2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7117a2655ade/
Changeset: 7117a2655ade
User: jmchilton
Date: 2013-11-21 15:02:50
Summary: Fix model/check.py for app being None such as when using create_db.sh
Thanks to Aaron Petkau for reporting this issue.
Affected #: 1 file
diff -r e6e9349e8da45a058fb5811eb89813694aeef729 -r 7117a2655ade212cfee20c9499d12b8ed5dc729b lib/galaxy/model/migrate/check.py
--- a/lib/galaxy/model/migrate/check.py
+++ b/lib/galaxy/model/migrate/check.py
@@ -57,7 +57,7 @@
migrate_to_current_version( engine, db_schema )
meta = MetaData( bind=engine )
- if getattr( app.config, 'database_auto_migrate', False ):
+ if app and getattr( app.config, 'database_auto_migrate', False ):
migrate()
return
https://bitbucket.org/galaxy/galaxy-central/commits/9a998cee3ea5/
Changeset: 9a998cee3ea5
User: jmchilton
Date: 2013-11-21 15:05:36
Summary: Merge.
Affected #: 1 file
diff -r 7117a2655ade212cfee20c9499d12b8ed5dc729b -r 9a998cee3ea5acaf0f058b4743da37787c916594 test/install_and_test_tool_shed_repositories/functional_tests.py
--- a/test/install_and_test_tool_shed_repositories/functional_tests.py
+++ b/test/install_and_test_tool_shed_repositories/functional_tests.py
@@ -43,6 +43,7 @@
from functional_tests import generate_config_file
from galaxy import eggs
+from galaxy.util import unicodify
eggs.require( "nose" )
eggs.require( "NoseHTML" )
@@ -1122,7 +1123,7 @@
# In keeping with the standard display layout, add the error message to the dict for each tool individually.
for dependency in repository.missing_tool_dependencies:
log.error( 'Missing tool dependency %s of type %s version %s: %s' % \
- ( str( dependency.name ), str( dependency.type ), str( dependency.version ), str( dependency.error_message ) ) )
+ ( str( dependency.name ), str( dependency.type ), str( dependency.version ), unicodify( dependency.error_message ) ) )
test_result = dict( type=dependency.type,
name=dependency.name,
version=dependency.version,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f6d687147f65/
Changeset: f6d687147f65
User: Dave Bouvier
Date: 2013-11-21 14:59:22
Summary: Handle unicode characters when logging tool dependency installation errors.
Affected #: 1 file
diff -r e6e9349e8da45a058fb5811eb89813694aeef729 -r f6d687147f65098a82854f5c7d6aaaa2dc602c8a test/install_and_test_tool_shed_repositories/functional_tests.py
--- a/test/install_and_test_tool_shed_repositories/functional_tests.py
+++ b/test/install_and_test_tool_shed_repositories/functional_tests.py
@@ -43,6 +43,7 @@
from functional_tests import generate_config_file
from galaxy import eggs
+from galaxy.util import unicodify
eggs.require( "nose" )
eggs.require( "NoseHTML" )
@@ -1122,7 +1123,7 @@
# In keeping with the standard display layout, add the error message to the dict for each tool individually.
for dependency in repository.missing_tool_dependencies:
log.error( 'Missing tool dependency %s of type %s version %s: %s' % \
- ( str( dependency.name ), str( dependency.type ), str( dependency.version ), str( dependency.error_message ) ) )
+ ( str( dependency.name ), str( dependency.type ), str( dependency.version ), unicodify( dependency.error_message ) ) )
test_result = dict( type=dependency.type,
name=dependency.name,
version=dependency.version,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e6e9349e8da4/
Changeset: e6e9349e8da4
User: dannon
Date: 2013-11-21 02:39:51
Summary: Add object_store_conf.xml to .hgignore
Affected #: 1 file
diff -r 672987cdb4bf67ed14915d7997618bf008ce844e -r e6e9349e8da45a058fb5811eb89813694aeef729 .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -60,6 +60,7 @@
job_conf.xml
data_manager_conf.xml
shed_data_manager_conf.xml
+object_store_conf.xml
config/*
static/welcome.html.*
static/welcome.html
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/672987cdb4bf/
Changeset: 672987cdb4bf
User: dannon
Date: 2013-11-21 01:59:01
Summary: Swap impersonate to select2 deferred load w/ filter. This adds a 'f_email' filter parameter to the Users api collection -- we should revisit this before the next stable release to decide how we want API filtering to actually work down the road.
