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commit/galaxy-central: fubar: Added sanitisation of the only user controllable parameter and removed use of shell in subprocess.popen to
by Bitbucket 10 Aug '12

10 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/18462a6cbf46/ changeset: 18462a6cbf46 user: fubar date: 2012-08-10 12:53:00 summary: Added sanitisation of the only user controllable parameter and removed use of shell in subprocess.popen to improve security and reduce breakage risk from ugly filenames pointed out by A Nonymous in https://bitbucket.org/galaxy/galaxy-central/issue/793/rgenetics-rgfastqcpy-… affected #: 2 files diff -r c6e1ef62c40b6c212210356fa59222b60645070b -r 18462a6cbf46566307eaa4fd33c8891b5979d699 tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -13,8 +13,13 @@ """ - -import os,sys,subprocess,optparse,shutil,tempfile +import re +import os +import sys +import subprocess +import optparse +import shutil +import tempfile from rgutils import getFileString class FastQC(): @@ -38,25 +43,26 @@ """ serr = '' - dummy,tlog = tempfile.mkstemp(prefix='rgFastQClog') + dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir) sout = open(tlog, 'w') fastq = os.path.basename(self.opts.input) - cl = [self.opts.executable,'-o %s' % self.opts.outputdir] + cl = [self.opts.executable,'--outdir=%s' % self.opts.outputdir] if self.opts.informat in ['sam','bam']: cl.append('-f %s' % self.opts.informat) if self.opts.contaminants <> None : cl.append('-c %s' % self.opts.contaminants) # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30 # use a symlink in a temporary directory so that the FastQC report reflects the history input file name - fastqinfilename = os.path.basename(self.opts.inputfilename).replace(' ','_') + fastqinfilename = re.sub('[^a-zA-Z0-9_]+', '', os.path.basename(self.opts.inputfilename)) link_name = os.path.join(self.opts.outputdir, fastqinfilename) os.symlink(self.opts.input, link_name) cl.append(link_name) - p = subprocess.Popen(' '.join(cl), shell=True, stderr=sout, stdout=sout, cwd=self.opts.outputdir) + sout.write('# FastQC cl = %s\n' % ' '.join(cl)) + sout.flush() + p = subprocess.Popen(cl, shell=False, stderr=sout, stdout=sout, cwd=self.opts.outputdir) retval = p.wait() sout.close() runlog = open(tlog,'r').readlines() - os.unlink(tlog) os.unlink(link_name) flist = os.listdir(self.opts.outputdir) # fastqc plays games with its output directory name. eesh odpath = None diff -r c6e1ef62c40b6c212210356fa59222b60645070b -r 18462a6cbf46566307eaa4fd33c8891b5979d699 tools/rgenetics/rgFastQC.xml --- a/tools/rgenetics/rgFastQC.xml +++ b/tools/rgenetics/rgFastQC.xml @@ -1,5 +1,5 @@ -<tool name="Fastqc: Fastqc QC" id="fastqc" version="0.5"> - <description>using FastQC from Babraham</description> +<tool name="FastQC:Read QC" id="fastqc" version="0.51"> + <description>reports using FastQC</description><command interpreter="python"> rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc" #if $contaminants.dataset and str($contaminants) > '' @@ -21,7 +21,7 @@ help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/></inputs><outputs> - <data format="html" name="html_file" label="${out_prefix}_${on_string}.html" /> + <data format="html" name="html_file" label="${out_prefix}_${input_file.name}.html" /></outputs><tests><test> @@ -51,15 +51,18 @@ - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application -**FastQC documentation** -This is a Galaxy interface to the external package FastQC_. -Specific documentation on FastQC can be found on that site. +----- + + +.. class:: infomark + +**FastQC** + +This is a Galaxy wrapper. It merely exposes the external package FastQC_ which is documented at FastQC_ +Kindly acknowledge it as well as this tool if you use it. FastQC incorporates the Picard-tools_ libraries for sam/bam processing. - .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - The contaminants file parameter was borrowed from the independently developed fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson. @@ -69,7 +72,10 @@ **Inputs and outputs** -This wrapper will accept any fastq file as well as sam or bam as the primary file to check. +FastQC_ is the best place to look for documentation - it's very good. +A summary follows below for those in a tearing hurry. + +This wrapper will accept a Galaxy fastq, sam or bam as the input read file to check. It will also take an optional file containing a list of contaminants information, in the form of a tab-delimited file with 2 columns, name and sequence. @@ -88,6 +94,8 @@ - Kmer Content All except Basic Statistics and Overrepresented sequences are plots. + .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ + .. _Picard-tools: http://picard.sourceforge.net/index.shtml </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Data providers: unified and comprehensive handling of differences between different chromosome naming schemes.
by Bitbucket 09 Aug '12

09 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c6e1ef62c40b/ changeset: c6e1ef62c40b user: jgoecks date: 2012-08-09 23:32:47 summary: Data providers: unified and comprehensive handling of differences between different chromosome naming schemes. affected #: 1 file diff -r 3b5db939aebe61addd6f0b8d0c14267cf16c4144 -r c6e1ef62c40b6c212210356fa59222b60645070b lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -44,6 +44,21 @@ if read[ end_pos_index ] > max_high: max_high = read[ end_pos_index ] return max_low, max_high + +def _convert_between_ucsc_and_ensemble_naming( chrom ): + ''' + Convert between UCSC chromosome ('chr1') naming conventions and Ensembl + naming conventions ('1') + ''' + if chrom.startswith( 'chr' ): + # Convert from UCSC to Ensembl + return chrom[ 3: ] + else: + # Convert from Ensembl to UCSC + return 'chr' + chrom + +def _chrom_naming_matches( chrom1, chrom2 ): + return ( chrom1.startswith( 'chr' ) and chrom2.startswith( 'chr' ) ) or ( not chrom1.startswith( 'chr' ) and not chrom2.startswith( 'chr' ) ) class TracksDataProvider( object ): """ Base class for tracks data providers. """ @@ -159,7 +174,7 @@ return filters def get_default_max_vals( self ): - return 5000; + return 5000 # # -- Base mixins and providers -- @@ -262,12 +277,9 @@ tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) - # If chrom is not found in indexes, try removing the first three - # characters (e.g. 'chr') and see if that works. This enables the - # provider to handle chrome names defined as chrXXX and as XXX. - chrom = str(chrom) - if chrom not in tabix.contigs and chrom.startswith("chr") and (chrom[3:] in tabix.contigs): - chrom = chrom[3:] + # If chrom not in data, try alternative. + if chrom not in tabix.contigs: + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) return tabix.fetch(reference=chrom, start=start, end=end) @@ -409,11 +421,6 @@ rval.append( payload ) continue - # Simpler way to add stuff, but type casting is not done. - # Name, score, strand, thick start, thick end. - #end = min( len( feature ), 8 ) - #payload.extend( feature[ 3:end ] ) - # Name, strand, thick start, thick end. if length >= 4: payload.append(feature[3]) @@ -470,6 +477,14 @@ """ def get_iterator( self, chrom=None, start=None, end=None ): + # Read first line in order to match chrom naming format. + line = source.readline() + dataset_chrom = line.split()[0] + if not _chrom_naming_matches( chrom, dataset_chrom ): + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + # Undo read. + source.seek( 0 ) + def line_filter_iter(): for line in open( self.original_dataset.file_name ): if line.startswith( "track" ) or line.startswith( "browser" ): @@ -483,6 +498,7 @@ or ( end is not None and feature_end < start ): continue yield line + return line_filter_iter() # @@ -601,6 +617,14 @@ """ def get_iterator( self, chrom, start, end ): + # Read first line in order to match chrom naming format. + line = source.readline() + dataset_chrom = line.split()[0] + if not _chrom_naming_matches( chrom, dataset_chrom ): + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + # Undo read. + source.seek( 0 ) + def line_filter_iter(): for line in open( self.original_dataset.file_name ): if line.startswith("#"): @@ -616,6 +640,7 @@ if variant_chrom != chrom or variant_start > end or variant_end < start: continue yield line + return line_filter_iter() class SummaryTreeDataProvider( TracksDataProvider ): @@ -639,15 +664,11 @@ st = summary_tree_from_file( self.converted_dataset.file_name ) self.CACHE[filename] = st - # If chrom is not found in blocks, try removing the first three - # characters (e.g. 'chr') and see if that works. This enables the - # provider to handle chrome names defined as chrXXX and as XXX. - if chrom in st.chrom_blocks: - pass - elif chrom[3:] in st.chrom_blocks: - chrom = chrom[3:] - else: - return None + # Look for chrom in tree using both naming conventions. + if chrom not in st.chrom_blocks: + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + if chrom not in st.chrom_blocks: + return None # Get or compute level. if level: @@ -684,7 +705,7 @@ self.CACHE[filename] = st # Check for data. - return st.chrom_blocks.get(chrom, None) is not None or (chrom and st.chrom_blocks.get(chrom[3:], None) is not None) + return st.chrom_blocks.get(chrom, None) or st.chrom_blocks.get(_convert_between_ucsc_and_ensemble_naming(chrom), None) class BamDataProvider( TracksDataProvider, FilterableMixin ): """ @@ -727,13 +748,11 @@ try: data = bamfile.fetch(start=start, end=end, reference=chrom) except ValueError, e: - # Some BAM files do not prefix chromosome names with chr, try without - if chrom.startswith( 'chr' ): - try: - data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) - except ValueError: - return None - else: + # Try alternative chrom naming. + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + try: + data = bamfile.fetch( start=start, end=end, reference=chrom ) + except ValueError: return None # Write reads in region. @@ -757,13 +776,11 @@ try: data = bamfile.fetch(start=start, end=end, reference=chrom) except ValueError, e: - # Some BAM files do not prefix chromosome names with chr, try without - if chrom.startswith( 'chr' ): - try: - data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) - except ValueError: - return None - else: + # Try alternative chrom naming. + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + try: + data = bamfile.fetch( start=start, end=end, reference=chrom ) + except ValueError: return None return data @@ -1034,12 +1051,9 @@ source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) - # If chrom is not found in indexes, try removing the first three - # characters (e.g. 'chr') and see if that works. This enables the - # provider to handle chrome names defined as chrXXX and as XXX. - chrom = str(chrom) - if chrom not in index.indexes and chrom[3:] in index.indexes: - chrom = chrom[3:] + if chrom not in index.indexes: + # Try alternative naming. + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) return index.find(chrom, start, end) @@ -1091,6 +1105,14 @@ a file offset. """ source = open( self.original_dataset.file_name ) + + # Read first line in order to match chrom naming format. + line = source.readline() + dataset_chrom = line.split()[0] + if not _chrom_naming_matches( chrom, dataset_chrom ): + chrom = _convert_between_ucsc_and_ensemble_naming( chrom ) + # Undo read. + source.seek( 0 ) def features_in_region_iter(): offset = 0 @@ -1100,6 +1122,7 @@ if feature.chrom == chrom and feature_end > start and feature_start < end: yield feature, offset offset += feature.raw_size + return features_in_region_iter() def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): 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: Fixes to recent changes that broke the ability to install a tool shed repository to a local Galaxy instance.
by Bitbucket 09 Aug '12

09 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3b5db939aebe/ changeset: 3b5db939aebe user: greg date: 2012-08-09 17:37:47 summary: Fixes to recent changes that broke the ability to install a tool shed repository to a local Galaxy instance. affected #: 3 files diff -r 1eab72ce0a483dd8bb09e43d549b119879d5435d -r 3b5db939aebe61addd6f0b8d0c14267cf16c4144 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -132,7 +132,7 @@ tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v - metadata_dict = generate_metadata_for_changeset_revision( self.app, relative_install_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( self.app, relative_install_dir, repository_clone_url ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() diff -r 1eab72ce0a483dd8bb09e43d549b119879d5435d -r 3b5db939aebe61addd6f0b8d0c14267cf16c4144 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -598,7 +598,7 @@ invalid_tool_configs.append( name ) break if can_set_metadata: - metadata_dict = generate_tool_metadata( name, tool, repository_clone_url, metadata_dict ) + metadata_dict = generate_tool_metadata( os.path.join( root, name ), tool, repository_clone_url, metadata_dict ) else: invalid_file_tups.extend( invalid_files_and_errors_tups ) # Find all exported workflows diff -r 1eab72ce0a483dd8bb09e43d549b119879d5435d -r 3b5db939aebe61addd6f0b8d0c14267cf16c4144 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -684,7 +684,7 @@ Generate the metadata for the installed tool shed repository, among other things. This method is called from Galaxy (never the tool shed) when an admin is installing a new repository or reinstalling an uninstalled repository. """ - metadata_dict = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) tool_shed_repository.metadata = metadata_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() @@ -779,7 +779,7 @@ message = "The repository information has been updated." elif params.get( 'set_metadata_button', False ): repository_clone_url = generate_clone_url( trans, repository ) - metadata_dict = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) if metadata_dict: repository.metadata = metadata_dict trans.sa_session.add( repository ) @@ -1479,7 +1479,7 @@ update_repository( repo, latest_ctx_rev ) # Update the repository metadata. tool_shed = clean_tool_shed_url( tool_shed_url ) - metadata_dict = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision 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: Fix imports broken in 9f790bc90769 using patch from Bjorn Gruning.
by Bitbucket 09 Aug '12

09 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1eab72ce0a48/ changeset: 1eab72ce0a48 user: greg date: 2012-08-09 12:46:13 summary: Fix imports broken in 9f790bc90769 using patch from Bjorn Gruning. affected #: 1 file diff -r a10bb73f579386e67c52383b4c0722cb693d7cf9 -r 1eab72ce0a483dd8bb09e43d549b119879d5435d lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -2,7 +2,8 @@ import galaxy.tools.data from datetime import date, datetime, timedelta from time import strftime, gmtime -from galaxy import tools, util +from galaxy import util +from galaxy.tools import parameters from galaxy.datatypes.checkers import * from galaxy.util.json import * from galaxy.tools.search import ToolBoxSearch @@ -255,7 +256,7 @@ invalid_files_and_errors_tups = [] correction_msg = '' for input_param in tool.input_params: - if isinstance( input_param, tools.parameters.basic.SelectToolParameter ) and input_param.is_dynamic: + if isinstance( input_param, parameters.basic.SelectToolParameter ) and input_param.is_dynamic: # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, make sure all requirements exist. options = input_param.dynamic_options or input_param.options if options: 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: Fixes for setting versions for tools included in a repository in the tool shed.
by Bitbucket 08 Aug '12

08 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a10bb73f5793/ changeset: a10bb73f5793 user: greg date: 2012-08-08 22:15:06 summary: Fixes for setting versions for tools included in a repository in the tool shed. affected #: 1 file diff -r 6a7d9d3714e99f613fb8dbcdb709e7e2a2b813e0 -r a10bb73f579386e67c52383b4c0722cb693d7cf9 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -122,7 +122,12 @@ else: for tool_dict in tool_dicts: # We have at least 2 changeset revisions to compare tool guids and tool ids. - parent_id = get_parent_id( trans, id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], changeset_revisions[ 0:index ] ) + parent_id = get_parent_id( trans, + id, + tool_dict[ 'id' ], + tool_dict[ 'version' ], + tool_dict[ 'guid' ], + changeset_revisions[ 0:index ] ) tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id if tool_versions_dict: repository_metadata.tool_versions = tool_versions_dict @@ -149,7 +154,8 @@ # Delete all repository_metadata records associated with the repository that have a changeset_revision that is not in changeset_revisions. # We sometimes see multiple records with the same changeset revision value - no idea how this happens. We'll assume we can delete the older # records, so we'll order by update_time descending and delete records that have the same changeset_revision we come across later.. - changeset_revisions_checked = [] + changeset_revisions_checked = [] + cleaned_changeset_revisions = [] for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ .order_by( trans.model.RepositoryMetadata.table.c.changeset_revision, @@ -159,6 +165,9 @@ if can_delete: trans.sa_session.delete( repository_metadata ) trans.sa_session.flush() + else: + cleaned_changeset_revisions.append( changeset_revision ) + return cleaned_changeset_revisions def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision is an ancestor of # current_changeset_revision which is associated with current_metadata_dict. A new repository_metadata record will be created only @@ -277,7 +286,7 @@ return file_path return None def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ): - downloadable = 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict + downloadable = is_downloadable( metadata_dict ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: repository_metadata.metadata = metadata_dict @@ -289,6 +298,7 @@ downloadable=downloadable ) trans.sa_session.add( repository_metadata ) trans.sa_session.flush() + return repository_metadata def generate_clone_url( trans, repository_id ): """Generate the URL for cloning a repository.""" repository = get_repository( trans, repository_id ) @@ -562,6 +572,8 @@ util.send_mail( frm, to, subject, body, trans.app.config ) except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) +def is_downloadable( metadata_dict ): + return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict def load_tool( trans, config_file ): """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 @@ -797,7 +809,7 @@ elif comparison == 'not equal and not subset': metadata_changeset_revision = ancestor_changeset_revision metadata_dict = ancestor_metadata_dict - create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = current_changeset_revision ancestor_metadata_dict = current_metadata_dict @@ -809,7 +821,7 @@ metadata_changeset_revision = current_changeset_revision metadata_dict = current_metadata_dict # We're at the end of the change log. - create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None @@ -820,7 +832,7 @@ metadata_dict = ancestor_metadata_dict if not ctx.children(): # We're at the end of the change log. - create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None @@ -830,10 +842,9 @@ except: pass # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. - clean_repository_metadata( trans, id, changeset_revisions ) + cleaned_changeset_revisions = clean_repository_metadata( trans, id, changeset_revisions ) # Set tool version information for all downloadable changeset revisions. - downloadable_changeset_revisions = [ rm.changeset_revision for rm in repository.downloadable_revisions ] - add_repository_metadata_tool_versions( trans, id, downloadable_changeset_revisions ) + add_repository_metadata_tool_versions( trans, id, cleaned_changeset_revisions ) def set_repository_metadata( trans, repository, content_alert_str='', **kwd ): """ Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset @@ -846,23 +857,22 @@ repo = hg.repository( get_configured_ui(), repo_dir ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, repo_dir, repository_clone_url ) if metadata_dict: + downloadable = is_downloadable( metadata_dict ) repository_metadata = None if new_tool_metadata_required( trans, repository, metadata_dict ) or new_workflow_metadata_required( trans, repository, metadata_dict ): # Create a new repository_metadata table row. - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - try: - trans.sa_session.flush() - # If this is the first record stored for this repository, see if we need to send any email alerts. - if len( repository.downloadable_revisions ) == 1: - handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) - except TypeError, e: - message = "Unable to save metadata for this repository, exception: %s" % str( e ) - status = 'error' + repository_metadata = create_or_update_repository_metadata( trans, + trans.security.encode_id( repository.id ), + repository, + repository.tip, + metadata_dict ) + # If this is the first record stored for this repository, see if we need to send any email alerts. + if len( repository.downloadable_revisions ) == 1: + handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: repository_metadata = get_latest_repository_metadata( trans, repository.id ) if repository_metadata: - downloadable = 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict + downloadable = is_downloadable( metadata_dict ) # Update the last saved repository_metadata table row. repository_metadata.changeset_revision = repository.tip repository_metadata.metadata = metadata_dict @@ -871,11 +881,22 @@ trans.sa_session.flush() else: # There are no tools in the repository, and we're setting metadata on the repository tip. - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() + repository_metadata = create_or_update_repository_metadata( trans, + trans.security.encode_id( repository.id ), + repository, + repository.tip, + metadata_dict ) if 'tools' in metadata_dict and repository_metadata and status != 'error': - add_repository_metadata_tool_versions( trans, trans.security.encode_id( repository.id ), [ repository_metadata.changeset_revision ] ) + # Set tool versions on the new downloadable change set. The order of the list of changesets is critical, so we use the repo's changelog. + downloadable_changeset_revisions = [ rm.changeset_revision for rm in repository.downloadable_revisions ] + changeset_revisions = [] + for changeset in repo.changelog: + changeset_revision = str( repo.changectx( changeset ) ) + if changeset_revision in downloadable_changeset_revisions: + changeset_revisions.append( changeset_revision ) + # Now append the latest changeset_revision we just updated above. + changeset_revisions.append( repository_metadata.changeset_revision ) + add_repository_metadata_tool_versions( trans, trans.security.encode_id( repository.id ), changeset_revisions ) elif len( repo ) == 1 and not invalid_file_tups: message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." 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: Apply changes to rendering tool help to the tool shed's version of the tool form mako template so tools can be displayed again in the tool shed.
by Bitbucket 08 Aug '12

08 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6a7d9d3714e9/ changeset: 6a7d9d3714e9 user: greg date: 2012-08-08 20:46:59 summary: Apply changes to rendering tool help to the tool shed's version of the tool form mako template so tools can be displayed again in the tool shed. affected #: 1 file diff -r 9af69e5a6db262ab5c277674c42cf0081259d0de -r 6a7d9d3714e99f613fb8dbcdb709e7e2a2b813e0 templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -186,12 +186,15 @@ <div class="toolHelp"><div class="toolHelpBody"><% + tool_help = tool.help + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ) ) # Convert to unicode to display non-ascii characters. - if type( tool.help ) is not unicode: - tool.help = unicode( tool.help, 'utf-8') + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') %> - ${tool.help} - </div> + ${tool_help} + </div></div> %endif %else: 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: carlfeberhard: fix for missing tool-data/shared/ucsc/publicbuilds.txt (related to test failure on functional.test_get_data.UploadData.test_0020_upload_file)
by Bitbucket 08 Aug '12

08 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9af69e5a6db2/ changeset: 9af69e5a6db2 user: carlfeberhard date: 2012-08-08 20:39:40 summary: fix for missing tool-data/shared/ucsc/publicbuilds.txt (related to test failure on functional.test_get_data.UploadData.test_0020_upload_file) affected #: 1 file diff -r 9f790bc90769df7a4f84f103707bdd8ceaf1115d -r 9af69e5a6db262ab5c277674c42cf0081259d0de buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -68,8 +68,13 @@ datatypes_conf.xml.sample universe_wsgi.ini.sample tool_data_table_conf.xml.sample +migrated_tools_conf.xml.sample +tool-data/shared/ensembl/builds.txt.sample +tool-data/shared/igv/igv_build_sites.txt.sample +tool-data/shared/ncbi/builds.txt.sample +tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/shared/ucsc/builds.txt.sample -migrated_tools_conf.xml.sample +tool-data/shared/ucsc/publicbuilds.txt.sample " DIRS=" 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: More fixes for setting metadata on repositories in the toool shed. Change set includes other miscellaneous fixes, including the elimination of some problematice historical code that managed temporary working directories which resulted in problematic race conditions.
by Bitbucket 08 Aug '12

08 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9f790bc90769/ changeset: 9f790bc90769 user: greg date: 2012-08-08 20:31:46 summary: More fixes for setting metadata on repositories in the toool shed. Change set includes other miscellaneous fixes, including the elimination of some problematice historical code that managed temporary working directories which resulted in problematic race conditions. affected #: 7 files diff -r 5f2db4a18d3d3bef78f0a330cc6073f34db7c88b -r 9f790bc90769df7a4f84f103707bdd8ceaf1115d lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -2,7 +2,7 @@ Manage automatic installation of tools configured in the xxx.xml files in ~/scripts/migrate_tools (e.g., 0002_tools.xml). All of the tools were at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool shed. """ -import urllib2 +import urllib2, tempfile from galaxy.tools import ToolSection from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * @@ -132,7 +132,7 @@ tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v - metadata_dict = generate_metadata_using_disk_files( self.toolbox, relative_install_dir, repository_clone_url ) + metadata_dict = generate_metadata_for_changeset_revision( self.app, relative_install_dir, repository_clone_url ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() @@ -142,7 +142,7 @@ else: tool_dependencies = None if 'tools' in metadata_dict: - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() repository_tools_tups = get_repository_tools_tups( self.app, metadata_dict ) if repository_tools_tups: sample_files = metadata_dict.get( 'sample_files', [] ) @@ -195,7 +195,7 @@ tool_shed_repository.includes_datatypes = True self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() datatypes_config = get_config_from_repository( self.app, 'datatypes_conf.xml', tool_shed_repository, diff -r 5f2db4a18d3d3bef78f0a330cc6073f34db7c88b -r 9f790bc90769df7a4f84f103707bdd8ceaf1115d lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -2,7 +2,7 @@ import galaxy.tools.data from datetime import date, datetime, timedelta from time import strftime, gmtime -from galaxy import util +from galaxy import tools, util from galaxy.datatypes.checkers import * from galaxy.util.json import * from galaxy.tools.search import ToolBoxSearch @@ -247,6 +247,52 @@ except: pass return converter_path, display_path +def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files ): + """ + Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make + sure the files exist. + """ + invalid_files_and_errors_tups = [] + correction_msg = '' + for input_param in tool.input_params: + if isinstance( input_param, tools.parameters.basic.SelectToolParameter ) and input_param.is_dynamic: + # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, make sure all requirements exist. + options = input_param.dynamic_options or input_param.options + if options: + if options.tool_data_table or options.missing_tool_data_table_name: + # Make sure the repository contains a tool_data_table_conf.xml.sample file. + sample_tool_data_table_conf = get_config_from_disk( 'tool_data_table_conf.xml.sample', repo_dir ) + if sample_tool_data_table_conf: + error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_tool_data_table_conf ) + if error: + invalid_files_and_errors_tups.append( ( 'tool_data_table_conf.xml.sample', correction_msg ) ) + else: + options.missing_tool_data_table_name = None + else: + correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample " + correction_msg += "to the repository that includes the required entry to correct this error.<br/>" + invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) + if options.index_file or options.missing_index_file: + # Make sure the repository contains the required xxx.loc.sample file. + index_file = options.index_file or options.missing_index_file + index_file_name = strip_path( index_file ) + sample_found = False + for sample_file in sample_files: + sample_file_name = strip_path( sample_file ) + if sample_file_name == '%s.sample' % index_file_name: + options.index_file = index_file_name + options.missing_index_file = None + if options.tool_data_table: + options.tool_data_table.missing_index_file = None + sample_found = True + break + if not sample_found: + correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) + correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) + invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( app ) + return invalid_files_and_errors_tups def config_elems_to_xml_file( app, config_elems, config_filename, tool_path ): # Persist the current in-memory list of config_elems to a file named by the value of config_filename. fd, filename = tempfile.mkstemp() @@ -383,7 +429,7 @@ def create_tool_dependency_objects( app, tool_shed_repository, current_changeset_revision, set_status=True ): # Create or update a ToolDependency for each entry in tool_dependencies_config. This method is called when installing a new tool_shed_repository. tool_dependency_objects = [] - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = get_config_from_repository( app, 'tool_dependencies.xml', @@ -501,6 +547,76 @@ if not can_generate_dependency_metadata: break return can_generate_dependency_metadata +def generate_metadata_for_changeset_revision( app, repository_files_dir, repository_clone_url ): + """ + Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, + the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's + disk files, so the value of repository_files_dir will not always be repository.repo_path (it could be a temporary directory containing a clone). + """ + metadata_dict = {} + invalid_file_tups = [] + invalid_tool_configs = [] + tool_dependencies_config = None + datatypes_config = get_config_from_disk( 'datatypes_conf.xml', repository_files_dir ) + if datatypes_config: + metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) + sample_files = get_sample_files_from_disk( repository_files_dir ) + if sample_files: + metadata_dict[ 'sample_files' ] = sample_files + # Find all tool configs and exported workflows. + for root, dirs, files in os.walk( repository_files_dir ): + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + if '.hg' in dirs: + dirs.remove( '.hg' ) + for name in files: + # Find all tool configs. + if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): + full_path = os.path.abspath( os.path.join( root, name ) ) + if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] + or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): + try: + # Make sure we're looking at a tool config and not a display application config or something else. + element_tree = util.parse_xml( full_path ) + element_tree_root = element_tree.getroot() + is_tool = element_tree_root.tag == 'tool' + except Exception, e: + print "Error parsing %s", full_path, ", exception: ", str( e ) + is_tool = False + if is_tool: + try: + tool = app.toolbox.load_tool( full_path ) + except Exception, e: + tool = None + invalid_tool_configs.append( name ) + if tool is not None: + invalid_files_and_errors_tups = check_tool_input_params( app, repository_files_dir, name, tool, sample_files ) + can_set_metadata = True + for tup in invalid_files_and_errors_tups: + if name in tup: + can_set_metadata = False + invalid_tool_configs.append( name ) + break + if can_set_metadata: + metadata_dict = generate_tool_metadata( name, tool, repository_clone_url, metadata_dict ) + else: + invalid_file_tups.extend( invalid_files_and_errors_tups ) + # Find all exported workflows + elif name.endswith( '.ga' ): + relative_path = os.path.join( root, name ) + fp = open( relative_path, 'rb' ) + workflow_text = fp.read() + fp.close() + exported_workflow_dict = from_json_string( workflow_text ) + if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) + if 'tools' in metadata_dict: + # This step must be done after metadata for tools has been defined. + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', repository_files_dir ) + if tool_dependencies_config: + metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) + if invalid_tool_configs: + metadata_dict [ 'invalid_tools' ] = invalid_tool_configs + return metadata_dict, invalid_file_tups def generate_package_dependency_metadata( elem, tool_dependencies_dict ): """The value of package_name must match the value of the "package" type in the tool config's <requirements> tag set.""" requirements_dict = {} @@ -517,58 +633,6 @@ if requirements_dict: tool_dependencies_dict[ dependency_key ] = requirements_dict return tool_dependencies_dict -def generate_metadata_using_disk_files( toolbox, relative_install_dir, repository_clone_url ): - """Generate metadata using only the repository files on disk - files are not retrieved from the repository manifest.""" - metadata_dict = {} - tool_dependencies_config = None - datatypes_config = get_config_from_disk( 'datatypes_conf.xml', relative_install_dir ) - if datatypes_config: - metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) - sample_files = get_sample_files_from_disk( relative_install_dir ) - if sample_files: - metadata_dict[ 'sample_files' ] = sample_files - # Find all tool configs and exported workflows. - for root, dirs, files in os.walk( relative_install_dir ): - if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: - if '.hg' in dirs: - dirs.remove( '.hg' ) - for name in files: - # Find all tool configs. - if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): - full_path = os.path.abspath( os.path.join( root, name ) ) - if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] - or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): - try: - # Make sure we're looking at a tool config and not a display application config or something else. - element_tree = util.parse_xml( full_path ) - element_tree_root = element_tree.getroot() - is_tool = element_tree_root.tag == 'tool' - except Exception, e: - log.debug( "Error parsing %s, exception: %s" % ( full_path, str( e ) ) ) - is_tool = False - if is_tool: - try: - tool = toolbox.load_tool( full_path ) - except Exception, e: - tool = None - if tool is not None: - tool_config = os.path.join( root, name ) - metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) - # Find all exported workflows - elif name.endswith( '.ga' ): - relative_path = os.path.join( root, name ) - fp = open( relative_path, 'rb' ) - workflow_text = fp.read() - fp.close() - exported_workflow_dict = from_json_string( workflow_text ) - if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': - metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) - if 'tools' in metadata_dict: - # This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) - return metadata_dict def generate_tool_guid( repository_clone_url, tool ): """ Generate a guid for the installed tool. It is critical that this guid matches the guid for @@ -1266,7 +1330,7 @@ def load_installed_datatypes( app, repository, relative_install_dir, deactivate=False ): # Load proprietary datatypes and return information needed for loading proprietary datatypes converters and display applications later. metadata = repository.metadata - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() repository_dict = None datatypes_config = get_config_from_repository( app, 'datatypes_conf.xml', @@ -1293,17 +1357,6 @@ def load_installed_display_applications( app, installed_repository_dict, deactivate=False ): # Load or deactivate proprietary datatype display applications app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, deactivate=deactivate ) -def make_tmp_directory(): - tmp_dir = os.getenv( 'TMPDIR', '' ) - if tmp_dir: - tmp_dir = tmp_dir.strip() - else: - home_dir = os.getenv( 'HOME' ) - tmp_dir = os.path.join( home_dir, 'tmp' ) - work_dir = os.path.join( tmp_dir, 'work_tmp' ) - if not os.path.exists( work_dir ): - os.makedirs( work_dir ) - return work_dir def open_repository_files_folder( trans, folder_path ): try: files_list = get_repository_files( trans, folder_path ) diff -r 5f2db4a18d3d3bef78f0a330cc6073f34db7c88b -r 9f790bc90769df7a4f84f103707bdd8ceaf1115d lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -1,4 +1,4 @@ -import urllib2 +import urllib2, tempfile from galaxy.web.controllers.admin import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * @@ -522,7 +522,7 @@ # Get the tool_shed_repository from one of the tool_dependencies. message = '' tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = get_config_from_repository( trans.app, 'tool_dependencies.xml', @@ -654,7 +654,7 @@ message += "from the installed repository's <b>Repository Actions</b> menu. " status = 'error' if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata: - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() # Install tool dependencies. update_tool_shed_repository_status( trans.app, tool_shed_repository, @@ -684,7 +684,7 @@ Generate the metadata for the installed tool shed repository, among other things. This method is called from Galaxy (never the tool shed) when an admin is installing a new repository or reinstalling an uninstalled repository. """ - metadata_dict = generate_metadata_using_disk_files( trans.app.toolbox, relative_install_dir, repository_clone_url ) + metadata_dict = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) tool_shed_repository.metadata = metadata_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() @@ -695,7 +695,7 @@ repository_tools_tups = get_repository_tools_tups( trans.app, metadata_dict ) if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() repository_tools_tups = handle_missing_data_table_entry( trans.app, tool_shed_repository, tool_shed_repository.changeset_revision, @@ -726,7 +726,7 @@ tool_shed_repository.includes_datatypes = True trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() datatypes_config = get_config_from_repository( trans.app, 'datatypes_conf.xml', tool_shed_repository, @@ -779,7 +779,7 @@ message = "The repository information has been updated." elif params.get( 'set_metadata_button', False ): repository_clone_url = generate_clone_url( trans, repository ) - metadata_dict = generate_metadata_using_disk_files( trans.app.toolbox, relative_install_dir, repository_clone_url ) + metadata_dict = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) if metadata_dict: repository.metadata = metadata_dict trans.sa_session.add( repository ) @@ -1479,7 +1479,7 @@ update_repository( repo, latest_ctx_rev ) # Update the repository metadata. tool_shed = clean_tool_shed_url( tool_shed_url ) - metadata_dict = generate_metadata_using_disk_files( trans.app.toolbox, relative_install_dir, repository_clone_url ) + metadata_dict = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision diff -r 5f2db4a18d3d3bef78f0a330cc6073f34db7c88b -r 9f790bc90769df7a4f84f103707bdd8ceaf1115d lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1,15 +1,13 @@ -import os, string, socket, logging, simplejson, binascii +import os, string, socket, logging, simplejson, binascii, tempfile from time import strftime from datetime import * from galaxy.datatypes.checkers import * from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * -from galaxy.util.shed_util import clone_repository, copy_sample_file, generate_datatypes_metadata, generate_tool_dependency_metadata, generate_tool_metadata -from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_config_from_disk, get_configured_ui -from galaxy.util.shed_util import get_named_tmpfile_from_ctx, get_sample_files_from_disk, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH -from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path, to_html_escaped -from galaxy.util.shed_util import to_html_str, update_repository +from galaxy.util.shed_util import clone_repository, generate_metadata_for_changeset_revision, get_changectx_for_changeset, get_config_from_disk +from galaxy.util.shed_util import get_configured_ui, get_named_tmpfile_from_ctx, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH +from galaxy.util.shed_util import reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -107,11 +105,8 @@ trans.sa_session.flush() return item_rating -## ---- Utility methods ------------------------------------------------------- - def add_repository_metadata_tool_versions( trans, id, changeset_revisions ): - # If a repository includes tools, build a dictionary of { 'tool id' : 'parent tool id' } - # pairs for each tool in each changeset revision. + # If a repository includes tools, build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision. for index, changeset_revision in enumerate( changeset_revisions ): tool_versions_dict = {} repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) @@ -120,9 +115,8 @@ if metadata: tool_dicts = metadata.get( 'tools', [] ) if index == 0: - # The first changset_revision is a special case because it will have no ancestor - # changeset_revisions in which to match tools. The parent tool id for tools in - # the first changeset_revision will be the "old_id" in the tool config. + # The first changset_revision is a special case because it will have no ancestor changeset_revisions in which to match tools. + # The parent tool id for tools in the first changeset_revision will be the "old_id" in the tool config. for tool_dict in tool_dicts: tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] else: @@ -134,43 +128,6 @@ repository_metadata.tool_versions = tool_versions_dict trans.sa_session.add( repository_metadata ) trans.sa_session.flush() -def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True ): - """Build a SelectField whose options are the changeset_rev strings of all downloadable revisions of the received repository.""" - repo = hg.repository( get_configured_ui(), repository.repo_path ) - options = [] - changeset_tups = [] - refresh_on_change_values = [] - for repository_metadata in repository.downloadable_revisions: - changeset_revision = repository_metadata.changeset_revision - ctx = get_changectx_for_changeset( repo, changeset_revision ) - if ctx: - rev = '%04d' % ctx.rev() - label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) - else: - rev = '-1' - label = "-1:%s" % changeset_revision - changeset_tups.append( ( rev, label, changeset_revision ) ) - refresh_on_change_values.append( changeset_revision ) - # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, - # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time. - for changeset_tup in sorted( changeset_tups ): - # Display the latest revision first. - options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) ) - if add_id_to_name: - name = 'changeset_revision_%d' % repository.id - else: - name = 'changeset_revision' - select_field = SelectField( name=name, - refresh_on_change=True, - refresh_on_change_values=refresh_on_change_values ) - for option_tup in options: - selected = selected_value and option_tup[1] == selected_value - select_field.add_option( option_tup[0], option_tup[1], selected=selected ) - return select_field -def changeset_is_downloadable( metadata_dict ): - # A RepositoryMetadata record will be created if metadata_dict includes only invalid stuff like 'invalid_tools', but in this case - # it won't be downloadable. - return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict def changeset_is_malicious( trans, id, changeset_revision, **kwd ): """Check the malicious flag in repository metadata for a specified change set""" repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) @@ -188,55 +145,6 @@ if user_email in admin_users: return True return False -def check_tool_input_params( trans, repo_dir, tool_config, tool, sample_files, invalid_files ): - """ - Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make - sure the files exist. - """ - can_set_metadata = True - correction_msg = '' - for input_param in tool.input_params: - if isinstance( input_param, tools.parameters.basic.SelectToolParameter ) and input_param.is_dynamic: - # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, make sure all requirements exist. - options = input_param.dynamic_options or input_param.options - if options: - if options.tool_data_table or options.missing_tool_data_table_name: - # Make sure the repository contains a tool_data_table_conf.xml.sample file. - sample_tool_data_table_conf = get_config_from_disk( 'tool_data_table_conf.xml.sample', repo_dir ) - if sample_tool_data_table_conf: - error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_tool_data_table_conf ) - if error: - can_set_metadata = False - invalid_files.append( ( 'tool_data_table_conf.xml.sample', correction_msg ) ) - else: - options.missing_tool_data_table_name = None - else: - can_set_metadata = False - correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample " - correction_msg += "to the repository that includes the required entry to correct this error.<br/>" - invalid_files.append( ( tool_config, correction_msg ) ) - if options.index_file or options.missing_index_file: - # Make sure the repository contains the required xxx.loc.sample file. - index_file = options.index_file or options.missing_index_file - index_file_name = strip_path( index_file ) - sample_found = False - for sample_file in sample_files: - sample_file_name = strip_path( sample_file ) - if sample_file_name == '%s.sample' % index_file_name: - options.index_file = index_file_name - options.missing_index_file = None - if options.tool_data_table: - options.tool_data_table.missing_index_file = None - sample_found = True - break - if not sample_found: - can_set_metadata = False - correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) - correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) - invalid_files.append( ( tool_config, correction_msg ) ) - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - reset_tool_data_tables( trans.app ) - return can_set_metadata, invalid_files def clean_repository_metadata( trans, id, changeset_revisions ): # Delete all repository_metadata records associated with the repository that have a changeset_revision that is not in changeset_revisions. # We sometimes see multiple records with the same changeset revision value - no idea how this happens. We'll assume we can delete the older @@ -369,12 +277,16 @@ return file_path return None def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ): + downloadable = 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: repository_metadata.metadata = metadata_dict + repository_metadata.downloadable = downloadable else: - repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) - repository_metadata.downloadable = changeset_is_downloadable( metadata_dict ) + repository_metadata = trans.model.RepositoryMetadata( repository_id=repository.id, + changeset_revision=changeset_revision, + metadata=metadata_dict, + downloadable=downloadable ) trans.sa_session.add( repository_metadata ) trans.sa_session.flush() def generate_clone_url( trans, repository_id ): @@ -387,69 +299,6 @@ return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) else: return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name ) -def generate_metadata_for_changeset_revision( trans, repository_files_dir, repository_clone_url ): - """ - Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, - the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's - disk files, so the value of repository_files_dir will not always be repository.repo_path (it could be a temporary directory containing a clone). - """ - metadata_dict = {} - invalid_files = [] - invalid_tool_configs = [] - tool_dependencies_config = None - datatypes_config = get_config_from_disk( 'datatypes_conf.xml', repository_files_dir ) - if datatypes_config: - metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) - sample_files = get_sample_files_from_disk( repository_files_dir ) - if sample_files: - metadata_dict[ 'sample_files' ] = sample_files - # Find all tool configs and exported workflows. - for root, dirs, files in os.walk( repository_files_dir ): - if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: - if '.hg' in dirs: - dirs.remove( '.hg' ) - for name in files: - # Find all tool configs. - if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): - full_path = os.path.abspath( os.path.join( root, name ) ) - if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] - or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): - try: - # Make sure we're looking at a tool config and not a display application config or something else. - element_tree = util.parse_xml( full_path ) - element_tree_root = element_tree.getroot() - is_tool = element_tree_root.tag == 'tool' - except Exception, e: - print "Error parsing %s", full_path, ", exception: ", str( e ) - is_tool = False - if is_tool: - try: - tool = trans.app.toolbox.load_tool( full_path ) - tool_config = os.path.join( root, name ) - except Exception, e: - tool = None - invalid_tool_configs.append( name ) - if tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, repository_files_dir, tool_config, tool, sample_files, invalid_files ) - if can_set_metadata: - metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) - # Find all exported workflows - elif name.endswith( '.ga' ): - relative_path = os.path.join( root, name ) - fp = open( relative_path, 'rb' ) - workflow_text = fp.read() - fp.close() - exported_workflow_dict = from_json_string( workflow_text ) - if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': - metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) - if 'tools' in metadata_dict: - # This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', repository_files_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) - if invalid_tool_configs: - metadata_dict [ 'invalid_tools' ] = invalid_tool_configs - return metadata_dict, invalid_files def generate_tool_guid( trans, repository, tool ): """ Generate a guid for the received tool. The form of the guid is @@ -588,10 +437,23 @@ .first() def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ): """Get metadata for a specified repository change set from the database""" - return trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), - trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ - .first() + # Make sure there are no duplicate records, and return the single unique record for the changeset_revision. Duplicate records were somehow + # creatd in the past. This may or may not be resolved, so when it is confirmed that the cause of duplicate records has been corrected, tweak + # this method accordingly. + all_metadata_records = trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), + trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ + .order_by( trans.model.RepositoryMetadata.table.c.update_time.desc() ) \ + .all() + if len( all_metadata_records ) > 1: + # Delete all recrds older than the last one updated. + for repository_metadata in all_metadata_records[ 1: ]: + trans.sa_session.delete( repository_metadata ) + trans.sa_session.flush() + return all_metadata_records[ 0 ] + elif all_metadata_records: + return all_metadata_records[ 0 ] + return None def get_repository_metadata_by_id( trans, id ): """Get repository metadata from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) @@ -762,7 +624,7 @@ ctx = get_changectx_for_changeset( repo, changeset_revision ) tool = None message = '' - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) if sample_files: trans.app.config.tool_data_path = work_dir @@ -913,7 +775,7 @@ print "Cloning repository revision: ", str( ctx.rev() ) clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) print "Generating metadata for changset revision: ", str( ctx.rev() ) - current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, work_dir, repository_clone_url ) + current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, work_dir, repository_clone_url ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: # We're at the first change set in the change log. @@ -969,7 +831,9 @@ pass # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. clean_repository_metadata( trans, id, changeset_revisions ) - add_repository_metadata_tool_versions( trans, id, changeset_revisions ) + # Set tool version information for all downloadable changeset revisions. + downloadable_changeset_revisions = [ rm.changeset_revision for rm in repository.downloadable_revisions ] + add_repository_metadata_tool_versions( trans, id, downloadable_changeset_revisions ) def set_repository_metadata( trans, repository, content_alert_str='', **kwd ): """ Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset @@ -980,8 +844,9 @@ repository_clone_url = generate_clone_url( trans, trans.security.encode_id( repository.id ) ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) - metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, repo_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, repo_dir, repository_clone_url ) if metadata_dict: + repository_metadata = None if new_tool_metadata_required( trans, repository, metadata_dict ) or new_workflow_metadata_required( trans, repository, metadata_dict ): # Create a new repository_metadata table row. repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) @@ -997,10 +862,11 @@ else: repository_metadata = get_latest_repository_metadata( trans, repository.id ) if repository_metadata: + downloadable = 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict # Update the last saved repository_metadata table row. repository_metadata.changeset_revision = repository.tip repository_metadata.metadata = metadata_dict - repository_metadata.downloadable = changeset_is_downloadable( metadata_dict ) + repository_metadata.downloadable = downloadable trans.sa_session.add( repository_metadata ) trans.sa_session.flush() else: @@ -1008,18 +874,20 @@ repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) trans.sa_session.add( repository_metadata ) trans.sa_session.flush() - elif len( repo ) == 1 and not invalid_files: + if 'tools' in metadata_dict and repository_metadata and status != 'error': + add_repository_metadata_tool_versions( trans, trans.security.encode_id( repository.id ), [ repository_metadata.changeset_revision ] ) + elif len( repo ) == 1 and not invalid_file_tups: message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" - if invalid_files: + if invalid_file_tups: if metadata_dict: message += "Metadata was defined for some items in revision '%s'. " % str( repository.tip ) message += "Correct the following problems if necessary and reset metadata.<br/>" else: message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip ) message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.<br/>" - for itc_tup in invalid_files: + for itc_tup in invalid_file_tups: tool_file, exception_msg = itc_tup if exception_msg.find( 'No such file or directory' ) >= 0: exception_items = exception_msg.split() diff -r 5f2db4a18d3d3bef78f0a330cc6073f34db7c88b -r 9f790bc90769df7a4f84f103707bdd8ceaf1115d lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -9,8 +9,8 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * -from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents, make_tmp_directory, NOT_TOOL_CONFIGS -from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, strip_path +from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents, NOT_TOOL_CONFIGS +from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, strip_path, to_html_escaped, update_repository from galaxy.tool_shed.encoding_util import * from common import * @@ -113,7 +113,7 @@ grids.GridColumn.__init__( self, col_name ) def get_value( self, trans, grid, repository ): """Display a SelectField whose options are the changeset_revision strings of all downloadable_revisions of this repository.""" - select_field = build_changeset_revision_select_field( trans, repository ) + select_field = build_changeset_revision_select_field( trans, repository, downloadable_only=False ) if len( select_field.options ) > 1: return select_field.get_html() return repository.revision @@ -268,7 +268,7 @@ grids.GridColumn.__init__( self, col_name ) def get_value( self, trans, grid, repository ): """Display a SelectField whose options are the changeset_revision strings of all download-able revisions of this repository.""" - select_field = build_changeset_revision_select_field( trans, repository ) + select_field = build_changeset_revision_select_field( trans, repository, downloadable_only=True ) if len( select_field.options ) > 1: return select_field.get_html() return repository.revision @@ -1346,19 +1346,14 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'error' ) webapp = get_webapp( trans, **kwd ) + repository_clone_url = generate_clone_url( trans, repository_id ) repository = get_repository( trans, repository_id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) ctx = get_changectx_for_changeset( repo, changeset_revision ) invalid_message = '' - metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans, - repo, - repository_id, - ctx, - changeset_revision, - repo_dir, - updating_tip=changeset_revision==repository.tip ) - for invalid_file_tup in invalid_files: + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, repo_dir, repository_clone_url ) + for invalid_file_tup in invalid_file_tups: invalid_tool_config, invalid_msg = invalid_file_tup invalid_tool_config_name = strip_path( invalid_tool_config ) if tool_config == invalid_tool_config_name: @@ -1554,7 +1549,8 @@ changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, - add_id_to_name=False ) + add_id_to_name=False, + downloadable_only=False ) revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: @@ -1657,7 +1653,8 @@ changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, - add_id_to_name=False ) + add_id_to_name=False, + downloadable_only=False ) return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', repository=repository, repository_metadata_id=repository_metadata_id, @@ -2128,7 +2125,8 @@ changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, - add_id_to_name=False ) + add_id_to_name=False, + downloadable_only=False ) revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: @@ -2185,7 +2183,8 @@ changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, - add_id_to_name=False ) + add_id_to_name=False, + downloadable_only=False ) return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", repository=repository, tool=tool, @@ -2197,3 +2196,42 @@ webapp=webapp, message=message, status=status ) + +# ----- Utility methods ----- +def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, downloadable_only=False ): + """Build a SelectField whose options are the changeset_rev strings of all downloadable revisions of the received repository.""" + repo = hg.repository( get_configured_ui(), repository.repo_path ) + options = [] + changeset_tups = [] + refresh_on_change_values = [] + if downloadable_only: + repository_metadata_revisions = repository.downloadable_revisions + else: + repository_metadata_revisions = repository.metadata_revisions + for repository_metadata in repository_metadata_revisions: + changeset_revision = repository_metadata.changeset_revision + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + rev = '-1' + label = "-1:%s" % changeset_revision + changeset_tups.append( ( rev, label, changeset_revision ) ) + refresh_on_change_values.append( changeset_revision ) + # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, + # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time. + for changeset_tup in sorted( changeset_tups ): + # Display the latest revision first. + options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) ) + if add_id_to_name: + name = 'changeset_revision_%d' % repository.id + else: + name = 'changeset_revision' + select_field = SelectField( name=name, + refresh_on_change=True, + refresh_on_change_values=refresh_on_change_values ) + for option_tup in options: + selected = selected_value and option_tup[1] == selected_value + select_field.add_option( option_tup[0], option_tup[1], selected=selected ) + return select_field diff -r 5f2db4a18d3d3bef78f0a330cc6073f34db7c88b -r 9f790bc90769df7a4f84f103707bdd8ceaf1115d lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -166,12 +166,13 @@ fp.close() class RepositoryMetadata( object ): - def __init__( self, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False ): + def __init__( self, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False ): self.repository_id = repository_id self.changeset_revision = changeset_revision self.metadata = metadata or dict() self.tool_versions = tool_versions or dict() self.malicious = malicious + self.downloadable = downloadable class ItemRatingAssociation( object ): def __init__( self, id=None, user=None, item=None, rating=0, comment='' ): diff -r 5f2db4a18d3d3bef78f0a330cc6073f34db7c88b -r 9f790bc90769df7a4f84f103707bdd8ceaf1115d templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako --- a/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako +++ b/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako @@ -43,14 +43,17 @@ ${render_msg( message, status )} %endif +<div class="warningmessage"> + Resetting metadata may take a while because this process clones each change set in each selected repository's change log to a temporary location on disk. + Wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as doing anything else will not be helpful. Watch + the tool shed paster log to pass the time if necessary. +</div> + <div class="toolForm"><div class="toolFormTitle">Reset all metadata on each selected repository</div><form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories' )}" method="post" ><div class="form-row"> - Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. Resetting metadata - may take a while because this process clones each change set in each selected repository's change log to a temporary location on disk. - Wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as doing anything else will not - be helpful. Watch the tool shed paster log to pass the time if necessary. + Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. </div><div style="clear: both"></div><div class="form-row"> 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: carlfeberhard: fix to mako import and some up-stack error reporting in tools
by Bitbucket 08 Aug '12

08 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5f2db4a18d3d/ changeset: 5f2db4a18d3d user: carlfeberhard date: 2012-08-08 18:30:25 summary: fix to mako import and some up-stack error reporting in tools affected #: 2 files diff -r 68d253239882008ee143fd46d946d1a8a828d21e -r 5f2db4a18d3d3bef78f0a330cc6073f34db7c88b lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -4,6 +4,7 @@ import pkg_resources pkg_resources.require( "simplejson" ) +pkg_resources.require( "Mako" ) import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback import simplejson @@ -2344,7 +2345,7 @@ command_line = command_line.replace( "\n", " " ).replace( "\r", " " ).strip() except Exception, e: # Modify exception message to be more clear - #e.args = ( 'Error substituting into command line. Params: %r, Command: %s' % ( param_dict, self.command ) ) + #e.args = ( 'Error substituting into command line. Params: %r, Command: %s' % ( param_dict, self.command ), ) raise if self.interpreter: # TODO: path munging for cluster/dataset server relocatability @@ -2441,7 +2442,7 @@ if code: return code( *args, **kwargs ) except Exception, e: - e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, e.args[0] ) ) + e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, e.args[0] ), ) raise def exec_before_job( self, app, inp_data, out_data, param_dict={} ): pass diff -r 68d253239882008ee143fd46d946d1a8a828d21e -r 5f2db4a18d3d3bef78f0a330cc6073f34db7c88b tools/new_operations/operation_filter.py --- a/tools/new_operations/operation_filter.py +++ b/tools/new_operations/operation_filter.py @@ -3,6 +3,9 @@ from galaxy import eggs from galaxy import jobs from galaxy.tools.parameters import DataToolParameter + +from galaxy.jobs.handler import JOB_ERROR + # Older py compatibility try: set() @@ -63,8 +66,8 @@ raise Exception( stderr ) except Exception, exc: - data.blurb = jobs.JOB_ERROR - data.state = jobs.JOB_ERROR + data.blurb = JOB_ERROR + data.state = JOB_ERROR ## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): ## pass Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Remove contrib/multiprocess.sh since run.sh can run all of the processes itself now.
by Bitbucket 08 Aug '12

08 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/68d253239882/ changeset: 68d253239882 user: natefoo date: 2012-08-08 17:12:42 summary: Remove contrib/multiprocess.sh since run.sh can run all of the processes itself now. affected #: 1 file diff -r 480b8c0003f1ab6fa78f88bd7854cf978f2ed575 -r 68d253239882008ee143fd46d946d1a8a828d21e contrib/multiproccess.sh --- a/contrib/multiproccess.sh +++ /dev/null @@ -1,26 +0,0 @@ -#!/bin/bash - -# copy this script to the top level galaxy directory and modify the following -# for your environment - -web_server_names=(web{0..2}) # server names: web0 web1 web2 -runner_server_names=(runner0) # server name: runner0 - -web_config='universe_wsgi.webapp.ini' -runner_config='universe_wsgi.runner.ini' - -# actually do the requested action - -if [ -z "$1" ]; then - echo "usage: multiprocess.sh <--daemon|--stop-daemon>" - exit 1 -fi - -for server_name in ${web_server_names[@]}; do - echo "[$server_name]" - python ./scripts/paster.py serve $web_config --server-name=$server_name --pid-file=$server_name.pid --log-file=$server_name.log $@ -done -for server_name in ${runner_server_names[@]}; do - echo "[$server_name]" - python ./scripts/paster.py serve $runner_config --server-name=$server_name --pid-file=$server_name.pid --log-file=$server_name.log $@ -done 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: inithello: Improved generation and display of local genome/indexes table. Handle missing tool data table entries.
by Bitbucket 08 Aug '12

08 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/480b8c0003f1/ changeset: 480b8c0003f1 user: inithello date: 2012-08-08 16:37:27 summary: Improved generation and display of local genome/indexes table. Handle missing tool data table entries. affected #: 4 files diff -r 4d22e26e595a278f96b814908b8dc24b3f77a06b -r 480b8c0003f1ab6fa78f88bd7854cf978f2ed575 lib/galaxy/web/controllers/data_admin.py --- a/lib/galaxy/web/controllers/data_admin.py +++ b/lib/galaxy/web/controllers/data_admin.py @@ -30,25 +30,28 @@ @web.expose @web.require_admin def manage_data( self, trans, **kwd ): - genomes = dict() if trans.app.config.get_bool( 'enable_beta_job_managers', False ) == False: - return trans.fill_template( '/admin/data_admin/betajob.mako' ) - for line in trans.app.tool_data_tables.data_tables[ 'all_fasta' ].data: - defstate = dict( state='Generate', style=self.jobstyles[ 'new' ] ) - indexers = dict( bowtie_indexes=defstate, bowtie2_indexes=defstate, bwa_indexes=defstate, perm_base_indexes=defstate, srma_indexes=defstate, sam_fa_indexes=defstate ) - dbkey = line[0] - name = line[2] - indexers[ 'name' ] = name - indexers[ 'fapath' ] = line[3] - genomes[ dbkey ] = indexers - for table in [ 'bowtie_indexes', 'bowtie2_indexes', 'bwa_indexes', 'srma_indexes' ]: - for line in trans.app.tool_data_tables.data_tables[ table ].data: - dbkey = line[0] - genomes[ dbkey ][ table ] = dict( state='Generated', style=self.jobstyles[ 'done' ] ) - for line in trans.app.tool_data_tables.data_tables[ 'sam_fa_indexes' ].data: - genomes[ line[1] ][ 'sam_fa_indexes' ] = dict( state='Generated', style=self.jobstyles[ 'done' ] ) - for line in trans.app.tool_data_tables.data_tables[ 'perm_base_indexes' ].data: - genomes[ line[1].split(':')[0] ][ 'perm_base_indexes' ] = dict( state='Generated', style=self.jobstyles[ 'done' ] ) + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='This feature requires that enable_beta_job_managers be set to True in your Galaxy configuration.' ) + if 'all_fasta' not in trans.app.tool_data_tables.data_tables: + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='The local data manager requires that an all_fasta entry exists in your tool_data_table_conf.xml.' ) + indextable = {} + dbkeys = [] + labels = { 'bowtie_indexes': 'Bowtie', 'bowtie2_indexes': 'Bowtie 2', 'bwa_indexes': 'BWA', 'srma_indexes': 'Picard', 'sam_fa_indexes': 'SAM', 'perm_base_indexes': 'PerM' } + tablenames = { 'Bowtie': 'bowtie_indexes', 'Bowtie 2': 'bowtie2_indexes', 'BWA': 'bwa_indexes', 'Picard': 'srma_indexes', 'SAM': 'sam_fa_indexes', 'PerM': 'perm_base_indexes' } + indexfuncs = dict( bowtie_indexes='bowtie', bowtie2_indexes='bowtie2', bwa_indexes='bwa', srma_indexes='picard', sam_fa_indexes='sam', perm_base_indexes='perm' ) + for genome in trans.app.tool_data_tables.data_tables[ 'all_fasta' ].data: + dbkey = genome[0] + dbkeys.append( dbkey ) + indextable[ dbkey ] = dict( indexes=dict(), name=genome[2], path=genome[3] ) + for genome in indextable: + for label in labels: + indextable[ genome ][ 'indexes' ][ label ] = 'Generate' + if label not in trans.app.tool_data_tables.data_tables: + indextable[ genome ][ 'indexes' ][ label ] = 'Disabled' + else: + for row in trans.app.tool_data_tables.data_tables[ label ].data: + if genome in row or row[0].startswith( genome ): + indextable[ genome ][ 'indexes' ][ label ] = 'Generated' jobgrid = [] sa_session = trans.app.model.context.current jobs = sa_session.query( model.GenomeIndexToolData ).order_by( model.GenomeIndexToolData.created_time.desc() ).filter_by( user_id=trans.get_user().id ).group_by( model.GenomeIndexToolData.deferred ).limit( 20 ).all() @@ -65,7 +68,8 @@ jobtype = 'index' indexers = ', '.join( params['indexes'] ) jobgrid.append( dict( jobtype=jobtype, indexers=indexers, rowclass=state, deferred=job.deferred.id, state=state, intname=job.deferred.params[ 'intname' ], dbkey=job.deferred.params[ 'dbkey' ] ) ) - return trans.fill_template( '/admin/data_admin/local_data.mako', jobgrid=jobgrid, genomes=genomes ) + styles = dict( Generate=self.jobstyles['new'], Generated=self.jobstyles['ok'], Disabled=self.jobstyles['error'] ) + return trans.fill_template( '/admin/data_admin/local_data.mako', jobgrid=jobgrid, indextable=indextable, labels=labels, dbkeys=dbkeys, styles=styles, indexfuncs=indexfuncs ) @web.expose @web.require_admin diff -r 4d22e26e595a278f96b814908b8dc24b3f77a06b -r 480b8c0003f1ab6fa78f88bd7854cf978f2ed575 templates/admin/data_admin/betajob.mako --- a/templates/admin/data_admin/betajob.mako +++ /dev/null @@ -1,35 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/library/common/common.mako" import="common_javascripts" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/galaxy/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.message_box_visible=False - self.active_view="user" - self.overlay_visible=False - self.has_accessible_datasets = False -%> -</%def> -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "autocomplete_tagging" )} -</%def> -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js("jquery.autocomplete", "autocomplete_tagging" )} -</%def> -## -## Override methods from base.mako and base_panels.mako -## -<p class="panel-error-message">This feature requires that enable_beta_job_managers be set to True in your Galaxy configuration.</p> \ No newline at end of file diff -r 4d22e26e595a278f96b814908b8dc24b3f77a06b -r 480b8c0003f1ab6fa78f88bd7854cf978f2ed575 templates/admin/data_admin/generic_error.mako --- /dev/null +++ b/templates/admin/data_admin/generic_error.mako @@ -0,0 +1,35 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/library/common/common.mako" import="common_javascripts" /> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/galaxy/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.message_box_visible=False + self.active_view="user" + self.overlay_visible=False + self.has_accessible_datasets = False +%> +</%def> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "autocomplete_tagging" )} +</%def> +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js("jquery.autocomplete", "autocomplete_tagging" )} +</%def> +## +## Override methods from base.mako and base_panels.mako +## +<p class="panel-error-message">${message}</p> \ No newline at end of file diff -r 4d22e26e595a278f96b814908b8dc24b3f77a06b -r 480b8c0003f1ab6fa78f88bd7854cf978f2ed575 templates/admin/data_admin/local_data.mako --- a/templates/admin/data_admin/local_data.mako +++ b/templates/admin/data_admin/local_data.mako @@ -44,6 +44,7 @@ td, th { padding-left: 10px; padding-right: 10px; } td.state-color-new { text-decoration: underline; } td.panel-done-message { background-image: none; padding: 0px 10px 0px 10px; } + td.panel-error-message { background-image: none; padding: 0px 10px 0px 10px; } </style><div class="toolForm"> %if message: @@ -52,19 +53,23 @@ <div class="toolFormTitle">Currently tracked builds <a class="action-button" href="${h.url_for( controller='data_admin', action='add_genome' )}">Add new</a></div><div class="toolFormBody"><h2>Locally cached data:</h2> - <h3>NOTE: Indexers queued here will not be reflected in the table until Galaxy is restarted.</h3> + <h3>NOTE: Indexes generated here will not be reflected in the table until Galaxy is restarted.</h3><table id="locfiles"> - <tr><th>Database ID</th><th>Name</th><th>Bowtie</th><th>Bowtie 2</th><th>BWA</th><th>Sam</th><th>Picard</th><th>PerM</th></tr> - %for dbkey in sorted(genomes.keys()): + <tr> + <th>DB Key</th> + <th>Name</th> + %for label in labels: + <th>${labels[label]}</th> + %endfor + </tr> + %for dbkey in sorted(dbkeys): <tr><td>${dbkey}</td> - <td>${genomes[dbkey]['name']}</td> - <td id="${dbkey}-bowtie" class="indexcell ${genomes[dbkey]['bowtie_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bowtie" data-dbkey="${dbkey}">${genomes[dbkey]['bowtie_indexes']['state']}</td> - <td id="${dbkey}-bowtie2" class="indexcell ${genomes[dbkey]['bowtie2_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bowtie2" data-dbkey="${dbkey}">${genomes[dbkey]['bowtie2_indexes']['state']}</td> - <td id="${dbkey}-bwa" class="indexcell ${genomes[dbkey]['bwa_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bwa" data-dbkey="${dbkey}">${genomes[dbkey]['bwa_indexes']['state']}</td> - <td id="${dbkey}-sam" class="indexcell ${genomes[dbkey]['sam_fa_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="sam" data-dbkey="${dbkey}">${genomes[dbkey]['sam_fa_indexes']['state']}</td> - <td id="${dbkey}-picard" class="indexcell ${genomes[dbkey]['srma_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="picard" data-dbkey="${dbkey}">${genomes[dbkey]['srma_indexes']['state']}</td> - <td id="${dbkey}-perm" class="indexcell ${genomes[dbkey]['perm_base_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="perm" data-dbkey="${dbkey}">${genomes[dbkey]['perm_base_indexes']['state']}</td> + <td>${indextable[dbkey]['name']}</td> + %for label in labels: + <td id="${dbkey}-${indexfuncs[label]}" class="indexcell ${styles[indextable[dbkey]['indexes'][label]]}" data-fapath="${indextable[dbkey]['path']}" data-longname="${indextable[dbkey]['name']}" data-index="${indexfuncs[label]}" data-dbkey="${dbkey}">${indextable[dbkey]['indexes'][label]}</td> + %endfor + </tr> %endfor </table> @@ -124,6 +129,7 @@ jsondata["name"] = $('#job-' + jobid).attr('data-name'); jsondata["dbkey"] = $('#job-' + jobid).attr('data-dbkey'); jsondata["indexes"] = $('#job-' + jobid).attr('data-indexes'); + tdid = jq(jsondata["dbkey"] + '-' + jsondata["indexes"]); newhtml = makeNewHTML(jsondata); $('#job-' + jobid).replaceWith(newhtml); if ($.inArray(jsondata["status"], finalstates) == -1) { @@ -133,7 +139,7 @@ }); } if (jsondata["status"] == 'done' || jsondata["status"] == 'ok') { - elem = $('#' + jsondata["dbkey"] + '-' + jsondata["indexes"]); + elem = $(tdid); elem.html('Generated'); elem.attr('class', 'indexcell panel-done-message'); } @@ -156,5 +162,8 @@ } }); }); - + + function jq(id) { + return '#' + id.replace(/(:|\.)/g,'\\$1'); + } </script> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Make workflows compatible with change made in 29680fa5c35e that makes tool help a template rather than static text. Bonus: images in tool help now display in workflow editor as well.
by Bitbucket 08 Aug '12

08 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4d22e26e595a/ changeset: 4d22e26e595a user: jgoecks date: 2012-08-08 14:39:39 summary: Make workflows compatible with change made in 29680fa5c35e that makes tool help a template rather than static text. Bonus: images in tool help now display in workflow editor as well. affected #: 2 files diff -r 4f17b0d16ff7b878fba9c6e8730998ee61c54c5e -r 4d22e26e595a278f96b814908b8dc24b3f77a06b lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -655,7 +655,7 @@ 'name': module.get_name(), 'tool_id': module.get_tool_id(), 'tool_state': module.get_state(), - 'tooltip': module.get_tooltip(), + 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), 'form_html': module.get_config_form(), @@ -732,7 +732,7 @@ 'tool_id': module.get_tool_id(), 'name': module.get_name(), 'tool_state': module.get_state(), - 'tooltip': module.get_tooltip(), + 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), 'tool_errors': module.get_errors(), 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), diff -r 4f17b0d16ff7b878fba9c6e8730998ee61c54c5e -r 4d22e26e595a278f96b814908b8dc24b3f77a06b lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -49,7 +49,7 @@ return self.name def get_tool_id( self ): return None - def get_tooltip( self ): + def get_tooltip( self, static_path='' ): return None ## ---- Configuration time ----------------------------------------------- @@ -258,8 +258,8 @@ return self.state.encode( self.tool, self.trans.app, secure=secure ) def get_errors( self ): return self.errors - def get_tooltip( self ): - return self.tool.help + def get_tooltip( self, static_path='' ): + return self.tool.help.render( static_path=static_path ) def get_data_inputs( self ): data_inputs = [] def callback( input, value, prefixed_name, prefixed_label ): 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: carlfeberhard: fix to rusted display_string in TestLibraryFeatures.test_100_add_ldda_to_folder3
by Bitbucket 07 Aug '12

07 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4f17b0d16ff7/ changeset: 4f17b0d16ff7 user: carlfeberhard date: 2012-08-07 21:57:13 summary: fix to rusted display_string in TestLibraryFeatures.test_100_add_ldda_to_folder3 affected #: 1 file diff -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c -r 4f17b0d16ff7b878fba9c6e8730998ee61c54c5e test/functional/test_library_templates.py --- a/test/functional/test_library_templates.py +++ b/test/functional/test_library_templates.py @@ -398,7 +398,7 @@ folder_id=self.security.encode_id( folder3.id ), upload_option='import_from_history', hda_ids=self.security.encode_id( hda.id ), - strings_displayed=[ '<input type="hidden" name="%s" value="Option1"/>' % select_field_name ] ) + strings_displayed=[ '<select name="%s" last_selected_value="Option1">' % select_field_name ] ) ldda = get_latest_ldda_by_name( filename ) assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Ensure repository metadata records are unique in the tool shed.
by Bitbucket 07 Aug '12

07 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1cb2fdf2c7cf/ changeset: 1cb2fdf2c7cf user: greg date: 2012-08-07 20:42:28 summary: Ensure repository metadata records are unique in the tool shed. affected #: 1 file diff -r ca835611e8c79a9b95c50acc28d670f7f81266e7 -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -238,10 +238,17 @@ reset_tool_data_tables( trans.app ) return can_set_metadata, invalid_files def clean_repository_metadata( trans, id, changeset_revisions ): - # Delete all repository_metadata reecords associated with the repository that have a changeset_revision that is not in changeset_revisions. + # Delete all repository_metadata records associated with the repository that have a changeset_revision that is not in changeset_revisions. + # We sometimes see multiple records with the same changeset revision value - no idea how this happens. We'll assume we can delete the older + # records, so we'll order by update_time descending and delete records that have the same changeset_revision we come across later.. + changeset_revisions_checked = [] for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ): - if repository_metadata.changeset_revision not in changeset_revisions: + .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ + .order_by( trans.model.RepositoryMetadata.table.c.changeset_revision, + trans.model.RepositoryMetadata.table.c.update_time.desc() ): + changeset_revision = repository_metadata.changeset_revision + can_delete = changeset_revision in changeset_revisions_checked or changeset_revision not in changeset_revisions + if can_delete: trans.sa_session.delete( repository_metadata ) trans.sa_session.flush() def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): @@ -874,9 +881,8 @@ if 'workflows' in metadata_dict: repository_metadata = get_latest_repository_metadata( trans, repository.id ) if repository_metadata: - if repository_metadata.metadata: - # The repository has metadata, so update the workflows value - no new record is needed. - return False + # The repository has metadata, so update the workflows value - no new record is needed. + return False else: # There is no saved repository metadata, so we need to create a new repository_metadata table record. return True 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: Fixes for setting metadata on repositories in the tool shed.
by Bitbucket 07 Aug '12

07 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ca835611e8c7/ changeset: ca835611e8c7 user: greg date: 2012-08-07 19:52:50 summary: Fixes for setting metadata on repositories in the tool shed. affected #: 11 files diff -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 -r ca835611e8c79a9b95c50acc28d670f7f81266e7 lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -1,4 +1,5 @@ import sys, config +from galaxy import tools import galaxy.tools.data import galaxy.quota import galaxy.datatypes.registry @@ -38,7 +39,7 @@ # Tool data tables - never pass a config file here because the tool shed should always have an empty dictionary! self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path ) # The tool shed has no toolbox, but this attribute is still required. - self.toolbox = None + self.toolbox = tools.ToolBox( [], self.config.tool_path, self ) # Load security policy self.security_agent = self.model.security_agent self.quota_agent = galaxy.quota.NoQuotaAgent( self.model ) diff -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 -r ca835611e8c79a9b95c50acc28d670f7f81266e7 lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -44,6 +44,7 @@ self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) # Tool stuff + self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() ) self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) @@ -55,6 +56,7 @@ else: self.tool_dependency_dir = None self.use_tool_dependencies = False + self.update_integrated_tool_panel = False self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) diff -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 -r ca835611e8c79a9b95c50acc28d670f7f81266e7 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -2,13 +2,14 @@ from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.web.form_builder import SelectField from galaxy.util import inflector from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui from common import * from repository import RepositoryListGrid, CategoryListGrid from galaxy import eggs -eggs.require('mercurial') +eggs.require( 'mercurial' ) from mercurial import hg import logging @@ -415,89 +416,6 @@ @web.expose @web.require_admin - def browse_repository_metadata( self, trans, **kwd ): - if 'operation' in kwd: - operation = kwd[ 'operation' ].lower() - if operation == "delete": - return self.delete_repository_metadata( trans, **kwd ) - if operation == "view_or_manage_repository_revision": - # The received id is a RepositoryMetadata object id, so we need to get the - # associated Repository and redirect to view_or_manage_repository with the - # changeset_revision. - repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] ) - repository = repository_metadata.repository - kwd[ 'id' ] = trans.security.encode_id( repository.id ) - kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision - kwd[ 'operation' ] = 'view_or_manage_repository' - return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repositories', - **kwd ) ) - return self.repository_metadata_list_grid( trans, **kwd ) - @web.expose - @web.require_admin - def delete_repository_metadata( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - id = kwd.get( 'id', None ) - if id: - ids = util.listify( id ) - count = 0 - for repository_metadata_id in ids: - repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) - trans.sa_session.delete( repository_metadata ) - trans.sa_session.flush() - count += 1 - if count: - message = "Deleted %d repository metadata %s" % ( count, inflector.cond_plural( len( ids ), "record" ) ) - else: - message = "No repository metadata ids received for deleting." - status = 'error' - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_repository_metadata', - message=util.sanitize_text( message ), - status=status ) ) - @web.expose - @web.require_admin - def reset_metadata_on_all_repositories( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - if 'reset_metadata_on_all_repositories_button' in kwd: - successful_count = 0 - unsuccessful_count = 0 - for repository in trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ): - try: - error_message, status = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) ) - if status not in [ 'ok' ] and error_message: - log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, error_message ) ) - unsuccessful_count += 1 - elif status in [ 'ok' ] and error_message: - log.debug( "Successfully reset metadata on repository %s, but encountered this problem: %s" % ( repository.name, error_message ) ) - successful_count += 1 - else: - log.debug( "Successfully reset metadata on repository %s" % repository.name ) - successful_count += 1 - except Exception, e: - log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) ) - unsuccessful_count += 1 - message = "Successfully reset metadata on %d %s. " % ( successful_count, - inflector.cond_plural( successful_count, "repository" ) ) - if unsuccessful_count: - message += "Error setting metadata on %d %s - see the paster log for details. " % ( unsuccessful_count, - inflector.cond_plural( unsuccessful_count, - "repository" ) ) - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_repository_metadata', - webapp='community', - message=util.sanitize_text( message ), - status=status ) ) - return trans.fill_template( '/webapps/community/admin/reset_metadata_on_all_repositories.mako', - message=message, - status=status ) - @web.expose - @web.require_admin def browse_repositories( self, trans, **kwd ): # We add params to the keyword dict in this method in order to rename the param # with an "f-" prefix, simulating filtering by clicking a search link. We have @@ -568,101 +486,24 @@ return self.repository_list_grid( trans, **kwd ) @web.expose @web.require_admin - def regenerate_statistics( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - if 'regenerate_statistics_button' in kwd: - trans.app.shed_counter.generate_statistics() - message = "Successfully regenerated statistics" - return trans.fill_template( '/webapps/community/admin/statistics.mako', - message=message, - status=status ) - @web.expose - @web.require_admin - def delete_repository( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - id = kwd.get( 'id', None ) - if id: - # Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. - ids = util.listify( id ) - count = 0 - deleted_repositories = "" - for repository_id in ids: - repository = get_repository( trans, repository_id ) - if not repository.deleted: - repository.deleted = True - trans.sa_session.add( repository ) - trans.sa_session.flush() - count += 1 - deleted_repositories += " %s " % repository.name - if count: - message = "Deleted %d %s: %s" % ( count, inflector.cond_plural( len( ids ), "repository" ), deleted_repositories ) - else: - message = "All selected repositories were already marked deleted." - else: - message = "No repository ids received for deleting." - status = 'error' - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_repositories', - message=util.sanitize_text( message ), - status=status ) ) - @web.expose - @web.require_admin - def undelete_repository( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - id = kwd.get( 'id', None ) - if id: - # Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. - ids = util.listify( id ) - count = 0 - undeleted_repositories = "" - for repository_id in ids: - repository = get_repository( trans, repository_id ) - if repository.deleted: - repository.deleted = False - trans.sa_session.add( repository ) - trans.sa_session.flush() - count += 1 - undeleted_repositories += " %s" % repository.name - if count: - message = "Undeleted %d %s: %s" % ( count, inflector.cond_plural( count, "repository" ), undeleted_repositories ) - else: - message = "No selected repositories were marked deleted, so they could not be undeleted." - else: - message = "No repository ids received for undeleting." - status = 'error' - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_repositories', - message=util.sanitize_text( message ), - status='done' ) ) - @web.expose - @web.require_admin - def manage_categories( self, trans, **kwd ): - if 'f-free-text-search' in kwd: - # Trick to enable searching repository name, description from the CategoryListGrid. - # What we've done is rendered the search box for the RepositoryListGrid on the grid.mako - # template for the CategoryListGrid. See ~/templates/webapps/community/category/grid.mako. - # Since we are searching repositories and not categories, redirect to browse_repositories(). - return self.browse_repositories( trans, **kwd ) + def browse_repository_metadata( self, trans, **kwd ): if 'operation' in kwd: - operation = kwd['operation'].lower() - if operation == "create": - return self.create_category( trans, **kwd ) - elif operation == "delete": - return self.mark_category_deleted( trans, **kwd ) - elif operation == "undelete": - return self.undelete_category( trans, **kwd ) - elif operation == "purge": - return self.purge_category( trans, **kwd ) - elif operation == "edit": - return self.edit_category( trans, **kwd ) - # Render the list view - return self.manage_category_list_grid( trans, **kwd ) + operation = kwd[ 'operation' ].lower() + if operation == "delete": + return self.delete_repository_metadata( trans, **kwd ) + if operation == "view_or_manage_repository_revision": + # The received id is a RepositoryMetadata object id, so we need to get the + # associated Repository and redirect to view_or_manage_repository with the + # changeset_revision. + repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] ) + repository = repository_metadata.repository + kwd[ 'id' ] = trans.security.encode_id( repository.id ) + kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision + kwd[ 'operation' ] = 'view_or_manage_repository' + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + **kwd ) ) + return self.repository_metadata_list_grid( trans, **kwd ) @web.expose @web.require_admin def create_category( self, trans, **kwd ): @@ -711,6 +552,61 @@ status=status ) @web.expose @web.require_admin + def delete_repository( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = kwd.get( 'id', None ) + if id: + # Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. + ids = util.listify( id ) + count = 0 + deleted_repositories = "" + for repository_id in ids: + repository = get_repository( trans, repository_id ) + if not repository.deleted: + repository.deleted = True + trans.sa_session.add( repository ) + trans.sa_session.flush() + count += 1 + deleted_repositories += " %s " % repository.name + if count: + message = "Deleted %d %s: %s" % ( count, inflector.cond_plural( len( ids ), "repository" ), deleted_repositories ) + else: + message = "All selected repositories were already marked deleted." + else: + message = "No repository ids received for deleting." + status = 'error' + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_repositories', + message=util.sanitize_text( message ), + status=status ) ) + @web.expose + @web.require_admin + def delete_repository_metadata( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = kwd.get( 'id', None ) + if id: + ids = util.listify( id ) + count = 0 + for repository_metadata_id in ids: + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + trans.sa_session.delete( repository_metadata ) + trans.sa_session.flush() + count += 1 + if count: + message = "Deleted %d repository metadata %s" % ( count, inflector.cond_plural( len( ids ), "record" ) ) + else: + message = "No repository metadata ids received for deleting." + status = 'error' + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_repository_metadata', + message=util.sanitize_text( message ), + status=status ) ) + @web.expose + @web.require_admin def edit_category( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -750,6 +646,124 @@ status=status ) @web.expose @web.require_admin + def manage_categories( self, trans, **kwd ): + if 'f-free-text-search' in kwd: + # Trick to enable searching repository name, description from the CategoryListGrid. + # What we've done is rendered the search box for the RepositoryListGrid on the grid.mako + # template for the CategoryListGrid. See ~/templates/webapps/community/category/grid.mako. + # Since we are searching repositories and not categories, redirect to browse_repositories(). + return self.browse_repositories( trans, **kwd ) + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "create": + return self.create_category( trans, **kwd ) + elif operation == "delete": + return self.mark_category_deleted( trans, **kwd ) + elif operation == "undelete": + return self.undelete_category( trans, **kwd ) + elif operation == "purge": + return self.purge_category( trans, **kwd ) + elif operation == "edit": + return self.edit_category( trans, **kwd ) + # Render the list view + return self.manage_category_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def regenerate_statistics( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if 'regenerate_statistics_button' in kwd: + trans.app.shed_counter.generate_statistics() + message = "Successfully regenerated statistics" + return trans.fill_template( '/webapps/community/admin/statistics.mako', + message=message, + status=status ) + @web.expose + @web.require_admin + def reset_metadata_on_selected_repositories( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository_names_by_owner = util.listify( kwd.get( 'repository_names_by_owner', None ) ) + if 'reset_metadata_on_selected_repositories_button' in kwd: + if repository_names_by_owner: + successful_count = 0 + unsuccessful_count = 0 + for repository_name_owner_str in repository_names_by_owner: + repository_name_owner_list = repository_name_owner_str.split( '__ESEP__' ) + name = repository_name_owner_list[ 0 ] + owner = repository_name_owner_list[ 1 ] + repository = get_repository_by_name_and_owner( trans, name, owner ) + try: + reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) ) + log.debug( "Successfully reset metadata on repository %s" % repository.name ) + successful_count += 1 + except Exception, e: + log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) ) + unsuccessful_count += 1 + message = "Successfully reset metadata on %d %s. " % ( successful_count, + inflector.cond_plural( successful_count, "repository" ) ) + if unsuccessful_count: + message += "Error setting metadata on %d %s - see the paster log for details. " % ( unsuccessful_count, + inflector.cond_plural( unsuccessful_count, + "repository" ) ) + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_repository_metadata', + webapp='community', + message=util.sanitize_text( message ), + status=status ) ) + else: + 'Select at least one repository to on which to reset all metadata.' + status = 'error' + repositories_select_field = SelectField( name='repository_names_by_owner', + multiple=True, + display='checkboxes' ) + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.deleted == False ) \ + .order_by( trans.model.Repository.table.c.name, + trans.model.Repository.table.c.user_id ): + owner = repository.user.username + option_label = '%s (%s)' % ( repository.name, owner ) + option_value = '%s__ESEP__%s' % ( repository.name, owner ) + repositories_select_field.add_option( option_label, option_value ) + return trans.fill_template( '/webapps/community/admin/reset_metadata_on_selected_repositories.mako', + repositories_select_field=repositories_select_field, + message=message, + status=status ) + @web.expose + @web.require_admin + def undelete_repository( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = kwd.get( 'id', None ) + if id: + # Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. + ids = util.listify( id ) + count = 0 + undeleted_repositories = "" + for repository_id in ids: + repository = get_repository( trans, repository_id ) + if repository.deleted: + repository.deleted = False + trans.sa_session.add( repository ) + trans.sa_session.flush() + count += 1 + undeleted_repositories += " %s" % repository.name + if count: + message = "Undeleted %d %s: %s" % ( count, inflector.cond_plural( count, "repository" ), undeleted_repositories ) + else: + message = "No selected repositories were marked deleted, so they could not be undeleted." + else: + message = "No repository ids received for undeleting." + status = 'error' + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_repositories', + message=util.sanitize_text( message ), + status='done' ) ) + @web.expose + @web.require_admin def mark_category_deleted( self, trans, **kwd ): # TODO: We should probably eliminate the Category.deleted column since it really makes no # sense to mark a category as deleted (category names and descriptions can be changed instead). @@ -776,33 +790,6 @@ status='done' ) ) @web.expose @web.require_admin - def undelete_category( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - id = kwd.get( 'id', None ) - if id: - ids = util.listify( id ) - count = 0 - undeleted_categories = "" - for category_id in ids: - category = get_category( trans, category_id ) - if category.deleted: - category.deleted = False - trans.sa_session.add( category ) - trans.sa_session.flush() - count += 1 - undeleted_categories += " %s" % category.name - message = "Undeleted %d categories: %s" % ( count, undeleted_categories ) - else: - message = "No category ids received for undeleting." - status = 'error' - trans.response.send_redirect( web.url_for( controller='admin', - action='manage_categories', - message=util.sanitize_text( message ), - status='done' ) ) - @web.expose - @web.require_admin def purge_category( self, trans, **kwd ): # This method should only be called for a Category that has previously been deleted. # Purging a deleted Category deletes all of the following from the database: @@ -832,3 +819,30 @@ action='manage_categories', message=util.sanitize_text( message ), status='done' ) ) + @web.expose + @web.require_admin + def undelete_category( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = kwd.get( 'id', None ) + if id: + ids = util.listify( id ) + count = 0 + undeleted_categories = "" + for category_id in ids: + category = get_category( trans, category_id ) + if category.deleted: + category.deleted = False + trans.sa_session.add( category ) + trans.sa_session.flush() + count += 1 + undeleted_categories += " %s" % category.name + message = "Undeleted %d categories: %s" % ( count, undeleted_categories ) + else: + message = "No category ids received for undeleting." + status = 'error' + trans.response.send_redirect( web.url_for( controller='admin', + action='manage_categories', + message=util.sanitize_text( message ), + status='done' ) ) diff -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 -r ca835611e8c79a9b95c50acc28d670f7f81266e7 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -5,10 +5,11 @@ from galaxy.tools import * 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_file, generate_datatypes_metadata, generate_tool_dependency_metadata, generate_tool_metadata -from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_configured_ui, get_named_tmpfile_from_ctx -from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH, make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables -from galaxy.util.shed_util import reversed_upper_bounded_changelog, strip_path, to_html_escaped, to_html_str, update_repository +from galaxy.util.shed_util import clone_repository, copy_sample_file, generate_datatypes_metadata, generate_tool_dependency_metadata, generate_tool_metadata +from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_config_from_disk, get_configured_ui +from galaxy.util.shed_util import get_named_tmpfile_from_ctx, get_sample_files_from_disk, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH +from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path, to_html_escaped +from galaxy.util.shed_util import to_html_str, update_repository from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -187,25 +188,23 @@ if user_email in admin_users: return True return False -def check_tool_input_params( trans, repo, repo_dir, ctx, xml_file_in_ctx, tool, sample_files, invalid_files, tool_data_path, dir ): +def check_tool_input_params( trans, repo_dir, tool_config, tool, sample_files, invalid_files ): """ Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make - sure the files exist. This method is called only from the tool shed when generating metadata for a specified changeset revision. + sure the files exist. """ can_set_metadata = True correction_msg = '' - # Keep track of copied files so they can be removed after metadata generation. - sample_files_copied = [] for input_param in tool.input_params: - if isinstance( input_param, galaxy.tools.parameters.basic.SelectToolParameter ) and input_param.is_dynamic: + if isinstance( input_param, tools.parameters.basic.SelectToolParameter ) and input_param.is_dynamic: # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, make sure all requirements exist. options = input_param.dynamic_options or input_param.options if options: if options.tool_data_table or options.missing_tool_data_table_name: # Make sure the repository contains a tool_data_table_conf.xml.sample file. - sample_tool_data_table_conf = get_config( 'tool_data_table_conf.xml.sample', repo, ctx, dir ) + sample_tool_data_table_conf = get_config_from_disk( 'tool_data_table_conf.xml.sample', repo_dir ) if sample_tool_data_table_conf: - error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, sample_tool_data_table_conf ) + error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_tool_data_table_conf ) if error: can_set_metadata = False invalid_files.append( ( 'tool_data_table_conf.xml.sample', correction_msg ) ) @@ -215,7 +214,7 @@ can_set_metadata = False correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample " correction_msg += "to the repository that includes the required entry to correct this error.<br/>" - invalid_files.append( ( xml_file_in_ctx, correction_msg ) ) + invalid_files.append( ( tool_config, correction_msg ) ) if options.index_file or options.missing_index_file: # Make sure the repository contains the required xxx.loc.sample file. index_file = options.index_file or options.missing_index_file @@ -224,13 +223,6 @@ for sample_file in sample_files: sample_file_name = strip_path( sample_file ) if sample_file_name == '%s.sample' % index_file_name: - # If sample_file_name is on disk, copy it to dir. - copied_sample_file = copy_file_from_disk( sample_file_name, repo_dir, dir ) - if not copied_sample_file: - # Get sample_file_name from the repository manifest. - copied_sample_file = copy_file_from_manifest( repo, ctx, sample_file_name, dir ) - copy_sample_file( trans.app, copied_sample_file, dest_path=tool_data_path ) - sample_files_copied.append( sample_file_name ) options.index_file = index_file_name options.missing_index_file = None if options.tool_data_table: @@ -241,10 +233,10 @@ can_set_metadata = False correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) - invalid_files.append( ( xml_file_in_ctx, correction_msg ) ) + invalid_files.append( ( tool_config, correction_msg ) ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) - return sample_files_copied, can_set_metadata, invalid_files + return can_set_metadata, invalid_files def clean_repository_metadata( trans, id, changeset_revisions ): # Delete all repository_metadata reecords associated with the repository that have a changeset_revision that is not in changeset_revisions. for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ @@ -254,11 +246,8 @@ trans.sa_session.flush() def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision is an ancestor of - # current_changeset_revision which is associated with current_metadata_dict. - # - # A new repository_metadata record will be created only when this method returns the string 'not equal and not subset'. However, we're - # currently also returning the strings 'no metadata', 'equal' and 'subset', depending upon how the 2 change sets compare. We'll leave - # things this way for the current time in case we discover a use for these additional result strings. + # current_changeset_revision which is associated with current_metadata_dict. A new repository_metadata record will be created only + # when this method returns the string 'not equal and not subset'. ancestor_datatypes = ancestor_metadata_dict.get( 'datatypes', [] ) ancestor_tools = ancestor_metadata_dict.get( 'tools', [] ) ancestor_guids = [ tool_dict[ 'guid' ] for tool_dict in ancestor_tools ] @@ -279,7 +268,7 @@ # Handle case where all metadata is the same. if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal': return 'equal' - if workflow_comparison == 'subset' and datatype_comparison == 'subset': + if workflow_comparison in [ 'equal', 'subset' ] and datatype_comparison in [ 'equal', 'subset' ]: is_subset = True for guid in ancestor_guids: if guid not in current_guids: @@ -391,103 +380,69 @@ return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) else: return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name ) -def generate_metadata_for_changeset_revision( trans, repo, id, ctx, changeset_revision, repo_dir, updating_tip=False ): - if updating_tip: - # If a push from the command line is occurring, update the repository files on disk before setting metadata. - update_repository( repo, str( ctx.rev() ) ) +def generate_metadata_for_changeset_revision( trans, repository_files_dir, repository_clone_url ): + """ + Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, + the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's + disk files, so the value of repository_files_dir will not always be repository.repo_path (it could be a temporary directory containing a clone). + """ metadata_dict = {} invalid_files = [] invalid_tool_configs = [] - original_tool_data_path = trans.app.config.tool_data_path - work_dir = make_tmp_directory() - datatypes_config = get_config( 'datatypes_conf.xml', repo, ctx, work_dir ) + tool_dependencies_config = None + datatypes_config = get_config_from_disk( 'datatypes_conf.xml', repository_files_dir ) if datatypes_config: - metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) - sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) + metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) + sample_files = get_sample_files_from_disk( repository_files_dir ) if sample_files: - trans.app.config.tool_data_path = work_dir - all_sample_files_copied = [] - # Handle the tool_data_table_conf.xml.sample file if it is included in the repository. - if 'tool_data_table_conf.xml.sample' in sample_files: - tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) - error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) - for filename in ctx: - # Find all tool configs. - ctx_file_name = strip_path( filename ) - if ctx_file_name not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): - is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, work_dir ) - if is_tool_config and valid and tool is not None: - sample_files_copied, can_set_metadata, invalid_files = check_tool_input_params( trans, - repo, - repo_dir, - ctx, - filename, - tool, - sample_files, - invalid_files, - original_tool_data_path, - work_dir ) - all_sample_files_copied.extend( sample_files_copied ) - if can_set_metadata: - # Update the list of metadata dictionaries for tools in metadata_dict. - repository_clone_url = generate_clone_url( trans, id ) - metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict ) - else: - invalid_tool_configs.append( ctx_file_name ) - elif is_tool_config: - if not error_message: - error_message = 'Unknown problems loading tool.' - # We have a tool config but it is invalid or the tool does not properly load. - invalid_files.append( ( ctx_file_name, error_message ) ) - invalid_tool_configs.append( ctx_file_name ) - # Find all exported workflows. - elif filename.endswith( '.ga' ): - try: - fctx = ctx[ filename ] - workflow_text = fctx.data() - exported_workflow_dict = from_json_string( workflow_text ) - if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': - metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict ) - except Exception, e: - invalid_files.append( ( ctx_file_name, str( e ) ) ) + metadata_dict[ 'sample_files' ] = sample_files + # Find all tool configs and exported workflows. + for root, dirs, files in os.walk( repository_files_dir ): + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + if '.hg' in dirs: + dirs.remove( '.hg' ) + for name in files: + # Find all tool configs. + if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): + full_path = os.path.abspath( os.path.join( root, name ) ) + if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] + or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): + try: + # Make sure we're looking at a tool config and not a display application config or something else. + element_tree = util.parse_xml( full_path ) + element_tree_root = element_tree.getroot() + is_tool = element_tree_root.tag == 'tool' + except Exception, e: + print "Error parsing %s", full_path, ", exception: ", str( e ) + is_tool = False + if is_tool: + try: + tool = trans.app.toolbox.load_tool( full_path ) + tool_config = os.path.join( root, name ) + except Exception, e: + tool = None + invalid_tool_configs.append( name ) + if tool is not None: + can_set_metadata, invalid_files = check_tool_input_params( trans, repository_files_dir, tool_config, tool, sample_files, invalid_files ) + if can_set_metadata: + metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) + # Find all exported workflows + elif name.endswith( '.ga' ): + relative_path = os.path.join( root, name ) + fp = open( relative_path, 'rb' ) + workflow_text = fp.read() + fp.close() + exported_workflow_dict = from_json_string( workflow_text ) + if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) if 'tools' in metadata_dict: - # Find tool_dependencies.xml if it exists. This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config( 'tool_dependencies.xml', repo, ctx, work_dir ) + # This step must be done after metadata for tools has been defined. + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', repository_files_dir ) if tool_dependencies_config: metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs - if sample_files: - # Don't forget to reset the value of trans.app.config.tool_data_path! - trans.app.config.tool_data_path = original_tool_data_path - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - reset_tool_data_tables( trans.app ) - try: - shutil.rmtree( work_dir ) - except: - pass - # Remove all copied sample files from both the original tool data path (~/shed-tool-data) and the temporary - # value of trans.app.config.tool_data_path, which is work_dir. - for copied_sample_file in all_sample_files_copied: - copied_file = copied_sample_file.replace( '.sample', '' ) - try: - os.unlink( os.path.join( trans.app.config.tool_data_path, copied_sample_file ) ) - except: - pass - try: - os.unlink( os.path.join( trans.app.config.tool_data_path, copied_file ) ) - except: - pass - if trans.app.config.tool_data_path == work_dir: - try: - os.unlink( os.path.join( original_tool_data_path, copied_sample_file ) ) - except: - pass - try: - os.unlink( os.path.join( original_tool_data_path, copied_file ) ) - except: - pass - return metadata_dict, invalid_files, deleted_sample_files + return metadata_dict, invalid_files def generate_tool_guid( trans, repository, tool ): """ Generate a guid for the received tool. The form of the guid is @@ -529,10 +484,10 @@ if deleted: return 'DELETED' return None -def get_latest_repository_metadata( trans, id ): +def get_latest_repository_metadata( trans, decoded_repository_id ): """Get last metadata defined for a specified repository from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ + .filter( trans.model.RepositoryMetadata.table.c.repository_id == decoded_repository_id ) \ .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \ .first() def get_list_of_copied_sample_files( repo, ctx, dir ): @@ -873,14 +828,13 @@ # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) return is_tool_config, valid, tool, error_message -def new_tool_metadata_required( trans, id, metadata_dict ): +def new_tool_metadata_required( trans, repository, metadata_dict ): """ - Compare the last saved metadata for each tool in the repository with the new metadata - in metadata_dict to determine if a new repository_metadata table record is required, or - if the last saved metadata record can updated instead. + Compare the last saved metadata for each tool in the repository with the new metadata in metadata_dict to determine if a new repository_metadata + table record is required, or if the last saved metadata record can be updated instead. """ if 'tools' in metadata_dict: - repository_metadata = get_latest_repository_metadata( trans, id ) + repository_metadata = get_latest_repository_metadata( trans, repository.id ) if repository_metadata: metadata = repository_metadata.metadata if metadata and 'tools' in metadata: @@ -908,20 +862,17 @@ # repository, so we can update the existing repository metadata. return False else: - # There is no saved repository metadata, so we need to create a new repository_metadata - # table record. + # There is no saved repository metadata, so we need to create a new repository_metadata table record. return True - # The received metadata_dict includes no metadata for tools, so a new repository_metadata table - # record is not needed. + # The received metadata_dict includes no metadata for tools, so a new repository_metadata table record is not needed. return False -def new_workflow_metadata_required( trans, id, metadata_dict ): +def new_workflow_metadata_required( trans, repository, metadata_dict ): """ - Currently everything about an exported workflow except the name is hard-coded, so there's - no real way to differentiate versions of exported workflows. If this changes at some future - time, this method should be enhanced accordingly. + Currently everything about an exported workflow except the name is hard-coded, so there's no real way to differentiate versions of + exported workflows. If this changes at some future time, this method should be enhanced accordingly. """ if 'workflows' in metadata_dict: - repository_metadata = get_latest_repository_metadata( trans, id ) + repository_metadata = get_latest_repository_metadata( trans, repository.id ) if repository_metadata: if repository_metadata.metadata: # The repository has metadata, so update the workflows value - no new record is needed. @@ -939,167 +890,128 @@ log.debug( "Resetting all metadata on repository: %s" % repository.name ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) - missing_sample_files = [] - if len( repo ) == 1: - error_message, status = set_repository_metadata( trans, id, repository.tip, **kwd ) - if error_message: - return error_message, status - else: - add_repository_metadata_tool_versions( trans, id, [ repository.tip ] ) - else: - # The list of changeset_revisions refers to repository_metadata records that have been created or updated. When the following loop - # completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list. - changeset_revisions = [] - # When a new repository_metadata record is created, it always uses the values of metadata_changeset_revision and metadata_dict. - metadata_changeset_revision = None - metadata_dict = None - ancestor_changeset_revision = None - ancestor_metadata_dict = None - for changeset in repo.changelog: - current_changeset_revision = str( repo.changectx( changeset ) ) - ctx = get_changectx_for_changeset( repo, current_changeset_revision ) - current_metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans, - repo, - id, - ctx, - current_changeset_revision, - repo_dir, - updating_tip=current_changeset_revision==repository.tip ) - for deleted_sample_file in deleted_sample_files: - if deleted_sample_file not in missing_sample_files: - missing_sample_files.append( deleted_sample_file ) - if current_metadata_dict: - if not metadata_changeset_revision and not metadata_dict: - # We're at the first change set in the change log. - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict - if ancestor_changeset_revision: - # Compare metadata from ancestor and current. The value of comparsion will be one of: - # 'no metadata' - no metadata for either ancestor or current, so continue from current - # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current - # 'subset' - ancestor metadata is a subset of current metadata, so continue from current - # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current metadata, so persist ancestor metadata. - comparison = compare_changeset_revisions( ancestor_changeset_revision, - ancestor_metadata_dict, - current_changeset_revision, - current_metadata_dict ) - if comparison in [ 'no metadata', 'equal', 'subset' ]: - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict - elif comparison == 'not equal and not subset': - metadata_changeset_revision = ancestor_changeset_revision - metadata_dict = ancestor_metadata_dict - create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) - changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict - else: - # We're at the beginning of the change log. + repository_clone_url = generate_clone_url( trans, id ) + # The list of changeset_revisions refers to repository_metadata records that have been created or updated. When the following loop + # completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list. + changeset_revisions = [] + # When a new repository_metadata record is created, it always uses the values of metadata_changeset_revision and metadata_dict. + metadata_changeset_revision = None + metadata_dict = None + ancestor_changeset_revision = None + ancestor_metadata_dict = None + home_dir = os.getcwd() + for changeset in repo.changelog: + work_dir = tempfile.mkdtemp() + current_changeset_revision = str( repo.changectx( changeset ) ) + ctx = repo.changectx( changeset ) + print "Cloning repository revision: ", str( ctx.rev() ) + clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) + print "Generating metadata for changset revision: ", str( ctx.rev() ) + current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, work_dir, repository_clone_url ) + if current_metadata_dict: + if not metadata_changeset_revision and not metadata_dict: + # We're at the first change set in the change log. + metadata_changeset_revision = current_changeset_revision + metadata_dict = current_metadata_dict + if ancestor_changeset_revision: + # Compare metadata from ancestor and current. The value of comparison will be one of: + # 'no metadata' - no metadata for either ancestor or current, so continue from current + # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current + # 'subset' - ancestor metadata is a subset of current metadata, so continue from current + # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current metadata, so persist ancestor metadata. + comparison = compare_changeset_revisions( ancestor_changeset_revision, + ancestor_metadata_dict, + current_changeset_revision, + current_metadata_dict ) + if comparison in [ 'no metadata', 'equal', 'subset' ]: ancestor_changeset_revision = current_changeset_revision ancestor_metadata_dict = current_metadata_dict - if not ctx.children(): - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict - # We're at the end of the change log. + elif comparison == 'not equal and not subset': + metadata_changeset_revision = ancestor_changeset_revision + metadata_dict = ancestor_metadata_dict create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = None - ancestor_metadata_dict = None - elif ancestor_metadata_dict: - # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + else: + # We're at the beginning of the change log. ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + if not ctx.children(): metadata_changeset_revision = current_changeset_revision - metadata_dict = ancestor_metadata_dict - if not ctx.children(): - # We're at the end of the change log. - create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) - changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = None - ancestor_metadata_dict = None - # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. - clean_repository_metadata( trans, id, changeset_revisions ) - add_repository_metadata_tool_versions( trans, id, changeset_revisions ) - if missing_sample_files: - message += "Metadata was successfully reset, but the following required sample files have been deleted from the repository so the version " - message += "of each file just prior to its deletion is being used. These files should be re-added to the repository as soon as possible: " - message += "<b>%s</b><br/>" % ', '.join( missing_sample_files ) - return message, 'ok' - return '', 'ok' -def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ): + metadata_dict = current_metadata_dict + # We're at the end of the change log. + create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + changeset_revisions.append( metadata_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None + elif ancestor_metadata_dict: + # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. + ancestor_changeset_revision = current_changeset_revision + metadata_changeset_revision = current_changeset_revision + metadata_dict = ancestor_metadata_dict + if not ctx.children(): + # We're at the end of the change log. + create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + changeset_revisions.append( metadata_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None + if os.path.exists( work_dir ): + try: + shutil.rmtree( work_dir ) + except: + pass + # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. + clean_repository_metadata( trans, id, changeset_revisions ) + add_repository_metadata_tool_versions( trans, id, changeset_revisions ) +def set_repository_metadata( trans, repository, content_alert_str='', **kwd ): """ - Set repository metadata on the repository tip, returning specific error messages (if any) to alert the repository owner that the changeset + Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset has problems. """ message = '' status = 'done' - repository = get_repository( trans, id ) + repository_clone_url = generate_clone_url( trans, trans.security.encode_id( repository.id ) ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) - ctx = get_changectx_for_changeset( repo, changeset_revision ) - metadata_dict = {} - invalid_files = [] - updating_tip = changeset_revision == repository.tip - if ctx is not None: - metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans, - repo, - id, - ctx, - changeset_revision, - repo_dir, - updating_tip=updating_tip ) - if metadata_dict: - if updating_tip: - if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ): - # Create a new repository_metadata table row. - repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) - trans.sa_session.add( repository_metadata ) - try: - trans.sa_session.flush() - # If this is the first record stored for this repository, see if we need to send any email alerts. - if len( repository.downloadable_revisions ) == 1: - handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) - except TypeError, e: - message = "Unable to save metadata for this repository probably due to a tool config file that doesn't conform to the Cheetah template syntax." - status = 'error' - else: - repository_metadata = get_latest_repository_metadata( trans, id ) - if repository_metadata: - # Update the last saved repository_metadata table row. - repository_metadata.changeset_revision = changeset_revision - repository_metadata.metadata = metadata_dict - repository_metadata.downloadable = changeset_is_downloadable( metadata_dict ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - else: - # There are no tools in the repository, and we're setting metadata on the repository tip. - repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - else: - # We're re-generating metadata for an old repository revision. - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, repo_dir, repository_clone_url ) + if metadata_dict: + if new_tool_metadata_required( trans, repository, metadata_dict ) or new_workflow_metadata_required( trans, repository, metadata_dict ): + # Create a new repository_metadata table row. + repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) + trans.sa_session.add( repository_metadata ) + try: + trans.sa_session.flush() + # If this is the first record stored for this repository, see if we need to send any email alerts. + if len( repository.downloadable_revisions ) == 1: + handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) + except TypeError, e: + message = "Unable to save metadata for this repository, exception: %s" % str( e ) + status = 'error' + else: + repository_metadata = get_latest_repository_metadata( trans, repository.id ) + if repository_metadata: + # Update the last saved repository_metadata table row. + repository_metadata.changeset_revision = repository.tip repository_metadata.metadata = metadata_dict repository_metadata.downloadable = changeset_is_downloadable( metadata_dict ) trans.sa_session.add( repository_metadata ) trans.sa_session.flush() - elif updating_tip and len( repo ) == 1 and not invalid_files: - message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( changeset_revision ) - message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." - status = "error" - else: - # Here ctx is None. - message = "This repository does not include revision '%s'." % str( changeset_revision ) - status = 'error' - if deleted_sample_files: - message += "Metadata was successfully reset, but the following required sample files have been deleted from the repository so the version " - message += "of each file just prior to its deletion is being used. These files should be re-added to the repository as soon as possible: " - message += "<b>%s</b><br/>" % ', '.join( deleted_sample_files ) + else: + # There are no tools in the repository, and we're setting metadata on the repository tip. + repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + elif len( repo ) == 1 and not invalid_files: + message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip ) + message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." + status = "error" if invalid_files: if metadata_dict: - message = "Metadata was defined for some items in revision '%s'. " % str( changeset_revision ) + message += "Metadata was defined for some items in revision '%s'. " % str( repository.tip ) message += "Correct the following problems if necessary and reset metadata.<br/>" else: - message = "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( changeset_revision ) + message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip ) message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.<br/>" for itc_tup in invalid_files: tool_file, exception_msg = itc_tup @@ -1118,18 +1030,14 @@ message += "<b>%s</b> - %s<br/>" % ( tool_file, correction_msg ) status = 'error' return message, status -def set_repository_metadata_due_to_new_tip( trans, id, repository, content_alert_str=None, **kwd ): +def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ): # Set metadata on the repository tip. - error_message, status = set_repository_metadata( trans, id, repository.tip, content_alert_str=content_alert_str, **kwd ) - if not error_message: - # If no error occurred in setting metadata on the repository tip, reset metadata on all changeset revisions for the repository. - # This will result in a more standardized set of valid repository revisions that can be installed. - error_message, status = reset_all_metadata_on_repository( trans, id, **kwd ) + error_message, status = set_repository_metadata( trans, repository, content_alert_str=content_alert_str, **kwd ) if error_message: # If there is an error, display it. return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', - id=id, + id=trans.security.encode_id( repository.id ), message=error_message, status='error' ) ) def update_for_browsing( trans, repository, current_working_dir, commit_message='' ): diff -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 -r ca835611e8c79a9b95c50acc28d670f7f81266e7 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1735,13 +1735,9 @@ status=status ) @web.expose def reset_all_metadata( self, trans, id, **kwd ): - error_message, status = reset_all_metadata_on_repository( trans, id, **kwd ) - if error_message: - message = error_message - status = 'error' - else: - message = "All repository metadata has been reset." - status = 'done' + reset_all_metadata_on_repository( trans, id, **kwd ) + message = "All repository metadata has been reset." + status = 'done' return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id, @@ -1890,7 +1886,7 @@ else: message += 'The selected files were deleted from the repository. ' kwd[ 'message' ] = message - set_repository_metadata_due_to_new_tip( trans, id, repository, **kwd ) + set_repository_metadata_due_to_new_tip( trans, repository, **kwd ) else: message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" @@ -1981,8 +1977,8 @@ action=caller, **kwd ) ) @web.expose - @web.require_login( "set repository metadata" ) - def set_metadata( self, trans, id, ctx_str, **kwd ): + @web.require_login( "set repository as malicious" ) + def set_malicious( self, trans, id, ctx_str, **kwd ): malicious = kwd.get( 'malicious', '' ) if kwd.get( 'malicious_button', False ): repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, ctx_str ) @@ -1995,11 +1991,6 @@ else: message = "The repository tip has been defined as <b>not</b> malicious." status = 'done' - else: - # The set_metadata_button was clicked - message, status = set_repository_metadata( trans, id, ctx_str, **kwd ) - if not message: - message = "Metadata for change set revision '%s' has been reset." % str( ctx_str ) return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id, diff -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 -r ca835611e8c79a9b95c50acc28d670f7f81266e7 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -3,7 +3,7 @@ from galaxy.model.orm import * from galaxy.datatypes.checkers import * from common import * -from galaxy.util.shed_util import get_configured_ui, reset_tool_data_tables, handle_sample_tool_data_table_conf_file +from galaxy.util.shed_util import get_configured_ui, reset_tool_data_tables, handle_sample_tool_data_table_conf_file, update_repository from galaxy import eggs eggs.require('mercurial') @@ -154,7 +154,7 @@ else: message += " %d files were removed from the repository root. " % len( files_to_remove ) kwd[ 'message' ] = message - set_repository_metadata_due_to_new_tip( trans, repository_id, repository, content_alert_str=content_alert_str, **kwd ) + set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) trans.response.send_redirect( web.url_for( controller='repository', diff -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 -r ca835611e8c79a9b95c50acc28d670f7f81266e7 templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -55,7 +55,7 @@ <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories', webapp='community' )}">Browse all repositories</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_all_repositories', webapp='community' )}">Reset all metadata</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories', webapp='community' )}">Reset selected metadata</a></div><div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata', webapp='community' )}">Browse metadata</a> diff -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 -r ca835611e8c79a9b95c50acc28d670f7f81266e7 templates/webapps/community/admin/reset_metadata_on_all_repositories.mako --- a/templates/webapps/community/admin/reset_metadata_on_all_repositories.mako +++ /dev/null @@ -1,19 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Reset metadata on each change set of the repositories in this tool shed</div> - <form name="reset_metadata_on_all_repositories" id="reset_metadata_on_all_repositories" action="${h.url_for( controller='admin', action='reset_metadata_on_all_repositories' )}" method="post" > - <div class="form-row"> - Click the button below to reset metadata on each change set of the repositories in this tool shed. - </div> - <div class="form-row"> - <input type="submit" name="reset_metadata_on_all_repositories_button" value="Reset metadata on all repositories"/> - </div> - </form> - </div> -</div> diff -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 -r ca835611e8c79a9b95c50acc28d670f7f81266e7 templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako --- /dev/null +++ b/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako @@ -0,0 +1,69 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="local_javascripts()"> + <script type="text/javascript"> + function checkAllFields() + { + var chkAll = document.getElementById('checkAll'); + var checks = document.getElementsByTagName('input'); + var boxLength = checks.length; + var allChecked = false; + var totalChecked = 0; + if ( chkAll.checked == true ) + { + for ( i=0; i < boxLength; i++ ) + { + if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1) + { + checks[i].checked = true; + } + } + } + else + { + for ( i=0; i < boxLength; i++ ) + { + if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1) + { + checks[i].checked = false + } + } + } + } + </script> +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${local_javascripts()} +</%def> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Reset all metadata on each selected repository</div> + <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories' )}" method="post" > + <div class="form-row"> + Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. Resetting metadata + may take a while because this process clones each change set in each selected repository's change log to a temporary location on disk. + Wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as doing anything else will not + be helpful. Watch the tool shed paster log to pass the time if necessary. + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="checkbox" id="checkAll" name=select_all_repositories_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_repositories_checkbox value="true"/><b>Select/unselect all repositories</b> + </div> + <div style="clear: both"></div> + <div class="form-row"> + ${repositories_select_field.get_html()} + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" name="reset_metadata_on_selected_repositories_button" value="Reset metadata on selected repositories"/> + </div> + </form> + </div> +</div> diff -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 -r ca835611e8c79a9b95c50acc28d670f7f81266e7 templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -340,7 +340,7 @@ <div class="toolForm"><div class="toolFormTitle">Malicious repository tip</div><div class="toolFormBody"> - <form name="malicious" id="malicious" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"> + <form name="malicious" id="malicious" action="${h.url_for( controller='repository', action='set_malicious', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"><div class="form-row"><label>Define repository tip as malicious:</label> ${malicious_check_box.get_html()} diff -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 -r ca835611e8c79a9b95c50acc28d670f7f81266e7 templates/webapps/community/repository/view_changelog.mako --- a/templates/webapps/community/repository/view_changelog.mako +++ b/templates/webapps/community/repository/view_changelog.mako @@ -107,7 +107,7 @@ else: ctx_parent_str = "%s:%s" % ( ctx_parent_rev, ctx_parent ) if changeset[ 'has_metadata' ]: - has_metadata_str = '<table border="0" bgcolor="#D8D8D8"><tr><td>Repository metadata is associated with this change set.</td></tr></table>' + has_metadata_str = '<table border="0"><tr><td bgcolor="#D8D8D8">Repository metadata is associated with this change set.</td></tr></table>' else: has_metadata_str = '' %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix mercurial command line handling for pushes from the command line that were broken in change set d19fbfefb676 for versions of mercurial older than 2.2.3. Pushes should now function correctly for those running mercurial older than version 2.2.3.
by Bitbucket 07 Aug '12

