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Rename global logger to LOGGER to be more PEP8 like
author
Diane Trout
<diane@caltech.edu>
Tue, 17 Apr 2012 00:51:55 +0000
(17:51 -0700)
committer
Diane Trout
<diane@caltech.edu>
Tue, 17 Apr 2012 00:51:55 +0000
(17:51 -0700)
htsworkflow/submission/daf.py
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diff --git
a/htsworkflow/submission/daf.py
b/htsworkflow/submission/daf.py
index 96037b9647c93146a9887334c3ec1ebdf9266b0d..a74d71a667d1cb788cbdaab24cdf8661738c9413 100644
(file)
--- a/
htsworkflow/submission/daf.py
+++ b/
htsworkflow/submission/daf.py
@@
-24,7
+24,7
@@
from htsworkflow.util.rdfhelp import \
fromTypedNode
from htsworkflow.util.hashfile import make_md5sum
fromTypedNode
from htsworkflow.util.hashfile import make_md5sum
-
logger
= logging.getLogger(__name__)
+
LOGGER
= logging.getLogger(__name__)
DAF_VARIABLE_NAMES = ("variables", "extraVariables")
VARIABLES_TERM_NAME = 'variables'
DAF_VARIABLE_NAMES = ("variables", "extraVariables")
VARIABLES_TERM_NAME = 'variables'
@@
-130,7
+130,7
@@
def parse_stream(stream):
if view_name is not None:
attributes['views'][view_name] = view_attributes
if view_name is not None:
attributes['views'][view_name] = view_attributes
-
logger
.debug("DAF Attributes" + pformat(attributes))
+
LOGGER
.debug("DAF Attributes" + pformat(attributes))
return attributes
return attributes
@@
-254,7
+254,7
@@
class UCSCSubmission(object):
otherwise specifies model to use
"""
if daf_file is None and model is None:
otherwise specifies model to use
"""
if daf_file is None and model is None:
-
logger
.error("We need a DAF or Model containing a DAF to work")
+
LOGGER
.error("We need a DAF or Model containing a DAF to work")
self.name = name
self.submissionSet = get_submission_uri(self.name)
self.name = name
self.submissionSet = get_submission_uri(self.name)
@@
-297,11
+297,11
@@
class UCSCSubmission(object):
"""Examine files in our result directory
"""
for lib_id, result_dir in result_map.items():
"""Examine files in our result directory
"""
for lib_id, result_dir in result_map.items():
-
logger
.info("Importing %s from %s" % (lib_id, result_dir))
+
LOGGER
.info("Importing %s from %s" % (lib_id, result_dir))
try:
self.import_submission_dir(result_dir, lib_id)
except MetadataLookupException, e:
try:
self.import_submission_dir(result_dir, lib_id)
except MetadataLookupException, e:
-
logger
.error("Skipping %s: %s" % (lib_id, str(e)))
+
LOGGER
.error("Skipping %s: %s" % (lib_id, str(e)))
def import_submission_dir(self, submission_dir, library_id):
"""Import a submission directories and update our model as needed
def import_submission_dir(self, submission_dir, library_id):
"""Import a submission directories and update our model as needed
@@
-324,10
+324,10
@@
class UCSCSubmission(object):
"""
path, filename = os.path.split(pathname)
"""
path, filename = os.path.split(pathname)
-
logger
.debug("Searching for view")
+
LOGGER
.debug("Searching for view")
view = self.find_view(filename)
if view is None:
view = self.find_view(filename)
if view is None:
-
logger
.warn("Unrecognized file: {0}".format(pathname))
+
LOGGER
.warn("Unrecognized file: {0}".format(pathname))
return None
if str(view) == str(libraryOntology['ignore']):
return None
return None
if str(view) == str(libraryOntology['ignore']):
return None
@@
-339,7
+339,7
@@
class UCSCSubmission(object):
dafTermOntology['name']))
if view_name is None:
errmsg = 'Could not find view name for {0}'
dafTermOntology['name']))
if view_name is None:
errmsg = 'Could not find view name for {0}'
-
logger
.warning(errmsg.format(str(view)))
+
LOGGER
.warning(errmsg.format(str(view)))
return
view_name = str(view_name)
return
view_name = str(view_name)
@@
-349,7
+349,7
@@
class UCSCSubmission(object):
RDF.Statement(self.submissionSet,
dafTermOntology['has_submission'],
submissionNode))
RDF.Statement(self.submissionSet,
dafTermOntology['has_submission'],
submissionNode))
-
logger
.debug("Adding statements to {0}".format(str(submissionNode)))
+
LOGGER
.debug("Adding statements to {0}".format(str(submissionNode)))
self.model.add_statement(RDF.Statement(submissionNode,
submissionOntology['has_view'],
submissionView))
self.model.add_statement(RDF.Statement(submissionNode,
submissionOntology['has_view'],
submissionView))
@@
-364,7
+364,7
@@
class UCSCSubmission(object):
submissionOntology['library'],
libNode))
submissionOntology['library'],
libNode))
-
logger
.debug("Adding statements to {0}".format(str(submissionView)))
+
LOGGER
.debug("Adding statements to {0}".format(str(submissionView)))
# add track specific information
self.model.add_statement(
RDF.Statement(submissionView, dafTermOntology['view'], view))
# add track specific information
self.model.add_statement(
RDF.Statement(submissionView, dafTermOntology['view'], view))
@@
-380,11
+380,11
@@
class UCSCSubmission(object):
# add file specific information
self.create_file_attributes(filename, submissionView, submission_uri, submission_dir)
# add file specific information
self.create_file_attributes(filename, submissionView, submission_uri, submission_dir)
-
logger
.debug("Done.")
+
LOGGER
.debug("Done.")
def create_file_attributes(self, filename, submissionView, submission_uri, submission_dir):
# add file specific information
def create_file_attributes(self, filename, submissionView, submission_uri, submission_dir):
# add file specific information
-
logger
.debug("Updating file md5sum")
+
LOGGER
.debug("Updating file md5sum")
fileNode = RDF.Node(RDF.Uri(submission_uri + '/' + filename))
submission_pathname = os.path.join(submission_dir, filename)
self.model.add_statement(
fileNode = RDF.Node(RDF.Uri(submission_uri + '/' + filename))
submission_pathname = os.path.join(submission_dir, filename)
self.model.add_statement(
@@
-399,7
+399,7
@@
class UCSCSubmission(object):
md5 = make_md5sum(submission_pathname)
if md5 is None:
errmsg = "Unable to produce md5sum for {0}"
md5 = make_md5sum(submission_pathname)
if md5 is None:
errmsg = "Unable to produce md5sum for {0}"
-
logger
.warning(errmsg.format(submission_pathname))
+
LOGGER
.warning(errmsg.format(submission_pathname))
else:
self.model.add_statement(
RDF.Statement(fileNode, dafTermOntology['md5sum'], md5))
else:
self.model.add_statement(
RDF.Statement(fileNode, dafTermOntology['md5sum'], md5))
@@
-513,7
+513,7
@@
class UCSCSubmission(object):
else:
msg = "Found wrong number of view names for {0} len = {1}"
msg = msg.format(str(view), len(names))
else:
msg = "Found wrong number of view names for {0} len = {1}"
msg = msg.format(str(view), len(names))
-
logger
.error(msg)
+
LOGGER
.error(msg)
raise RuntimeError(msg)
def _get_filename_view_map(self):
raise RuntimeError(msg)
def _get_filename_view_map(self):
@@
-528,11
+528,11
@@
class UCSCSubmission(object):
for s in self.model.find_statements(filename_query):
view_name = s.subject
literal_re = s.object.literal_value['string']
for s in self.model.find_statements(filename_query):
view_name = s.subject
literal_re = s.object.literal_value['string']
-
logger
.debug("Found: %s" % (literal_re,))
+
LOGGER
.debug("Found: %s" % (literal_re,))
try:
filename_re = re.compile(literal_re)
except re.error, e:
try:
filename_re = re.compile(literal_re)
except re.error, e:
-
logger
.error("Unable to compile: %s" % (literal_re,))
+
LOGGER
.error("Unable to compile: %s" % (literal_re,))
patterns[literal_re] = view_name
return patterns
patterns[literal_re] = view_name
return patterns