1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4bcc1949021b/
Changeset: 4bcc1949021b
User: davebgx
Date: 2014-06-13 23:32:51
Summary: Fetch eggs after initializing sample files, per John Chilton's comment.
Affected #: 1 file
diff -r fb4ac45f7827a92fa637899fb5da43a350bc857b -r 4bcc1949021ba358ea3e1dbf624d0014e8fab525 scripts/common_startup.sh
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -8,19 +8,6 @@
[ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0
[ "$arg" = "--skip-samples" ] && COPY_SAMPLE_FILES=0
done
-if [ $FETCH_EGGS -eq 1 ]; then
- python ./scripts/check_eggs.py -q
- if [ $? -ne 0 ]; then
- echo "Some eggs are out of date, attempting to fetch..."
- python ./scripts/fetch_eggs.py
- if [ $? -eq 0 ]; then
- echo "Fetch successful."
- else
- echo "Fetch failed."
- exit 1
- fi
- fi
-fi
SAMPLES="
tool_shed_wsgi.ini.sample
@@ -60,4 +47,17 @@
fi
done
fi
-
+
+if [ $FETCH_EGGS -eq 1 ]; then
+ python ./scripts/check_eggs.py -q
+ if [ $? -ne 0 ]; then
+ echo "Some eggs are out of date, attempting to fetch..."
+ python ./scripts/fetch_eggs.py
+ if [ $? -eq 0 ]; then
+ echo "Fetch successful."
+ else
+ echo "Fetch failed."
+ exit 1
+ fi
+ fi
+fi
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/c8e9e10e1a5a/
Changeset: c8e9e10e1a5a
User: dan
Date: 2014-06-13 22:31:25
Summary: Add set methods to ToolDataTableManager.
Affected #: 1 file
diff -r 6e39473e4c51151ef71ef0f5a5e05134e5d5aaa4 -r c8e9e10e1a5a2c69e94224629e8b086112e15bff lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -34,6 +34,9 @@
def __getitem__( self, key ):
return self.data_tables.__getitem__( key )
+ def __setitem__( self, key, value ):
+ return self.data_tables.__setitem__( key, value )
+
def __contains__( self, key ):
return self.data_tables.__contains__( key )
@@ -43,6 +46,9 @@
except KeyError:
return default
+ def set( self, name, value ):
+ self[ name ] = value
+
def get_tables( self ):
return self.data_tables
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/6e39473e4c51/
Changeset: 6e39473e4c51
User: dan
Date: 2014-06-13 22:09:53
Summary: In TabularToolDataTable use .get_fields() instead of .data directly.
Affected #: 1 file
diff -r e5eae98697a2f5bc4fdab711ebc1ae8d48ccde20 -r 6e39473e4c51151ef71ef0f5a5e05134e5d5aaa4 lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -335,7 +335,7 @@
return rval
def get_version_fields( self ):
- return ( self._loaded_content_version, self.data )
+ return ( self._loaded_content_version, self.get_fields() )
def parse_column_spec( self, config_element ):
"""
@@ -422,7 +422,7 @@
return default
rval = default
# Look for table entry.
- for fields in self.data:
+ for fields in self.get_fields():
if fields[ query_col ] == query_val:
rval = fields[ return_col ]
break
@@ -444,7 +444,7 @@
is_error = False
if self.largest_index < len( fields ):
fields = self._replace_field_separators( fields )
- if fields not in self.data or allow_duplicates:
+ if fields not in self.get_fields() or allow_duplicates:
self.data.append( fields )
else:
log.debug( "Attempted to add fields (%s) to data table '%s', but this entry already exists and allow_duplicates is False.", fields, self.name )
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/ea6698177726/
Changeset: ea6698177726
User: dan
Date: 2014-06-13 19:30:23
Summary: Handle update_state for Conditional tool parameters when a currently valid current_case value has not been provided.
Affected #: 2 files
diff -r 8a608db6cf83b653a433f43b501f4047f63d248b -r ea6698177726a9e94931dcd818db52f5c0e2aec3 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2392,7 +2392,18 @@
# Get value of test param and determine current case
value, test_param_error = \
check_param( trans, input.test_param, test_incoming, context, source=source )
- current_case = input.get_current_case( value, trans )
+ try:
+ current_case = input.get_current_case( value, trans )
+ except ValueError, e:
+ #load default initial value
+ if not test_param_error:
+ test_param_error = str( e )
+ if trans is not None:
+ history = trans.get_history()
+ else:
+ history = None
+ value = input.test_param.get_initial_value( trans, context, history=history )
+ current_case = input.get_current_case( value, trans )
if current_case != old_current_case:
# Current case has changed, throw away old state
group_state = state[input.name] = {}
diff -r 8a608db6cf83b653a433f43b501f4047f63d248b -r ea6698177726a9e94931dcd818db52f5c0e2aec3 lib/galaxy/tools/parameters/grouping.py
--- a/lib/galaxy/tools/parameters/grouping.py
+++ b/lib/galaxy/tools/parameters/grouping.py
@@ -472,7 +472,7 @@
for index, case in enumerate( self.cases ):
if str_value == case.value:
return index
- raise Exception( "No case matched value:", self.name, str_value )
+ raise ValueError( "No case matched value:", self.name, str_value )
def value_to_basic( self, value, app ):
rval = dict()
current_case = rval['__current_case__'] = value['__current_case__']
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/8a608db6cf83/
Changeset: 8a608db6cf83
User: jmchilton
Date: 2014-06-13 16:14:38
Summary: Small clarification in previous doc addition.
Affected #: 1 file
diff -r c9c07643e04ece14e27c07c4aa73b3578202c47b -r 8a608db6cf83b653a433f43b501f4047f63d248b lib/galaxy/webapps/galaxy/api/history_contents.py
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -240,7 +240,8 @@
'content' = [the encoded id from the HDCA]
create new history dataset collection (for type 'dataset_collection')
- 'source' = 'new_collection'
+ 'source' = 'new_collection' (default 'source' if type is
+ 'dataset_collection' - no need to specify this)
'collection_type' = For example, "list", "paired", "list:paired".
'name' = Name of new dataset collection.
'element_identifiers' = Recursive list structure defining collection.
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/c9c07643e04e/
Changeset: c9c07643e04e
User: jmchilton
Date: 2014-06-13 16:08:56
Summary: Add some quick docs for creating dataset collections through API.
For full worked examples see bioblend and API tests.
Affected #: 1 file
diff -r 05500f5c6710816865536335a42eb9e00caf6f03 -r c9c07643e04ece14e27c07c4aa73b3578202c47b lib/galaxy/webapps/galaxy/api/history_contents.py
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -217,27 +217,54 @@
def create( self, trans, history_id, payload, **kwd ):
"""
create( self, trans, history_id, payload, **kwd )
- * POST /api/histories/{history_id}/contents
+ * POST /api/histories/{history_id}/contents/{type}
create a new HDA by copying an accessible LibraryDataset
:type history_id: str
:param history_id: encoded id string of the new HDA's History
+ :type type: str
+ :param type: Type of history content - 'dataset' (default) or
+ 'dataset_collection'.
:type payload: dict
:param payload: dictionary structure containing::
- copy from library:
+ copy from library (for type 'dataset'):
'source' = 'library'
'content' = [the encoded id from the library dataset]
- copy from HDA:
+ copy from history dataset (for type 'dataset'):
'source' = 'hda'
'content' = [the encoded id from the HDA]
+ copy from history dataset collection (for type 'dataset_collection')
+ 'source' = 'hdca'
+ 'content' = [the encoded id from the HDCA]
+
+ create new history dataset collection (for type 'dataset_collection')
+ 'source' = 'new_collection'
+ 'collection_type' = For example, "list", "paired", "list:paired".
+ 'name' = Name of new dataset collection.
+ 'element_identifiers' = Recursive list structure defining collection.
+ Each element must have 'src' which can be
+ 'hda', 'ldda', 'hdca', or 'new_collection',
+ as well as a 'name' which is the name of
+ element (e.g. "forward" or "reverse" for
+ paired datasets, or arbitrary sample names
+ for instance for lists). For all src's except
+ 'new_collection' - a encoded 'id' attribute
+ must be included wiht element as well.
+ 'new_collection' sources must defined a
+ 'collection_type' and their own list of
+ (potentially) nested 'element_identifiers'.
+
..note:
Currently, a user can only copy an HDA from a history that the user owns.
:rtype: dict
:returns: dictionary containing detailed information for the new HDA
"""
+ # TODO: Flush out create new collection documentation above, need some
+ # examples. See also bioblend and API tests for specific examples.
+
# get the history, if anon user and requesting current history - allow it
if( ( trans.user == None )
and ( history_id == trans.security.encode_id( trans.history.id ) ) ):
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