07 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f4e633e6ab4e/ changeset: f4e633e6ab4e user: greg date: 2012-08-07 19:43:36 summary: Fix mercurial command line handling for pushes from the command line that were broken in change set d19fbfefb676 for versions of mercurial older than 2.2.3. Pushes should now function correctly for those running mercurial older than version 2.2.3. affected #: 2 files diff -r 3f17b65c590758f03c517cc564d59efcc5f3998c -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 lib/galaxy/webapps/community/controllers/hg.py --- a/lib/galaxy/webapps/community/controllers/hg.py +++ b/lib/galaxy/webapps/community/controllers/hg.py @@ -1,9 +1,12 @@ import os, logging from galaxy.web.base.controller import * from galaxy.webapps.community.controllers.common import * +from galaxy.util.shed_util import update_repository from galaxy import eggs eggs.require('mercurial') +import mercurial.__version__ +from mercurial import hg, ui, commands from mercurial.hgweb.hgwebdir_mod import hgwebdir from mercurial.hgweb.request import wsgiapplication @@ -14,17 +17,32 @@ def handle_request( self, trans, **kwd ): # The os command that results in this method being called will look something like # hg clone http://test@127.0.0.1:9009/repos/test/convert_characters1 + hg_version = mercurial.__version__.version cmd = kwd.get( 'cmd', None ) wsgi_app = wsgiapplication( make_web_app ) - if cmd == 'pushkey': - # This results from an "hg push" from the command line. When doing this, the following 6 commands, in order, - # will be retrieved from environ: capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey + # In mercurial version 2.2.3, section 15.2. Command changes includes a new feature: pushkey: add hooks for pushkey/listkeys (see + # http://mercurial.selenic.com/wiki/WhatsNew#Mercurial_2.2.3_.282012-07-01.29) Older versions require checking for 'listkeys'. + push_from_command_line = ( hg_version < '2.2.3' and cmd == 'listkeys' ) or ( hg_version >= '2.2.3' and cmd == 'pushkey' ) + if push_from_command_line: + # When doing an "hg push" from the command line, the following commands, in order, will be retrieved from environ, depending + # upon the mercurial version being used. There is a weakness if the mercurial version < '2.2.3' because several commands include + # listkeys, so repository metadata will be set, but only for the files currently on disk, so doing so is not too expensive. + # If mercurial version < '2.2.3: + # capabilities -> batch -> branchmap -> unbundle -> listkeys + # If mercurial version >= '2.2.3': + # capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey path_info = kwd.get( 'path_info', None ) if path_info: owner, name = path_info.split( '/' ) repository = get_repository_by_name_and_owner( trans, name, owner ) if repository: - error_message, status = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) ) + if hg_version < '2.2.3': + # We're forced to update the repository so the disk files include the changes in the push. This is handled in the + # pushkey hook in mercurial version 2.2.3 and newer. + repo = hg.repository( ui.ui(), repository.repo_path ) + update_repository( repo ) + # Set metadata using the repository files on disk. + error_message, status = set_repository_metadata( trans, repository ) if status not in [ 'ok' ] and error_message: log.debug( "Error resetting metadata on repository '%s': %s" % ( str( repository.name ), str( error_message ) ) ) elif status in [ 'ok' ] and error_message: diff -r 3f17b65c590758f03c517cc564d59efcc5f3998c -r f4e633e6ab4e3f319f02a33fd21cbccfda2a80c1 lib/galaxy/webapps/community/framework/middleware/hg.py --- a/lib/galaxy/webapps/community/framework/middleware/hg.py +++ b/lib/galaxy/webapps/community/framework/middleware/hg.py @@ -8,11 +8,13 @@ from galaxy.webapps.community import model from galaxy.util.hash_util import new_secure_hash +import mercurial.__version__ log = logging.getLogger(__name__) class Hg( object ): def __init__( self, app, config ): + print "mercurial version is:", mercurial.__version__.version self.app = app self.config = config # Authenticate this mercurial request using basic authentication @@ -56,7 +58,7 @@ connection.close() if cmd == 'unbundle': # This is an hg push from the command line. When doing this, the following 7 commands, in order, - # will be retrieved from environ: + # will be retrieved from environ (see the docs at http://mercurial.selenic.com/wiki/WireProtocol) # between -> capabilities -> heads -> branchmap -> unbundle -> unbundle -> listkeys # # The mercurial API unbundle() ( i.e., hg push ) method ultimately requires authorization. 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: smcmanus: Removed offending code from last checkin - sorry for the foul-up
by Bitbucket 07 Aug '12

07 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3f17b65c5907/ changeset: 3f17b65c5907 user: smcmanus date: 2012-08-07 19:35:39 summary: Removed offending code from last checkin - sorry for the foul-up affected #: 2 files diff -r fc9b4ae154efd2d8fb02c3637835a82767898be4 -r 3f17b65c590758f03c517cc564d59efcc5f3998c tools/filters/changeCase.pl --- a/tools/filters/changeCase.pl +++ b/tools/filters/changeCase.pl @@ -56,10 +56,3 @@ close IN; close OUT; - -sleep(10); -if ( 0 == floor(4 * rand()) % 4 ) { - print "Exiting randomly - no actual error\n"; - exit 2; -} -sleep(50); diff -r fc9b4ae154efd2d8fb02c3637835a82767898be4 -r 3f17b65c590758f03c517cc564d59efcc5f3998c tools/filters/changeCase.xml --- a/tools/filters/changeCase.xml +++ b/tools/filters/changeCase.xml @@ -1,10 +1,5 @@ <tool id="ChangeCase" name="Change Case"><description> of selected columns</description> - <parallelism method="multi" - split_inputs="input" - split_mode="number_of_parts" - split_size="8" - merge_outputs="out_file1" /><stdio><exit_code range="1:" err_level="fatal" /></stdio> 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: jgoecks: Update track icons when decomposing a composite track into individual tracks.
by Bitbucket 07 Aug '12

07 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fc9b4ae154ef/ changeset: fc9b4ae154ef user: jgoecks date: 2012-08-07 15:52:14 summary: Update track icons when decomposing a composite track into individual tracks. affected #: 1 file diff -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc -r fc9b4ae154efd2d8fb02c3637835a82767898be4 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -4067,6 +4067,7 @@ track; for (var i = 0; i < this.drawables.length; i++) { track = this.drawables[i]; + track.update_icons(); group.add_drawable(track); track.container = group; group.content_div.append(track.container_div); 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: jgoecks: Use mako template in tool help so that dynamic image paths can be used. Fixes #141
by Bitbucket 07 Aug '12

