def command(self):
self.load_wsgi_app()
qlbplates = Session.query(QLBPlate).\
filter(and_(QLBPlate.file_id != None, QLBPlate.plate_id != None)).\
order_by(desc(QLBPlate.id)).\
options(joinedload_all(QLBPlate.plate, innerjoin=True))
for qlbplate in qlbplates:
qlbplate.plate.score = Plate.compute_score(qlbplate.plate)
print "%s: %s points" % (qlbplate.plate.id, qlbplate.plate.score)
Session.commit()
def plate_from_qlp(qlbplate):
"""
Given a QLBPlate, find out what information we can automatically determine
from the file name and location.
"""
dirname = qlbplate.file.dirname
basename = qlbplate.file.basename
complete_name = basename[:-4] # -- .qlp
# assign box 2
boxes = Session.query(Box2).all()
# TODO: rename as to not contain timestamp?
# TODO-- this is probably bad (assumes parent directory like Box 2 Alpha 03)
plate_name = qlbplate.file.dirname.split('/')[-1]
plate = Plate(name=plate_name, program_version=qlbplate.host_software,
run_time=datetime.strptime(qlbplate.host_datetime, '%Y:%m:%d %H:%M:%S') if qlbplate.host_datetime else None)
for b in boxes:
if qlbplate.file.dirname.startswith(b.src_dir):
plate.box2 = b
return plate
def __scan_plate(file_source, image_source, path_id, path, mtime_dict, plate_type=None, file_lists=None):
"""
The method responsible for taking a QLP file on disk and creating
thumbnails and adding/updating records in the database based off
the contents of that file.
This is a nasty abstraction, I apologize.
TODO: make this more natural along add/update line, do not require use of
mtime_dict or file_list (or return file_list as files touched)
Returns the Plate object of the added/updated plate, or None if there was
no touch/error.
:param file_source: The source of the QLP files (QLStorageSource)
:param image_source: The source/sink of thumbnails (QLStorageSource)
:param path_id: The unique identifier of the plate file. Computed by run_id()
:param path: The actual file path of the QLP.
:param mtime_dict: A mapping between plates and their last updated times. This will
indicate whether or not a plate is 'dirty' with respect to the DB.
:param plate_type: A plate type. Supplying this will indicate that the special metrics
corresponding to that plate type should be computed during the scan.
:param file_lists: A logging object used in the scan to record files that are missing,
poorly processed, etc. Side-effected by this method.
"""
if not file_lists:
file_lists = defaultdict(list)
# if the file is not being tracked, attempt to add it
if not mtime_dict.has_key(path_id):
print "Adding plate: %s" % path
qlbfile, qlplate, valid_file = add_qlp_file_record(file_source, path)
if not valid_file:
print "Invalid file: %s" % path
file_lists['invalid_plates'].append(path)
return None
elif path.endswith('HFE_Plate.qlp'):
qlbfile.read_status = -7
print "Ignoring HFE Plate: %s" % path
Session.commit()
return None
elif qlbfile.version is 'Unknown':
qlbfile.read_status = -8
print "Ignoring plate run with unknown QS version: %s" % path
Session.commit()
return None
if(qlbfile.version_tuple < (0,1,1,9)):
# we don't recognize the QLP file version, ditch
qlbfile.read_status = -2
Session.commit()
return None
qlbplate, valid_plate = add_qlp_plate_record(qlplate, qlbfile)
if not valid_plate:
# invalid plate
print "Could not read plate: %s" % path
qlbfile.read_status = -20
Session.commit()
file_lists['unreadable_plates'].append(path)
return None
for well_name, proc_qlwell in sorted(qlplate.analyzed_wells.items()):
# remove empty/blank wells generated by eng group
if (well_name is None or well_name == ''):
del qlplate.analyzed_wells[well_name]
