(p){r.push(this.source.join("\n "));return Function.apply(this,r)}else{var m="function "+(this.name||"")+"("+r.join(",")+") {\n "+this.source.join("\n ")+"}";Handlebars.log(Handlebars.logger.DEBUG,m+"\n\n");return m}},appendContent:function(i){this.source.push(this.appendToBuffer(this.quotedString(i)))},append:function(){var i=this.popStack();this.source.push("if("+i+" || "+i+" === 0) { "+this.appendToBuffer(i)+" }");if(this.environment.isSimple){this.source.push("else { "+this.appendToBuffer("''")+" }")}},appendEscaped:function(){var j=this.nextOpcode(1),i="";this.context.aliases.escapeExpression="this.escapeExpression";if(j[0]==="appendContent"){i=" + "+this.quotedString(j[1][0]);this.eat(j)}this.source.push(this.appendToBuffer("escapeExpression("+this.popStack()+")"+i))},getContext:function(i){if(this.lastContext!==i){this.lastContext=i}},lookupWithHelpers:function(k,l){if(k){var i=this.nextStack();this.usingKnownHelper=false;var j;if(!l&&this.options.knownHelpers[k]){j=i+" = "+this.nameLookup("helpers",k,"helper");this.usingKnownHelper=true}else{if(l||this.options.knownHelpersOnly){j=i+" = "+this.nameLookup("depth"+this.lastContext,k,"context")}else{this.register("foundHelper",this.nameLookup("helpers",k,"helper"));j=i+" = foundHelper || "+this.nameLookup("depth"+this.lastContext,k,"context")}}j+=";";this.source.push(j)}else{this.pushStack("depth"+this.lastContext)}},lookup:function(j){var i=this.topStack();this.source.push(i+" = ("+i+" === null || "+i+" === undefined || "+i+" === false ? "+i+" : "+this.nameLookup(i,j,"context")+");")},pushStringParam:function(i){this.pushStack("depth"+this.lastContext);this.pushString(i)},pushString:function(i){this.pushStack(this.quotedString(i))},push:function(i){this.pushStack(i)},invokeMustache:function(k,j,i){this.populateParams(k,this.quotedString(j),"{}",null,i,function(l,n,m){if(!this.usingKnownHelper){this.context.aliases.helperMissing="helpers.helperMissing";this.context.aliases.undef="void 0";this.source.push("else if("+m+"=== undef) { "+l+" = helperMissing.call("+n+"); }");if(l!==m){this.source.push("else { "+l+" = "+m+"; }")}}})},invokeProgram:function(k,l,j){var i=this.programExpression(this.inverse);var m=this.programExpression(k);this.populateParams(l,null,m,i,j,function(n,p,o){if(!this.usingKnownHelper){this.context.aliases.blockHelperMissing="helpers.blockHelperMissing";this.source.push("else { "+n+" = blockHelperMissing.call("+p+"); }")}})},populateParams:function(p,k,t,q,x,w){var l=x||this.options.stringParams||q||this.options.data;var j=this.popStack(),v;var n=[],m,o,u;if(l){this.register("tmp1",t);u="tmp1"}else{u="{ hash: {} }"}if(l){var s=(x?this.popStack():"{}");this.source.push("tmp1.hash = "+s+";")}if(this.options.stringParams){this.source.push("tmp1.contexts = [];")}for(var r=0;r<p;r++){m=this.popStack();n.push(m);if(this.options.stringParams){this.source.push("tmp1.contexts.push("+this.popStack()+");")}}if(q){this.source.push("tmp1.fn = tmp1;");this.source.push("tmp1.inverse = "+q+";")}if(this.options.data){this.source.push("tmp1.data = data;")}n.push(u);this.populateCall(n,j,k||j,w,t!=="{}")},populateCall:function(n,j,k,q,o){var m=["depth0"].concat(n).join(", ");var i=["depth0"].concat(k).concat(n).join(", ");var p=this.nextStack();if(this.usingKnownHelper){this.source.push(p+" = "+j+".call("+m+");")}else{this.context.aliases.functionType='"function"';var l=o?"foundHelper && ":"";this.source.push("if("+l+"typeof "+j+" === functionType) { "+p+" = "+j+".call("+m+"); }")}q.call(this,p,i,j);this.usingKnownHelper=false},invokePartial:function(i){params=[this.nameLookup("partials",i,"partial"),"'"+i+"'",this.popStack(),"helpers","partials"];if(this.options.data){params.push("data")}this.pushStack("self.invokePartial("+params.join(", ")+");")},assignToHash:function(i){var j=this.popStack();var k=this.topStack();this.source.push(k+"['"+i+"'] = "+j+";")},compiler:e,compileChildren:function(j,n){var p=j.children,r,q;for(var o=0,k=p.length;o<k;o++){r=p[o];q=new this.compiler();this.context.programs.push("");var m=this.context.programs.length;r.index=m;r.name="program"+m;this.context.programs[m]=q.compile(r,n,this.context)}},programExpression:function(k){if(k==null){return"self.noop"}var p=this.environment.children[k],o=p.depths.list;var n=[p.index,p.name,"data"];for(var m=0,j=o.length;m<j;m++){depth=o[m];if(depth===1){n.push("depth0")}else{n.push("depth"+(depth-1))}}if(o.length===0){return"self.program("+n.join(", ")+")"}else{n.shift();return"self.programWithDepth("+n.join(", ")+")"}},register:function(i,j){this.useRegister(i);this.source.push(i+" = "+j+";")},useRegister:function(i){if(!this.context.registers[i]){this.context.registers[i]=true;this.context.registers.list.push(i)}},pushStack:function(i){this.source.push(this.nextStack()+" = "+i+";");return"stack"+this.stackSlot},nextStack:function(){this.stackSlot++;if(this.stackSlot>this.stackVars.length){this.stackVars.push("stack"+this.stackSlot)}return"stack"+this.stackSlot},popStack:function(){return"stack"+this.stackSlot--},topStack:function(){return"stack"+this.stackSlot},quotedString:function(i){return'"'+i.replace(/\\/g,"\\\\").replace(/"/g,'\\"').replace(/\n/g,"\\n").replace(/\r/g,"\\r")+'"'}};var a=("break else new var case finally return void catch for switch while continue function this with default if throw delete in try do instanceof typeof abstract enum int short boolean export interface static byte extends long super char final native synchronized class float package throws const goto private transient debugger implements protected volatile double import public let yield").split(" ");var d=e.RESERVED_WORDS={};for(var c=0,b=a.length;c<b;c++){d[a[c]]=true}e.isValidJavaScriptVariableName=function(i){if(!e.RESERVED_WORDS[i]&&/^[a-zA-Z_$][0-9a-zA-Z_$]+$/.test(i)){return true}return false}})(Handlebars.Compiler,Handlebars.JavaScriptCompiler);Handlebars.precompile=function(d,c){c=c||{};var b=Handlebars.parse(d);var a=new Handlebars.Compiler().compile(b,c);return new Handlebars.JavaScriptCompiler().compile(a,c)};Handlebars.compile=function(b,a){a=a||{};var d;function c(){var g=Handlebars.parse(b);var f=new Handlebars.Compiler().compile(g,a);var e=new Handlebars.JavaScriptCompiler().compile(f,a,undefined,true);return Handlebars.template(e)}return function(f,e){if(!d){d=c()}return d.call(this,f,e)}};Handlebars.VM={template:function(a){var b={escapeExpression:Handlebars.Utils.escapeExpression,invokePartial:Handlebars.VM.invokePartial,programs:[],program:function(d,e,f){var c=this.programs[d];if(f){return Handlebars.VM.program(e,f)}else{if(c){return c}else{c=this.programs[d]=Handlebars.VM.program(e);return c}}},programWithDepth:Handlebars.VM.programWithDepth,noop:Handlebars.VM.noop};return function(d,c){c=c||{};return a.call(b,Handlebars,d,c.helpers,c.partials,c.data)}},programWithDepth:function(b,d,c){var a=Array.prototype.slice.call(arguments,2);return function(f,e){e=e||{};return b.apply(this,[f,e.data||d].concat(a))}},program:function(a,b){return function(d,c){c=c||{};return a(d,c.data||b)}},noop:function(){return""},invokePartial:function(a,b,d,e,c,f){options={helpers:e,partials:c,data:f};if(a===undefined){throw new Handlebars.Exception("The partial "+b+" could not be found")}else{if(a instanceof Function){return a(d,options)}else{if(!Handlebars.compile){throw new Handlebars.Exception("The partial "+b+" could not be compiled when running in runtime-only mode")}else{c[b]=Handlebars.compile(a);return c[b](d,options)}}}}};Handlebars.template=Handlebars.VM.template; 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\ No newline at end of file diff -r 11649eacb329e0f84e64d8c07d316c26182d8be1 -r 24501c5f17a6310f39f5e3a5d55f8a00d7a67213 static/scripts/packed/tools/rgenetics/checkbox_and_radiobutton.js --- /dev/null +++ b/static/scripts/packed/tools/rgenetics/checkbox_and_radiobutton.js @@ -0,0 +1,1 @@ +function checkBox(A,x,r,u,q,s,B,y,t,C,w,p,D){var z=13;var v=true;if(arguments.length==z){this.id=A;this.parentNode=x;this.x=r;this.y=u;this.checkboxId=q;this.checkcrossId=s;this.checkedStatus=B;this.labelText=y;this.textStyles=t;if(!this.textStyles["font-size"]){this.textStyles["font-size"]=12}this.labelDistance=C;this.labelYOffset=w;this.radioButtonGroup=p;this.functionToCall=D;this.exists=true;this.label=undefined}else{v=false;alert("Error in checkbox ("+A+"): wrong nr of arguments! You have to pass over "+z+" parameters.")}if(v){this.timer=new Timer(this);if(this.radioButtonGroup){this.timerMs=0}else{this.timerMs=200}this.createCheckBox()}else{alert("Could not create checkbox with id '"+A+"' due to errors in the constructor parameters")}}checkBox.prototype.createCheckBox=function(){if(typeof(this.parentNode)=="string"){this.parentNode=document.getElementById(this.parentNode)}this.checkBox=document.createElementNS(svgNS,"use");this.checkBox.setAttributeNS(null,"x",this.x);this.checkBox.setAttributeNS(null,"y",this.y);this.checkBox.setAttributeNS(xlinkNS,"href","#"+this.checkboxId);this.checkBox.addEventListener("click",this,false);this.checkBox.setAttributeNS(null,"cursor","pointer");this.parentNode.appendChild(this.checkBox);this.checkCross=document.createElementNS(svgNS,"use");this.checkCross.setAttributeNS(null,"x",this.x);this.checkCross.setAttributeNS(null,"y",this.y);this.checkCross.setAttributeNS(xlinkNS,"href","#"+this.checkcrossId);this.parentNode.appendChild(this.checkCross);if(this.checkedStatus==false){this.checkCross.setAttributeNS(null,"display","none")}if(this.labelText){if(this.labelText.length>0){this.label=document.createElementNS(svgNS,"text");for(var d in this.textStyles){var e=this.textStyles[d];if(d=="font-size"){e+="px"}this.label.setAttributeNS(null,d,e)}this.label.setAttributeNS(null,"x",(this.x+this.labelDistance));this.label.setAttributeNS(null,"y",(this.y+this.labelYOffset));this.label.setAttributeNS(null,"cursor","pointer");var f=document.createTextNode(this.labelText);this.label.appendChild(f);this.label.setAttributeNS(null,"pointer-events","all");this.label.addEventListener("click",this,false);this.parentNode.appendChild(this.label)}}if(this.radioButtonGroup){this.radioButtonGroup.addCheckBox(this)}};checkBox.prototype.handleEvent=function(b){if(b.type=="click"){if(this.checkedStatus==true){this.checkCross.setAttributeNS(null,"display","none");this.checkedStatus=false}else{this.checkCross.setAttributeNS(null,"display","inline");this.checkedStatus=true}}this.timer.setTimeout("fireFunction",this.timerMs)};checkBox.prototype.fireFunction=function(){if(this.radioButtonGroup){this.radioButtonGroup.selectById(this.id,true)}else{if(typeof(this.functionToCall)=="function"){this.functionToCall(this.id,this.checkedStatus,this.labelText)}if(typeof(this.functionToCall)=="object"){this.functionToCall.checkBoxChanged(this.id,this.checkedStatus,this.labelText)}if(typeof(this.functionToCall)==undefined){return}}};checkBox.prototype.check=function(b){this.checkCross.setAttributeNS(null,"display","inherit");this.checkedStatus=true;if(b){this.timer.setTimeout("fireFunction",this.timerMs)}};checkBox.prototype.uncheck=function(b){this.checkCross.setAttributeNS(null,"display","none");this.checkedStatus=false;if(b){this.timer.setTimeout("fireFunction",this.timerMs)}};checkBox.prototype.moveTo=function(c,d){this.x=c;this.y=d;this.checkBox.setAttributeNS(null,"x",this.x);this.checkBox.setAttributeNS(null,"y",this.y);this.checkCross.setAttributeNS(null,"x",this.x);this.checkCross.setAttributeNS(null,"y",this.y);if(this.labelText){this.label.setAttributeNS(null,"x",(this.x+this.labelDistance));this.label.setAttributeNS(null,"y",(this.y+this.labelYOffset))}};checkBox.prototype.remove=function(b){this.checkBox.removeEventListener("click",this,false);this.parentNode.removeChild(this.checkBox);this.parentNode.removeChild(this.checkCross);if(this.label){this.parentNode.removeChild(this.label)}this.exists=false};checkBox.prototype.setLabelText=function(e){this.labelText=e;if(this.label){this.label.firstChild.nodeValue=e}else{if(this.labelText.length>0){this.label=document.createElementNS(svgNS,"text");for(var d in this.textStyles){value=this.textStyles[d];if(d=="font-size"){value+="px"}this.label.setAttributeNS(null,d,value)}this.label.setAttributeNS(null,"x",(this.x+this.labelDistance));this.label.setAttributeNS(null,"y",(this.y+this.textStyles["font-size"]*0.3));var f=document.createTextNode(this.labelText);this.label.appendChild(f);this.parentNode.appendChild(this.label)}}};function radioButtonGroup(f,e){var d=2;if(arguments.length==d){this.id=f;if(typeof(e)=="function"||typeof(e)=="object"||typeof(e)==undefined){this.functionToCall=e}else{alert("Error in radiobutton with ("+f+"): argument functionToCall is not of type 'function', 'object' or undefined!")}this.checkBoxes=new Array();this.selectedId=undefined;this.selectedIndex=undefined;this.timer=new Timer(this);this.timerMs=200}else{alert("Error in radiobutton with ("+f+"): wrong nr of arguments! You have to pass over "+d+" parameters.")}}radioButtonGroup.prototype.addCheckBox=function(b){this.checkBoxes.push(b);if(b.checkedStatus){this.selectedId=b.id;this.selectedIndex=this.checkBoxes.length-1}};radioButtonGroup.prototype.selectById=function(h,f){var g=false;for(var e=0;e<this.checkBoxes.length;e++){if(this.checkBoxes[e].id==h){this.selectedId=h;this.selectedIndex=e;if(this.checkBoxes[e].checkedStatus==false){this.checkBoxes[e].check(false)}g=true}else{this.checkBoxes[e].uncheck(false)}}if(g){if(f){this.timer.setTimeout("fireFunction",this.timerMs)}}else{alert("Error in radiobutton with ("+this.id+"): could not find checkbox with id '"+h+"'")}};radioButtonGroup.prototype.selectByLabelname=function(f,e){var g=-1;for(var h=0;h<this.checkBoxes.length;h++){if(this.checkBoxes[h].labelText==f){g=this.checkBoxes[h].id}}if(g==-1){alert("Error in radiobutton with ("+this.id+"): could not find checkbox with label '"+f+"'")}else{this.selectById(g,e)}};radioButtonGroup.prototype.fireFunction=function(){if(typeof(this.functionToCall)=="function"){this.functionToCall(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText)}if(typeof(this.functionToCall)=="object"){this.functionToCall.radioButtonChanged(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText)}if(typeof(this.functionToCall)==undefined){return}}; \ No newline at end of file diff -r 11649eacb329e0f84e64d8c07d316c26182d8be1 -r 24501c5f17a6310f39f5e3a5d55f8a00d7a67213 static/scripts/packed/tools/rgenetics/helper_functions.js --- /dev/null +++ b/static/scripts/packed/tools/rgenetics/helper_functions.js @@ -0,0 +1,1 @@ +var svgNS="http://www.w3.org/2000/svg";var xlinkNS="http://www.w3.org/1999/xlink";var cartoNS="http://www.carto.net/attrib";var attribNS="http://www.carto.net/attrib";var batikNS="http://xml.apache.org/batik/ext";function toPolarDir(e,f){var d=(Math.atan2(f,e));return(d)}function 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k=m[0].length;if(k>3){while(k>0){if(k>3){g=l+m[0].substr(k-3,3)+g}else{g=m[0].substr(0,k)+g}k-=3}}else{g=m[0]}if(m[1]){g=g+"."+m[1]}return g}function statusChange(b){document.getElementById("statusText").firstChild.nodeValue="Statusbar: "+b}function scaleObject(j,l){var m=j.currentTarget;var n=m.getAttributeNS(null,"x");var g=m.getAttributeNS(null,"y");var k="scale("+l+") translate("+(n*1/l-n)+" "+(g*1/l-g)+")";m.setAttributeNS(null,"transform",k)}function getTransformToRootElement(d){try{var f=d.getTransformToElement(document.documentElement)}catch(e){var f=d.getCTM();while((d=d.parentNode)!=document){f=d.getCTM().multiply(f)}}return f}function getTransformToElement(e,j){try{var g=e.getTransformToElement(j)}catch(f){var g=e.getCTM();while((e=e.parentNode)!=j){g=e.getCTM().multiply(g)}}return g}function hsv2rgb(n,r,t){var f=new Object();if(r==0){f.red=Math.round(t*255);f.green=Math.round(t*255);f.blue=Math.round(t*255)}else{var o=n/60;var p=Math.floor(o);var m=o-p;if(p%2==0){m=1-m}var q=t*(1-r);var u=t*(1-r*m);switch(p){case 0:f.red=t;f.green=u;f.blue=q;break;case 1:f.red=u;f.green=t;f.blue=q;break;case 2:f.red=q;f.green=t;f.blue=u;break;case 3:f.red=q;f.green=u;f.blue=t;break;case 4:f.red=u;f.green=q;f.blue=t;break;case 5:f.red=t;f.green=q;f.blue=u;break;case 6:f.red=t;f.green=u;f.blue=q;break}f.red=Math.round(f.red*255);f.green=Math.round(f.green*255);f.blue=Math.round(f.blue*255)}return f}function rgb2hsv(j,e,f){var g=new Object();j=j/255;e=e/255;f=f/255;myMax=Math.max(j,Math.max(e,f));myMin=Math.min(j,Math.min(e,f));v=myMax;if(myMax>0){s=(myMax-myMin)/myMax}else{s=0}if(s>0){myDiff=myMax-myMin;rc=(myMax-j)/myDiff;gc=(myMax-e)/myDiff;bc=(myMax-f)/myDiff;if(j==myMax){h=(bc-gc)/6}if(e==myMax){h=(2+rc-bc)/6}if(f==myMax){h=(4+gc-rc)/6}}else{h=0}if(h<0){h+=1}g.hue=Math.round(h*360);g.sat=s;g.val=v;return g}function arrayPopulate(e,d){var f=new Array();if(e.length!