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record file size information for a file in the triple store
author
Diane Trout
<diane@caltech.edu>
Fri, 27 Mar 2015 18:03:45 +0000
(11:03 -0700)
committer
Diane Trout
<diane@caltech.edu>
Fri, 27 Mar 2015 18:13:12 +0000
(11:13 -0700)
htsworkflow/submission/submission.py
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diff --git
a/htsworkflow/submission/submission.py
b/htsworkflow/submission/submission.py
index 897053fbc148477c108d232635958db45488dfc5..ed4d898ec919fdb66909ad810bd249e860f38b2a 100644
(file)
--- a/
htsworkflow/submission/submission.py
+++ b/
htsworkflow/submission/submission.py
@@
-123,6
+123,7
@@
class Submission(object):
# add file specific information
fileNode = self.make_file_node(pathname, an_analysis)
self.add_md5s(filename, fileNode, analysis_dir)
# add file specific information
fileNode = self.make_file_node(pathname, an_analysis)
self.add_md5s(filename, fileNode, analysis_dir)
+ self.add_file_size(filename, fileNode, analysis_dir)
self.add_fastq_metadata(filename, fileNode)
self.add_label(file_type, fileNode, libNode)
self.model.add_statement(
self.add_fastq_metadata(filename, fileNode)
self.add_label(file_type, fileNode, libNode)
self.model.add_statement(
@@
-168,6
+169,13
@@
class Submission(object):
self.model.add_statement(
RDF.Statement(fileNode, dafTermOntology['md5sum'], md5))
self.model.add_statement(
RDF.Statement(fileNode, dafTermOntology['md5sum'], md5))
+ def add_file_size(self, filename, fileNode, analysis_dir):
+ LOGGER.debug("Updating file size")
+ submission_pathname = os.path.join(analysis_dir, filename)
+ file_size = os.stat(submission_pathname).st_size
+ self.model.add_statement(
+ RDF.Statement(fileNode, dafTermOntology['file_size'], toTypedNode(file_size)))
+
def add_fastq_metadata(self, filename, fileNode):
# How should I detect if this is actually a fastq file?
try:
def add_fastq_metadata(self, filename, fileNode):
# How should I detect if this is actually a fastq file?
try: