1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/7d278a17747a/
changeset: 7d278a17747a
user: carlfeberhard
date: 2012-11-21 20:02:58
summary: history panel: documenting fix to show display and edit attributes buttons for HDA in the error state.
affected #: 2 files
diff -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 -r 7d278a17747ad9cb35b1af5ec011e46f814c339a static/scripts/mvc/dataset/hda-base.js
--- a/static/scripts/mvc/dataset/hda-base.js
+++ b/static/scripts/mvc/dataset/hda-base.js
@@ -181,7 +181,8 @@
* @returns {jQuery} rendered DOM
*/
_render_displayButton : function(){
- // don't show display if not in ready state, error'd, or not accessible
+ // don't show display if not in ready state or not accessible
+ // DO show if in error (ala previous history panel)
if( ( !this.model.inReadyState() )
//|| ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR )
|| ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE )
diff -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 -r 7d278a17747ad9cb35b1af5ec011e46f814c339a static/scripts/mvc/dataset/hda-edit.js
--- a/static/scripts/mvc/dataset/hda-edit.js
+++ b/static/scripts/mvc/dataset/hda-edit.js
@@ -64,8 +64,8 @@
* @returns {jQuery} rendered DOM
*/
_render_editButton : function(){
- // don't show edit while uploading
- //TODO??: error?
+ // don't show edit while uploading, in-accessible
+ // DO show if in error (ala previous history panel)
//TODO??: not viewable/accessible are essentially the same (not viewable set from accessible)
if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD )
//|| ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/43e41e09206d/
changeset: 43e41e09206d
user: greg
date: 2012-11-21 16:50:52
summary: More shed_util refactoring.
affected #: 2 files
diff -r 5376431b78bf67afc967eb7dbebde50a02e69518 -r 43e41e09206d2ddc52f4a46114303ef9fd067251 lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -168,16 +168,6 @@
os.close( fd )
shutil.move( filename, os.path.abspath( config_filename ) )
os.chmod( config_filename, 0644 )
-def copy_disk_sample_files_to_dir( trans, repo_files_dir, dest_path ):
- sample_files = []
- for root, dirs, files in os.walk( repo_files_dir ):
- if root.find( '.hg' ) < 0:
- for name in files:
- if name.endswith( '.sample' ):
- relative_path = os.path.join( root, name )
- copy_sample_file( trans.app, relative_path, dest_path=dest_path )
- sample_files.append( name )
- return sample_files
def clean_tool_shed_url( tool_shed_url ):
if tool_shed_url.find( ':' ) > 0:
# Eliminate the port, if any, since it will result in an invalid directory name.
@@ -544,17 +534,6 @@
if converter_path and display_path:
break
return converter_path, display_path
-def get_ctx_file_path_from_manifest( filename, repo, changeset_revision ):
- """Get the ctx file path for the latest revision of filename from the repository manifest up to the value of changeset_revision."""
- stripped_filename = strip_path( filename )
- for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ):
- manifest_changeset_revision = str( repo.changectx( changeset ) )
- manifest_ctx = repo.changectx( changeset )
- for ctx_file in manifest_ctx.files():
- ctx_file_name = strip_path( ctx_file )
- if ctx_file_name == stripped_filename:
- return manifest_ctx, ctx_file
- return None, None
def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ):
url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) )
response = urllib2.urlopen( url )
@@ -564,38 +543,6 @@
def get_installed_tool_shed_repository( trans, id ):
"""Get a repository on the Galaxy side from the database via id"""
return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
-def get_list_of_copied_sample_files( repo, ctx, dir ):
- """
- Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy
- each discovered file to dir and return the list of filenames. If a .sample file was added in a changeset and then deleted in a later
- changeset, it will be returned in the deleted_sample_files list. The caller will set the value of app.config.tool_data_path to dir in
- order to load the tools and generate metadata for them.
- """
- deleted_sample_files = []
- sample_files = []
- for changeset in reversed_upper_bounded_changelog( repo, ctx ):
- changeset_ctx = repo.changectx( changeset )
- for ctx_file in changeset_ctx.files():
- ctx_file_name = strip_path( ctx_file )
- # If we decide in the future that files deleted later in the changelog should not be used, we can use the following if statement.
- # if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files:
- if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files:
- fctx = get_file_context_from_ctx( changeset_ctx, ctx_file )
- if fctx in [ 'DELETED' ]:
- # Since the possibly future used if statement above is commented out, the same file that was initially added will be
- # discovered in an earlier changeset in the change log and fall through to the else block below. In other words, if
- # a file named blast2go.loc.sample was added in change set 0 and then deleted in changeset 3, the deleted file in changeset
- # 3 will be handled here, but the later discovered file in changeset 0 will be handled in the else block below. In this
- # way, the file contents will always be found for future tools even though the file was deleted.