=d.length){alert("error: arrays do not have the same length!")}else{for(i=0;i<e.length;i++){f[e[i]]=d[i]}}return f}function getData(m,n,l,k,g,j){this.url=m;this.callBackFunction=n;this.returnFormat=l;this.method=k;this.additionalParams=j;if(k!="get"&&k!="post"){alert("Error in network request: parameter 'method' must be 'get' or 'post'")}this.postText=g;this.xmlRequest=null}getData.prototype.getData=function(){if(window.getURL){if(this.method=="get"){getURL(this.url,this)}if(this.method=="post"){postURL(this.url,this.postText,this)}}else{if(window.XMLHttpRequest){var c=this;this.xmlRequest=new XMLHttpRequest();if(this.method=="get"){if(this.returnFormat=="xml"){this.xmlRequest.overrideMimeType("text/xml")}this.xmlRequest.open("GET",this.url,true)}if(this.method=="post"){this.xmlRequest.open("POST",this.url,true)}this.xmlRequest.onreadystatechange=function(){c.handleEvent()};if(this.method=="get"){this.xmlRequest.send(null)}if(this.method=="post"){var d=true;if(!this.postText){d=false;alert("Error in network post request: missing parameter 'postText'!")}if(typeof(this.postText)!="string"){d=false;alert("Error in network post request: parameter 'postText' has to be of type 'string')")}if(d){this.xmlRequest.send(this.postText)}}}else{alert("your browser/svg viewer neither supports window.getURL nor window.XMLHttpRequest!")}}};getData.prototype.operationComplete=function(c){if(c.success){if(this.returnFormat=="xml"){var d=parseXML(c.content,document);if(typeof(this.callBackFunction)=="function"){this.callBackFunction(d.firstChild,this.additionalParams)}if(typeof(this.callBackFunction)=="object"){this.callBackFunction.receiveData(d.firstChild,this.additionalParams)}}if(this.returnFormat=="json"){if(typeof(this.callBackFunction)=="function"){this.callBackFunction(c.content,this.additionalParams)}if(typeof(this.callBackFunction)=="object"){this.callBackFunction.receiveData(c.content,this.additionalParams)}}}else{alert("something went wrong with dynamic loading of geometry!")}};getData.prototype.handleEvent=function(){if(this.xmlRequest.readyState==4){if(this.returnFormat=="xml"){var b=document.importNode(this.xmlRequest.responseXML.documentElement,true);if(typeof(this.callBackFunction)=="function"){this.callBackFunction(b,this.additionalParams)}if(typeof(this.callBackFunction)=="object"){this.callBackFunction.receiveData(b,this.additionalParams)}}if(this.returnFormat=="json"){if(typeof(this.callBackFunction)=="function"){this.callBackFunction(this.xmlRequest.responseText,this.additionalParams)}if(typeof(this.callBackFunction)=="object"){this.callBackFunction.receiveData(this.xmlRequest.responseText,this.additionalParams)}}}};function serializeNode(d){if(typeof XMLSerializer!="undefined"){return new XMLSerializer().serializeToString(d)}else{if(typeof d.xml!="undefined"){return d.xml}else{if(typeof printNode!="undefined"){return printNode(d)}else{if(typeof Packages!="undefined"){try{var e=new java.io.StringWriter();Packages.org.apache.batik.dom.util.DOMUtilities.writeNode(d,e);return e.toString()}catch(f){alert("Sorry, your SVG viewer does not support the printNode/serialize function.");return""}}else{alert("Sorry, your SVG viewer does not support the printNode/serialize function.");return""}}}}}function startAnimation(b){document.getElementById(b).beginElement()}; \ No newline at end of file diff -r 11649eacb329e0f84e64d8c07d316c26182d8be1 -r 24501c5f17a6310f39f5e3a5d55f8a00d7a67213 static/scripts/packed/tools/rgenetics/timer.js --- /dev/null +++ b/static/scripts/packed/tools/rgenetics/timer.js @@ -0,0 +1,1 @@ +function Timer(){this.obj=(arguments.length)?arguments[0]:window;return this}Timer.prototype.setInterval=function(h,g){var e=Timer.getNew();var f=Timer.buildCall(this.obj,e,arguments);Timer.set[e].timer=window.setInterval(f,g);return e};Timer.prototype.setTimeout=function(d,f){var e=Timer.getNew();Timer.buildCall(this.obj,e,arguments);Timer.set[e].timer=window.setTimeout("Timer.callOnce("+e+");",f);return e};Timer.prototype.clearInterval=function(b){if(!Timer.set[b]){return}window.clearInterval(Timer.set[b].timer);Timer.set[b]=null};Timer.prototype.clearTimeout=function(b){if(!Timer.set[b]){return}window.clearTimeout(Timer.set[b].timer);Timer.set[b]=null};Timer.set=new Array();Timer.buildCall=function(h,i,f){var j="";Timer.set[i]=new Array();if(h!=window){Timer.set[i].obj=h;j="Timer.set["+i+"].obj."}j+=f[0]+"(";if(f.length>2){Timer.set[i][0]=f[2];j+="Timer.set["+i+"][0]";for(var g=1;(g+2)<f.length;g++){Timer.set[i][g]=f[g+2];j+=", Timer.set["+i+"]["+g+"]"}}j+=");";Timer.set[i].call=j;return j};Timer.callOnce=function(i){if(!Timer.set[i]){return}eval(Timer.set[i].call);Timer.set[i]=null};Timer.getNew=function(){var b=0;while(Timer.set[b]){b++}return b}; \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/892d346ba649/ changeset: 892d346ba649 user: jgoecks date: 2012-04-02 16:19:21 summary: Merge. affected #: 1 file diff -r 24501c5f17a6310f39f5e3a5d55f8a00d7a67213 -r 892d346ba6493249f503a43bface1ca8f4a4c167 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -138,6 +138,7 @@ --excludeAnnotation "${annotation}" #end for #end if + ${analysis_param_type.multiallelic} ' ## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': ## -p '--annotation "SnpEff"' @@ -145,7 +146,6 @@ ## #else: ## -p '--excludeAnnotation "SnpEff"' ## #end if - ${analysis_param_type.multiallelic} #end if </command><inputs> https://bitbucket.org/galaxy/galaxy-central/changeset/d02ee3fe8f4e/ changeset: d02ee3fe8f4e user: jgoecks date: 2012-04-02 16:43:14 summary: Put tool panel definition