Affected #: 2 files
diff -r 7a882c5fdd34636ae5ca98f63709c13a6648c3cf -r 672987cdb4bf67ed14915d7997618bf008ce844e lib/galaxy/webapps/galaxy/api/users.py
--- a/lib/galaxy/webapps/galaxy/api/users.py
+++ b/lib/galaxy/webapps/galaxy/api/users.py
@@ -14,7 +14,7 @@
class UserAPIController( BaseAPIController, UsesTagsMixin, CreatesUsersMixin, CreatesApiKeysMixin ):
@web.expose_api
- def index( self, trans, deleted='False', **kwd ):
+ def index( self, trans, deleted='False', f_email=None, **kwd ):
"""
GET /api/users
GET /api/users/deleted
@@ -23,6 +23,8 @@
rval = []
query = trans.sa_session.query( trans.app.model.User )
deleted = util.string_as_bool( deleted )
+ if f_email:
+ query = query.filter(trans.app.model.User.email.like("%%%s%%" % f_email))
if deleted:
query = query.filter( trans.app.model.User.table.c.deleted == True )
# only admins can see deleted users
diff -r 7a882c5fdd34636ae5ca98f63709c13a6648c3cf -r 672987cdb4bf67ed14915d7997618bf008ce844e templates/admin/impersonate.mako
--- a/templates/admin/impersonate.mako
+++ b/templates/admin/impersonate.mako
@@ -14,11 +14,8 @@
<label>
User to impersonate:
</label>
- <select name="email" class='text-and-autocomplete-select'>
- %for email in emails:
- <option>${email}</option>
- %endfor
- </select>
+ <input type="hidden" id="email_select" name="email">
+ </input></div><div class="form-row"><input type="submit" name="impersonate_button" value="Impersonate"/>
@@ -26,4 +23,35 @@
</form></div></div>
+ <script type="text/javascript">
+ /* This should be ripped out and made generic at some point for the
+ * various API bindings available, and once the API can filter list
+ * queries (term, below) */
+ $("#email_select").select2({
+ placeholder: "Select a user",
+ ajax: {
+ url: "/api/users/",
+ dataType: 'json',
+ quietMillis: 250,
+ matcher: function(term, text) { return text.toUpperCase().indexOf(term.toUpperCase())>=0; },
+ data: function (term) {
+ return {
+ f_email: term
+ };
+ },
+ results: function (data) {
+ var results = [];
+ $.each(data, function(index, item){
+ results.push({
+ id: item.email,
+ text: item.email
+ });
+ });
+ return {
+ results: results
+ };
+ }
+ }
+ });
+ </script>
%endif
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/23afd47845fe/
Changeset: 23afd47845fe
User: jmchilton
Date: 2013-11-20 23:44:09
Summary: Add stderr and stdout to provenance information.
Affected #: 1 file
diff -r ef45d85b1f579c5bb4b07284dd96ad8403003c03 -r 23afd47845fec9b8169712d0e78ee8d2baf0d96d lib/galaxy/webapps/galaxy/api/provenance.py
--- a/lib/galaxy/webapps/galaxy/api/provenance.py
+++ b/lib/galaxy/webapps/galaxy/api/provenance.py
@@ -48,6 +48,8 @@
"uuid": ( lambda uuid: str( uuid ) if uuid else None )( item.dataset.uuid),
"tool_id": job.tool_id,
"parameters": self._get_job_record(trans, job, follow),
+ "stderr": job.stderr,
+ "stdout": job.stdout,
}
return None
https://bitbucket.org/galaxy/galaxy-central/commits/bd8b3e2a9938/
Changeset: bd8b3e2a9938
User: jmchilton
Date: 2013-11-20 23:44:09
Summary: Allow raw display of composite files via API.
Affected #: 1 file
diff -r 23afd47845fec9b8169712d0e78ee8d2baf0d96d -r bd8b3e2a99389f0564a1ff0dbfb9e3d56e56f990 lib/galaxy/webapps/galaxy/api/datasets.py
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -265,7 +265,12 @@
except KeyError:
pass
if raw:
- rval = open( hda.file_name )
+ if filename and filename != 'index':
+ file_path = trans.app.object_store.get_filename(hda.dataset, extra_dir='dataset_%s_files' % hda.dataset.id, alt_name=filename)
+ else:
+ file_path = hda.file_name
+ rval = open( file_path )
+
else:
rval = hda.datatype.display_data( trans, hda, preview, filename, to_ext, chunk, **display_kwd )
https://bitbucket.org/galaxy/galaxy-central/commits/7a882c5fdd34/
Changeset: 7a882c5fdd34
User: jmchilton
Date: 2013-11-20 23:44:09
Summary: Allow simple use of multi-page tools via API.