- if ctx_file_name not in deleted_sample_files:
- deleted_sample_files.append( ctx_file_name )
- else:
- sample_files.append( ctx_file_name )
- tmp_ctx_file_name = os.path.join( dir, ctx_file_name.replace( '.sample', '' ) )
- fh = open( tmp_ctx_file_name, 'wb' )
- fh.write( fctx.data() )
- fh.close()
- return sample_files, deleted_sample_files
def get_repository_owner( cleaned_repository_url ):
items = cleaned_repository_url.split( 'repos' )
repo_path = items[ 1 ]
@@ -916,31 +863,6 @@
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 load_tool_from_tmp_config( trans, repo, ctx, ctx_file, work_dir ):
- tool = None
- message = ''
- tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir )
- if tmp_tool_config:
- element_tree = util.parse_xml( tmp_tool_config )
- element_tree_root = element_tree.getroot()
- # Look for code files required by the tool config.
- tmp_code_files = []
- for code_elem in element_tree_root.findall( 'code' ):
- code_file_name = code_elem.get( 'file' )
- tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir )
- if tmp_code_file_name:
- tmp_code_files.append( tmp_code_file_name )
- tool, valid, message = load_tool_from_config( trans.app, tmp_tool_config )
- for tmp_code_file in tmp_code_files:
- try:
- os.unlink( tmp_code_file )
- except:
- pass
- try:
- os.unlink( tmp_tool_config )
- except:
- pass
- return tool, message
def panel_entry_per_tool( tool_section_dict ):
# Return True if tool_section_dict looks like this.
# {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]}
diff -r 5376431b78bf67afc967eb7dbebde50a02e69518 -r 43e41e09206d2ddc52f4a46114303ef9fd067251 lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -284,6 +284,28 @@
else:
message = ''
return message
+def copy_disk_sample_files_to_dir( trans, repo_files_dir, dest_path ):
+ sample_files = []
+ for root, dirs, files in os.walk( repo_files_dir ):
+ if root.find( '.hg' ) < 0:
+ for name in files:
+ if name.endswith( '.sample' ):
+ relative_path = os.path.join( root, name )
+ copy_sample_file( trans.app, relative_path, dest_path=dest_path )
+ sample_files.append( name )
+ return sample_files
+def copy_file_from_manifest( repo, ctx, filename, dir ):
+ """Copy the latest version of the file named filename from the repository manifest to the directory to which dir refers."""
+ for changeset in reversed_upper_bounded_changelog( repo, ctx ):
+ changeset_ctx = repo.changectx( changeset )
+ fctx = get_file_context_from_ctx( changeset_ctx, filename )
+ if fctx and fctx not in [ 'DELETED' ]:
+ file_path = os.path.join( dir, filename )
+ fh = open( file_path, 'wb' )
+ fh.write( fctx.data() )
+ fh.close()
+ return file_path
+ return None
def copy_sample_file( app, filename, dest_path=None ):
"""Copy xxx.sample to dest_path/xxx.sample and dest_path/xxx. The default value for dest_path is ~/tool-data."""
if dest_path is None:
@@ -603,10 +625,12 @@
is_valid = False
if is_valid:
for repository_elem in root.findall( 'repository' ):
- repository_dependencies_tups.append( ( repository_elem.attrib[ 'toolshed' ],
- repository_elem.attrib[ 'name' ],
- repository_elem.attrib[ 'owner'],
- repository_elem.attrib[ 'changeset_revision' ] ) )
+ repository_dependencies_tup = ( repository_elem.attrib[ 'toolshed' ],
+ repository_elem.attrib[ 'name' ],
+ repository_elem.attrib[ 'owner'],
+ repository_elem.attrib[ 'changeset_revision' ] )
+ if repository_dependencies_tup not in repository_dependencies_tups:
+ repository_dependencies_tups.append( repository_dependencies_tup )
if repository_dependencies_tups:
metadata_dict[ 'repository_dependencies' ] = repository_dependencies_tups
return metadata_dict
@@ -723,6 +747,17 @@
# quiet = True
_ui.setconfig( 'ui', 'quiet', True )
return _ui
+def get_ctx_file_path_from_manifest( filename, repo, changeset_revision ):
+ """Get the ctx file path for the latest revision of filename from the repository manifest up to the value of changeset_revision."""
