2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7094bb55cc8a/
Changeset: 7094bb55cc8a
User: jmchilton
Date: 2014-06-29 20:31:33
Summary: Spelling fix in method name.
Affected #: 2 files
diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r
7094bb55cc8aa7f3ee71fcd2286a5576add79e4c lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2931,7 +2931,7 @@
Find any additional datasets generated by a tool and attach (for
cases where number of outputs is not known in advance).
"""
- return output_collect.collect_primary_datatasets( self, output,
job_working_directory )
+ return output_collect.collect_primary_datasets( self, output,
job_working_directory )
def to_dict( self, trans, link_details=False, io_details=False ):
""" Returns dict of tool. """
diff -r 381a36069c14bf20c98955c01ab00e7838257943 -r
7094bb55cc8aa7f3ee71fcd2286a5576add79e4c lib/galaxy/tools/parameters/output_collect.py
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/tools/parameters/output_collect.py
@@ -14,7 +14,7 @@
DEFAULT_EXTRA_FILENAME_PATTERN =
r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?"
-def collect_primary_datatasets( tool, output, job_working_directory ):
+def collect_primary_datasets( tool, output, job_working_directory ):
app = tool.app
sa_session = tool.sa_session
new_primary_datasets = {}
https://bitbucket.org/galaxy/galaxy-central/commits/4de240e5a781/
Changeset: 4de240e5a781
User: jmchilton
Date: 2014-06-29 20:31:33
Summary: Allow discovered datasets to use input data format in 'ext'
definition.
Affected #: 4 files
diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r
4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1181,6 +1181,13 @@
out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ]
)
out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets
] )
+ input_ext = 'data'
+ for _, data in inp_data.items():
+ # For loop odd, but sort simulating behavior in galaxy.tools.actions
+ if not data:
+ continue
+ input_ext = data.ext
+
param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not
re-use self.param_dict here? ##dunno...probably should, this causes
tools.parameters.basic.UnvalidatedValue to be used in following methods instead of
validated and transformed values during i.e. running workflows
param_dict = self.tool.params_from_strings( param_dict, self.app )
# Check for and move associated_files
@@ -1191,7 +1198,7 @@
# Create generated output children and primary datasets and add to param_dict
collected_datasets = {
'children': self.tool.collect_child_datasets(out_data,
self.working_directory),
- 'primary': self.tool.collect_primary_datasets(out_data,
self.working_directory)
+ 'primary': self.tool.collect_primary_datasets(out_data,
self.working_directory, input_ext)
}
param_dict.update({'__collected_datasets__': collected_datasets})
# Certain tools require tasks to be completed after job execution
diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r
4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2926,12 +2926,12 @@
self.sa_session.flush()
return children
- def collect_primary_datasets( self, output, job_working_directory ):
+ def collect_primary_datasets( self, output, job_working_directory, input_ext ):
"""
Find any additional datasets generated by a tool and attach (for
cases where number of outputs is not known in advance).
"""
- return output_collect.collect_primary_datasets( self, output,
job_working_directory )
+ return output_collect.collect_primary_datasets( self, output,
job_working_directory, input_ext )
def to_dict( self, trans, link_details=False, io_details=False ):
""" Returns dict of tool. """
diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r
4de240e5a7819c768b8267c19e477530dab54370 lib/galaxy/tools/parameters/output_collect.py
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/tools/parameters/output_collect.py
@@ -14,7 +14,7 @@
DEFAULT_EXTRA_FILENAME_PATTERN =
r"primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?"
-def collect_primary_datasets( tool, output, job_working_directory ):
+def collect_primary_datasets( tool, output, job_working_directory, input_ext ):
app = tool.app
sa_session = tool.sa_session
new_primary_datasets = {}
@@ -66,6 +66,8 @@
designation = fields_match.designation
visible = fields_match.visible
ext = fields_match.ext
+ if ext == "input":
+ ext = input_ext
dbkey = fields_match.dbkey
# Create new primary dataset
primary_data = app.model.HistoryDatasetAssociation( extension=ext,
diff -r 7094bb55cc8aa7f3ee71fcd2286a5576add79e4c -r
4de240e5a7819c768b8267c19e477530dab54370
test/functional/tools/multi_output_configured.xml
--- a/test/functional/tools/multi_output_configured.xml
+++ b/test/functional/tools/multi_output_configured.xml
@@ -8,19 +8,24 @@
echo "1" > subdir2/CUSTOM_1.txt;
echo "2" > subdir2/CUSTOM_2.tabular;
echo "3" > subdir2/CUSTOM_3.txt;
+ mkdir subdir3;
+ echo "Foo" > subdir3/Foo;
</command><inputs>
- <param name="input" type="integer" value="7" />
+ <param name="num_param" type="integer" value="7"
/>
+ <param name="input" type="data"
/></inputs><outputs><data format="txt"
name="report"><discover_datasets
pattern="__designation_and_ext__" directory="subdir1"
/><discover_datasets
pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)"
directory="subdir2" />
+ <discover_datasets pattern="__designation__"
directory="subdir3" ext="input"
/></data></outputs><tests><test>
- <param name="input" value="7" />
+ <param name="num_param" value="7" />
+ <param name="input" ftype="txt"
value="simple_line.txt"/><output
name="report"><assert_contents><has_line line="Hello"
/>
@@ -37,6 +42,9 @@
<discovered_dataset designation="2"
ftype="tabular"><assert_contents><has_line line="2"
/></assert_contents></discovered_dataset>
+ <discovered_dataset designation="Foo" ftype="txt">
+ <assert_contents><has_line line="Foo"
/></assert_contents>
+ </discovered_dataset></output></test></tests>
Repository URL:
https://bitbucket.org/galaxy/galaxy-central/
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