in page rather than using AJAX to retrieve. affected #: 4 files diff -r 892d346ba6493249f503a43bface1ca8f4a4c167 -r d02ee3fe8f4ec295913b4acb0b3c1932ddd3b22f lib/galaxy/web/controllers/tools.py --- a/lib/galaxy/web/controllers/tools.py +++ b/lib/galaxy/web/controllers/tools.py @@ -18,7 +18,6 @@ in_panel = util.string_as_bool( kwds.get( 'in_panel', 'True' ) ) if in_panel: panel_elts = [] - # Taken from tool_menu.mako: for key, val in self.app.toolbox.tool_panel.items(): panel_elts.append( val.to_dict( trans ) ) rval = panel_elts diff -r 892d346ba6493249f503a43bface1ca8f4a4c167 -r d02ee3fe8f4ec295913b4acb0b3c1932ddd3b22f static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ b/static/scripts/backbone/tools.js @@ -341,10 +341,6 @@ */ initialize: function(options) { this.collection.tool_search.on("change:results", this.handle_search_results, this); - - var self = this; - // Wait for collection to load before rendering. - this.collection.bind("reset", function() { self.render(); }); }, render: function() { diff -r 892d346ba6493249f503a43bface1ca8f4a4c167 -r d02ee3fe8f4ec295913b4acb0b3c1932ddd3b22f static/scripts/packed/backbone/tools.js --- a/static/scripts/packed/backbone/tools.js +++ b/static/scripts/packed/backbone/tools.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=Backbone.Model.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var ToolLinkView=Backbone.View.extend({tagName:"div",template:Handlebars.templates.tool_link,initialize:function(){this.model.on("change:hidden",this.update_visible,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolPanelLabelView=Backbone.View.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,initialize:function(){this.model.on("change:hidden",this.update_visible,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolPanelSectionView=Backbone.View.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.$el.children(".toolSectionBody").toggle("fast");this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").show("fast"):this.$el.children(".toolSectionBody").hide("fast"))},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(b){this.collection.tool_search.on("change:results",this.handle_search_results,this);var a=this;this.collection.bind("reset",function(){a.render()})},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:elt,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file +var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=Backbone.Model.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var ToolLinkView=Backbone.View.extend({tagName:"div",template:Handlebars.templates.tool_link,initialize:function(){this.model.on("change:hidden",this.update_visible,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolPanelLabelView=Backbone.View.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,initialize:function(){this.model.on("change:hidden",this.update_visible,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolPanelSectionView=Backbone.View.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.$el.children(".toolSectionBody").toggle("fast");this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").show("fast"):this.$el.children(".toolSectionBody").hide("fast"))},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:elt,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file diff -r 892d346ba6493249f503a43bface1ca8f4a4c167 -r d02ee3fe8f4ec295913b4acb0b3c1932ddd3b22f templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -20,9 +20,14 @@ ${h.js( "galaxy.base", "json2", "autocomplete_tagging", "backbone/tools" )} <% + # Set up for creating tool panel. show_tool_search = "true" if trans.user and trans.user.preferences.get( "show_tool_search", "False" ) == "False": show_tool_search = "false" + + dictified_panel = [] + for key, val in trans.app.toolbox.tool_panel.items(): + dictified_panel.append( val.to_dict( trans ) ) %><script type="text/javascript"> @@ -36,11 +41,11 @@ // Set up tool panel. tool_panel = new ToolPanel( { tool_search: tool_search } ); - tool_panel.fetch(); - + tool_panel.reset( tool_panel.parse( ${h.to_json_string( dictified_panel )} ) ); // Set up tool panel view and initialize. tool_panel_view = new ToolPanelView( {collection: tool_panel} ); + tool_panel_view.render(); $('body').prepend(tool_panel_view.$el); // Minsize init hint. https://bitbucket.org/galaxy/galaxy-central/changeset/de70d3eb7565/ changeset: de70d3eb7565 user: jgoecks date: 2012-04-02 17:36:35 summary: Show/hide tool search based on user preferences. affected #: 2 files diff -r d02ee3fe8f4ec295913b4acb0b3c1932ddd3b22f -r de70d3eb756529bc37f00495a5f2f2357915eb1c static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ b/static/scripts/backbone/tools.js @@ -101,7 +101,7 @@ * indicates that query was not run; if not null, results are from search using * query. */ -var ToolSearch = Backbone.Model.extend({ +var ToolSearch = BaseModel.extend({ defaults: { spinner_url: "", search_url: "", @@ -320,6 +320,9 @@ render: function() { this.$el.append( this.template(this.model.toJSON()) ); + if (!this.model.is_visible()) { + this.