projects
/
htsworkflow.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Generate manifest files for ENCODE3
[htsworkflow.git]
/
htsworkflow
/
submission
/
submission.py
diff --git
a/htsworkflow/submission/submission.py
b/htsworkflow/submission/submission.py
index 77a1b68e4db763ab83eb50135f9613e8264ce973..3320f1caf3174e6d5636c4dd20841188771050d9 100644
(file)
--- a/
htsworkflow/submission/submission.py
+++ b/
htsworkflow/submission/submission.py
@@
-122,6
+122,11
@@
class Submission(object):
RDF.Statement(fileNode,
rdfNS['type'],
file_type))
RDF.Statement(fileNode,
rdfNS['type'],
file_type))
+ self.model.add_statement(
+ RDF.Statement(fileNode,
+ libraryOntology['library'],
+ libNode))
+
LOGGER.debug("Done.")
def make_file_node(self, pathname, submissionNode):
LOGGER.debug("Done.")
def make_file_node(self, pathname, submissionNode):
@@
-129,7
+134,8
@@
class Submission(object):
"""
# add file specific information
path, filename = os.path.split(pathname)
"""
# add file specific information
path, filename = os.path.split(pathname)
- fileNode = RDF.Node(RDF.Uri('file://'+ os.path.abspath(pathname)))
+ pathname = os.path.abspath(pathname)
+ fileNode = RDF.Node(RDF.Uri('file://'+ pathname))
self.model.add_statement(
RDF.Statement(submissionNode,
dafTermOntology['has_file'],
self.model.add_statement(
RDF.Statement(submissionNode,
dafTermOntology['has_file'],
@@
-138,6
+144,10
@@
class Submission(object):
RDF.Statement(fileNode,
dafTermOntology['filename'],
filename))
RDF.Statement(fileNode,
dafTermOntology['filename'],
filename))
+ self.model.add_statement(
+ RDF.Statement(fileNode,
+ dafTermOntology['relative_path'],
+ os.path.relpath(pathname)))
return fileNode
def add_md5s(self, filename, fileNode, analysis_dir):
return fileNode
def add_md5s(self, filename, fileNode, analysis_dir):
@@
-176,7
+186,12
@@
class Submission(object):
libraryOntology['has_mappings'],
dafTermOntology['has_file']))
parser = RDF.Parser(name='rdfa')
libraryOntology['has_mappings'],
dafTermOntology['has_file']))
parser = RDF.Parser(name='rdfa')
- new_statements = parser.parse_as_stream(libNode.uri)
+ try:
+ new_statements = parser.parse_as_stream(libNode.uri)
+ except RDF.RedlandError as e:
+ LOGGER.error(e)
+ return
+ LOGGER.debug("Scanning %s", str(libNode.uri))
toadd = []
for s in new_statements:
# always add "collections"
toadd = []
for s in new_statements:
# always add "collections"
@@
-310,7
+325,8
@@
class Submission(object):
paired = ['Barcoded Illumina',
'Multiplexing',
'Nextera',
paired = ['Barcoded Illumina',
'Multiplexing',
'Nextera',
- 'Paired End (non-multiplexed)',]
+ 'Paired End (non-multiplexed)',
+ 'Dual Index Illumina',]
if library_type in single:
return False
elif library_type in paired:
if library_type in single:
return False
elif library_type in paired: