toTypedNode, \
fromTypedNode
from htsworkflow.util.hashfile import make_md5sum
-
+from htsworkflow.submission.fastqname import FastqName
from htsworkflow.submission.daf import \
MetadataLookupException, \
get_submission_uri
an_analysis))
# add file specific information
- fileNode = self.link_file_to_classes(pathname,
- an_analysis,
- an_analysis_uri,
- analysis_dir)
+ fileNode = self.make_file_node(pathname, an_analysis)
self.add_md5s(filename, fileNode, analysis_dir)
+ self.add_fastq_metadata(filename, fileNode)
self.model.add_statement(
RDF.Statement(fileNode,
rdfNS['type'],
file_type))
LOGGER.debug("Done.")
- def link_file_to_classes(self, pathname, submissionNode, submission_uri, analysis_dir):
+ def make_file_node(self, pathname, submissionNode):
+ """Create file node and attach it to its submission.
+ """
# add file specific information
path, filename = os.path.split(pathname)
fileNode = RDF.Node(RDF.Uri('file://'+ os.path.abspath(pathname)))
self.model.add_statement(
RDF.Statement(fileNode, dafTermOntology['md5sum'], md5))
+ def add_fastq_metadata(self, filename, fileNode):
+ # How should I detect if this is actually a fastq file?
+ try:
+ fqname = FastqName(filename=filename)
+ except ValueError:
+ # currently its just ignore it if the fastq name parser fails
+ return
+
+ terms = [('flowcell', libraryOntology['flowcell_id']),
+ ('lib_id', libraryOntology['library_id']),
+ ('lane', libraryOntology['lane_number']),
+ ('read', libraryOntology['read']),
+ ('cycle', libraryOntology['read_length'])]
+ for file_term, model_term in terms:
+ value = fqname.get(file_term)
+ if value is not None:
+ s = RDF.Statement(fileNode, model_term, toTypedNode(value))
+ self.model.append(s)
+
def _add_library_details_to_model(self, libNode):
# attributes that can have multiple values
set_attributes = set((libraryOntology['has_lane'],