07 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/29680fa5c35e/ changeset: 29680fa5c35e user: jgoecks date: 2012-08-07 15:40:51 summary: Use mako template in tool help so that dynamic image paths can be used. Fixes #141 affected #: 58 files diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -8,6 +8,7 @@ import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback import simplejson import binascii +from mako.template import Template from UserDict import DictMixin from galaxy.util.odict import odict from galaxy.util.bunch import Bunch @@ -1068,7 +1069,8 @@ break def parse_help( self, root ): """ - Parse the help text for the tool. Formatted in reStructuredText. + Parse the help text for the tool. Formatted in reStructuredText, but + stored as Mako to allow for dynamic image paths. This implementation supports multiple pages. """ # TODO: Allow raw HTML or an external link. @@ -1080,7 +1082,7 @@ help_pages = self.help.findall( "page" ) help_header = self.help.text try: - self.help = util.rst_to_html(self.help.text) + self.help = Template( util.rst_to_html(self.help.text) ) except: log.exception( "error in help for tool %s" % self.name ) # Multiple help page case @@ -1090,7 +1092,7 @@ help_footer = help_footer + help_page.tail # Each page has to rendered all-together because of backreferences allowed by rst try: - self.help_by_page = [ util.rst_to_html( help_header + x + help_footer ) + self.help_by_page = [ Template( util.rst_to_html( help_header + x + help_footer ) ) for x in self.help_by_page ] except: log.exception( "error in multi-page help for tool %s" % self.name ) diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -332,6 +332,9 @@ else: tool_help = tool.help + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ) ) + # Convert to unicode to display non-ascii characters. if type( tool_help ) is not unicode: tool_help = unicode( tool_help, 'utf-8') diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/discreteWavelet/execute_dwt_IvC_all.xml --- a/tools/discreteWavelet/execute_dwt_IvC_all.xml +++ b/tools/discreteWavelet/execute_dwt_IvC_all.xml @@ -101,11 +101,11 @@ The second output file: -.. image:: ./static/operation_icons/dwt_IvC_1.png -.. image:: ./static/operation_icons/dwt_IvC_2.png -.. image:: ./static/operation_icons/dwt_IvC_3.png -.. image:: ./static/operation_icons/dwt_IvC_4.png -.. image:: ./static/operation_icons/dwt_IvC_5.png +.. image:: ${static_path}/operation_icons/dwt_IvC_1.png +.. image:: ${static_path}/operation_icons/dwt_IvC_2.png +.. image:: ${static_path}/operation_icons/dwt_IvC_3.png +.. image:: ${static_path}/operation_icons/dwt_IvC_4.png +.. image:: ${static_path}/operation_icons/dwt_IvC_5.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml --- a/tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml +++ b/tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml @@ -101,11 +101,11 @@ The second output file: -.. image:: ./static/operation_icons/dwt_cor_aVa_1.png -.. image:: ./static/operation_icons/dwt_cor_aVa_2.png -.. image:: ./static/operation_icons/dwt_cor_aVa_3.png -.. image:: ./static/operation_icons/dwt_cor_aVa_4.png -.. image:: ./static/operation_icons/dwt_cor_aVa_5.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_1.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_2.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_3.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_4.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_5.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/discreteWavelet/execute_dwt_cor_aVb_all.xml --- a/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml +++ b/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml @@ -106,16 +106,16 @@ The second output file: -.. image:: ./static/operation_icons/dwt_cor_aVb_all_1.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_2.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_3.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_4.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_5.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_6.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_7.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_8.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_9.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_10.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_1.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_2.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_3.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_4.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_5.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_6.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_7.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_8.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_9.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_10.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/discreteWavelet/execute_dwt_var_perClass.xml --- a/tools/discreteWavelet/execute_dwt_var_perClass.xml +++ b/tools/discreteWavelet/execute_dwt_var_perClass.xml @@ -98,7 +98,7 @@ The third output file: -.. image:: ./static/operation_icons/dwt_var_perClass.png +.. image:: ${static_path}/operation_icons/dwt_var_perClass.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/evolution/add_scores.xml --- a/tools/evolution/add_scores.xml +++ b/tools/evolution/add_scores.xml @@ -43,8 +43,8 @@ The input can be any interval_ format dataset. The output is also in interval format. (`Dataset missing?`_) -.. _interval: ./static/formatHelp.html#interval -.. _Dataset missing?: ./static/formatHelp.html +.. _interval: ${static_path}/formatHelp.html#interval +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/evolution/codingSnps.xml --- a/tools/evolution/codingSnps.xml +++ b/tools/evolution/codingSnps.xml @@ -94,9 +94,9 @@ The gene dataset is in BED_ format with 12 columns. The output dataset is also interval. (`Dataset missing?`_) -.. _interval: ./static/formatHelp.html#interval -.. _BED: ./static/formatHelp.html#bed -.. _Dataset missing?: ./static/formatHelp.html +.. _interval: ${static_path}/formatHelp.html#interval +.. _BED: ${static_path}/formatHelp.html#bed +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/fastx_toolkit/fasta_clipping_histogram.xml --- a/tools/fastx_toolkit/fasta_clipping_histogram.xml +++ b/tools/fastx_toolkit/fasta_clipping_histogram.xml @@ -1,6 +1,6 @@ <tool id="cshl_fasta_clipping_histogram" name="Length Distribution"><description>chart</description> - <requirements><requirement type="package">fastx_toolkit</requirement></requirements> + <requirements><requirement type="package">fastx_toolkit</requirement></requirements><command>fasta_clipping_histogram.pl $input $outfile</command><inputs> @@ -25,13 +25,13 @@ In the following library, most sequences are 24-mers to 27-mers. This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place). -.. image:: ./static/fastx_icons/fasta_clipping_histogram_1.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png In the following library, most sequences are 19,22 or 23-mers. This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place). -.. image:: ./static/fastx_icons/fasta_clipping_histogram_2.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_2.png ----- @@ -81,7 +81,7 @@ Each sequence is counts as one, to produce the following chart: -.. image:: ./static/fastx_icons/fasta_clipping_histogram_3.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png Example 2 - The following FASTA file have multiplicity counts:: @@ -95,7 +95,7 @@ The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart: -.. image:: ./static/fastx_icons/fasta_clipping_histogram_4.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_4.png Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts. diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/fastx_toolkit/fastq_quality_boxplot.xml --- a/tools/fastx_toolkit/fastq_quality_boxplot.xml +++ b/tools/fastx_toolkit/fastq_quality_boxplot.xml @@ -32,16 +32,16 @@ An excellent quality library (median quality is 40 for almost all 36 cycles): -.. image:: ./static/fastx_icons/fastq_quality_boxplot_1.png +.. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_1.png A relatively good quality library (median quality degrades towards later cycles): -.. image:: ./static/fastx_icons/fastq_quality_boxplot_2.png +.. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_2.png A low quality library (median drops quickly): -.. image:: ./static/fastx_icons/fastq_quality_boxplot_3.png +.. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_3.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/fastx_toolkit/fastx_barcode_splitter.xml --- a/tools/fastx_toolkit/fastx_barcode_splitter.xml +++ b/tools/fastx_toolkit/fastx_barcode_splitter.xml @@ -1,6 +1,6 @@ <tool id="cshl_fastx_barcode_splitter" name="Barcode Splitter"><description></description> - <requirements><requirement type="package">fastx_toolkit</requirement></requirements> + <requirements><requirement type="package">fastx_toolkit</requirement></requirements><command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command><inputs> @@ -62,7 +62,7 @@ **Output Example** -.. image:: ./static/fastx_icons/barcode_splitter_output_example.png +.. image:: ${static_path}/fastx_icons/barcode_splitter_output_example.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/fastx_toolkit/fastx_clipper.xml --- a/tools/fastx_toolkit/fastx_clipper.xml +++ b/tools/fastx_toolkit/fastx_clipper.xml @@ -1,6 +1,6 @@ <tool id="cshl_fastx_clipper" name="Clip" version="1.0.1" ><description>adapter sequences</description> - <requirements><requirement type="package">fastx_toolkit</requirement></requirements> + <requirements><requirement type="package">fastx_toolkit</requirement></requirements><command> zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS #if $input.ext == "fastqsanger": @@ -82,7 +82,7 @@ **Clipping Illustration:** -.. image:: ./static/fastx_icons/fastx_clipper_illustration.png +.. image:: ${static_path}/fastx_icons/fastx_clipper_illustration.png @@ -93,7 +93,7 @@ **Clipping Example:** -.. image:: ./static/fastx_icons/fastx_clipper_example.png +.. image:: ${static_path}/fastx_icons/fastx_clipper_example.png diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/fastx_toolkit/fastx_nucleotides_distribution.xml --- a/tools/fastx_toolkit/fastx_nucleotides_distribution.xml +++ b/tools/fastx_toolkit/fastx_nucleotides_distribution.xml @@ -1,6 +1,6 @@ <tool id="cshl_fastx_nucleotides_distribution" name="Draw nucleotides distribution chart"><description></description> - <requirements><requirement type="package">fastx_toolkit</requirement></requirements> + <requirements><requirement type="package">fastx_toolkit</requirement></requirements><command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command><inputs> @@ -26,19 +26,19 @@ The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_1.png In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_2.png The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_3.png But most of the time, the chart will look rather random: -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_4.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml +++ b/tools/maf/interval2maf.xml @@ -110,7 +110,7 @@ Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are trimmed because they extend beyond boundaries of the interval: -.. image:: ./static/images/maf_icons/interval2maf.png +.. image:: ${static_path}/images/maf_icons/interval2maf.png ------- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/maf/interval2maf_pairwise.xml --- a/tools/maf/interval2maf_pairwise.xml +++ b/tools/maf/interval2maf_pairwise.xml @@ -37,7 +37,7 @@ Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are trimmed because they extend beyond boundaries of the interval: -.. image:: ./static/images/maf_icons/interval2maf.png +.. image:: ${static_path}/images/maf_icons/interval2maf.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/maf/interval_maf_to_merged_fasta.xml --- a/tools/maf/interval_maf_to_merged_fasta.xml +++ b/tools/maf/interval_maf_to_merged_fasta.xml @@ -101,7 +101,7 @@ Here three MAF blocks overlapping a single interval are stitched together. Space between blocks 2 and 3 is filled with gaps: -.. image:: ./static/images/maf_icons/stitchMaf.png +.. image:: ${static_path}/images/maf_icons/stitchMaf.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/metag_tools/blat_mapping.xml --- a/tools/metag_tools/blat_mapping.xml +++ b/tools/metag_tools/blat_mapping.xml @@ -35,7 +35,7 @@ Showing reads coverage on human chromosome 22 (partial result) in UCSC Genome Browser Custom Track: - .. image:: ./static/images/blat_mapping_example.png + .. image:: ${static_path}/images/blat_mapping_example.png :width: 600 </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/metag_tools/convert_SOLiD_color2nuc.xml --- a/tools/metag_tools/convert_SOLiD_color2nuc.xml +++ b/tools/metag_tools/convert_SOLiD_color2nuc.xml @@ -65,7 +65,7 @@ Each di-nucleotide is represented by a single digit: 0 to 3. The matrix is symmetric, thus the leading nucleotide is necessary to determine the sequence (otherwise there are four possibilities). - .. image:: ./static/images/dualcolorcode.png + .. image:: ${static_path}/images/dualcolorcode.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/metag_tools/short_reads_figure_score.xml --- a/tools/metag_tools/short_reads_figure_score.xml +++ b/tools/metag_tools/short_reads_figure_score.xml @@ -56,7 +56,7 @@ Quality scores are summarized as boxplot (Roche 454 FLX data): -.. image:: ./static/images/short_reads_boxplot.png +.. image:: ${static_path}/images/short_reads_boxplot.png where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines: diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/mutation/visualize.xml --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -96,7 +96,7 @@ Visualization output: -.. image:: ./static/images/mutation_visualization_example.png +.. image:: ${static_path}/images/mutation_visualization_example.png :width: 150 Here the left-most column represents the position and the background color is the reference base color. Each column on its right describe each sample. diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/basecoverage.xml --- a/tools/new_operations/basecoverage.xml +++ b/tools/new_operations/basecoverage.xml @@ -38,7 +38,7 @@ **Example** -.. image:: ./static/operation_icons/gops_baseCoverage.gif +.. image:: ${static_path}/operation_icons/gops_baseCoverage.gif </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/cluster.xml --- a/tools/new_operations/cluster.xml +++ b/tools/new_operations/cluster.xml @@ -86,11 +86,11 @@ Find Clusters: -.. image:: ./static/operation_icons/gops_clusterFind.gif +.. image:: ${static_path}/operation_icons/gops_clusterFind.gif Merge Clusters: -.. image:: ./static/operation_icons/gops_clusterMerge.gif +.. image:: ${static_path}/operation_icons/gops_clusterMerge.gif </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/complement.xml --- a/tools/new_operations/complement.xml +++ b/tools/new_operations/complement.xml @@ -55,7 +55,7 @@ **Example** -.. image:: ./static/operation_icons/gops_complement.gif +.. image:: ${static_path}/operation_icons/gops_complement.gif </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/concat.xml --- a/tools/new_operations/concat.xml +++ b/tools/new_operations/concat.xml @@ -53,7 +53,7 @@ **Example** -.. image:: ./static/operation_icons/gops_concatenate.gif +.. image:: ${static_path}/operation_icons/gops_concatenate.gif </help></tool> \ No newline at end of file diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/get_flanks.xml --- a/tools/new_operations/get_flanks.xml +++ b/tools/new_operations/get_flanks.xml @@ -58,7 +58,7 @@ chr22 500 800 NM_174568 0 + -.. image:: ./static/operation_icons/flanks_ex1.gif +.. image:: ${static_path}/operation_icons/flanks_ex1.gif **Example 2** @@ -70,7 +70,7 @@ chr22 500 800 NM_028946 0 - -.. image:: ./static/operation_icons/flanks_ex2.gif +.. image:: ${static_path}/operation_icons/flanks_ex2.gif </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/intersect.xml --- a/tools/new_operations/intersect.xml +++ b/tools/new_operations/intersect.xml @@ -133,11 +133,11 @@ Overlapping Intervals: -.. image:: ./static/operation_icons/gops_intersectOverlappingIntervals.gif +.. image:: ${static_path}/operation_icons/gops_intersectOverlappingIntervals.gif Overlapping Pieces of Intervals: -.. image:: ./static/operation_icons/gops_intersectOverlappingPieces.gif +.. image:: ${static_path}/operation_icons/gops_intersectOverlappingPieces.gif </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/join.xml --- a/tools/new_operations/join.xml +++ b/tools/new_operations/join.xml @@ -94,23 +94,23 @@ **Examples** -.. image:: ./static/operation_icons/gops_joinRecordsList.gif +.. image:: ${static_path}/operation_icons/gops_joinRecordsList.gif Only records that are joined (inner join): -.. image:: ./static/operation_icons/gops_joinInner.gif +.. image:: ${static_path}/operation_icons/gops_joinInner.gif All records of first dataset: -.. image:: ./static/operation_icons/gops_joinLeftOuter.gif +.. image:: ${static_path}/operation_icons/gops_joinLeftOuter.gif All records of second dataset: -.. image:: ./static/operation_icons/gops_joinRightOuter.gif +.. image:: ${static_path}/operation_icons/gops_joinRightOuter.gif All records of both datasets: -.. image:: ./static/operation_icons/gops_joinFullOuter.gif +.. image:: ${static_path}/operation_icons/gops_joinFullOuter.gif </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/merge.xml --- a/tools/new_operations/merge.xml +++ b/tools/new_operations/merge.xml @@ -52,7 +52,7 @@ **Example** -.. image:: ./static/operation_icons/gops_merge.gif +.. image:: ${static_path}/operation_icons/gops_merge.gif </help></tool> \ No newline at end of file diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/new_operations/subtract.xml --- a/tools/new_operations/subtract.xml +++ b/tools/new_operations/subtract.xml @@ -114,11 +114,11 @@ Intervals with no overlap: -.. image:: ./static/operation_icons/gops_subtractOverlappingIntervals.gif +.. image:: ${static_path}/operation_icons/gops_subtractOverlappingIntervals.gif Non-overlapping pieces of intervals: -.. image:: ./static/operation_icons/gops_subtractOverlappingPieces.gif +.. image:: ${static_path}/operation_icons/gops_subtractOverlappingPieces.gif </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/ngs_simulation/ngs_simulation.xml --- a/tools/ngs_simulation/ngs_simulation.xml +++ b/tools/ngs_simulation/ngs_simulation.xml @@ -188,7 +188,7 @@ Plot output (png): -.. image:: ./static/images/ngs_simulation.png +.. image:: ${static_path}/images/ngs_simulation.png Summary output (txt):: diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/beam.xml --- a/tools/phenotype_association/beam.xml +++ b/tools/phenotype_association/beam.xml @@ -59,9 +59,9 @@ The input dataset must be in lped_ format. The output datasets are both tabular_. (`Dataset missing?`_) -.. _lped: ./static/formatHelp.html#lped -.. _tabular: ./static/formatHelp.html#tabular -.. _Dataset missing?: ./static/formatHelp.html +.. _lped: ${static_path}/formatHelp.html#lped +.. _tabular: ${static_path}/formatHelp.html#tabular +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/ctd.xml --- a/tools/phenotype_association/ctd.xml +++ b/tools/phenotype_association/ctd.xml @@ -246,7 +246,7 @@ Home page: http://ctdbase.org -.. _tabular: ./static/formatHelp.html#tab +.. _tabular: ${static_path}/formatHelp.html#tab ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/funDo.xml --- a/tools/phenotype_association/funDo.xml +++ b/tools/phenotype_association/funDo.xml @@ -34,7 +34,7 @@ There is no input dataset. The output is in interval_ format. -.. _interval: ./static/formatHelp.html#interval +.. _interval: ${static_path}/formatHelp.html#interval ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/gpass.xml --- a/tools/phenotype_association/gpass.xml +++ b/tools/phenotype_association/gpass.xml @@ -39,9 +39,9 @@ The input dataset must be in lped_ format, and the output is tabular_. (`Dataset missing?`_) -.. _lped: ./static/formatHelp.html#lped -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _lped: ${static_path}/formatHelp.html#lped +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/hilbertvis.xml --- a/tools/phenotype_association/hilbertvis.xml +++ b/tools/phenotype_association/hilbertvis.xml @@ -63,8 +63,8 @@ The input format is interval_, and the output is an image in PDF format. (`Dataset missing?`_) -.. _interval: ./static/formatHelp.html#interval -.. _Dataset missing?: ./static/formatHelp.html +.. _interval: ${static_path}/formatHelp.html#interval +.. _Dataset missing?: ${static_path}/formatHelp.html ----- @@ -75,7 +75,7 @@ visualization onto a two-dimensional square. For example, here is a diagram showing the path of a level-2 Hilbert curve. -.. image:: ./static/images/hilbertvisDiagram.png +.. image:: ${static_path}/images/hilbertvisDiagram.png The shade of each pixel represents the value for the corresponding bin of consecutive genomic positions, calculated according to the specified @@ -99,11 +99,11 @@ Here are some examples from the HilbertVis homepage, using ChIP-Seq data. -.. image:: ./static/images/hilbertvis1.png +.. image:: ${static_path}/images/hilbertvis1.png ----- -.. image:: ./static/images/hilbertvis2.png +.. image:: ${static_path}/images/hilbertvis2.png ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/ldtools.xml --- a/tools/phenotype_association/ldtools.xml +++ b/tools/phenotype_association/ldtools.xml @@ -34,8 +34,8 @@ The input and output datasets are tabular_. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/linkToDavid.xml --- a/tools/phenotype_association/linkToDavid.xml +++ b/tools/phenotype_association/linkToDavid.xml @@ -76,9 +76,9 @@ a link to the DAVID website as described below. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _html: ./static/formatHelp.html#html -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _html: ${static_path}/formatHelp.html#html +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/linkToGProfile.xml --- a/tools/phenotype_association/linkToGProfile.xml +++ b/tools/phenotype_association/linkToGProfile.xml @@ -48,9 +48,9 @@ The output dataset is html_ with a link to g:Profiler. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _html: ./static/formatHelp.html#html -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _html: ${static_path}/formatHelp.html#html +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/lps.xml --- a/tools/phenotype_association/lps.xml +++ b/tools/phenotype_association/lps.xml @@ -180,9 +180,9 @@ There is a second output dataset (a log) that is in text_ format. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _text: ./static/formatHelp.html#text -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _text: ${static_path}/formatHelp.html#text +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/pass.xml --- a/tools/phenotype_association/pass.xml +++ b/tools/phenotype_association/pass.xml @@ -39,9 +39,9 @@ The input is in GFF_ format, and the output is tabular_. (`Dataset missing?`_) -.. _GFF: ./static/formatHelp.html#gff -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _GFF: ${static_path}/formatHelp.html#gff +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/sift.xml --- a/tools/phenotype_association/sift.xml +++ b/tools/phenotype_association/sift.xml @@ -97,8 +97,8 @@ The input and output datasets are tabular_. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/phenotype_association/snpFreq.xml --- a/tools/phenotype_association/snpFreq.xml +++ b/tools/phenotype_association/snpFreq.xml @@ -44,8 +44,8 @@ and includes all of the input data plus the additional columns described below. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/plotting/bar_chart.xml --- a/tools/plotting/bar_chart.xml +++ b/tools/plotting/bar_chart.xml @@ -52,7 +52,7 @@ Graphing columns 2 and 3 while using column 1 for X Tick Labels will produce the following plot: -.. image:: ./static/images/bar_chart.png +.. image:: ${static_path}/images/bar_chart.png :height: 324 :width: 540 diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/plotting/boxplot.xml --- a/tools/plotting/boxplot.xml +++ b/tools/plotting/boxplot.xml @@ -95,7 +95,7 @@ * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1) * Whiskers show outliers at max. 1.5*IQR -.. image:: ./static/images/solid_qual.png +.. image:: ${static_path}/images/solid_qual.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/plotting/histogram2.xml --- a/tools/plotting/histogram2.xml +++ b/tools/plotting/histogram2.xml @@ -70,7 +70,7 @@ - Create a histogram on column 2 of the above dataset. -.. image:: ./static/images/histogram2.png +.. image:: ${static_path}/images/histogram2.png </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/plotting/scatterplot.xml --- a/tools/plotting/scatterplot.xml +++ b/tools/plotting/scatterplot.xml @@ -65,7 +65,7 @@ - Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset. -.. image:: ./static/images/scatterplot.png +.. image:: ${static_path}/images/scatterplot.png </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/plotting/xy_plot.xml --- a/tools/plotting/xy_plot.xml +++ b/tools/plotting/xy_plot.xml @@ -143,6 +143,6 @@ - Series 1: Red Dashed-Line plot between columns 1 and 2 - Series 2: Blue Circular-Point plot between columns 3 and 2 -.. image:: ./static/images/xy_example.jpg +.. image:: ${static_path}/images/xy_example.jpg </help></tool> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/regVariation/compute_q_values.xml --- a/tools/regVariation/compute_q_values.xml +++ b/tools/regVariation/compute_q_values.xml @@ -141,13 +141,13 @@ 0.03115264 0.009750824 1 -.. image:: ./static/operation_icons/p_hist.png +.. image:: ${static_path}/operation_icons/p_hist.png -.. image:: ./static/operation_icons/q_hist.png +.. image:: ${static_path}/operation_icons/q_hist.png -.. image:: ./static/operation_icons/Q_plots.png +.. image:: ${static_path}/operation_icons/Q_plots.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/regVariation/draw_stacked_barplots.xml --- a/tools/regVariation/draw_stacked_barplots.xml +++ b/tools/regVariation/draw_stacked_barplots.xml @@ -52,7 +52,7 @@ The stacked bars plot representing the data in the input file. -.. image:: ./static/operation_icons/stacked_bars_plot.png +.. image:: ${static_path}/operation_icons/stacked_bars_plot.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/rgenetics/rgManQQ.xml --- a/tools/rgenetics/rgManQQ.xml +++ b/tools/rgenetics/rgManQQ.xml @@ -86,7 +86,7 @@ improbable p values are above the red line which is drawn at the Bonferroni FWER control level (0.05/n where n is the number of tests - this is highly conservative for correlated SNPs typical of GWA) -.. image:: ./static/images/Armitagep_manhattan.png +.. image:: ${static_path}/images/Armitagep_manhattan.png A quantile-quantile (QQ) plot is a good way to see systematic departures from the null expectation of uniform p-values from a genomic analysis. If the QQ plot shows departure from the null (ie a uniform 0-1 @@ -94,7 +94,7 @@ interesting results to look at. A log scale will help emphasise departures from the null at low p values more clear -.. image:: ./static/images/Armitagep_qqplot.png +.. image:: ${static_path}/images/Armitagep_qqplot.png ----- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/rgenetics/rgWebLogo3.xml --- a/tools/rgenetics/rgWebLogo3.xml +++ b/tools/rgenetics/rgWebLogo3.xml @@ -106,7 +106,7 @@ A typical output looks like this -.. image:: ./static/images/rgWebLogo3_test.jpg +.. image:: ${static_path}/images/rgWebLogo3_test.jpg ---- diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml +++ b/tools/samtools/pileup_parser.xml @@ -320,7 +320,7 @@ To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows: -.. image:: ./static/images/pileup_parser_help1.png +.. image:: ${static_path}/images/pileup_parser_help1.png Running the tool with these parameters will return:: @@ -336,7 +336,7 @@ In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters: -.. image:: ./static/images/pileup_parser_help2.png +.. image:: ${static_path}/images/pileup_parser_help2.png will report everything from the original file:: @@ -355,7 +355,7 @@ If you set the **Print total number of differences?** to **Yes** the tool will print an additional column with the total number of reads where a devinat base is above the quality threshold. So, seetiing parametrs like this: -.. image:: ./static/images/pileup_parser_help3.png +.. image:: ${static_path}/images/pileup_parser_help3.png will produce this:: @@ -371,7 +371,7 @@ Setting **Print quality and base string?** to **Yes** as shown here: -.. image:: ./static/images/pileup_parser_help4.png +.. image:: ${static_path}/images/pileup_parser_help4.png will produce this:: diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/solid_tools/solid_qual_boxplot.xml --- a/tools/solid_tools/solid_qual_boxplot.xml +++ b/tools/solid_tools/solid_qual_boxplot.xml @@ -29,7 +29,7 @@ * Whiskers show outliers at max. 1.5*IQR -.. image:: ./static/images/solid_qual.png +.. image:: ${static_path}/images/solid_qual.png ------ diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/stats/cor.xml --- a/tools/stats/cor.xml +++ b/tools/stats/cor.xml @@ -47,19 +47,19 @@ - **Pearson's Correlation** reflects the degree of linear relationship between two variables. It ranges from +1 to -1. A correlation of +1 means that there is a perfect positive linear relationship between variables. The formula for Pearson's correlation is: - .. image:: ./static/images/pearson.png + .. image:: ${static_path}/images/pearson.png where n is the number of items - **Kendall's rank correlation** is used to measure the degree of correspondence between two rankings and assessing the significance of this correspondence. The formula for Kendall's rank correlation is: - .. image:: ./static/images/kendall.png + .. image:: ${static_path}/images/kendall.png where n is the number of items, and P is the sum. - **Spearman's rank correlation** assesses how well an arbitrary monotonic function could describe the relationship between two variables, without making any assumptions about the frequency distribution of the variables. The formula for Spearman's rank correlation is - .. image:: ./static/images/spearman.png + .. image:: ${static_path}/images/spearman.png where D is the difference between the ranks of corresponding values of X and Y, and N is the number of pairs of values. diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/stats/generate_matrix_for_pca_lda.xml --- a/tools/stats/generate_matrix_for_pca_lda.xml +++ b/tools/stats/generate_matrix_for_pca_lda.xml @@ -35,12 +35,12 @@ - Input file (Source file First) -.. image:: ./static/images/tools/lda/first_matrix_generator_example_file.png +.. image:: ${static_path}/images/tools/lda/first_matrix_generator_example_file.png - Input file (Source file Second) -.. image:: ./static/images/tools/lda/second_matrix_generator_example_file.png +.. image:: ${static_path}/images/tools/lda/second_matrix_generator_example_file.png </help> diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/taxonomy/gi2taxonomy.xml --- a/tools/taxonomy/gi2taxonomy.xml +++ b/tools/taxonomy/gi2taxonomy.xml @@ -50,7 +50,7 @@ and you want to obtain full taxonomic representation for GIs listed in *targetGI* column. If you set parameters as shown here: -.. image:: ./static/images/fetchTax.png +.. image:: ${static_path}/images/fetchTax.png the tool will generate the following output (you may need to scroll sideways to see the entire line):: diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/taxonomy/poisson2test.xml --- a/tools/taxonomy/poisson2test.xml +++ b/tools/taxonomy/poisson2test.xml @@ -48,12 +48,12 @@ Equation 1: -.. image:: ./static/images/poisson2test_eqn1.png +.. image:: ${static_path}/images/poisson2test_eqn1.png Equation 2: -.. image:: ./static/images/poisson2test_eqn2.png +.. image:: ${static_path}/images/poisson2test_eqn2.png X = number of reads falling in a particular taxon in location 1 diff -r 81692d707741d1933c3f7007148b59e7c9e28698 -r 29680fa5c35e6c22a6b7208015237b95d4bce2cc tools/taxonomy/t2ps_wrapper.xml --- a/tools/taxonomy/t2ps_wrapper.xml +++ b/tools/taxonomy/t2ps_wrapper.xml @@ -62,14 +62,14 @@ Drawing the tree with default parameters (without changing anything in the interface) will produce this tree: -.. image:: ./static/images/t2ps_ideal.png +.. image:: ${static_path}/images/t2ps_ideal.png :width: 500 (for explanation of colors and numbers on the tree scroll to the bottom of this help section) Here *Class* rank represent terminal nodes (leaves) of the tree because it is the default setting of the "*show ranks from root to*" drop-down. Changing the drop-down to "*Subspecies*" will produce this: -.. image:: ./static/images/t2ps_ideal_ssp.png +.. image:: ${static_path}/images/t2ps_ideal_ssp.png :width: 1000 -------- @@ -87,7 +87,7 @@ A full tree for this dataset will look like this: -.. image:: ./static/images/t2ps_missing_nodes.png +.. image:: ${static_path}/images/t2ps_missing_nodes.png :width: 1000 Missing nodes are simply omitted from the tree (there are no gray boxes corresponding to "n") but the branch length is maintained so that taxa belonging to the same taxonomic rank are always aligned with each other @@ -98,11 +98,11 @@ You can use the "*maximum number of leaves*" to restrict the tree to a specified number of leaves (external nodes). Using the following setting on the above dataset (note *show ranks from root to* set to *show entire tree* and *maximum number of leaves* is set *3*): -.. image:: ./static/images/t2ps_autoscale.png +.. image:: ${static_path}/images/t2ps_autoscale.png will produce this tree: -.. image:: ./static/images/t2ps_autoscale_tree.png +.. image:: ${static_path}/images/t2ps_autoscale_tree.png :width: 1000 Here the tree is automatically trimmed at a taxonomic rank that will only have 3 outer nodes. This is very useful for initial evaluation of very large trees where you want to only see, say, 1,000 outer nodes at once. @@ -113,11 +113,11 @@ Branches of the tree are colored according to the heatmap below. The "bluer" the branch the lesser the number of leaves it leads to and vice versa. -.. image:: ./static/images/t2ps_heatmap.png +.. image:: ${static_path}/images/t2ps_heatmap.png Each node is labeled with taxonomic name and the number of tree leaves belonging to this taxonomic group: -.. image:: ./static/images/t2ps_node_label.png +.. image:: ${static_path}/images/t2ps_node_label.png 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: scot...@gatech.edu: Added minor changes, including model accessors, for cancelling PBS tasks
by Bitbucket 06 Aug '12

06 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/81692d707741/ changeset: 81692d707741 user: scot...(a)gatech.edu date: 2012-08-06 05:45:11 summary: Added minor changes, including model accessors, for cancelling PBS tasks affected #: 6 files diff -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 -r 81692d707741d1933c3f7007148b59e7c9e28698 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -100,7 +100,7 @@ def get_id_tag(self): # For compatability with drmaa, which uses job_id right now, and TaskWrapper - return str(self.job_id) + return self.get_job().get_id_tag() def get_param_dict( self ): """ @@ -869,7 +869,7 @@ def get_id_tag(self): # For compatibility with drmaa job runner and TaskWrapper, instead of using job_id directly - return "%s_%s" % (self.job_id, self.task_id) + return self.get_task().get_id_tag() def get_param_dict( self ): """ diff -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 -r 81692d707741d1933c3f7007148b59e7c9e28698 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -1,4 +1,4 @@ -import os, logging, threading, time +import os, logging, threading, time, traceback from datetime import timedelta from Queue import Queue, Empty @@ -305,7 +305,9 @@ return # submit - galaxy_job_id = job_wrapper.job_id + # The job tag includes the job and the task identifier + # (if a TaskWrapper was passed in): + galaxy_job_id = job_wrapper.get_id_tag() log.debug("(%s) submitting file %s" % ( galaxy_job_id, job_file ) ) log.debug("(%s) command is: %s" % ( galaxy_job_id, command_line ) ) job_id = pbs.pbs_submit(c, job_attrs, job_file, pbs_queue_name, None) @@ -375,7 +377,8 @@ ( failures, statuses ) = self.check_all_jobs() for pbs_job_state in self.watched: job_id = pbs_job_state.job_id - galaxy_job_id = pbs_job_state.job_wrapper.job_id + #galaxy_job_id = pbs_job_state.job_wrapper.job_id + galaxy_job_id = pbs_job_state.job_wrapper.get_id_tag() old_state = pbs_job_state.old_state pbs_server_name = self.determine_pbs_server( pbs_job_state.runner_url ) if pbs_server_name in failures: @@ -562,6 +565,8 @@ """ Separated out so we can use the worker threads for it. """ + # NB: The stop_job method was modified to limit exceptions being sent up here, + # so the wrapper's fail method will now be called in case of error: if pbs_job_state.stop_job: self.stop_job( self.sa_session.query( self.app.model.Job ).get( pbs_job_state.job_wrapper.job_id ) ) pbs_job_state.job_wrapper.fail( pbs_job_state.fail_message ) @@ -606,14 +611,30 @@ def stop_job( self, job ): """Attempts to delete a job from the PBS queue""" - pbs_server_name = self.determine_pbs_server( str( job.job_runner_name ) ) - c = pbs.pbs_connect( pbs_server_name ) - if c <= 0: - log.debug("(%s/%s) Connection to PBS server for job delete failed" % ( job.id, job.job_runner_external_id ) ) - return - pbs.pbs_deljob( c, str( job.job_runner_external_id ), '' ) - pbs.pbs_disconnect( c ) - log.debug( "(%s/%s) Removed from PBS queue before job completion" % ( job.id, job.job_runner_external_id ) ) + job_tag = ( "(%s/%s)" + % ( job.get_id_tag(), job.get_job_runner_external_id() ) ) + log.debug( "%s Stopping PBS job" % job_tag ) + + # Declare the connection handle c so that it can be cleaned up: + c = None + + try: + pbs_server_name = self.determine_pbs_server( job.get_job_runner_name() ) + c = pbs.pbs_connect( pbs_server_name ) + if c <= 0: + log.debug("%s Connection to PBS server for job delete failed" + % job_tag ) + return + pbs.pbs_deljob( c, job.get_job_runner_external_id(), '' ) + log.debug( "%s Removed from PBS queue before job completion" + % job_tag ) + except: + e = traceback.format_exc() + log.debug( "%s Unable to stop job: %s" % ( job_tag, e ) ) + finally: + # Cleanup: disconnect from the server. + if ( None != c ): + pbs.pbs_disconnect( c ) def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" @@ -622,17 +643,17 @@ pbs_job_state.efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.ecfile = "%s/%s.ec" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job.id) - pbs_job_state.job_id = str( job.job_runner_external_id ) + pbs_job_state.job_id = str( job.get_job_runner_external_id() ) pbs_job_state.runner_url = job_wrapper.get_job_runner_url() job_wrapper.command_line = job.command_line pbs_job_state.job_wrapper = job_wrapper if job.state == model.Job.states.RUNNING: - log.debug( "(%s/%s) is still in running state, adding to the PBS queue" % ( job.id, job.job_runner_external_id ) ) + log.debug( "(%s/%s) is still in running state, adding to the PBS queue" % ( job.id, job.get_job_runner_external_id() ) ) pbs_job_state.old_state = 'R' pbs_job_state.running = True self.monitor_queue.put( pbs_job_state ) elif job.state == model.Job.states.QUEUED: - log.debug( "(%s/%s) is still in PBS queued state, adding to the PBS queue" % ( job.id, job.job_runner_external_id ) ) + log.debug( "(%s/%s) is still in PBS queued state, adding to the PBS queue" % ( job.id, job.get_job_runner_external_id() ) ) pbs_job_state.old_state = 'Q' pbs_job_state.running = False self.monitor_queue.put( pbs_job_state ) diff -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 -r 81692d707741d1933c3f7007148b59e7c9e28698 lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -197,12 +197,6 @@ % ( job.get_id(), task.get_id() ) ) job_wrapper.app.job_manager.job_handler.dispatcher.stop( task ) -# DELETEME: -# else: -# log.debug( "cancel_job for job %d: Task %d is in state %s and does not need to be cancelled" -# % ( job.get_id(), task.get_id(), task_state ) ) - - def put( self, job_wrapper ): """Add a job to the queue (by job identifier)""" # Change to queued state before handing to worker thread so the runner won't pick it up again diff -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 -r 81692d707741d1933c3f7007148b59e7c9e28698 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -188,6 +188,12 @@ def get_tasks( self ): # The tasks member is pert of a reference in the SQL Alchemy schema: return self.tasks + def get_id_tag( self ): + """ + Return a tag that can be useful in identifying a Job. + This returns the Job's get_id + """ + return "%s" % self.id; def set_session_id( self, session_id ): self.session_id = session_id @@ -328,6 +334,12 @@ def get_id( self ): # This is defined in the SQL Alchemy schema: return self.id + def get_id_tag( self ): + """ + Return an id tag suitable for identifying the task. + This combines the task's job id and the task's own id. + """ + return "%s:%s" % ( self.job.get_id(), self.get_id() ) def get_command_line( self ): return self.command_line def get_parameters( self ): diff -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 -r 81692d707741d1933c3f7007148b59e7c9e28698 tools/filters/changeCase.pl --- a/tools/filters/changeCase.pl +++ b/tools/filters/changeCase.pl @@ -56,3 +56,10 @@ close IN; close OUT; + +sleep(10); +if ( 0 == floor(4 * rand()) % 4 ) { + print "Exiting randomly - no actual error\n"; + exit 2; +} +sleep(50); diff -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 -r 81692d707741d1933c3f7007148b59e7c9e28698 tools/filters/changeCase.xml --- a/tools/filters/changeCase.xml +++ b/tools/filters/changeCase.xml @@ -1,5 +1,13 @@ <tool id="ChangeCase" name="Change Case"><description> of selected columns</description> + <parallelism method="multi" + split_inputs="input" + split_mode="number_of_parts" + split_size="8" + merge_outputs="out_file1" /> + <stdio> + <exit_code range="1:" err_level="fatal" /> + </stdio><command interpreter="perl">changeCase.pl $input "$cols" $delimiter $casing $out_file1</command><inputs><param name="input" format="txt" type="data" label="From"/> @@ -71,4 +79,4 @@ WINDOWS is BAD </help> -</tool> \ No newline at end of file +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: minor docstring adds in /scripts
by Bitbucket 03 Aug '12