continue
raw_qlwell = None
# TODO: abstract?
well_loc = "%s_%s_RAW.qlb" % (path[:-4], well_name)
# process QLP only
if not os.path.isfile(well_loc):
print "Could not find well file: %s" % well_loc
file_lists['missing_wells'].append(well_loc)
well_file = None
# proceed, as file may just not have been delivered
valid_file = True
else:
well_file, raw_qlwell, valid_file = add_qlb_file_record(file_source, well_loc)
if not valid_file:
print "Invalid well file: %s" % well_loc
file_lists['invalid_wells'].append(well_loc)
continue
qlbwell, valid_well = add_qlb_well_record(well_file, well_name, proc_qlwell, raw_qlwell)
if valid_well:
qlbplate.wells.append(qlbwell)
# bug 829: if there are invalid wells, do not process the plate;
# wait for the well files to complete processing, get on next run
#
#
if file_lists['invalid_wells']:
print "Skipping plate processing (invalid well): %s" % path
Session.rollback()
return None # continue plate
plate_meta = plate_from_qlp(qlbplate)
Session.add(plate_meta)
qlbplate.plate = plate_meta
validation_test = get_product_validation_plate(qlplate, plate_meta)
if not validation_test:
if not apply_setup_to_plate(qlplate, plate_meta):
apply_template_to_plate(qlplate, plate_meta)
# OK, try it now
try:
for well in qlbplate.wells:
if well.file_id != -1:
well.file.read_status = 1
qlbplate.file.read_status = 1
Session.commit()
write_images_stats_for_plate(qlbplate, qlplate, image_source, override_plate_type=plate_type)
Session.commit()
qlbplate.plate.score = Plate.compute_score(qlbplate.plate)
Session.commit()
if validation_test:
validation_test.plate_id = qlbplate.plate.id
Session.add(validation_test)
Session.commit()
file_lists['added_plates'].append(path)
return plate_meta
except Exception, e:
print e
print "Could not process new plate: %s" % path
file_lists['unwritable_plates'].append(path)
Session.rollback()
elif time_equals(mtime_dict[path_id][1], datetime.fromtimestamp(os.stat(path).st_mtime)):
return None
else:
# strategy: reprocess the plate and update.
qlbfile = Session.query(QLBFile).get(mtime_dict[path_id][0])
if not qlbfile:
print "No file for path: %s" % path
return None
elif path.endswith('HFE_Plate.qlp'):
qlbfile.mtime = datetime.fromtimestamp(os.stat(path).st_mtime)
Session.commit()
return None
qlbplates = Session.query(QLBPlate).filter_by(file_id=qlbfile.id).\
options(joinedload_all(QLBPlate.wells, QLBWell.channels)).all()
if not qlbplates:
print "No plate for read file: %s" % path
return None
qlbplate = qlbplates[0]
if not qlbplate.plate_id:
print "No plate for read file (plate deleted): %s" % path
qlbfile.mtime = datetime.fromtimestamp(os.stat(path).st_mtime)
Session.commit()
return None
print "Updating plate %s/%s: %s" % (qlbplate.plate_id, qlbplate.id, path)
qlplate = get_plate(path)
updated = update_qlp_plate_record(qlbplate, qlplate)
if not updated:
print "Could not read updated file"
Session.rollback()
qlbplate.file.read_status = -30
Session.commit()
file_lists['unreadable_plates'].append(path)
return None
# this is basically the same as on add -- abstract?
#
# TODO (GitHub Issue 30): handle case where a previously analyzed well is switched to 'Not Used'
for well_name, proc_qlwell in sorted(qlplate.analyzed_wells.items()):
raw_qlwell = None
# TODO: abstract?
well_loc = "%s_%s_RAW.qlb" % (path[:-4], well_name)
qlbwells = [well for well in qlbplate.wells if well.well_name == well_name]
if not qlbwells:
# add qlb file record
if not os.path.isfile(well_loc):
print "Could not find well file: %s" % well_loc
well_file = None
valid_file = True
file_lists['missing_wells'].append(well_loc)
else:
well_file, raw_qlwell, valid_file = add_qlb_file_record(file_source, well_loc)
if not valid_file:
print "Invalid well file: %s" % well_loc
file_lists['invalid_wells'].append(well_loc)
continue
qlbwell, valid_well = add_qlb_well_record(well_file, well_name, proc_qlwell, raw_qlwell)
if valid_well:
qlbplate.wells.append(qlbwell)
else:
file_lists['invalid_wells'].append(well_loc)
print "Could not add well %s: %s" % (well_name, well_loc)
else:
qlbwell = qlbwells[0]
if not os.path.isfile(well_loc):
print "Could not find well file to update: %s" % well_loc
file_lists['missing_wells'].append(well_loc)
update_qlb_well_record(qlbwell, well_name, proc_qlwell, None)
else:
if qlbwell.file_id == -1:
well_file, raw_qlwell, valid_file = add_qlb_file_record(file_source, well_loc)
if valid_file:
qlbwell.file = well_file
update_qlb_well_record(qlbwell, well_name, proc_qlwell, raw_qlwell)
# in lieu of updating plate meta (though it maybe should be done)
qlbplate.plate.program_version = qlbplate.host_software
try:
for well in qlbplate.wells:
if well.file_id != -1 and well.file:
well.file.read_status = 1
qlbplate.file.read_status = 1
qlbfile.mtime = datetime.fromtimestamp(os.stat(path).st_mtime)
Session.commit()
# this is where updating the dirty bits would come in handy
write_images_stats_for_plate(qlbplate, qlplate, image_source, overwrite=True, override_plate_type=plate_type)
Session.commit()
qlbplate.plate.score = Plate.compute_score(qlbplate.plate)
Session.commit()
file_lists['updated_plates'].append(path)
return qlbplate.plate
except Exception, e:
print e
print "Could not update plate %s/%s: %s" % (qlbplate.plate_id, qlbplate.id, path)
file_lists['unwritable_plates'].append(path)
Session.rollback()