In tools module, when process_state=='populate' (i.e. coming from tool API without existing tool_state specified), populate and validate state of all pages of tools.
Affected #: 1 file
diff -r bd8b3e2a99389f0564a1ff0dbfb9e3d56e56f990 -r 7a882c5fdd34636ae5ca98f63709c13a6648c3cf lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1811,7 +1811,8 @@
from API). May want an incremental version of the API also at some point,
that is why this is not just called for_api.
"""
- state, state_new = self.__fetch_state( trans, incoming, history )
+ all_pages = ( process_state == "populate" ) # If process_state = update, handle all pages at once.
+ state, state_new = self.__fetch_state( trans, incoming, history, all_pages=all_pages )
if state_new:
# This feels a bit like a hack. It allows forcing full processing
# of inputs even when there is no state in the incoming dictionary
@@ -1837,7 +1838,7 @@
error_message = "One or more errors were found in the input you provided. The specific errors are marked below."
return "tool_form.mako", dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message )
# If we've completed the last page we can execute the tool
- elif state.page == self.last_page:
+ elif all_pages or state.page == self.last_page:
return self.__handle_tool_execute( trans, incoming, params, history )
# Otherwise move on to the next page
else:
@@ -1891,7 +1892,7 @@
return 'message.mako', dict( status='info', message="The interface for this tool cannot be displayed", refresh_frames=['everything'] )
return 'tool_form.mako', dict( errors=errors, tool_state=state )
- def __fetch_state( self, trans, incoming, history ):
+ def __fetch_state( self, trans, incoming, history, all_pages ):
# Get the state or create if not found
if "tool_state" in incoming:
encoded_state = string_to_object( incoming["tool_state"] )
@@ -1899,7 +1900,7 @@
state.decode( encoded_state, self, trans.app )
new = False
else:
- state = self.new_state( trans, history=history )
+ state = self.new_state( trans, history=history, all_pages=all_pages )
new = True
return state, new
@@ -1917,15 +1918,17 @@
# Update state for all inputs on the current page taking new
# values from `incoming`.
if process_state == "update":
- errors = self.update_state( trans, self.inputs_by_page[state.page], state.inputs, incoming, old_errors=old_errors or {}, source=source )
+ inputs = self.inputs_by_page[state.page]
+ errors = self.update_state( trans, inputs, state.inputs, incoming, old_errors=old_errors or {}, source=source )
elif process_state == "populate":
- errors = self.populate_state( trans, self.inputs_by_page[state.page], state.inputs, incoming, history, source=source )
+ inputs = self.inputs
+ errors = self.populate_state( trans, inputs, state.inputs, incoming, history, source=source )
else:
raise Exception("Unknown process_state type %s" % process_state)
# If the tool provides a `validate_input` hook, call it.
validate_input = self.get_hook( 'validate_input' )
if validate_input:
- validate_input( trans, errors, state.inputs, self.inputs_by_page[state.page] )
+ validate_input( trans, errors, state.inputs, inputs )
params = state.inputs
return errors, params
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/30d30843b57f/
Changeset: 30d30843b57f
User: Dave Bouvier
Date: 2013-11-20 22:51:02
Summary: Fix string interpolation in a log message.
Affected #: 1 file
diff -r d0fe08c597a40b32a5d6c9a57b4be07f610fdfc7 -r 30d30843b57f5b8fe809ed2c226cf41e82b8465e lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
--- a/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
+++ b/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
@@ -86,7 +86,7 @@
now = strftime( "%Y-%m-%d %H:%M:%S" )
print "#############################################################################"
- print "# %s - Validating repositories of type %s on %s..." % ( TOOL_DEPENDENCY_DEFINITION, now )
+ print "# %s - Validating repositories of type %s on %s..." % ( TOOL_DEPENDENCY_DEFINITION, now, config_parser.get( config_section, 'host' ) )
print "# This tool shed is configured to listen on %s:%s" % ( config_parser.get( config_section, 'host' ), config_parser.get( config_section, 'port' ) )
app = RepositoriesApplication( config )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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