03 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ba56d4746f7a/ changeset: ba56d4746f7a user: carlfeberhard date: 2012-08-03 19:31:48 summary: minor docstring adds in /scripts affected #: 7 files diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/check_eggs.py --- a/scripts/check_eggs.py +++ b/scripts/check_eggs.py @@ -1,7 +1,11 @@ #!/usr/bin/env python """ -usage: check_eggs.py +Compares local dependency eggs to those in eggs.ini, displaying a warning if +any are out of date. + +usage: check_eggs.py [options] """ + import os, sys, logging from optparse import OptionParser diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/check_python.py --- a/scripts/check_python.py +++ b/scripts/check_python.py @@ -1,3 +1,8 @@ +""" +If the current installed python version is not 2.5 to 2.7, prints an error +message to stderr and returns 1 +""" + import os, sys msg = """ERROR: Your Python version is: %s diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/create_db.py --- a/scripts/create_db.py +++ b/scripts/create_db.py @@ -1,3 +1,21 @@ +""" +Creates the initial galaxy database schema using the settings defined in +universe_wsgi.ini. + +This script is also wrapped by create_db.sh. + +.. note: pass '-c /location/to/your_config.ini' for non-standard ini file +locations. + +.. note: if no database_connection is set in universe_wsgi.ini, the default, +sqlite database will be constructed. + Using the database_file setting in universe_wsgi.ini will create the file + at the settings location (??) + +.. seealso: universe_wsgi.ini, specifically the settings: database_connection +and database file +""" + import sys, os.path, logging new_path = [ os.path.join( os.getcwd(), "lib" ) ] diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/dist-scramble.py --- a/scripts/dist-scramble.py +++ b/scripts/dist-scramble.py @@ -1,3 +1,36 @@ +""" +Scrambles eggs for distribution on multiple platforms. + +(from http://wiki.g2.bx.psu.edu/Admin/Config/Eggs) +This is mostly designed for use by Galaxy Developers at Penn State who are +building eggs for distribution via the Galaxy Eggs distribution site. +dist-scramble.py uses the dist-eggs.ini config file to determine what platforms +to build for, and which hosts to build on. + +dist-scramble.py works the same way as scramble.py: :: + +% python scripts/dist-scramble.py galaxy_egg + +Called with only the egg argument, dist-scramble.py will build for all the +platforms under the all group in its config file (for platform-specific eggs) +or the noplatform group (for platform-inspecific eggs). The [[hosts]|section +contains information about which hosts will be used for building on each desired +platform. If you don't want to build for all the platforms listed under the all +group, you can add a platform argument (any lvalue in the [hosts]] or [groups] +section is valid): :: + +% python scripts/dist-scramble.py galaxy_egg linux + +The platform argument is ignored for platform-inspecific eggs. An assumption is +made that your Galaxy distribution is located at the same place on all of the +hosts on which you're building (i.e. via a network filesystem). + +Once dist-scramble.py finishes, it will output a list of platforms on which it +failed to scramble the egg. Successful eggs will be put in a new dist-eggs +subdirectory of your Galaxy distribution. These eggs can then be copied to your +distribution site. +""" + import os, sys, logging from optparse import OptionParser diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/drmaa_external_killer.py --- a/scripts/drmaa_external_killer.py +++ b/scripts/drmaa_external_killer.py @@ -1,4 +1,9 @@ #!/usr/bin/env python + +""" +Terminates a DRMAA job if given a job id and (appropriate) user id. +""" + import os import sys import errno diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/drmaa_external_runner.py --- a/scripts/drmaa_external_runner.py +++ b/scripts/drmaa_external_runner.py @@ -1,4 +1,11 @@ #!/usr/bin/env python + +""" +Submit a DRMAA job given a user id and a job template file (in JSON format) +defining any or all of the following: args, remoteCommand, outputPath, +errorPath, nativeSpecification, name, email, project +""" + import os import sys import errno diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/fetch_eggs.py --- a/scripts/fetch_eggs.py +++ b/scripts/fetch_eggs.py @@ -1,3 +1,10 @@ +""" +Connects to the Galaxy Eggs distribution site and downloads any eggs needed. + +If eggs for your platform are unavailable, fetch_eggs.py will direct you to run +scramble.py. +""" + import os, sys, logging from optparse import OptionParser Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster and data providers: fix and document one-off/coordinate systems used for different track types.
by Bitbucket 03 Aug '12

03 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/53aacf94c5fc/ changeset: 53aacf94c5fc user: jgoecks date: 2012-08-03 17:20:43 summary: Trackster and data providers: fix and document one-off/coordinate systems used for different track types. affected #: 2 files diff -r da7821adf629620b239c9f5c5e1381eaf4c3ff7b -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -688,7 +688,8 @@ class BamDataProvider( TracksDataProvider, FilterableMixin ): """ - Provides access to intervals from a sorted indexed BAM file. + Provides access to intervals from a sorted indexed BAM file. Position data + is reported in 1-based, closed format, i.e. SAM/BAM format. """ def get_filters( self ): @@ -987,6 +988,10 @@ return f, BigBedFile(file=f) class BigWigDataProvider ( BBIDataProvider ): + """ + Provides data from BigWig files; position data is reported in 1-based + coordinate system, i.e. wiggle format. + """ def _get_dataset( self ): if self.converted_dataset is not None: f = open( self.converted_dataset.file_name ) diff -r da7821adf629620b239c9f5c5e1381eaf4c3ff7b -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -4201,6 +4201,9 @@ } }); +/** + * Track displays continuous/numerical data. Track expects position data in 1-based format, i.e. wiggle format. + */ var LineTrack = function (view, container, obj_dict) { var track = this; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; @@ -4420,6 +4423,9 @@ } }); +/** + * A track that displays features/regions. Track expects position data in BED format, i.e. 0-based, half-open. + */ var FeatureTrack = function(view, container, obj_dict) { // // Preinitialization: do things that need to be done before calling Track and TiledTrack @@ -4913,6 +4919,9 @@ extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); +/** + * Track that displays mapped reads. Track expects position data in 1-based, closed format, i.e. SAM/BAM format. + */ var ReadTrack = function (view, container, obj_dict) { FeatureTrack.call(this, view, container, obj_dict); @@ -5847,7 +5856,8 @@ // Go left if it clips base_offset -= cig_len; } - var seq_start = feature_start + base_offset, + // -1 for feature start because data is using 1-based offset but display is 0-based. + var seq_start = (feature_start - 1) + base_offset, s_start = Math.floor( Math.max(0, (seq_start - tile_low) * w_scale) ), s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low) * w_scale) ); 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: carlfeberhard: fixes for tool search clear-btn (to use templating); added bootstrap.js to tool menu iframe
by Bitbucket 02 Aug '12