+ stripped_filename = strip_path( filename )
+ for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ):
+ manifest_changeset_revision = str( repo.changectx( changeset ) )
+ manifest_ctx = repo.changectx( changeset )
+ for ctx_file in manifest_ctx.files():
+ ctx_file_name = strip_path( ctx_file )
+ if ctx_file_name == stripped_filename:
+ return manifest_ctx, ctx_file
+ return None, None
def get_file_context_from_ctx( ctx, filename ):
# We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories
# within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to
@@ -743,6 +778,77 @@
if deleted:
return 'DELETED'
return None
+def get_list_of_copied_sample_files( repo, ctx, dir ):
+ """
+ Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy
+ each discovered file to dir and return the list of filenames. If a .sample file was added in a changeset and then deleted in a later
+ changeset, it will be returned in the deleted_sample_files list. The caller will set the value of app.config.tool_data_path to dir in
+ order to load the tools and generate metadata for them.
+ """
+ deleted_sample_files = []
+ sample_files = []
+ for changeset in reversed_upper_bounded_changelog( repo, ctx ):
+ changeset_ctx = repo.changectx( changeset )
+ for ctx_file in changeset_ctx.files():
+ ctx_file_name = strip_path( ctx_file )
+ # If we decide in the future that files deleted later in the changelog should not be used, we can use the following if statement.
+ # if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files:
+ if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files:
+ fctx = get_file_context_from_ctx( changeset_ctx, ctx_file )
+ if fctx in [ 'DELETED' ]:
+ # Since the possibly future used if statement above is commented out, the same file that was initially added will be
+ # discovered in an earlier changeset in the change log and fall through to the else block below. In other words, if
+ # a file named blast2go.loc.sample was added in change set 0 and then deleted in changeset 3, the deleted file in changeset
+ # 3 will be handled here, but the later discovered file in changeset 0 will be handled in the else block below. In this
+ # way, the file contents will always be found for future tools even though the file was deleted.
+ if ctx_file_name not in deleted_sample_files:
+ deleted_sample_files.append( ctx_file_name )
+ else:
+ sample_files.append( ctx_file_name )
+ tmp_ctx_file_name = os.path.join( dir, ctx_file_name.replace( '.sample', '' ) )
+ fh = open( tmp_ctx_file_name, 'wb' )
+ fh.write( fctx.data() )
+ fh.close()
+ return sample_files, deleted_sample_files
+def get_named_tmpfile_from_ctx( ctx, filename, dir ):
+ filename = strip_path( filename )
+ for ctx_file in ctx.files():
+ ctx_file_name = strip_path( ctx_file )
+ if filename == ctx_file_name:
+ try:
+ # If the file was moved, its destination file contents will be returned here.
+ fctx = ctx[ ctx_file ]
+ except LookupError, e:
+ # Continue looking in case the file was moved.
+ fctx = None
+ continue
+ if fctx:
+ fh = tempfile.NamedTemporaryFile( 'wb', dir=dir )
+ tmp_filename = fh.name
+ fh.close()
+ fh = open( tmp_filename, 'wb' )
+ fh.write( fctx.data() )
+ fh.close()
+ return tmp_filename
+ return None
+def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ):
+ parent_id = None
+ # Compare from most recent to oldest.
+ changeset_revisions.reverse()
+ for changeset_revision in changeset_revisions:
+ repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
+ metadata = repository_metadata.metadata
+ tools_dicts = metadata.get( 'tools', [] )
+ for tool_dict in tools_dicts:
+ if tool_dict[ 'guid' ] == guid:
+ # The tool has not changed between the compared changeset revisions.
+ continue
+ if tool_dict[ 'id' ] == old_id and tool_dict[ 'version' ] != version:
+ # The tool version is different, so we've found the parent.
+ return tool_dict[ 'guid' ]
+ if parent_id is None:
+ # The tool did not change through all of the changeset revisions.
+ return old_id
def get_readme_file_names( repository_name ):
readme_files = [ 'readme', 'read_me', 'install' ]
valid_filenames = [ r for r in readme_files ]
@@ -803,27 +909,20 @@
elif all_metadata_records:
return all_metadata_records[ 0 ]
return None
-def get_named_tmpfile_from_ctx( ctx, filename, dir ):
- filename = strip_path( filename )
- for ctx_file in ctx.files():
- ctx_file_name = strip_path( ctx_file )
- if filename == ctx_file_name:
- try:
- # If the file was moved, its destination file contents will be returned here.
- fctx = ctx[ ctx_file ]
- except LookupError, e:
- # Continue looking in case the file was moved.