$el.hide(); + } return this; }, diff -r d02ee3fe8f4ec295913b4acb0b3c1932ddd3b22f -r de70d3eb756529bc37f00495a5f2f2357915eb1c templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -21,9 +21,9 @@ <% # Set up for creating tool panel. - show_tool_search = "true" + tool_search_hidden = "false" if trans.user and trans.user.preferences.get( "show_tool_search", "False" ) == "False": - show_tool_search = "false" + tool_search_hidden = "true" dictified_panel = [] for key, val in trans.app.toolbox.tool_panel.items(): @@ -37,7 +37,7 @@ // Set up search. tool_search = new ToolSearch( {spinner_url: "${h.url_for('/static/images/loading_small_white_bg.gif')}", search_url: "${h.url_for( controller='root', action='tool_search' )}", - visible: ${show_tool_search} } ); + hidden: ${tool_search_hidden} } ); // Set up tool panel. tool_panel = new ToolPanel( { tool_search: tool_search } ); https://bitbucket.org/galaxy/galaxy-central/changeset/b8559675ee18/ changeset: b8559675ee18 user: jgoecks date: 2012-04-02 17:38:44 summary: Disable recently used tools menu for now. affected #: 1 file diff -r de70d3eb756529bc37f00495a5f2f2357915eb1c -r b8559675ee18d77397bd572b2d22525137677afb templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -173,7 +173,8 @@ else: action = "SHOW_RECENT" %> - menu_options[ ${action} ] = toggle_recently_used_fn; + // TODO: make compatible with new tool menu. + //menu_options[ ${action} ] = toggle_recently_used_fn; %endif https://bitbucket.org/galaxy/galaxy-central/changeset/9b403ed9ec16/ changeset: 9b403ed9ec16 user: jgoecks date: 2012-04-02 17:48:40 summary: Add a base view that supports hiding and showing objects. affected #: 2 files diff -r b8559675ee18d77397bd572b2d22525137677afb -r 9b403ed9ec16789e2100e9921bed956789b47613 static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ b/static/scripts/backbone/tools.js @@ -203,54 +203,54 @@ * they are controllers are well and the HTML is the real view in the MVC architecture. */ -// TODO: implement a BaseModelView for handling model visibility. +/** + * Base view that handles visibility based on model's hidden attribute. + */ +var BaseView = Backbone.View.extend({ + initialize: function() { + this.model.on("change:hidden", this.update_visible, this); + }, + update_visible: function() { + ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); + } +}); /** * Link to a tool. */ -var ToolLinkView = Backbone.View.extend({ +var ToolLinkView = BaseView.extend({ tagName: 'div', template: Handlebars.templates.tool_link, - initialize: function() { - this.model.on("change:hidden", this.update_visible, this); - }, + render: function() { this.$el.append( this.template(this.model.toJSON()) ); return this; - }, - update_visible: function() { - ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); } }); /** * Panel label/section header. */ -var ToolPanelLabelView = Backbone.View.extend({ +var ToolPanelLabelView = BaseView.extend({ tagName: 'div', className: 'toolPanelLabel', template: Handlebars.templates.panel_label, - initialize: function() { - this.model.on("change:hidden", this.update_visible, this); - }, + render: function() { this.$el.append( this.template(this.model.toJSON()) ); return this; }, - update_visible: function() { - ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); - } }); /** * Panel section. */ -var ToolPanelSectionView = Backbone.View.extend({ +var ToolPanelSectionView = BaseView.extend({ tagName: 'div', className: 'toolSectionWrapper', template: Handlebars.templates.panel_section, initialize: function() { - this.model.on("change:hidden", this.update_visible, this); + BaseView.prototype.initialize.call(this); this.model.on("change:open", this.update_open, this); }, render: function() { @@ -297,13 +297,6 @@ this.$el.children(".toolSectionBody").show("fast") : this.$el.children(".toolSectionBody").hide("fast") ); - }, - - /** - * Update section and section elements visibility after search. - */ - update_visible: function() { - ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); } }); diff -r b8559675ee18d77397bd572b2d22525137677afb -r 9b403ed9ec16789e2100e9921bed956789b47613 static/scripts/packed/backbone/tools.js --- a/static/scripts/packed/backbone/tools.js +++ b/static/scripts/packed/backbone/tools.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=Backbone.Model.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var ToolLinkView=Backbone.View.extend({tagName:"div",template:Handlebars.templates.tool_link,initialize:function(){this.model.on("change:hidden",this.update_visible,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolPanelLabelView=Backbone.View.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,initialize:function(){this.model.on("change:hidden",this.update_visible,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolPanelSectionView=Backbone.View.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.$el.children(".toolSectionBody").toggle("fast");this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").show("fast"):this.$el.children(".toolSectionBody").hide("fast"))},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:elt,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file +var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this)},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.$el.children(".toolSectionBody").toggle("fast");this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").show("fast"):this.$el.children(".toolSectionBody").hide("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:elt,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/319c7ee6873c/ changeset: 319c7ee6873c user: jgoecks date: 2012-04-02 17:52:39 summary: Merge. affected #: 6 files diff -r 9b403ed9ec16789e2100e9921bed956789b47613 -r 319c7ee6873c53e57aa6b37271cb7c6afb067612 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -223,7 +223,7 @@ if not os.path.exists(path): return self._construct_path(obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name) - def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, **kwargs): """ Construct the expected absolute path for accessing the object identified by `obj`.id. diff -r 9b403ed9ec16789e2100e9921bed956789b47613 -r 319c7ee6873c53e57aa6b37271cb7c6afb067612 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2181,7 +2181,7 @@ sa_session=self.sa_session ) self.app.security_agent.copy_dataset_permissions( outdata.dataset, child_dataset.dataset ) # Move data from temp location to dataset location - self.app.object_store.update_from_file(child_dataset.dataset, filename, create=True) + self.app.object_store.update_from_file(child_dataset.dataset, file_name=filename, create=True) self.sa_session.add( child_dataset ) self.sa_session.flush() child_dataset.set_size() @@ -2248,7 +2248,7 @@ self.sa_session.add( primary_data ) self.sa_session.flush() # Move data from temp location to dataset location - self.app.object_store.update_from_file(primary_data.dataset, filename, create=True) + self.app.object_store.update_from_file(primary_data.dataset, file_name=filename, create=True) primary_data.set_size() primary_data.name = "%s (%s)" % ( outdata.name, designation ) primary_data.info = outdata.info diff -r 9b403ed9ec16789e2100e9921bed956789b47613 -r 319c7ee6873c53e57aa6b37271cb7c6afb067612 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -367,6 +367,22 @@ shed_tool_conf = shed_tool_conf.replace( './', '', 1 ) shed_tool_conf_select_field = None tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) + if includes_tools: + # If we're installing a single repository that contains a readme file, get it's contents to display. + decoded_repo_info_dict = tool_shed_decode( repo_info_dict ) + if len( decoded_repo_info_dict ) == 1: + name = decoded_repo_info_dict.keys()[ 0 ] + repo_info_tuple = decoded_repo_info_dict[ name ] + description, repository_clone_url, changeset_revision = repo_info_tuple + owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) ) + url = '%s/repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( tool_shed_url, name, owner, changeset_revision ) + response = urllib2.urlopen( url ) + readme_text = response.read() + response.close() + else: + readme_text = '' + else: + readme_text = '' return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict, @@ -375,6 +391,7 @@ shed_tool_conf_select_field=shed_tool_conf_select_field, tool_panel_section_select_field=tool_panel_section_select_field, new_tool_panel_section=new_tool_panel_section, + readme_text=readme_text, message=message, status=status ) @web.expose diff -r 9b403ed9ec16789e2100e9921bed956789b47613 -r 319c7ee6873c53e57aa6b37271cb7c6afb067612 lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -86,6 +86,7 @@ self.cloud_controller_instance = False self.server_name = '' self.job_manager = '' + self.default_job_handlers = [] self.job_handlers = [] self.tool_handlers = [] self.tool_runners = [] diff -r 9b403ed9ec16789e2100e9921bed956789b47613 -r 319c7ee6873c53e57aa6b37271cb7c6afb067612 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -773,6 +773,25 @@ ( galaxy_url, url_for( '/', qualified=True ), encoded_repo_info_dict, str( includes_tools ) ) return trans.response.send_redirect( url ) @web.expose + def get_readme( self, trans, **kwd ): + """ + If the received changeset_revision includes a file named readme (case ignored), return it's contents. + """ + name = kwd[ 'name' ] + owner = kwd[ 'owner' ] + changeset_revision = kwd[ 'changeset_revision' ] + repository = get_repository_by_name_and_owner( trans, name, owner ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + for root, dirs, files in os.walk( repo_dir ): + for name in files: + if name.lower() in [ 'readme', 'read_me' ]: + f = open( os.path.join( root, name ), 'r' ) + text = f.read() + f.close() + return str( text ) + return '' + @web.expose def get_tool_versions( self, trans, **kwd ): """ For each valid /downloadable change set (up to the received changeset_revision) in the diff -r 9b403ed9ec16789e2100e9921bed956789b47613 -r 319c7ee6873c53e57aa6b37271cb7c6afb067612 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -62,3 +62,13 @@ </form></div></div> +%if readme_text: + <div class="toolForm"> + <div class="toolFormTitle">Repository README file (may contain important installation or license information)</div> + <div class="toolFormBody"> + <div class="form-row"> + <pre>${readme_text}</pre> + </div> + </div> + </div> +%endif Repository URL: 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commit/galaxy-central: greg: If installing a single tool shed repository that contains a readme file, display its contents on the tool panel section selection page.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/41aa295fa871/ changeset: 41aa295fa871 user: greg date: 2012-04-02 17:25:46 summary: If installing a single tool shed repository that contains a readme file, display its contents on the tool panel section selection page. affected #: 4 files diff -r e8e6bb539b85533d8aff54adbacfcfd548ba8a8e -r 41aa295fa871ef7f81f12a701ec59acc16c3ae9c lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -367,6 +367,22 @@ shed_tool_conf = shed_tool_conf.replace( './', '', 1 ) shed_tool_conf_select_field = None tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) + if includes_tools: + # If we're installing a single repository that contains a readme file, get it's contents to display. + decoded_repo_info_dict = tool_shed_decode( repo_info_dict ) + if len( decoded_repo_info_dict ) == 1: + name = decoded_repo_info_dict.keys()[ 0 ] + repo_info_tuple = decoded_repo_info_dict[ name ] + description, repository_clone_url, changeset_revision = repo_info_tuple + owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) ) + url = '%s/repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( tool_shed_url, name, owner, changeset_revision ) + response = urllib2.urlopen( url ) + readme_text = response.read() + response.close() + else: + readme_text = '' + else: + readme_text = '' return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict, @@ -375,6 +391,7 @@ shed_tool_conf_select_field=shed_tool_conf_select_field, tool_panel_section_select_field=tool_panel_section_select_field, new_tool_panel_section=new_tool_panel_section, + readme_text=readme_text, message=message, status=status ) @web.expose diff -r e8e6bb539b85533d8aff54adbacfcfd548ba8a8e -r 41aa295fa871ef7f81f12a701ec59acc16c3ae9c lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -86,6 +86,7 @@ self.cloud_controller_instance = False self.server_name = '' self.job_manager = '' + self.default_job_handlers = [] self.job_handlers = [] self.tool_handlers = [] self.tool_runners = [] diff -r e8e6bb539b85533d8aff54adbacfcfd548ba8a8e -r 41aa295fa871ef7f81f12a701ec59acc16c3ae9c lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -773,6 +773,25 @@ ( galaxy_url, url_for( '/', qualified=True ), encoded_repo_info_dict, str( includes_tools ) ) return trans.response.send_redirect( url ) @web.expose + def get_readme( self, trans, **kwd ): + """ + If the received changeset_revision includes a file named readme (case ignored), return it's contents. + """ + name = kwd[ 'name' ] + owner = kwd[ 'owner' ] + changeset_revision = kwd[ 'changeset_revision' ] + repository = get_repository_by_name_and_owner( trans, name, owner ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + for root, dirs, files in os.walk( repo_dir ): + for name in files: + if name.lower() in [ 'readme', 'read_me' ]: + f = open( os.path.join( root, name ), 'r' ) + text = f.read() + f.close() + return str( text ) + return '' + @web.expose def get_tool_versions( self, trans, **kwd ): """ For each valid /downloadable change set (up to the received changeset_revision) in the diff -r e8e6bb539b85533d8aff54adbacfcfd548ba8a8e -r 41aa295fa871ef7f81f12a701ec59acc16c3ae9c templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -62,3 +62,13 @@ </form></div></div> +%if readme_text: + <div class="toolForm"> + <div class="toolFormTitle">Repository README file (may contain important installation or license information)</div> + <div class="toolFormBody"> + <div class="form-row"> + <pre>${readme_text}</pre> + </div> + </div> + </div> +%endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for DiskObjectStore._construct_path recieving extra keywords.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e8e6bb539b85/ changeset: e8e6bb539b85 user: dan date: 2012-04-02 17:00:56 summary: Fix for DiskObjectStore._construct_path recieving extra keywords. affected #: 1 file diff -r 6ceefdcedee595904231c4bc2ee78417bfec637a -r e8e6bb539b85533d8aff54adbacfcfd548ba8a8e lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -223,7 +223,7 @@ if not os.path.exists(path): return self._construct_path(obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name) - def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, **kwargs): """ Construct the expected absolute path for accessing the object identified by `obj`.id. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for call to object_store.update_from_file for collect primary data in tools/__init__.py.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6ceefdcedee5/ changeset: 6ceefdcedee5 user: dan date: 2012-04-02 16:48:27 summary: Fix for call to object_store.update_from_file for collect primary data in tools/__init__.py. affected #: 1 file diff -r 24b474fd29bcfddabd996e985c72872e21c8c0f8 -r 6ceefdcedee595904231c4bc2ee78417bfec637a lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2180,7 +2180,7 @@ sa_session=self.sa_session ) self.app.security_agent.copy_dataset_permissions( outdata.dataset, child_dataset.dataset ) # Move data from temp location to dataset location - self.app.object_store.update_from_file(child_dataset.dataset, filename, create=True) + self.app.object_store.update_from_file(child_dataset.dataset, file_name=filename, create=True) self.sa_session.add( child_dataset ) self.sa_session.flush() child_dataset.set_size() @@ -2247,7 +2247,7 @@ self.sa_session.add( primary_data ) self.sa_session.flush() # Move data from temp location to dataset location - self.app.object_store.update_from_file(primary_data.dataset, filename, create=True) + self.app.object_store.update_from_file(primary_data.dataset, file_name=filename, create=True) primary_data.set_size() primary_data.name = "%s (%s)" % ( outdata.name, designation ) primary_data.info = outdata.info Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for --multiallelic in Unified Genotyper.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/24b474fd29bc/ changeset: 24b474fd29bc user: dan date: 2012-04-02 16:09:00 summary: Fix for --multiallelic in Unified Genotyper. affected #: 1 file diff -r 4dd7564268fcd4f5bd3275fa3b5da012b7adefb5 -r 24b474fd29bcfddabd996e985c72872e21c8c0f8 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -138,6 +138,7 @@ --excludeAnnotation "${annotation}" #end for #end if + ${analysis_param_type.multiallelic} ' ## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': ## -p '--annotation "SnpEff"' @@ -145,7 +146,6 @@ ## #else: ## -p '--excludeAnnotation "SnpEff"' ## #end if - ${analysis_param_type.multiallelic} #end if </command><inputs> 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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