02 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/da7821adf629/ changeset: da7821adf629 user: carlfeberhard date: 2012-08-02 22:43:59 summary: fixes for tool search clear-btn (to use templating); added bootstrap.js to tool menu iframe affected #: 6 files diff -r 59cc544ee6573507fa9ce2ca69aeb82907870cf2 -r da7821adf629620b239c9f5c5e1381eaf4c3ff7b static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -757,8 +757,14 @@ .search-spinner { position: absolute; display: none; - right: 8px; - top: 10px; + right: 5px; + top: 9px; +} + +#search-clear-btn { + position: absolute; + right: 4px; + top: 8px; } // Messages diff -r 59cc544ee6573507fa9ce2ca69aeb82907870cf2 -r da7821adf629620b239c9f5c5e1381eaf4c3ff7b static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -2,7 +2,7 @@ audio,canvas,video{display:inline-block;*display:inline;*zoom:1;} audio:not([controls]){display:none;} html{font-size:100%;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%;} -a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} +a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} a:hover,a:active{outline:0;} sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline;} sup{top:-0.5em;} @@ -19,12 +19,12 @@ .clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";} .clearfix:after{clear:both;} .hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;} -.input-block-level{display:block;width:100%;min-height:28px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;} +.input-block-level{display:block;width:100%;min-height:28px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;} article,aside,details,figcaption,figure,footer,header,hgroup,nav,section{display:block;} audio,canvas,video{display:inline-block;*display:inline;*zoom:1;} audio:not([controls]){display:none;} html{font-size:100%;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%;} -a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} +a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} a:hover,a:active{outline:0;} sub,sup{position:relative;font-size:75%;line-height:0;vertical-align:baseline;} sup{top:-0.5em;} @@ -41,7 +41,7 @@ .clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";} .clearfix:after{clear:both;} .hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;} -.input-block-level{display:block;width:100%;min-height:28px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;} +.input-block-level{display:block;width:100%;min-height:28px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;} body{margin:0;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;color:#111111;background-color:#ffffff;} a{color:#303030;text-decoration:none;} a:hover{color:#0a0a0a;text-decoration:underline;} @@ -67,7 +67,7 @@ dt,dd{line-height:16px;} dt{font-weight:bold;line-height:15px;} dd{margin-left:8px;} -.dl-horizontal dt{float:left;width:120px;clear:left;text-align:right;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;} +.dl-horizontal dt{float:left;width:120px;clear:left;text-align:right;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;} .dl-horizontal dd{margin-left:130px;} hr{margin:16px 0;border:0;border-top:1px solid #eeeeee;border-bottom:1px solid #ffffff;} strong{font-weight:bold;} @@ -75,7 +75,7 @@ .muted{color:#999999;} abbr[title]{cursor:help;border-bottom:1px dotted #999999;} abbr.initialism{font-size:90%;text-transform:uppercase;} -blockquote{padding:0 0 0 15px;margin:0 0 16px;border-left:5px solid #eeeeee;}blockquote p{margin-bottom:0;font-size:16px;font-weight:300;line-height:20px;} +blockquote{padding:0 0 0 15px;margin:0 0 16px;border-left:5px solid #eeeeee;}blockquote p{margin-bottom:0;font-size:16px;font-weight:300;line-height:20px;font-size:16px;font-weight:300;line-height:20px;} blockquote small{display:block;line-height:16px;color:#999999;}blockquote small:before{content:'\2014 \00A0';} blockquote.pull-right{float:right;padding-right:15px;padding-left:0;border-right:5px solid #eeeeee;border-left:0;}blockquote.pull-right p,blockquote.pull-right small{text-align:right;} q:before,q:after,blockquote:before,blockquote:after{content:"";} @@ -89,71 +89,71 @@ .table caption+thead tr:first-child th,.table caption+thead tr:first-child td,.table colgroup+thead tr:first-child th,.table colgroup+thead tr:first-child td,.table thead:first-child tr:first-child th,.table thead:first-child tr:first-child td{border-top:0;} .table tbody+tbody{border-top:2px solid #dddddd;} .table-condensed th,.table-condensed td{padding:4px 5px;} -.table-bordered{border:1px solid #dddddd;border-collapse:separate;*border-collapse:collapsed;border-left:0;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;}.table-bordered th,.table-bordered td{border-left:1px solid #dddddd;} +.table-bordered{border:1px solid #dddddd;border-collapse:separate;*border-collapse:collapsed;border-left:0;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;}.table-bordered th,.table-bordered td{border-left:1px solid #dddddd;} .table-bordered caption+thead tr:first-child th,.table-bordered caption+tbody tr:first-child th,.table-bordered caption+tbody tr:first-child td,.table-bordered colgroup+thead tr:first-child th,.table-bordered colgroup+tbody tr:first-child th,.table-bordered colgroup+tbody tr:first-child td,.table-bordered thead:first-child tr:first-child th,.table-bordered tbody:first-child tr:first-child th,.table-bordered tbody:first-child tr:first-child td{border-top:0;} .table-bordered thead:first-child tr:first-child th:first-child,.table-bordered tbody:first-child tr:first-child td:first-child{-webkit-border-top-left-radius:4px;border-top-left-radius:4px;-moz-border-radius-topleft:4px;} .table-bordered thead:first-child tr:first-child th:last-child,.table-bordered tbody:first-child tr:first-child td:last-child{-webkit-border-top-right-radius:4px;border-top-right-radius:4px;-moz-border-radius-topright:4px;} -.table-bordered thead:last-child tr:last-child th:first-child,.table-bordered tbody:last-child tr:last-child td:first-child{-webkit-border-radius:0 0 0 4px;-moz-border-radius:0 0 0 4px;border-radius:0 0 0 4px;-webkit-border-bottom-left-radius:4px;border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;} +.table-bordered thead:last-child tr:last-child th:first-child,.table-bordered tbody:last-child tr:last-child td:first-child{-webkit-border-radius:0 0 0 4px;-moz-border-radius:0 0 0 4px;border-radius:0 0 0 4px;-webkit-border-radius:0 0 0 4px;-moz-border-radius:0 0 0 4px;border-radius:0 0 0 4px;-webkit-border-bottom-left-radius:4px;border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;} .table-bordered thead:last-child tr:last-child 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14px;font-size:14px;line-height:normal;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;} +.btn:hover{color:#333333;text-decoration:none;background-color:#e6e6e6;*background-color:#d9d9d9;background-position:0 -15px;-webkit-transition:background-position 0.1s linear;-moz-transition:background-position 0.1s linear;-ms-transition:background-position 0.1s linear;-o-transition:background-position 0.1s linear;transition:background-position 0.1s linear;-webkit-transition:background-position 0.1s linear;-moz-transition:background-position 0.1s linear;-ms-transition:background-position 0.1s linear;-o-transition:background-position 0.1s linear;transition:background-position 0.1s linear;} +.btn:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} +.btn.active,.btn:active{background-color:#e6e6e6;background-color:#d9d9d9 \9;background-image:none;outline:0;-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);} +.btn.disabled,.btn[disabled]{cursor:default;background-color:#e6e6e6;background-image:none;opacity:0.65;filter:alpha(opacity=65);opacity:0.65;filter:alpha(opacity=65);-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none;-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none;} +.btn-large{padding:9px 14px;font-size:14px;line-height:normal;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;} .btn-large [class^="icon-"]{margin-top:1px;} .btn-small{padding:5px 9px;font-size:10px;line-height:14px;} .btn-small [class^="icon-"]{margin-top:-1px;} @@ -161,27 +161,27 @@ .btn-primary,.btn-primary:hover,.btn-warning,.btn-warning:hover,.btn-danger,.btn-danger:hover,.btn-success,.btn-success:hover,.btn-info,.btn-info:hover,.btn-inverse,.btn-inverse:hover{color:#ffffff;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);} .btn-primary.active,.btn-warning.active,.btn-danger.active,.btn-success.active,.btn-info.active,.btn-inverse.active{color:rgba(255, 255, 255, 0.75);} .btn{border-color:#ccc;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);} -.btn-primary{background-color:#0050cd;background-image:-moz-linear-gradient(top, #0064cd, #0031cd);background-image:-ms-linear-gradient(top, #0064cd, #0031cd);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#0064cd), to(#0031cd));background-image:-webkit-linear-gradient(top, #0064cd, #0031cd);background-image:-o-linear-gradient(top, 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0.25);*background-color:#222222;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);}.btn-inverse:hover,.btn-inverse:active,.btn-inverse.active,.btn-inverse.disabled,.btn-inverse[disabled]{background-color:#222222;*background-color:#151515;} .btn-inverse:active,.btn-inverse.active{background-color:#080808 \9;} .btn-inverse:hover,.btn-inverse:active,.btn-inverse.active,.btn-inverse.disabled,.btn-inverse[disabled]{background-color:#222222;*background-color:#151515;} .btn-inverse:active,.btn-inverse.active{background-color:#080808 \9;} @@ -189,26 +189,26 @@ button.btn.btn-large,input[type="submit"].btn.btn-large{*padding-top:7px;*padding-bottom:7px;} button.btn.btn-small,input[type="submit"].btn.btn-small{*padding-top:3px;*padding-bottom:3px;} button.btn.btn-mini,input[type="submit"].btn.btn-mini{*padding-top:1px;*padding-bottom:1px;} -.btn-group{position:relative;*zoom:1;*margin-left:.3em;}.btn-group:before,.btn-group:after{display:table;content:"";} +.btn-group{position:relative;*zoom:1;*zoom:1;*margin-left:.3em;*margin-left:.3em;}.btn-group:before,.btn-group:after{display:table;content:"";} .btn-group:after{clear:both;} .btn-group:before,.btn-group:after{display:table;content:"";} .btn-group:after{clear:both;} .btn-group:first-child{*margin-left:0;} .btn-group:first-child{*margin-left:0;} .btn-group+.btn-group{margin-left:5px;} -.btn-toolbar{margin-top:8px;margin-bottom:8px;}.btn-toolbar .btn-group{display:inline-block;*display:inline;*zoom:1;} -.btn-group>.btn{position:relative;float:left;margin-left:-1px;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} +.btn-toolbar{margin-top:8px;margin-bottom:8px;}.btn-toolbar .btn-group{display:inline-block;*display:inline;*zoom:1;*display:inline;*zoom:1;} +.btn-group>.btn{position:relative;float:left;margin-left:-1px;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} .btn-group>.btn:first-child{margin-left:0;-webkit-border-top-left-radius:4px;-moz-border-radius-topleft:4px;border-top-left-radius:4px;-webkit-border-bottom-left-radius:4px;-moz-border-radius-bottomleft:4px;border-bottom-left-radius:4px;} .btn-group>.btn:last-child,.btn-group>.dropdown-toggle{-webkit-border-top-right-radius:4px;-moz-border-radius-topright:4px;border-top-right-radius:4px;-webkit-border-bottom-right-radius:4px;-moz-border-radius-bottomright:4px;border-bottom-right-radius:4px;} .btn-group>.btn.large:first-child{margin-left:0;-webkit-border-top-left-radius:6px;-moz-border-radius-topleft:6px;border-top-left-radius:6px;-webkit-border-bottom-left-radius:6px;-moz-border-radius-bottomleft:6px;border-bottom-left-radius:6px;} .btn-group>.btn.large:last-child,.btn-group>.large.dropdown-toggle{-webkit-border-top-right-radius:6px;-moz-border-radius-topright:6px;border-top-right-radius:6px;-webkit-border-bottom-right-radius:6px;-moz-border-radius-bottomright:6px;border-bottom-right-radius:6px;} .btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active{z-index:2;} .btn-group .dropdown-toggle:active,.btn-group.open .dropdown-toggle{outline:0;} -.btn-group>.dropdown-toggle{padding-left:8px;padding-right:8px;-webkit-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);*padding-top:4px;*padding-bottom:4px;} +.btn-group>.dropdown-toggle{padding-left:8px;padding-right:8px;-webkit-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-webkit-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 1px 0 0 rgba(255,255,255,.125), inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);*padding-top:4px;*padding-bottom:4px;} .btn-group>.btn-mini.dropdown-toggle{padding-left:5px;padding-right:5px;} .btn-group>.btn-small.dropdown-toggle{*padding-top:4px;*padding-bottom:4px;} .btn-group>.btn-large.dropdown-toggle{padding-left:12px;padding-right:12px;} -.btn-group.open .dropdown-toggle{background-image:none;-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);} +.btn-group.open .dropdown-toggle{background-image:none;-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);} .btn-group.open .btn.dropdown-toggle{background-color:#e6e6e6;} .btn-group.open .btn-primary.dropdown-toggle{background-color:#0031cd;} .btn-group.open .btn-warning.dropdown-toggle{background-color:#f89406;} @@ -217,13 +217,13 @@ .btn-group.open .btn-info.dropdown-toggle{background-color:#2f96b4;} .btn-group.open .btn-inverse.dropdown-toggle{background-color:#222222;} .btn .caret{margin-top:7px;margin-left:0;} -.btn:hover .caret,.open.btn-group .caret{opacity:1;filter:alpha(opacity=100);} +.btn:hover .caret,.open.btn-group .caret{opacity:1;filter:alpha(opacity=100);opacity:1;filter:alpha(opacity=100);} .btn-mini .caret{margin-top:5px;} .btn-small .caret{margin-top:6px;} .btn-large .caret{margin-top:6px;border-left-width:5px;border-right-width:5px;border-top-width:5px;} .dropup .btn-large .caret{border-bottom:5px solid #000000;border-top:0;} -.btn-primary .caret,.btn-warning .caret,.btn-danger .caret,.btn-info .caret,.btn-success .caret,.btn-inverse .caret{border-top-color:#ffffff;border-bottom-color:#ffffff;opacity:0.75;filter:alpha(opacity=75);} -.alert{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;} +.btn-primary .caret,.btn-warning .caret,.btn-danger .caret,.btn-info .caret,.btn-success .caret,.btn-inverse .caret{border-top-color:#ffffff;border-bottom-color:#ffffff;opacity:0.75;filter:alpha(opacity=75);opacity:0.75;filter:alpha(opacity=75);} +.alert{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;} .alert-heading{color:inherit;} .alert .close{position:relative;top:-2px;right:-21px;line-height:18px;} .alert-success{background-color:#ccffcc;border-color:#1a9900;color:#006600;} @@ -243,8 +243,8 @@ .nav-list>li>a{padding:3px 15px;} .nav-list>.active>a,.nav-list>.active>a:hover{color:#ffffff;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.2);background-color:#303030;} .nav-list [class^="icon-"]{margin-right:2px;} -.nav-list .divider{*width:100%;height:1px;margin:7px 1px;*margin:-5px 0 5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;} -.nav-tabs,.nav-pills{*zoom:1;}.nav-tabs:before,.nav-pills:before,.nav-tabs:after,.nav-pills:after{display:table;content:"";} +.nav-list .divider{*width:100%;height:1px;margin:7px 1px;*margin:-5px 0 5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;*width:100%;height:1px;margin:7px 1px;*margin:-5px 0 5px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;} +.nav-tabs,.nav-pills{*zoom:1;*zoom:1;}.nav-tabs:before,.nav-pills:before,.nav-tabs:after,.nav-pills:after{display:table;content:"";} .nav-tabs:after,.nav-pills:after{clear:both;} .nav-tabs:before,.nav-pills:before,.nav-tabs:after,.nav-pills:after{display:table;content:"";} .nav-tabs:after,.nav-pills:after{clear:both;} @@ -252,29 +252,29 @@ .nav-tabs>li>a,.nav-pills>li>a{padding-right:12px;padding-left:12px;margin-right:2px;line-height:14px;} .nav-tabs{border-bottom:1px solid #ddd;} .nav-tabs>li{margin-bottom:-1px;} -.nav-tabs>li>a{padding-top:8px;padding-bottom:8px;line-height:16px;border:1px solid transparent;-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;}.nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #999999;} +.nav-tabs>li>a{padding-top:8px;padding-bottom:8px;line-height:16px;border:1px solid transparent;-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;}.nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #999999;} .nav-tabs>.active>a,.nav-tabs>.active>a:hover{color:#555555;background-color:#ffffff;border:1px solid #999;border-bottom-color:transparent;cursor:default;} -.nav-pills>li>a{padding-top:8px;padding-bottom:8px;margin-top:2px;margin-bottom:2px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;} +.nav-pills>li>a{padding-top:8px;padding-bottom:8px;margin-top:2px;margin-bottom:2px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;-webkit-border-radius:5px;-moz-border-radius:5px;border-radius:5px;} .nav-pills>.active>a,.nav-pills>.active>a:hover{color:#ffffff;background-color:#303030;} .nav-stacked>li{float:none;} .nav-stacked>li>a{margin-right:0;} .nav-tabs.nav-stacked{border-bottom:0;} -.nav-tabs.nav-stacked>li>a{border:1px solid #ddd;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} -.nav-tabs.nav-stacked>li:first-child>a{-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;} -.nav-tabs.nav-stacked>li:last-child>a{-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;} +.nav-tabs.nav-stacked>li>a{border:1px solid #ddd;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} +.nav-tabs.nav-stacked>li:first-child>a{-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;-webkit-border-radius:4px 4px 0 0;-moz-border-radius:4px 4px 0 0;border-radius:4px 4px 0 0;} +.nav-tabs.nav-stacked>li:last-child>a{-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;} .nav-tabs.nav-stacked>li>a:hover{border-color:#ddd;z-index:2;} .nav-pills.nav-stacked>li>a{margin-bottom:3px;} .nav-pills.nav-stacked>li:last-child>a{margin-bottom:1px;} -.nav-tabs .dropdown-menu{-webkit-border-radius:0 0 5px 5px;-moz-border-radius:0 0 5px 5px;border-radius:0 0 5px 5px;} -.nav-pills .dropdown-menu{-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.nav-tabs .dropdown-menu{-webkit-border-radius:0 0 5px 5px;-moz-border-radius:0 0 5px 5px;border-radius:0 0 5px 5px;-webkit-border-radius:0 0 5px 5px;-moz-border-radius:0 0 5px 5px;border-radius:0 0 5px 5px;} +.nav-pills .dropdown-menu{-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} .nav-tabs .dropdown-toggle .caret,.nav-pills .dropdown-toggle .caret{border-top-color:#303030;border-bottom-color:#303030;margin-top:6px;} .nav-tabs .dropdown-toggle:hover .caret,.nav-pills .dropdown-toggle:hover .caret{border-top-color:#0a0a0a;border-bottom-color:#0a0a0a;} .nav-tabs .active .dropdown-toggle .caret,.nav-pills .active .dropdown-toggle .caret{border-top-color:#333333;border-bottom-color:#333333;} .nav>.dropdown.active>a:hover{color:#000000;cursor:pointer;} .nav-tabs .open .dropdown-toggle,.nav-pills .open .dropdown-toggle,.nav>li.dropdown.open.active>a:hover{color:#ffffff;background-color:#999999;border-color:#999999;} -.nav li.dropdown.open .caret,.nav li.dropdown.open.active .caret,.nav li.dropdown.open a:hover .caret{border-top-color:#ffffff;border-bottom-color:#ffffff;opacity:1;filter:alpha(opacity=100);} +.nav li.dropdown.open .caret,.nav li.dropdown.open.active .caret,.nav li.dropdown.open a:hover .caret{border-top-color:#ffffff;border-bottom-color:#ffffff;opacity:1;filter:alpha(opacity=100);opacity:1;filter:alpha(opacity=100);} .tabs-stacked .open>a:hover{border-color:#999999;} -.tabbable{*zoom:1;}.tabbable:before,.tabbable:after{display:table;content:"";} +.tabbable{*zoom:1;*zoom:1;}.tabbable:before,.tabbable:after{display:table;content:"";} .tabbable:after{clear:both;} .tabbable:before,.tabbable:after{display:table;content:"";} .tabbable:after{clear:both;} @@ -284,46 +284,46 @@ .tab-content>.active,.pill-content>.active{display:block;} .tabs-below>.nav-tabs{border-top:1px solid #ddd;} .tabs-below>.nav-tabs>li{margin-top:-1px;margin-bottom:0;} -.tabs-below>.nav-tabs>li>a{-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;}.tabs-below>.nav-tabs>li>a:hover{border-bottom-color:transparent;border-top-color:#ddd;} +.tabs-below>.nav-tabs>li>a{-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;}.tabs-below>.nav-tabs>li>a:hover{border-bottom-color:transparent;border-top-color:#ddd;} .tabs-below>.nav-tabs>.active>a,.tabs-below>.nav-tabs>.active>a:hover{border-color:transparent #ddd #ddd #ddd;} .tabs-left>.nav-tabs>li,.tabs-right>.nav-tabs>li{float:none;} .tabs-left>.nav-tabs>li>a,.tabs-right>.nav-tabs>li>a{min-width:74px;margin-right:0;margin-bottom:3px;} .tabs-left>.nav-tabs{float:left;margin-right:19px;border-right:1px solid #ddd;} -.tabs-left>.nav-tabs>li>a{margin-right:-1px;-webkit-border-radius:4px 0 0 4px;-moz-border-radius:4px 0 0 4px;border-radius:4px 0 0 4px;} +.tabs-left>.nav-tabs>li>a{margin-right:-1px;-webkit-border-radius:4px 0 0 4px;-moz-border-radius:4px 0 0 4px;border-radius:4px 0 0 4px;-webkit-border-radius:4px 0 0 4px;-moz-border-radius:4px 0 0 4px;border-radius:4px 0 0 4px;} .tabs-left>.nav-tabs>li>a:hover{border-color:#eeeeee #dddddd #eeeeee #eeeeee;} .tabs-left>.nav-tabs .active>a,.tabs-left>.nav-tabs .active>a:hover{border-color:#ddd transparent #ddd #ddd;*border-right-color:#ffffff;} .tabs-right>.nav-tabs{float:right;margin-left:19px;border-left:1px solid #ddd;} -.tabs-right>.nav-tabs>li>a{margin-left:-1px;-webkit-border-radius:0 4px 4px 0;-moz-border-radius:0 4px 4px 0;border-radius:0 4px 4px 0;} +.tabs-right>.nav-tabs>li>a{margin-left:-1px;-webkit-border-radius:0 4px 4px 0;-moz-border-radius:0 4px 4px 0;border-radius:0 4px 4px 0;-webkit-border-radius:0 4px 4px 0;-moz-border-radius:0 4px 4px 0;border-radius:0 4px 4px 0;} .tabs-right>.nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #eeeeee #dddddd;} .tabs-right>.nav-tabs .active>a,.tabs-right>.nav-tabs .active>a:hover{border-color:#ddd #ddd #ddd transparent;*border-left-color:#ffffff;} .navbar{*position:relative;*z-index:2;overflow:visible;margin-bottom:16px;} -.navbar-inner{min-height:32px;padding-left:20px;padding-right:20px;background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-ms-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(top, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#333333', endColorstr='#2c3143', GradientType=0);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);-moz-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);} +.navbar-inner{min-height:32px;padding-left:20px;padding-right:20px;background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-ms-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(top, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#333333', endColorstr='#2c3143', GradientType=0);background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-ms-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(top, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#333333', endColorstr='#2c3143', GradientType=0);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);-moz-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);-webkit-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);-moz-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);} .navbar .container{width:auto;} .nav-collapse.collapse{height:auto;} .navbar{color:#999999;}.navbar .brand:hover{text-decoration:none;} .navbar .brand{float:left;display:block;padding:4px 20px 8px;margin-left:-20px;font-size:20px;font-weight:200;line-height:1;color:#999999;} .navbar .navbar-text{margin-bottom:0;line-height:32px;} .navbar .navbar-link{color:#999999;}.navbar .navbar-link:hover{color:#ffffff;} -.navbar .btn,.navbar .btn-group{margin-top:1px;} +.navbar .btn,.navbar .btn-group{margin-top:1px;margin-top:1px;} .navbar .btn-group .btn{margin:0;} -.navbar-form{margin-bottom:0;*zoom:1;}.navbar-form:before,.navbar-form:after{display:table;content:"";} +.navbar-form{margin-bottom:0;*zoom:1;*zoom:1;}.navbar-form:before,.navbar-form:after{display:table;content:"";} .navbar-form:after{clear:both;} .navbar-form:before,.navbar-form:after{display:table;content:"";} .navbar-form:after{clear:both;} -.navbar-form input,.navbar-form select,.navbar-form .radio,.navbar-form .checkbox{margin-top:1px;} +.navbar-form input,.navbar-form select,.navbar-form .radio,.navbar-form .checkbox{margin-top:1px;margin-top:1px;} .navbar-form input,.navbar-form select{display:inline-block;margin-bottom:0;} .navbar-form input[type="image"],.navbar-form input[type="checkbox"],.navbar-form input[type="radio"]{margin-top:3px;} .navbar-form .input-append,.navbar-form .input-prepend{margin-top:6px;white-space:nowrap;}.navbar-form .input-append input,.navbar-form .input-prepend input{margin-top:0;} -.navbar-search{position:relative;float:left;margin-top:2px;margin-bottom:0;}.navbar-search .search-query{padding:4px 9px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:13px;font-weight:normal;line-height:1;color:#ffffff;background-color:#5f6990;border:1px solid #222634;-webkit-box-shadow:inset 0 1px 2px rgba(0,0,0,.1), 0 1px 0 rgba(255,255,255,.15);-moz-box-shadow:inset 0 1px 2px rgba(0,0,0,.1), 0 1px 0 rgba(255,255,255,.15);box-shadow:inset 0 1px 2px rgba(0,0,0,.1), 0 1px 0 rgba(255,255,255,.15);-webkit-transition:none;-moz-transition:none;-ms-transition:none;-o-transition:none;transition:none;}.navbar-search .search-query:-moz-placeholder{color:#cccccc;} +.navbar-search{position:relative;float:left;margin-top:2px;margin-top:2px;margin-bottom:0;}.navbar-search .search-query{padding:4px 9px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:13px;font-weight:normal;line-height:1;font-size:13px;font-weight:normal;line-height:1;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:13px;font-weight:normal;line-height:1;font-size:13px;font-weight:normal;line-height:1;color:#ffffff;background-color:#5f6990;border:1px solid #222634;-webkit-box-shadow:inset 0 1px 2px rgba(0,0,0,.1), 0 1px 0 rgba(255,255,255,.15);-moz-box-shadow:inset 0 1px 2px rgba(0,0,0,.1), 0 1px 0 rgba(255,255,255,.15);box-shadow:inset 0 1px 2px rgba(0,0,0,.1), 0 1px 0 rgba(255,255,255,.15);-webkit-box-shadow:inset 0 1px 2px rgba(0,0,0,.1), 0 1px 0 rgba(255,255,255,.15);-moz-box-shadow:inset 0 1px 2px rgba(0,0,0,.1), 0 1px 0 rgba(255,255,255,.15);box-shadow:inset 0 1px 2px rgba(0,0,0,.1), 0 1px 0 rgba(255,255,255,.15);-webkit-transition:none;-moz-transition:none;-ms-transition:none;-o-transition:none;transition:none;-webkit-transition:none;-moz-transition:none;-ms-transition:none;-o-transition:none;transition:none;}.navbar-search .search-query:-moz-placeholder{color:#cccccc;} .navbar-search .search-query:-ms-input-placeholder{color:#cccccc;} .navbar-search .search-query::-webkit-input-placeholder{color:#cccccc;} .navbar-search .search-query:-moz-placeholder{color:#cccccc;} .navbar-search .search-query:-ms-input-placeholder{color:#cccccc;} .navbar-search .search-query::-webkit-input-placeholder{color:#cccccc;} -.navbar-search .search-query:focus,.navbar-search .search-query.focused{padding:5px 10px;color:#333333;text-shadow:0 1px 0 #ffffff;background-color:#ffffff;border:0;-webkit-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);-moz-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);box-shadow:0 0 3px rgba(0, 0, 0, 0.15);outline:0;} +.navbar-search .search-query:focus,.navbar-search .search-query.focused{padding:5px 10px;color:#333333;text-shadow:0 1px 0 #ffffff;background-color:#ffffff;border:0;-webkit-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);-moz-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);box-shadow:0 0 3px rgba(0, 0, 0, 0.15);-webkit-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);-moz-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);box-shadow:0 0 3px rgba(0, 0, 0, 0.15);outline:0;} .navbar-fixed-top,.navbar-fixed-bottom{position:fixed;right:0;left:0;z-index:1030;margin-bottom:0;} -.navbar-fixed-top .navbar-inner,.navbar-fixed-bottom .navbar-inner{padding-left:0;padding-right:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} -.navbar-fixed-top .container,.navbar-fixed-bottom .container{width:940px;} +.navbar-fixed-top .navbar-inner,.navbar-fixed-bottom .navbar-inner{padding-left:0;padding-right:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;} +.navbar-fixed-top .container,.navbar-fixed-bottom .container{width:940px;width:940px;} .navbar-fixed-top{top:0;} .navbar-fixed-bottom{bottom:0;} .navbar .nav{position:relative;left:0;display:block;float:left;margin:0 10px 0 0;} @@ -336,42 +336,42 @@ .navbar .nav .active>a,.navbar .nav .active>a:hover{color:#ffffff;text-decoration:none;background-color:rgba(0, 0, 0, 0.5);} .navbar .divider-vertical{height:32px;width:1px;margin:0 9px;overflow:hidden;background-color:#2c3143;border-right:1px solid #333333;} .navbar .nav.pull-right{margin-left:10px;margin-right:0;} -.navbar .btn-navbar{display:none;float:right;padding:7px 10px;margin-left:5px;margin-right:5px;background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-ms-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(top, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#333333', endColorstr='#2c3143', GradientType=0);border-color:#2c3143 #2c3143 #0e0f15;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);*background-color:#2c3143;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 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#2c3143);background-image:-ms-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(top, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#333333', endColorstr='#2c3143', GradientType=0);border-color:#2c3143 #2c3143 #0e0f15;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);*background-color:#2c3143;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.075);}.navbar .btn-navbar:hover,.navbar .btn-navbar:active,.navbar .btn-navbar.active,.navbar .btn-navbar.disabled,.navbar .btn-navbar[disabled]{background-color:#2c3143;*background-color:#222634;} .navbar .btn-navbar:active,.navbar .btn-navbar.active{background-color:#181a24 \9;} .navbar .btn-navbar:hover,.navbar .btn-navbar:active,.navbar .btn-navbar.active,.navbar .btn-navbar.disabled,.navbar .btn-navbar[disabled]{background-color:#2c3143;*background-color:#222634;} .navbar .btn-navbar:active,.navbar .btn-navbar.active{background-color:#181a24 \9;} -.navbar .btn-navbar .icon-bar{display:block;width:18px;height:2px;background-color:#f5f5f5;-webkit-border-radius:1px;-moz-border-radius:1px;border-radius:1px;-webkit-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);-moz-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);} +.navbar .btn-navbar .icon-bar{display:block;width:18px;height:2px;background-color:#f5f5f5;-webkit-border-radius:1px;-moz-border-radius:1px;border-radius:1px;-webkit-border-radius:1px;-moz-border-radius:1px;border-radius:1px;-webkit-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);-moz-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);-webkit-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);-moz-box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);box-shadow:0 1px 0 rgba(0, 0, 0, 0.25);} .btn-navbar .icon-bar+.icon-bar{margin-top:3px;} .navbar .dropdown-menu:before{content:'';display:inline-block;border-left:7px solid transparent;border-right:7px solid transparent;border-bottom:7px solid #ccc;border-bottom-color:rgba(0, 0, 0, 0.2);position:absolute;top:-7px;left:9px;} .navbar .dropdown-menu:after{content:'';display:inline-block;border-left:6px solid transparent;border-right:6px solid transparent;border-bottom:6px solid #ffffff;position:absolute;top:-6px;left:10px;} .navbar-fixed-bottom .dropdown-menu:before{border-top:7px solid #ccc;border-top-color:rgba(0, 0, 0, 0.2);border-bottom:0;bottom:-7px;top:auto;} .navbar-fixed-bottom .dropdown-menu:after{border-top:6px solid #ffffff;border-bottom:0;bottom:-6px;top:auto;} .navbar .nav li.dropdown .dropdown-toggle .caret,.navbar .nav li.dropdown.open .caret{border-top-color:#ffffff;border-bottom-color:#ffffff;} -.navbar .nav li.dropdown.active .caret{opacity:1;filter:alpha(opacity=100);} +.navbar .nav li.dropdown.active .caret{opacity:1;filter:alpha(opacity=100);opacity:1;filter:alpha(opacity=100);} .navbar .nav li.dropdown.open>.dropdown-toggle,.navbar .nav li.dropdown.active>.dropdown-toggle,.navbar .nav li.dropdown.open.active>.dropdown-toggle{background-color:transparent;} .navbar .nav li.dropdown.active>.dropdown-toggle:hover{color:#ffffff;} .navbar .pull-right .dropdown-menu,.navbar .dropdown-menu.pull-right{left:auto;right:0;}.navbar .pull-right .dropdown-menu:before,.navbar .dropdown-menu.pull-right:before{left:auto;right:12px;} .navbar .pull-right .dropdown-menu:after,.navbar .dropdown-menu.pull-right:after{left:auto;right:13px;} -.breadcrumb{padding:7px 14px;margin:0 0 16px;list-style:none;background-color:#fbfbfb;background-image:-moz-linear-gradient(top, #ffffff, #f5f5f5);background-image:-ms-linear-gradient(top, #ffffff, #f5f5f5);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#f5f5f5));background-image:-webkit-linear-gradient(top, #ffffff, #f5f5f5);background-image:-o-linear-gradient(top, #ffffff, #f5f5f5);background-image:linear-gradient(top, #ffffff, #f5f5f5);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#f5f5f5', GradientType=0);border:1px solid #ddd;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;}.breadcrumb li{display:inline-block;*display:inline;*zoom:1;text-shadow:0 1px 0 #ffffff;} +.breadcrumb{padding:7px 14px;margin:0 0 16px;list-style:none;background-color:#fbfbfb;background-image:-moz-linear-gradient(top, #ffffff, #f5f5f5);background-image:-ms-linear-gradient(top, #ffffff, #f5f5f5);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#f5f5f5));background-image:-webkit-linear-gradient(top, #ffffff, #f5f5f5);background-image:-o-linear-gradient(top, #ffffff, #f5f5f5);background-image:linear-gradient(top, #ffffff, #f5f5f5);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#f5f5f5', GradientType=0);background-color:#fbfbfb;background-image:-moz-linear-gradient(top, #ffffff, #f5f5f5);background-image:-ms-linear-gradient(top, #ffffff, #f5f5f5);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#f5f5f5));background-image:-webkit-linear-gradient(top, #ffffff, #f5f5f5);background-image:-o-linear-gradient(top, #ffffff, #f5f5f5);background-image:linear-gradient(top, #ffffff, #f5f5f5);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#f5f5f5', GradientType=0);border:1px solid #ddd;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;}.breadcrumb li{display:inline-block;*display:inline;*zoom:1;*display:inline;*zoom:1;text-shadow:0 1px 0 #ffffff;} .breadcrumb .divider{padding:0 5px;color:#999999;} .breadcrumb .active a{color:#333333;} .pagination{height:32px;margin:16px 0;} -.pagination ul{display:inline-block;*display:inline;*zoom:1;margin-left:0;margin-bottom:0;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;-webkit-box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);} +.pagination ul{display:inline-block;*display:inline;*zoom:1;*display:inline;*zoom:1;margin-left:0;margin-bottom:0;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;-webkit-box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);-webkit-box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);-moz-box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);box-shadow:0 1px 2px rgba(0, 0, 0, 0.05);} .pagination li{display:inline;} .pagination a{float:left;padding:0 14px;line-height:30px;text-decoration:none;border:1px solid #ddd;border-left-width:0;} .pagination a:hover,.pagination .active a{background-color:#f5f5f5;} .pagination .active a{color:#999999;cursor:default;} .pagination .disabled span,.pagination .disabled a,.pagination .disabled a:hover{color:#999999;background-color:transparent;cursor:default;} -.pagination li:first-child a{border-left-width:1px;-webkit-border-radius:3px 0 0 3px;-moz-border-radius:3px 0 0 3px;border-radius:3px 0 0 3px;} -.pagination li:last-child a{-webkit-border-radius:0 3px 3px 0;-moz-border-radius:0 3px 3px 0;border-radius:0 3px 3px 0;} +.pagination li:first-child a{border-left-width:1px;-webkit-border-radius:3px 0 0 3px;-moz-border-radius:3px 0 0 3px;border-radius:3px 0 0 3px;-webkit-border-radius:3px 0 0 3px;-moz-border-radius:3px 0 0 3px;border-radius:3px 0 0 3px;} +.pagination li:last-child a{-webkit-border-radius:0 3px 3px 0;-moz-border-radius:0 3px 3px 0;border-radius:0 3px 3px 0;-webkit-border-radius:0 3px 3px 0;-moz-border-radius:0 3px 3px 0;border-radius:0 3px 3px 0;} .pagination-centered{text-align:center;} .pagination-right{text-align:right;} -.pager{margin-left:0;margin-bottom:16px;list-style:none;text-align:center;*zoom:1;}.pager:before,.pager:after{display:table;content:"";} +.pager{margin-left:0;margin-bottom:16px;list-style:none;text-align:center;*zoom:1;*zoom:1;}.pager:before,.pager:after{display:table;content:"";} .pager:after{clear:both;} .pager:before,.pager:after{display:table;content:"";} .pager:after{clear:both;} .pager li{display:inline;} -.pager a{display:inline-block;padding:5px 14px;background-color:#fff;border:1px solid #ddd;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;} +.pager a{display:inline-block;padding:5px 14px;background-color:#fff;border:1px solid #ddd;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;-webkit-border-radius:15px;-moz-border-radius:15px;border-radius:15px;} .pager a:hover{text-decoration:none;background-color:#f5f5f5;} .pager .next a{float:right;} .pager .previous a{float:left;} @@ -381,13 +381,13 @@ .modal-open .popover{z-index:2060;} .modal-open .tooltip{z-index:2070;} .modal-backdrop{position:fixed;top:0;right:0;bottom:0;left:0;z-index:1040;background-color:#000000;}.modal-backdrop.fade{opacity:0;} -.modal-backdrop,.modal-backdrop.fade.in{opacity:0.8;filter:alpha(opacity=80);} -.modal{position:fixed;top:50%;left:50%;z-index:1050;overflow:auto;width:560px;margin:-250px 0 0 -280px;background-color:#ffffff;border:1px solid #999;border:1px solid rgba(0, 0, 0, 0.3);*border:1px solid #999;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;}.modal.fade{-webkit-transition:opacity .3s linear, top .3s ease-out;-moz-transition:opacity .3s linear, top .3s ease-out;-ms-transition:opacity .3s linear, top .3s ease-out;-o-transition:opacity .3s linear, top .3s ease-out;transition:opacity .3s linear, top .3s ease-out;top:-25%;} +.modal-backdrop,.modal-backdrop.fade.in{opacity:0.8;filter:alpha(opacity=80);opacity:0.8;filter:alpha(opacity=80);} +.modal{position:fixed;top:50%;left:50%;z-index:1050;overflow:auto;width:560px;margin:-250px 0 0 -280px;background-color:#ffffff;border:1px solid #999;border:1px solid rgba(0, 0, 0, 0.3);*border:1px solid #999;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;}.modal.fade{-webkit-transition:opacity .3s linear, top .3s ease-out;-moz-transition:opacity .3s linear, top .3s ease-out;-ms-transition:opacity .3s linear, top .3s ease-out;-o-transition:opacity .3s linear, top .3s ease-out;transition:opacity .3s linear, top .3s ease-out;-webkit-transition:opacity .3s linear, top .3s ease-out;-moz-transition:opacity .3s linear, top .3s ease-out;-ms-transition:opacity .3s linear, top .3s ease-out;-o-transition:opacity .3s linear, top .3s ease-out;transition:opacity .3s linear, top .3s ease-out;top:-25%;} .modal.fade.in{top:50%;} .modal-header{padding:9px 15px;border-bottom:1px solid #eee;}.modal-header .close{margin-top:2px;} .modal-body{overflow-y:auto;max-height:400px;padding:15px;} .modal-form{margin-bottom:0;} -.modal-footer{padding:14px 15px 15px;margin-bottom:0;text-align:right;background-color:#f5f5f5;border-top:1px solid #ddd;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;*zoom:1;}.modal-footer:before,.modal-footer:after{display:table;content:"";} +.modal-footer{padding:14px 15px 15px;margin-bottom:0;text-align:right;background-color:#f5f5f5;border-top:1px solid #ddd;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-border-radius:0 0 6px 6px;-moz-border-radius:0 0 6px 6px;border-radius:0 0 6px 6px;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;-webkit-box-shadow:inset 0 1px 0 #ffffff;-moz-box-shadow:inset 0 1px 0 #ffffff;box-shadow:inset 0 1px 0 #ffffff;*zoom:1;*zoom:1;}.modal-footer:before,.modal-footer:after{display:table;content:"";} .modal-footer:after{clear:both;} .modal-footer:before,.modal-footer:after{display:table;content:"";} .modal-footer:after{clear:both;} @@ -397,35 +397,35 @@ .popover.right{margin-left:5px;} .popover.bottom{margin-top:5px;} .popover.left{margin-left:-5px;} -.popover.top .arrow{bottom:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-top:5px solid #000000;} -.popover.right .arrow{top:50%;left:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-right:5px solid #000000;} -.popover.bottom .arrow{top:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-bottom:5px solid #000000;} -.popover.left .arrow{top:50%;right:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;} +.popover.top .arrow{bottom:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-top:5px solid #000000;bottom:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-top:5px solid #000000;} +.popover.right .arrow{top:50%;left:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-right:5px solid #000000;top:50%;left:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-right:5px solid #000000;} +.popover.bottom .arrow{top:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-bottom:5px solid #000000;top:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-bottom:5px solid #000000;} +.popover.left .arrow{top:50%;right:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;top:50%;right:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;} .popover .arrow{position:absolute;width:0;height:0;} -.popover-inner{padding:3px;width:280px;overflow:hidden;background:#000000;background:rgba(0, 0, 0, 0.8);-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);} -.popover-title{padding:9px 15px;line-height:1;background-color:#f5f5f5;border-bottom:1px solid #eee;-webkit-border-radius:3px 3px 0 0;-moz-border-radius:3px 3px 0 0;border-radius:3px 3px 0 0;} -.popover-content{padding:14px;background-color:#ffffff;-webkit-border-radius:0 0 3px 3px;-moz-border-radius:0 0 3px 3px;border-radius:0 0 3px 3px;-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;}.popover-content 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#f9f9f9);background-image:linear-gradient(top, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f5f5f5', endColorstr='#f9f9f9', GradientType=0);-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} -.progress .bar{width:0%;height:18px;color:#ffffff;font-size:12px;text-align:center;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);background-color:#0e90d2;background-image:-moz-linear-gradient(top, #149bdf, #0480be);background-image:-ms-linear-gradient(top, #149bdf, #0480be);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#149bdf), to(#0480be));background-image:-webkit-linear-gradient(top, #149bdf, #0480be);background-image:-o-linear-gradient(top, #149bdf, #0480be);background-image:linear-gradient(top, #149bdf, #0480be);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#149bdf', endColorstr='#0480be', GradientType=0);-webkit-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-moz-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;-webkit-transition:width 0.6s ease;-moz-transition:width 0.6s ease;-ms-transition:width 0.6s ease;-o-transition:width 0.6s ease;transition:width 0.6s ease;} -.progress-striped .bar{background-color:#149bdf;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px;} +.popover-inner{padding:3px;width:280px;overflow:hidden;background:#000000;background:rgba(0, 0, 0, 0.8);-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-webkit-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);-moz-box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);box-shadow:0 3px 7px rgba(0, 0, 0, 0.3);} +.popover-title{padding:9px 15px;line-height:1;background-color:#f5f5f5;border-bottom:1px solid #eee;-webkit-border-radius:3px 3px 0 0;-moz-border-radius:3px 3px 0 0;border-radius:3px 3px 0 0;-webkit-border-radius:3px 3px 0 0;-moz-border-radius:3px 3px 0 0;border-radius:3px 3px 0 0;} +.popover-content{padding:14px;background-color:#ffffff;-webkit-border-radius:0 0 3px 3px;-moz-border-radius:0 0 3px 3px;border-radius:0 0 3px 3px;-webkit-border-radius:0 0 3px 3px;-moz-border-radius:0 0 3px 3px;border-radius:0 0 3px 3px;-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;-webkit-background-clip:padding-box;-moz-background-clip:padding-box;background-clip:padding-box;}.popover-content p,.popover-content ul,.popover-content ol{margin-bottom:0;} +@-webkit-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-ms-keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}@-o-keyframes progress-bar-stripes{from{background-position:0 0;} to{background-position:40px 0;}}@keyframes progress-bar-stripes{from{background-position:40px 0;} to{background-position:0 0;}}.progress{overflow:hidden;height:18px;margin-bottom:18px;background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-ms-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(top, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f5f5f5', endColorstr='#f9f9f9', GradientType=0);background-color:#f7f7f7;background-image:-moz-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-ms-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f5f5f5), to(#f9f9f9));background-image:-webkit-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:-o-linear-gradient(top, #f5f5f5, #f9f9f9);background-image:linear-gradient(top, #f5f5f5, #f9f9f9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f5f5f5', endColorstr='#f9f9f9', GradientType=0);-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.progress .bar{width:0%;height:18px;color:#ffffff;font-size:12px;text-align:center;text-shadow:0 -1px 0 rgba(0, 0, 0, 0.25);background-color:#0e90d2;background-image:-moz-linear-gradient(top, #149bdf, #0480be);background-image:-ms-linear-gradient(top, #149bdf, #0480be);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#149bdf), to(#0480be));background-image:-webkit-linear-gradient(top, #149bdf, #0480be);background-image:-o-linear-gradient(top, #149bdf, #0480be);background-image:linear-gradient(top, #149bdf, #0480be);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#149bdf', endColorstr='#0480be', GradientType=0);background-color:#0e90d2;background-image:-moz-linear-gradient(top, #149bdf, #0480be);background-image:-ms-linear-gradient(top, #149bdf, #0480be);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#149bdf), to(#0480be));background-image:-webkit-linear-gradient(top, #149bdf, #0480be);background-image:-o-linear-gradient(top, #149bdf, #0480be);background-image:linear-gradient(top, #149bdf, #0480be);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#149bdf', endColorstr='#0480be', GradientType=0);-webkit-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-moz-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-webkit-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-moz-box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);box-shadow:inset 0 -1px 0 rgba(0, 0, 0, 0.15);-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;-webkit-transition:width 0.6s ease;-moz-transition:width 0.6s ease;-ms-transition:width 0.6s ease;-o-transition:width 0.6s ease;transition:width 0.6s ease;-webkit-transition:width 0.6s ease;-moz-transition:width 0.6s ease;-ms-transition:width 0.6s ease;-o-transition:width 0.6s ease;transition:width 0.6s ease;} +.progress-striped .bar{background-color:#149bdf;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#149bdf;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px;-webkit-background-size:40px 40px;-moz-background-size:40px 40px;-o-background-size:40px 40px;background-size:40px 40px;} .progress.active .bar{-webkit-animation:progress-bar-stripes 2s linear infinite;-moz-animation:progress-bar-stripes 2s linear infinite;-ms-animation:progress-bar-stripes 2s linear infinite;-o-animation:progress-bar-stripes 2s linear infinite;animation:progress-bar-stripes 2s linear infinite;} -.progress-danger .bar{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-ms-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(top, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0);} -.progress-danger.progress-striped .bar{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} -.progress-success .bar{background-color:#5eb95e;background-image:-moz-linear-gradient(top, #62c462, #57a957);background-image:-ms-linear-gradient(top, #62c462, #57a957);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));background-image:-webkit-linear-gradient(top, #62c462, #57a957);background-image:-o-linear-gradient(top, #62c462, #57a957);background-image:linear-gradient(top, #62c462, #57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#57a957', GradientType=0);} -.progress-success.progress-striped .bar{background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} -.progress-info .bar{background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-ms-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(top, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#339bb9', GradientType=0);} -.progress-info.progress-striped .bar{background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} -.progress-warning .bar{background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-ms-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(top, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fbb450', endColorstr='#f89406', GradientType=0);} -.progress-warning.progress-striped .bar{background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-danger .bar{background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-ms-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(top, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0);background-color:#dd514c;background-image:-moz-linear-gradient(top, #ee5f5b, #c43c35);background-image:-ms-linear-gradient(top, #ee5f5b, #c43c35);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ee5f5b), to(#c43c35));background-image:-webkit-linear-gradient(top, #ee5f5b, #c43c35);background-image:-o-linear-gradient(top, #ee5f5b, #c43c35);background-image:linear-gradient(top, #ee5f5b, #c43c35);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ee5f5b', endColorstr='#c43c35', GradientType=0);} +.progress-danger.progress-striped .bar{background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#ee5f5b;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-success .bar{background-color:#5eb95e;background-image:-moz-linear-gradient(top, #62c462, #57a957);background-image:-ms-linear-gradient(top, #62c462, #57a957);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));background-image:-webkit-linear-gradient(top, #62c462, #57a957);background-image:-o-linear-gradient(top, #62c462, #57a957);background-image:linear-gradient(top, #62c462, #57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#57a957', GradientType=0);background-color:#5eb95e;background-image:-moz-linear-gradient(top, #62c462, #57a957);background-image:-ms-linear-gradient(top, #62c462, #57a957);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#62c462), to(#57a957));background-image:-webkit-linear-gradient(top, #62c462, #57a957);background-image:-o-linear-gradient(top, #62c462, #57a957);background-image:linear-gradient(top, #62c462, #57a957);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#62c462', endColorstr='#57a957', GradientType=0);} +.progress-success.progress-striped .bar{background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#62c462;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-info .bar{background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-ms-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(top, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#339bb9', GradientType=0);background-color:#4bb1cf;background-image:-moz-linear-gradient(top, #5bc0de, #339bb9);background-image:-ms-linear-gradient(top, #5bc0de, #339bb9);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#5bc0de), to(#339bb9));background-image:-webkit-linear-gradient(top, #5bc0de, #339bb9);background-image:-o-linear-gradient(top, #5bc0de, #339bb9);background-image:linear-gradient(top, #5bc0de, #339bb9);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#5bc0de', endColorstr='#339bb9', GradientType=0);} +.progress-info.progress-striped .bar{background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#5bc0de;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} +.progress-warning .bar{background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-ms-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(top, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fbb450', endColorstr='#f89406', GradientType=0);background-color:#faa732;background-image:-moz-linear-gradient(top, #fbb450, #f89406);background-image:-ms-linear-gradient(top, #fbb450, #f89406);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fbb450), to(#f89406));background-image:-webkit-linear-gradient(top, #fbb450, #f89406);background-image:-o-linear-gradient(top, #fbb450, #f89406);background-image:linear-gradient(top, #fbb450, #f89406);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#fbb450', endColorstr='#f89406', GradientType=0);} +.progress-warning.progress-striped .bar{background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-color:#fbb450;background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(0.25, rgba(255, 255, 255, 0.15)), color-stop(0.25, transparent), color-stop(0.5, transparent), color-stop(0.5, rgba(255, 255, 255, 0.15)), color-stop(0.75, rgba(255, 255, 255, 0.15)), color-stop(0.75, transparent), to(transparent));background-image:-webkit-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-ms-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:-o-linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(-45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);} .accordion{margin-bottom:16px;} -.accordion-group{margin-bottom:2px;border:1px solid #e5e5e5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} +.accordion-group{margin-bottom:2px;border:1px solid #e5e5e5;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} .accordion-heading{border-bottom:0;} .accordion-heading .accordion-toggle{display:block;padding:8px 15px;} .accordion-toggle{cursor:pointer;} .accordion-inner{padding:9px 15px;border-top:1px solid #e5e5e5;} .carousel{position:relative;margin-bottom:16px;line-height:1;} .carousel-inner{overflow:hidden;width:100%;position:relative;} -.carousel .item{display:none;position:relative;-webkit-transition:0.6s ease-in-out left;-moz-transition:0.6s ease-in-out left;-ms-transition:0.6s ease-in-out left;-o-transition:0.6s ease-in-out left;transition:0.6s ease-in-out left;} +.carousel .item{display:none;position:relative;-webkit-transition:0.6s ease-in-out left;-moz-transition:0.6s ease-in-out left;-ms-transition:0.6s ease-in-out left;-o-transition:0.6s ease-in-out left;transition:0.6s ease-in-out left;-webkit-transition:0.6s ease-in-out left;-moz-transition:0.6s ease-in-out left;-ms-transition:0.6s ease-in-out left;-o-transition:0.6s ease-in-out left;transition:0.6s ease-in-out left;} .carousel .item>img{display:block;line-height:1;} .carousel .active,.carousel .next,.carousel .prev{display:block;} .carousel .active{left:0;} @@ -435,11 +435,11 @@ .carousel .next.left,.carousel .prev.right{left:0;} .carousel .active.left{left:-100%;} .carousel .active.right{left:100%;} -.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#ffffff;text-align:center;background:#222222;border:3px solid #ffffff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:0.5;filter:alpha(opacity=50);}.carousel-control.right{left:auto;right:15px;} -.carousel-control:hover{color:#ffffff;text-decoration:none;opacity:0.9;filter:alpha(opacity=90);} +.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#ffffff;text-align:center;background:#222222;border:3px solid #ffffff;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;-webkit-border-radius:23px;-moz-border-radius:23px;border-radius:23px;opacity:0.5;filter:alpha(opacity=50);opacity:0.5;filter:alpha(opacity=50);}.carousel-control.right{left:auto;right:15px;} +.carousel-control:hover{color:#ffffff;text-decoration:none;opacity:0.9;filter:alpha(opacity=90);opacity:0.9;filter:alpha(opacity=90);} .carousel-caption{position:absolute;left:0;right:0;bottom:0;padding:10px 15px 5px;background:#333333;background:rgba(0, 0, 0, 0.75);} .carousel-caption h4,.carousel-caption p{color:#ffffff;} -.hero-unit{padding:60px;margin-bottom:30px;background-color:#eeeeee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;color:inherit;letter-spacing:-1px;} +.hero-unit{padding:60px;margin-bottom:30px;background-color:#eeeeee;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px;}.hero-unit h1{margin-bottom:0;font-size:60px;line-height:1;color:inherit;letter-spacing:-1px;} .hero-unit p{font-size:18px;font-weight:200;line-height:24px;color:inherit;} .pull-right{float:right;} .pull-left{float:left;} @@ -453,15 +453,15 @@ .nav-tabs{border-bottom:1px solid #999999;} .nav-tabs>li>a:hover{border-color:#eeeeee #eeeeee #999999;} .nav-tabs>.active>a,.nav-tabs>.active>a:hover{border:1px solid #999999;border-bottom-color:transparent;} -.bs-tooltip{position:absolute;z-index:1020;display:block;visibility:visible;padding:5px;font-size:11px;opacity:0;filter:alpha(opacity=0);}.bs-tooltip.in{opacity:0.8;filter:alpha(opacity=80);} +.bs-tooltip{position:absolute;z-index:1020;display:block;visibility:visible;padding:5px;font-size:11px;opacity:0;filter:alpha(opacity=0);opacity:0;filter:alpha(opacity=0);}.bs-tooltip.in{opacity:0.8;filter:alpha(opacity=80);opacity:0.8;filter:alpha(opacity=80);} .bs-tooltip.top{margin-top:-2px;} .bs-tooltip.right{margin-left:2px;} .bs-tooltip.bottom{margin-top:2px;} .bs-tooltip.left{margin-left:-2px;} -.bs-tooltip.top .tooltip-arrow{bottom:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-top:5px solid #000000;} -.bs-tooltip.left .tooltip-arrow{top:50%;right:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;} -.bs-tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-bottom:5px solid #000000;} -.bs-tooltip.right .tooltip-arrow{top:50%;left:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-right:5px solid #000000;} +.bs-tooltip.top .tooltip-arrow{bottom:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-top:5px solid #000000;bottom:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-top:5px solid #000000;} +.bs-tooltip.left .tooltip-arrow{top:50%;right:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;top:50%;right:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-left:5px solid #000000;} +.bs-tooltip.bottom .tooltip-arrow{top:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-bottom:5px solid #000000;top:0;left:50%;margin-left:-5px;border-left:5px solid transparent;border-right:5px solid transparent;border-bottom:5px solid #000000;} +.bs-tooltip.right .tooltip-arrow{top:50%;left:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-right:5px solid #000000;top:50%;left:0;margin-top:-5px;border-top:5px solid transparent;border-bottom:5px solid transparent;border-right:5px solid #000000;} .bs-tooltip .tooltip-inner{max-width:200px;padding:3px 8px;color:#ffffff;text-align:center;text-decoration:none;background-color:#000000;} .bs-tooltip .tooltip-arrow{position:absolute;width:0;height:0;} @font-face{font-family:'FontAwesome';src:url('../images/fonts/fontawesome-webfont.eot');src:url('../images/fonts/fontawesome-webfont.eot?#iefix') format('embedded-opentype'),url('../images/fonts/fontawesome-webfont.woff') format('woff'),url('../images/fonts/fontawesome-webfont.ttf') format('truetype'),url('../images/fonts/fontawesome-webfont.svgz#FontAwesomeRegular') format('svg'),url('../images/fonts/fontawesome-webfont.svg#FontAwesomeRegular') format('svg');font-weight:normal;font-style:normal;}.ficon,[class^="ficon"]:before,[class*=" ficon"]:before{font-family:FontAwesome;font-weight:normal;font-style:normal;display:inline-block;} @@ -611,9 +611,9 @@ .ficon.github-sign:before{content:"\f092";} .ficon.upload-alt:before{content:"\f093";} .ficon.lemon:before{content:"\f094";} -.unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;} -.parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%;} -.clear{*zoom:1;}.clear:before,.clear:after{display:table;content:"";} +.unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;} +.parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%;} +.clear{*zoom:1;*zoom:1;}.clear:before,.clear:after{display:table;content:"";} .clear:after{clear:both;} .clear:before,.clear:after{display:table;content:"";} .clear:after{clear:both;} @@ -637,13 +637,13 @@ #center{left:250px;right:250px;overflow:hidden;z-index:1;} #right-border{right:250px;} #right{width:250px;right:0px;z-index:200;border-left:solid #999999 1px;} -.subnavbar{background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-bottom:solid #999999 1px;border-top:solid #999999 1px;padding:5px;color:#555;} -.unified-panel-header{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;height:30px;z-index:1000;text-shadow:rgba(255, 255, 255, 0.8) 0 1px 0;background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-bottom:solid #999999 1px;margin:0;padding:0;padding-right:10px;padding-left:10px;font-weight:bold;color:#555;}.unified-panel-header a{color:#555;} +.subnavbar{background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-bottom:solid #999999 1px;border-top:solid #999999 1px;padding:5px;color:#555;} +.unified-panel-header{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;height:30px;z-index:1000;text-shadow:rgba(255, 255, 255, 0.8) 0 1px 0;background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);background-color:#fafafa;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), color-stop(25%, #ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #ffffff, #ffffff 25%, #e6e6e6);background-image:-ms-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:-o-linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-image:linear-gradient(#ffffff, #ffffff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-bottom:solid #999999 1px;margin:0;padding:0;padding-right:10px;padding-left:10px;font-weight:bold;color:#555;}.unified-panel-header a{color:#555;} .unified-panel-header-inner{padding-top:8px;} -.unified-panel-footer{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);color:#555;}.unified-panel-footer a{color:#555;} +.unified-panel-footer{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);color:#555;}.unified-panel-footer a{color:#555;} .unified-panel-footer .drag{position:absolute;top:0;right:0;padding:0 5px;text-align:center;height:25px;width:20px;background-image:url(../images/visualization/draggable_horizontal.png);background-repeat:no-repeat;background-position:50% 50%;cursor:w-resize;} #right>.unified-panel-footer .drag{left:0;} -.panel-collapse{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;position:absolute;height:25px;line-height:25px;width:100%;z-index:1000;color:#555;z-index:10000;position:fixed;left:0;top:inherit;bottom:0;padding:0 5px;text-align:center;width:20px;background:none;border-right:solid #999999 1px;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);font-family:FontAwesome;font-weight:normal;font-style:normal;display:inline-block;font-size:1.3333333333333333em;}.panel-collapse a{color:#555;} +.panel-collapse{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;position:absolute;bottom:0;height:25px;line-height:25px;width:100%;z-index:1000;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);color:#555;z-index:10000;position:fixed;left:0;top:inherit;bottom:0;padding:0 5px;text-align:center;width:20px;background:none;border-right:solid #999999 1px;border-top:solid #999999 1px;background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);background-color:#f0f0f0;background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#f2f2f2), color-stop(25%, #f2f2f2), to(#e6e6e6));background-image:-webkit-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-ms-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:-o-linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-image:linear-gradient(#f2f2f2, #f2f2f2 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#f2f2f2', endColorstr='#e6e6e6', GradientType=0);font-family:FontAwesome;font-weight:normal;font-style:normal;display:inline-block;font-size:1.3333333333333333em;}.panel-collapse a{color:#555;} .panel-collapse .drag{position:absolute;top:0;right:0;padding:0 5px;text-align:center;height:25px;width:20px;background-image:url(../images/visualization/draggable_horizontal.png);background-repeat:no-repeat;background-position:50% 50%;cursor:w-resize;} .panel-collapse:before{content:'\f053';} .panel-collapse.hidden:before{content:'\f054';} @@ -652,7 +652,7 @@ .menu-bg{background:whiteSmoke top repeat-x;} div.unified-panel-body{position:absolute;top:30px;bottom:0;width:100%;margin-top:1px;} #left>div.unified-panel-body,#right>div.unified-panel-body{bottom:25px;} -.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;padding-right:0.5em;padding-left:0.5em;}.panel-header-button:hover{color:maroon;-webkit-transition:color 0.25s linear;-moz-transition:color 0.25s linear;-ms-transition:color 0.25s linear;-o-transition:color 0.25s linear;transition:color 0.25s linear;} +.panel-header-button{color:#333;text-decoration:none;display:inline-block;cursor:pointer;margin:-1px;padding:1px;margin-top:-0.2em;padding-right:0.5em;padding-left:0.5em;}.panel-header-button:hover{color:maroon;-webkit-transition:color 0.25s linear;-moz-transition:color 0.25s linear;-ms-transition:color 0.25s linear;-o-transition:color 0.25s linear;transition:color 0.25s linear;-webkit-transition:color 0.25s linear;-moz-transition:color 0.25s linear;-ms-transition:color 0.25s linear;-o-transition:color 0.25s linear;transition:color 0.25s linear;} .panel-header-button .caret{margin-top:7px;} .panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px;} #overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} @@ -661,18 +661,18 @@ .panel-warning-message{background-image:url(warn_small.png);background-color:#ffffcc;} .panel-done-message{background-image:url(ok_small.png);background-color:#ccffcc;} .panel-info-message{background-image:url(info_small.png);background-color:#d9edf7;} -#masthead{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;*position:relative;*z-index:2;overflow:visible;margin-bottom:16px;color:#999999;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;border-bottom:solid #444444 1px;z-index:15000;padding:0;}#masthead .brand:hover{text-decoration:none;} +#masthead{-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;*position:relative;*z-index:2;overflow:visible;margin-bottom:16px;color:#999999;position:absolute;top:0;left:0;width:100%;min-width:900px;height:32px;border-bottom:solid #444444 1px;z-index:15000;padding:0;}#masthead .brand:hover{text-decoration:none;} #masthead .brand{float:left;display:block;padding:4px 20px 8px;margin-left:-20px;font-size:20px;font-weight:200;line-height:1;color:#999999;} #masthead .navbar-text{margin-bottom:0;line-height:32px;} #masthead .navbar-link{color:#999999;}#masthead .navbar-link:hover{color:#ffffff;} -#masthead .btn,#masthead .btn-group{margin-top:1px;} +#masthead .btn,#masthead .btn-group{margin-top:1px;margin-top:1px;} #masthead .btn-group .btn{margin:0;} #masthead .nav{z-index:10000;background-color:#2c3143;} #masthead .nav>li>a{padding:6px 10px 8px;cursor:pointer;}#masthead .nav>li>a:hover{color:gold;} #masthead .dropdown-menu a,#masthead .dropdown-menu a:hover{text-decoration:none;} #masthead .title{position:absolute;left:0;top:0;font-family:verdana;font-weight:bold;font-size:20px;line-height:1;color:white;padding:5px 20px 12px;margin-left:-15px;z-index:2000;}#masthead .title img{display:inline;width:26px;vertical-align:top;} #masthead .title a{color:white;text-decoration:none;} -#masthead .masthead-inner{min-height:32px;padding-left:20px;padding-right:20px;background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-ms-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(top, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#333333', endColorstr='#2c3143', GradientType=0);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);-moz-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);padding-left:0;padding-right:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;height:32px;} +#masthead .masthead-inner{min-height:32px;padding-left:20px;padding-right:20px;background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-ms-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(top, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#333333', endColorstr='#2c3143', GradientType=0);background-color:#303239;background-image:-moz-linear-gradient(top, #333333, #2c3143);background-image:-ms-linear-gradient(top, #333333, #2c3143);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#333333), to(#2c3143));background-image:-webkit-linear-gradient(top, #333333, #2c3143);background-image:-o-linear-gradient(top, #333333, #2c3143);background-image:linear-gradient(top, #333333, #2c3143);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#333333', endColorstr='#2c3143', GradientType=0);-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);-moz-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);-webkit-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);-moz-box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);box-shadow:0 1px 3px rgba(0,0,0,.25), inset 0 -1px 0 rgba(0,0,0,.1);padding-left:0;padding-right:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;height:32px;} #masthead a:hover{text-decoration:underline;} .quota-meter-container{position:absolute;top:0;right:0;height:32px;} .quota-meter{position:absolute;top:8px;right:8px;height:16px;width:100px;background-color:#c1c9e5;} @@ -712,17 +712,17 @@ select,input,textarea{font:inherit;} .form-row select,.form-row textarea,.form-row input[type="text"],.form-row input[type="file"],.form-row input[type="password"]{max-width:90%;} textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:16px;border:1px solid #999999;padding:3px;} -.search-query{display:inline-block;padding:4px;font-size:12px;line-height:16px;color:#555555;border:1px solid #999999;padding-left:14px !important;padding-right:14px !important;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto;} -.search-query:focus{border-color:rgba(24, 132, 218, 0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);outline:0;outline:thin dotted \9;} +.search-query{display:inline-block;padding:4px;font-size:12px;line-height:16px;color:#555555;border:1px solid #999999;padding-left:14px !important;padding-right:14px !important;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto;} +.search-query:focus{border-color:rgba(24, 132, 218, 0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);outline:0;outline:thin dotted \9;} .search-spinner{position:absolute;display:none;right:5px;top:9px;} -.search-clear-btn{position:absolute;right:4px;top:8px;} -.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:36px;padding-left:52px;background-image:url(error_large.png);background-repeat:no-repeat;background-position:10px 10px;} +#search-clear-btn{position:absolute;right:4px;top:8px;} +.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:36px;padding-left:52px;background-image:url(error_large.png);background-repeat:no-repeat;background-position:10px 10px;} .errormessagelarge{background-color:#ffcccc;border-color:#ff3355;color:#660000;padding-left:52px;} .warningmessagelarge{background-image:url(warn_large.png);border-color:#aaaa66;background-color:#ffffcc;} .donemessagelarge{background-color:#ccffcc;border-color:#1a9900;color:#006600;padding-left:52px;background-image:url(ok_large.png);} -.infomessagelarge{border-color:#1b7183;color:#134158;background-image:url(info_large.png);border-color:#6666aa;background-color:#d9edf7;} +.infomessagelarge{background-color:#d9edf7;border-color:#1b7183;color:#134158;background-image:url(info_large.png);border-color:#6666aa;background-color:#d9edf7;} .screencastBox{padding-left:10px;border-color:#AAAA66;background-color:#FFFFCC;background-image:none;} -.errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;padding:5px;padding-left:25px;min-height:15px;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} +.errormessage,.warningmessage,.donemessage,.infomessage,.errormessagesmall,.warningmessagesmall,.donemessagesmall,.infomessagesmall{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;padding:5px;padding-left:25px;min-height:15px;background-image:url(error_small.png);background-repeat:no-repeat;background-position:5px 5px;} .errormessage{background-color:#ffcccc;border-color:#ff3355;color:#660000;} .warningmessage,.warningmessagesmall{background-image:url(warn_small.png);} .donemessage,.donemessagesmall{background-color:#ccffcc;border-color:#1a9900;color:#006600;background-image:url(ok_small.png);} @@ -789,7 +789,7 @@ .state-fg-ok{color:#66AA66;} .state-fg-error{color:#AA6666;} .state-fg-deleted{color:#3399FF;} -.action-button{display:inline-block;*display:inline;*zoom:1;padding:4px 10px 4px;margin-bottom:0;font-size:12px;line-height:16px;*line-height:20px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);vertical-align:middle;cursor:pointer;background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-color:#e6e6e6 #e6e6e6 #bfbfbf;*background-color:#e6e6e6;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);border:1px solid #999999;*border:0;border-bottom-color:#808080;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;*margin-left:.3em;-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);border-color:#ccc;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);padding:2px 10px 2px;border-color:#999999;border-color:rgba(0, 0, 0, 0.4) rgba(0, 0, 0, 0.4) rgba(0, 0, 0, 0.4);}.action-button:hover,.action-button:active,.action-button.active,.action-button.disabled,.action-button[disabled]{background-color:#e6e6e6;*background-color:#d9d9d9;} +.action-button{display:inline-block;*display:inline;*zoom:1;*display:inline;*zoom:1;padding:4px 10px 4px;margin-bottom:0;font-size:12px;line-height:16px;*line-height:20px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);vertical-align:middle;cursor:pointer;background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-color:#e6e6e6 #e6e6e6 #bfbfbf;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-color:#e6e6e6 #e6e6e6 #bfbfbf;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);*background-color:#e6e6e6;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-color:#e6e6e6 #e6e6e6 #bfbfbf;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-color:#e6e6e6 #e6e6e6 #bfbfbf;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);*background-color:#e6e6e6;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);border:1px solid #999999;*border:0;border-bottom-color:#808080;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;*margin-left:.3em;*margin-left:.3em;-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);border-color:#ccc;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);padding:2px 10px 2px;border-color:#999999;border-color:rgba(0, 0, 0, 0.4) rgba(0, 0, 0, 0.4) rgba(0, 0, 0, 0.4);}.action-button:hover,.action-button:active,.action-button.active,.action-button.disabled,.action-button[disabled]{background-color:#e6e6e6;*background-color:#d9d9d9;} .action-button:active,.action-button.active{background-color:#cccccc \9;} .action-button:hover,.action-button:active,.action-button.active,.action-button.disabled,.action-button[disabled]{background-color:#e6e6e6;*background-color:#d9d9d9;} .action-button:active,.action-button.active{background-color:#cccccc \9;} @@ -798,20 +798,20 @@ .action-button [class^="ficon"],.action-button [class*=" ficon"]{line-height:.9em;} a.action-button{text-decoration:none;} .action-button>img{vertical-align:middle;} -.action-button:active{background-color:#e6e6e6;background-color:#d9d9d9 \9;background-image:none;outline:0;-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);color:inherit;} -.menubutton{*display:inline;*zoom:1;padding:4px 10px 4px;margin-bottom:0;font-size:12px;line-height:16px;*line-height:20px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);vertical-align:middle;background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-color:#e6e6e6 #e6e6e6 #bfbfbf;*background-color:#e6e6e6;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);border:1px solid #999999;*border:0;border-bottom-color:#808080;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;*margin-left:.3em;-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);border-color:#ccc;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);padding:2px 10px 2px;border-color:#999999;border-color:rgba(0, 0, 0, 0.4) rgba(0, 0, 0, 0.4) rgba(0, 0, 0, 0.4);display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;}.menubutton:hover,.menubutton:active,.menubutton.active,.menubutton.disabled,.menubutton[disabled]{background-color:#e6e6e6;*background-color:#d9d9d9;} +.action-button:active{background-color:#e6e6e6;background-color:#d9d9d9 \9;background-image:none;outline:0;-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);color:inherit;} +.menubutton{display:inline-block;*display:inline;*zoom:1;*display:inline;*zoom:1;padding:4px 10px 4px;margin-bottom:0;font-size:12px;line-height:16px;*line-height:20px;color:#333333;text-align:center;text-shadow:0 1px 1px rgba(255, 255, 255, 0.75);vertical-align:middle;cursor:pointer;background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-color:#e6e6e6 #e6e6e6 #bfbfbf;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-color:#e6e6e6 #e6e6e6 #bfbfbf;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);*background-color:#e6e6e6;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-color:#e6e6e6 #e6e6e6 #bfbfbf;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);background-color:#f5f5f5;background-image:-moz-linear-gradient(top, #ffffff, #e6e6e6);background-image:-ms-linear-gradient(top, #ffffff, #e6e6e6);background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#ffffff), to(#e6e6e6));background-image:-webkit-linear-gradient(top, #ffffff, #e6e6e6);background-image:-o-linear-gradient(top, #ffffff, #e6e6e6);background-image:linear-gradient(top, #ffffff, #e6e6e6);background-repeat:repeat-x;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffff', endColorstr='#e6e6e6', GradientType=0);border-color:#e6e6e6 #e6e6e6 #bfbfbf;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);*background-color:#e6e6e6;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);border:1px solid #999999;*border:0;border-bottom-color:#808080;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;*margin-left:.3em;*margin-left:.3em;-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 1px 0 rgba(255,255,255,.2), 0 1px 2px rgba(0,0,0,.05);border-color:#ccc;border-color:rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.1) rgba(0, 0, 0, 0.25);padding:2px 10px 2px;border-color:#999999;border-color:rgba(0, 0, 0, 0.4) rgba(0, 0, 0, 0.4) rgba(0, 0, 0, 0.4);display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;}.menubutton:hover,.menubutton:active,.menubutton.active,.menubutton.disabled,.menubutton[disabled]{background-color:#e6e6e6;*background-color:#d9d9d9;} .menubutton:active,.menubutton.active{background-color:#cccccc \9;} .menubutton:hover,.menubutton:active,.menubutton.active,.menubutton.disabled,.menubutton[disabled]{background-color:#e6e6e6;*background-color:#d9d9d9;} .menubutton:active,.menubutton.active{background-color:#cccccc \9;} .menubutton:first-child{*margin-left:0;} .menubutton:first-child{*margin-left:0;} .menubutton [class^="ficon"],.menubutton [class*=" ficon"]{line-height:.9em;} -.menubutton:active{background-color:#e6e6e6;background-color:#d9d9d9 \9;background-image:none;outline:0;-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);color:inherit;} -.menubutton:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} +.menubutton:active{background-color:#e6e6e6;background-color:#d9d9d9 \9;background-image:none;outline:0;-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-webkit-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);-moz-box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);box-shadow:inset 0 2px 4px rgba(0,0,0,.15), 0 1px 2px rgba(0,0,0,.05);color:inherit;} +.menubutton:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px;} .menubutton a{text-decoration:none;} .menubutton .label,.menubutton>label{position:relative;display:inline-block;border-right:none;text-decoration:none;text-align:left;max-height:32px;line-height:16px;overflow:hidden;text-overflow:ellipsis;} .menubutton.popup .label{border-right:solid #999999 1px;padding-right:6px;} -.menubutton.popup,.menubutton.popup.split{padding-right:18px;}.menubutton.popup:after,.menubutton.popup.split:after{margin-top:6px;position:absolute;top:2px;right:6px;display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.3;filter:alpha(opacity=30);} +.menubutton.popup,.menubutton.popup.split{padding-right:18px;}.menubutton.popup:after,.menubutton.popup.split:after{margin-top:6px;position:absolute;top:2px;right:6px;display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.3;filter:alpha(opacity=30);opacity:0.3;filter:alpha(opacity=30);} div.popmenu-wrapper{position:absolute;top:100%;z-index:20000;}div.popmenu-wrapper ul.dropdown-menu{display:block;position:relative;float:none;} ul.dropdown-menu a{text-decoration:none;} ul.dropdown-menu li.head>a{text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);font-size:11px;font-weight:bold;line-height:16px;color:#999999;text-transform:uppercase;} @@ -909,4 +909,4 @@ div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px 0px;} div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} -.text-and-autocomplete-select{background:none;position:relative;padding-right:18px;}.text-and-autocomplete-select:after{margin-top:6px;position:absolute;top:2px;right:6px;width:10px;height:10px;display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.3;filter:alpha(opacity=30);opacity:0.8;filter:alpha(opacity=80);} +.text-and-autocomplete-select{background:none;position:relative;padding-right:18px;}.text-and-autocomplete-select:after{margin-top:6px;position:absolute;top:2px;right:6px;width:10px;height:10px;display:inline-block;width:0;height:0;vertical-align:top;border-top:4px solid #000000;border-right:4px solid transparent;border-left:4px solid transparent;content:"";opacity:0.3;filter:alpha(opacity=30);opacity:0.3;filter:alpha(opacity=30);opacity:0.8;filter:alpha(opacity=80);opacity:0.8;filter:alpha(opacity=80);} diff -r 59cc544ee6573507fa9ce2ca69aeb82907870cf2 -r da7821adf629620b239c9f5c5e1381eaf4c3ff7b static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -559,7 +559,7 @@ query_changed: function( evData ) { // check for the 'clear key' (ESC) first if( ( this.model.attributes.clear_key ) - && ( this.model.attributes.clear_key == evData.which ) ){ + && ( this.model.attributes.clear_key === evData.which ) ){ this.clear(); return false; } diff -r 59cc544ee6573507fa9ce2ca69aeb82907870cf2 -r da7821adf629620b239c9f5c5e1381eaf4c3ff7b static/scripts/templates/compiled/tool_search.js --- a/static/scripts/templates/compiled/tool_search.js +++ b/static/scripts/templates/compiled/tool_search.js @@ -9,14 +9,10 @@ foundHelper = helpers.search_hint_string; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.search_hint_string; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\" id=\"tool-search-query\" autocomplete=\"off\" class=\"search-query parent-width\" />\n<img src=\""; - foundHelper = helpers.clear_btn_url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.clear_btn_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\" id=\"search-clear-btn\" class=\"search-clear-btn\"/>\n<img src=\""; + buffer += escapeExpression(stack1) + "\" id=\"tool-search-query\" autocomplete=\"off\" class=\"search-query parent-width\" />\n<a id=\"search-clear-btn\" class=\"icon-button cross-circle tooltip\" title=\"clear search (esc)\"></a>\n<img src=\""; foundHelper = helpers.spinner_url; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.spinner_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\" id=\"search-spinner\" class=\"search-spinner\"/>\n"; + buffer += escapeExpression(stack1) + "\" id=\"search-spinner\" class=\"search-spinner\"/>"; return buffer;}); })(); \ No newline at end of file diff -r 59cc544ee6573507fa9ce2ca69aeb82907870cf2 -r da7821adf629620b239c9f5c5e1381eaf4c3ff7b static/scripts/templates/tool_search.handlebars --- a/static/scripts/templates/tool_search.handlebars +++ b/static/scripts/templates/tool_search.handlebars @@ -1,3 +1,3 @@ <input type="text" name="query" value="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> -<img src="{{clear_btn_url}}" id="search-clear-btn" class="search-clear-btn"/> -<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> +<a id="search-clear-btn" class="icon-button cross-circle tooltip" title="clear search (esc)"></a> +<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> \ No newline at end of file diff -r 59cc544ee6573507fa9ce2ca69aeb82907870cf2 -r da7821adf629620b239c9f5c5e1381eaf4c3ff7b templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -17,7 +17,7 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.templates( "tool_link", "panel_section", "tool_search" )} - ${h.js( "galaxy.base", "json2", "autocomplete_tagging", "mvc/tools" )} + ${h.js( "galaxy.base", "json2", "autocomplete_tagging", "mvc/tools", "bootstrap" )} <% # Set up for creating tool panel. @@ -34,7 +34,6 @@ $(function() { // Set up search. tool_search = new ToolSearch( {spinner_url: "${h.url_for('/static/images/loading_small_white_bg.gif')}", - clear_btn_url: "${h.url_for('/static/images/fugue/cross-circle-bw.png')}", search_url: "${h.url_for( controller='root', action='tool_search' )}", hidden: ${tool_search_hidden} } ); @@ -66,6 +65,8 @@ JSON.stringify({"search_active" : search_active})); }); */ + + $( '.tooltip' ).tooltip(); // TODO: is this necessary? $( "a[minsizehint]" ).click( function() { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: smcmanus: Eliminated debug statements (mostly already commented out) under DELETEME tags
by Bitbucket 02 Aug '12