- fctx = None
- continue
- if fctx:
- fh = tempfile.NamedTemporaryFile( 'wb', dir=dir )
- tmp_filename = fh.name
- fh.close()
- fh = open( tmp_filename, 'wb' )
- fh.write( fctx.data() )
- fh.close()
- return tmp_filename
- return None
+def get_relative_path_to_repository_file( root, name, relative_install_dir, work_dir, shed_config_dict, resetting_all_metadata_on_repository ):
+ if resetting_all_metadata_on_repository:
+ full_path_to_file = os.path.join( root, name )
+ stripped_path_to_file = full_path_to_file.replace( work_dir, '' )
+ if stripped_path_to_file.startswith( '/' ):
+ stripped_path_to_file = stripped_path_to_file[ 1: ]
+ relative_path_to_file = os.path.join( relative_install_dir, stripped_path_to_file )
+ else:
+ relative_path_to_file = os.path.join( root, name )
+ if relative_install_dir and \
+ shed_config_dict.get( 'tool_path' ) and \
+ relative_path_to_file.startswith( os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) ):
+ relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ]
+ return relative_path_to_file
def get_sample_files_from_disk( repository_files_dir, tool_path = None, relative_install_dir=None, resetting_all_metadata_on_repository=False ):
if resetting_all_metadata_on_repository:
# Keep track of the location where the repository is temporarily cloned so that we can strip it when setting metadata.
@@ -852,38 +951,6 @@
relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :]
sample_file_metadata_paths.append( relative_path_to_sample_file )
return sample_file_metadata_paths, sample_file_copy_paths
-def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ):
- parent_id = None
- # Compare from most recent to oldest.
- changeset_revisions.reverse()
- for changeset_revision in changeset_revisions:
- repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
- metadata = repository_metadata.metadata
- tools_dicts = metadata.get( 'tools', [] )
- for tool_dict in tools_dicts:
- if tool_dict[ 'guid' ] == guid:
- # The tool has not changed between the compared changeset revisions.
- continue
- if tool_dict[ 'id' ] == old_id and tool_dict[ 'version' ] != version:
- # The tool version is different, so we've found the parent.
- return tool_dict[ 'guid' ]
- if parent_id is None:
- # The tool did not change through all of the changeset revisions.
- return old_id
-def get_relative_path_to_repository_file( root, name, relative_install_dir, work_dir, shed_config_dict, resetting_all_metadata_on_repository ):
- if resetting_all_metadata_on_repository:
- full_path_to_file = os.path.join( root, name )
- stripped_path_to_file = full_path_to_file.replace( work_dir, '' )
- if stripped_path_to_file.startswith( '/' ):
- stripped_path_to_file = stripped_path_to_file[ 1: ]
- relative_path_to_file = os.path.join( relative_install_dir, stripped_path_to_file )
- else:
- relative_path_to_file = os.path.join( root, name )
- if relative_install_dir and \
- shed_config_dict.get( 'tool_path' ) and \
- relative_path_to_file.startswith( os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) ):
- relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ]
- return relative_path_to_file
def handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_dependency_dict, new_dependency_dict ):
"""
This method is called when a Galaxy admin is getting updates for an installed tool shed repository in order to cover the case where an
@@ -969,6 +1036,31 @@
valid = False
error_message = str( e )
return tool, valid, error_message
+def load_tool_from_tmp_config( trans, repo, ctx, ctx_file, work_dir ):
+ tool = None
+ message = ''
+ tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir )
+ if tmp_tool_config:
+ element_tree = util.parse_xml( tmp_tool_config )
+ element_tree_root = element_tree.getroot()
+ # Look for code files required by the tool config.
+ tmp_code_files = []
+ for code_elem in element_tree_root.findall( 'code' ):
+ code_file_name = code_elem.get( 'file' )
+ tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir )
+ if tmp_code_file_name:
+ tmp_code_files.append( tmp_code_file_name )
+ tool, valid, message = load_tool_from_config( trans.app, tmp_tool_config )
+ for tmp_code_file in tmp_code_files:
+ try:
+ os.unlink( tmp_code_file )
+ except:
+ pass
+ try:
+ os.unlink( tmp_tool_config )
+ except:
+ pass
+ return tool, message
def open_repository_files_folder( trans, folder_path ):
try:
files_list = get_repository_files( trans, folder_path )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/46339150e5e1/
changeset: 46339150e5e1
user: carlfeberhard
date: 2012-11-20 21:42:01
summary: scatterplot: fix column selection broken in 7002f41
affected #: 1 file
diff -r 7002f41bcaa3b1a5f5023e3c2d523488812873df -r 46339150e5e134fb2eb57e4945617841e03a5a3f static/scripts/viz/scatterplot.js
--- a/static/scripts/viz/scatterplot.js
+++ b/static/scripts/viz/scatterplot.js
@@ -939,7 +939,7 @@
var selections = {};
this.$dataSettingsPanel.find( 'div.column-select select' ).each( function(){
var $this = $( this ),
- val = $this.val();
+ val = parseInt( $this.val(), 10 ) - 1;
selections[ $this.attr( 'name' ) ] = {
colIndex : val,
colName : $this.children( '[value="' + val + '"]' ).text()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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