02 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/59cc544ee657/ changeset: 59cc544ee657 user: smcmanus date: 2012-08-02 19:06:43 summary: Eliminated debug statements (mostly already commented out) under DELETEME tags affected #: 4 files diff -r c2ff2d01a23a778c4778e6a466eaf3592486cbee -r 59cc544ee6573507fa9ce2ca69aeb82907870cf2 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -976,8 +976,6 @@ def set_runner( self, runner_url, external_id ): task = self.get_task() self.sa_session.refresh( task ) - # DELETEME: - #log.debug( "************** Setting task %d runner name to %s" % ( task.get_id(), runner_url ) ) task.task_runner_name = runner_url task.task_runner_external_id = external_id # DBTODO Check task job_runner_stuff diff -r c2ff2d01a23a778c4778e6a466eaf3592486cbee -r 59cc544ee6573507fa9ce2ca69aeb82907870cf2 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -392,9 +392,6 @@ runner_name = "tasks" else: runner_name = ( job_wrapper.get_job_runner_url().split(":", 1) )[0] - # DELETEME - #log.debug( "__get_runner_name: runner_name = %s; URL: %s" - # % (runner_name, job_wrapper.get_job_runner_url()) ) return runner_name def put( self, job_wrapper ): @@ -419,8 +416,6 @@ # Note that Jobs and Tasks have runner_names, which are distinct from # the job_runner_name and task_runner_name. - # DELETEME - this next block is for debug only. - log.debug( "DefaultJobDispatcher: Stopping job %d" % job.get_id() ) if ( isinstance( job, model.Job ) ): log.debug( "Stopping job %d:", job.get_id() ) elif( isinstance( job, model.Task ) ): diff -r c2ff2d01a23a778c4778e6a466eaf3592486cbee -r 59cc544ee6573507fa9ce2ca69aeb82907870cf2 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -87,9 +87,6 @@ stderr = stderr_file, env = os.environ, preexec_fn = os.setpgrp ) - # DELETEME (debug): - log.debug( "Job %s: PID %d" - % ( job_wrapper.get_id_tag(), proc.pid ) ) job_wrapper.set_runner( 'local:///', proc.pid ) job_wrapper.change_state( model.Job.states.RUNNING ) if self.app.config.output_size_limit > 0: diff -r c2ff2d01a23a778c4778e6a466eaf3592486cbee -r 59cc544ee6573507fa9ce2ca69aeb82907870cf2 lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -103,9 +103,6 @@ count_complete = 0 tasks_complete = True for tw in task_wrappers: -# # DELETEME - debug -# log.debug( "Checking task wrapper %d; tasks_complete = %s" -# % (tw.task_id, tasks_complete) ) task_state = tw.get_state() if ( model.Task.states.ERROR == task_state ): log.debug( "Canceling job %d: Task %d returned an error" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: btn/esc to clear tool search (bb issue #774)
by Bitbucket 02 Aug '12

02 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c2ff2d01a23a/ changeset: c2ff2d01a23a user: carlfeberhard date: 2012-08-02 18:21:49 summary: btn/esc to clear tool search (bb issue #774) affected #: 8 files diff -r 8402d189f38ba88a0f83c9f76ad56cc05c82f363 -r c2ff2d01a23a778c4778e6a466eaf3592486cbee static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -714,7 +714,8 @@ textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:16px;border:1px solid #999999;padding:3px;} .search-query{display:inline-block;padding:4px;font-size:12px;line-height:16px;color:#555555;border:1px solid #999999;padding-left:14px !important;padding-right:14px !important;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto;} .search-query:focus{border-color:rgba(24, 132, 218, 0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);-moz-box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);box-shadow:inset 0 1px 1px rgba(0, 0, 0, 0.075),0 0 8px rgba(82, 168, 236, 0.6);outline:0;outline:thin dotted \9;} -.search-spinner{position:absolute;display:none;right:8px;top:10px;} +.search-spinner{position:absolute;display:none;right:5px;top:9px;} +.search-clear-btn{position:absolute;right:4px;top:8px;} .errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:8px 35px 8px 14px;margin-bottom:16px;text-shadow:0 1px 0 rgba(255, 255, 255, 0.5);background-color:#ffffcc;border:1px solid #ffdd33;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;color:#666600;min-height:36px;padding-left:52px;background-image:url(error_large.png);background-repeat:no-repeat;background-position:10px 10px;} .errormessagelarge{background-color:#ffcccc;border-color:#ff3355;color:#660000;padding-left:52px;} .warningmessagelarge{background-image:url(warn_large.png);border-color:#aaaa66;background-color:#ffffcc;} diff -r 8402d189f38ba88a0f83c9f76ad56cc05c82f363 -r c2ff2d01a23a778c4778e6a466eaf3592486cbee static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -270,11 +270,16 @@ */ var ToolSearch = BaseModel.extend({ defaults: { + search_hint_string: "search tools", + min_chars_for_search: 3, spinner_url: "", + clear_btn_url: "", search_url: "", visible: true, query: "", - results: null + results: null, + // ESC (27) will clear the input field and tool search filters + clear_key: 27 }, initialize: function() { @@ -288,7 +293,7 @@ var query = this.attributes.query; // If query is too short, do not search. - if (query.length < 3) { + if (query.length < this.attributes.min_chars_for_search) { this.set("results", null); return; } @@ -300,15 +305,23 @@ clearTimeout(this.timer); } // Start a new ajax-request in X ms + $("#search-clear-btn").hide(); $("#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(); + $("#search-clear-btn").show(); }, "json" ); }, 200 ); + }, + + clear_search: function() { + this.set("query", ""); + this.set("results", null); } + }); /** @@ -520,7 +533,8 @@ events: { 'click': 'focus_and_select', - 'keyup :input': 'query_changed' + 'keyup :input': 'query_changed', + 'click #search-clear-btn': 'clear' }, render: function() { @@ -535,7 +549,20 @@ this.$el.find(":input").focus().select(); }, - query_changed: function() { + clear: function() { + this.model.clear_search(); + this.$el.find(":input").val(this.model.attributes.search_hint_string); + this.focus_and_select(); + return false; + }, + + query_changed: function( evData ) { + // check for the 'clear key' (ESC) first + if( ( this.model.attributes.clear_key ) + && ( this.model.attributes.clear_key == evData.which ) ){ + this.clear(); + return false; + } this.model.set("query", this.$el.find(":input").val()); } }); diff -r 8402d189f38ba88a0f83c9f76ad56cc05c82f363 -r c2ff2d01a23a778c4778e6a466eaf3592486cbee static/scripts/templates/compiled/panel_section.js --- a/static/scripts/templates/compiled/panel_section.js +++ b/static/scripts/templates/compiled/panel_section.js @@ -2,24 +2,21 @@ 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; + var buffer = "", stack1, foundHelper, functionType="function", 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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "\">\n <a href=\"javascript:void(0)\"><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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } 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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } 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 8402d189f38ba88a0f83c9f76ad56cc05c82f363 -r c2ff2d01a23a778c4778e6a466eaf3592486cbee static/scripts/templates/compiled/tool_form.js --- a/static/scripts/templates/compiled/tool_form.js +++ b/static/scripts/templates/compiled/tool_form.js @@ -2,60 +2,47 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['tool_form'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, stack2, foundHelper, tmp1, self=this, functionType="function", helperMissing=helpers.helperMissing, undef=void 0, escapeExpression=this.escapeExpression; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; function program1(depth0,data) { - var buffer = "", stack1; + var buffer = "", stack1, foundHelper; buffer += "\n <div class=\"form-row\">\n <label for=\""; 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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "\">"; foundHelper = helpers.label; - stack1 = foundHelper || depth0.label; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "label", { hash: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.label; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + ":</label>\n <div class=\"form-row-input\">\n "; foundHelper = helpers.html; - stack1 = foundHelper || depth0.html; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "html", { hash: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.html; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n <div class=\"toolParamHelp\" style=\"clear: both;\">\n "; foundHelper = helpers.help; - stack1 = foundHelper || depth0.help; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "help", { hash: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.help; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "\n </div>\n <div style=\"clear: both;\"></div>\n </div>\n "; return buffer;} buffer += "<div class=\"toolFormTitle\">"; 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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + " (version "; foundHelper = helpers.version; - stack1 = foundHelper || depth0.version; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "version", { hash: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.version; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + ")</div>\n <div class=\"toolFormBody\">\n "; - foundHelper = helpers.inputs; - stack1 = foundHelper || depth0.inputs; - stack2 = helpers.each; - tmp1 = self.program(1, program1, data); - tmp1.hash = {}; - tmp1.fn = tmp1; - tmp1.inverse = self.noop; - stack1 = stack2.call(depth0, stack1, tmp1); + stack1 = depth0.inputs; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n <div class=\"form-row form-actions\">\n <input type=\"submit\" class=\"btn btn-primary\" name=\"runtool_btn\" value=\"Execute\">\n</div>\n<div class=\"toolHelp\">\n <div class=\"toolHelpBody\">"; foundHelper = helpers.help; - stack1 = foundHelper || depth0.help; - if(typeof stack1 === functionType) { stack1 = stack1.call(depth0, { hash: {} }); } - else if(stack1=== undef) { stack1 = helperMissing.call(depth0, "help", { hash: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.help; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "</div>\n</div>"; return buffer;}); })(); \ No newline at end of file diff -r 8402d189f38ba88a0f83c9f76ad56cc05c82f363 -r c2ff2d01a23a778c4778e6a466eaf3592486cbee static/scripts/templates/compiled/tool_link.js --- a/static/scripts/templates/compiled/tool_link.js +++ b/static/scripts/templates/compiled/tool_link.js @@ -2,39 +2,33 @@ 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; + var buffer = "", stack1, foundHelper, functionType="function", 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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } 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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.link; stack1 = typeof stack1 === functionType ? stack1() : stack1; } 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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.target; stack1 = typeof stack1 === functionType ? stack1() : stack1; } 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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.min_width; stack1 = typeof stack1 === functionType ? stack1() : stack1; } 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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } 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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.description; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1); return buffer;}); })(); \ No newline at end of file diff -r 8402d189f38ba88a0f83c9f76ad56cc05c82f363 -r c2ff2d01a23a778c4778e6a466eaf3592486cbee static/scripts/templates/compiled/tool_search.js --- a/static/scripts/templates/compiled/tool_search.js +++ b/static/scripts/templates/compiled/tool_search.js @@ -2,14 +2,21 @@ 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; + var buffer = "", stack1, foundHelper, functionType="function", 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=\""; + buffer += "<input type=\"text\" name=\"query\" value=\""; + foundHelper = helpers.search_hint_string; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.search_hint_string; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" id=\"tool-search-query\" autocomplete=\"off\" class=\"search-query parent-width\" />\n<img src=\""; + foundHelper = helpers.clear_btn_url; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.clear_btn_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" id=\"search-clear-btn\" class=\"search-clear-btn\"/>\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: {} }); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.spinner_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "\" id=\"search-spinner\" class=\"search-spinner\"/>\n"; return buffer;}); })(); \ No newline at end of file diff -r 8402d189f38ba88a0f83c9f76ad56cc05c82f363 -r c2ff2d01a23a778c4778e6a466eaf3592486cbee static/scripts/templates/tool_search.handlebars --- a/static/scripts/templates/tool_search.handlebars +++ b/static/scripts/templates/tool_search.handlebars @@ -1,2 +1,3 @@ -<input type="text" name="query" value="search tools" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> +<input type="text" name="query" value="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> +<img src="{{clear_btn_url}}" id="search-clear-btn" class="search-clear-btn"/><img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> diff -r 8402d189f38ba88a0f83c9f76ad56cc05c82f363 -r c2ff2d01a23a778c4778e6a466eaf3592486cbee templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -34,9 +34,10 @@ $(function() { // Set up search. tool_search = new ToolSearch( {spinner_url: "${h.url_for('/static/images/loading_small_white_bg.gif')}", - search_url: "${h.url_for( controller='root', action='tool_search' )}", + clear_btn_url: "${h.url_for('/static/images/fugue/cross-circle-bw.png')}", + search_url: "${h.url_for( controller='root', action='tool_search' )}", hidden: ${tool_search_hidden} } ); - + // Set up tool panel. tool_panel = new ToolPanel( { tool_search: tool_search } ); tool_panel.reset( tool_panel.parse( ${h.to_json_string( dictified_panel )} ) ); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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