def update_reprocess_analysis_group_data(analysis_group, reprocess_config, config, logger):
"""
Given an analysis_gropu and repocessor, relaod each into qtools
"""
update_status = 0
plates = analysis_group.plates
# remove old metrics if present
for plate in plates:
pm = [pm for pm in plate.metrics if pm.reprocess_config_id == reprocess_config.id]
# should only be of length 1, but just to be safe
for p in pm:
Session.delete(p)
# TODO: how to make this whole operation transactional
Session.commit()
plate_ids = [plate.id for plate in plates]
data_root = config['qlb.reprocess_root']
file_source = QLPReprocessedFileSource(data_root, reprocess_config)
for id in plate_ids:
dbplate = dbplate_tree(id)
# TODO: right abstraction?
plate_path = file_source.full_path(analysis_group, dbplate)
print "Reading/updating metrics for %s" % plate_path
qlplate = get_plate(plate_path)
if not qlplate:
print "Could not read plate: %s" % plate_path
continue
plate_metrics = get_beta_plate_metrics(dbplate, qlplate, reprocess_config)
Session.add(plate_metrics)
del qlplate
Session.commit()
return update_status
def command(self):
from qtools.lib.mplot import plot_cluster_2d, cleanup as plt_cleanup
app = self.load_wsgi_app()
image_root = app.config['qlb.image_store']
image_source = QLBImageSource(image_root)
# enforce config.ini
if len(self.args) < 2:
raise ValueError, self.__class_.usage
analysis_group_id = int(self.args[0])
if len(self.args) == 3:
reprocess_config = Session.query(ReprocessConfig).filter_by(code=self.args[1]).one()
reprocess_config_id = reprocess_config.id
else:
reprocess_config = None
reprocess_config_id = None
if reprocess_config:
data_root = app.config['qlb.reprocess_root']
storage = QLPReprocessedFileSource(data_root, reprocess_config)
else:
storage = QLStorageSource(app.config)
analysis_group = Session.query(AnalysisGroup).get(analysis_group_id)
if not analysis_group:
raise ValueError, "No analysis group for id %s" % analysis_group_id
plates = analysis_group.plates
for plate in plates:
# TODO: UGH THIS CODE INVARIANT SUCKS (should merge QLReprocessedFile/QLStorageSources)
if reprocess_config:
plate_path = storage.full_path(analysis_group, plate)
else:
plate_path = storage.plate_path(plate)
print "Reading %s" % plate_path
qlplate = get_plate(plate_path)
if not qlplate:
print "Could not read plate: %s" % plate.name
continue
print "Generating thumbnails for %s" % plate.name
for name, qlwell in sorted(qlplate.analyzed_wells.items()):
# TODO abstract into utility image generation function (thumbnail.py?)
threshold_fallback = qlwell.clustering_method == QLWell.CLUSTERING_TYPE_THRESHOLD
fig = plot_cluster_2d(qlwell.peaks,
width=60,
height=60,
thresholds=[qlwell.channels[0].statistics.threshold,
qlwell.channels[1].statistics.threshold],
boundaries=[0,0,12000,24000],
show_axes=False,
antialiased=True,
unclassified_alpha=0.5,
use_manual_clusters=not well_channel_automatic_classification(qlwell),
highlight_thresholds=threshold_fallback)
image_path = image_source.get_path('%s/%s_2d.png' % (plate.qlbplate.id, name))
print image_path
fig.savefig(image_path, format='png', dpi=72)
plt_cleanup(fig)
def command(self):
app = self.load_wsgi_app()
# enforce config.ini
if len(self.args) < 2:
raise ValueError, self.__class__.usage
analysis_group_id = int(self.args[0])
if len(self.args) == 3:
reprocess_config = Session.query(ReprocessConfig).filter_by(code=self.args[1]).one()
reprocess_config_id = reprocess_config.id
else:
reprocess_config = None
reprocess_config_id = None
analysis_group = Session.query(AnalysisGroup).get(analysis_group_id)
if not analysis_group:
raise ValueError, "No analysis group for id %s" % analysis_group_id
plates = analysis_group.plates
# todo: add in reprocess config id
for plate in plates:
pm = [pm for pm in plate.metrics if pm.reprocess_config_id == reprocess_config_id]
# should only be of length 1, but just to be safe
for p in pm:
Session.delete(p)
# TODO: how to make this whole operation transactional
Session.commit()
# this is a little tricky in the ORM world. only get the
# ids of the analysis_group plates, so that you can load the plate
# and all the necessary children
plate_ids = [plate.id for plate in plates]
if reprocess_config_id is None:
storage = QLStorageSource(app.config)
for id in plate_ids:
dbplate = dbplate_tree(id)
plate_path = storage.plate_path(dbplate)
print "Reading/updating metrics for %s" % plate_path
qlplate = get_plate(plate_path)
if not qlplate:
print "Could not read plate: %s" % plate_path
continue
plate_metrics = get_beta_plate_metrics(dbplate, qlplate)
Session.add(plate_metrics)
del qlplate
else:
data_root = app.config['qlb.reprocess_root']
file_source = QLPReprocessedFileSource(data_root, reprocess_config)
for id in plate_ids:
dbplate = dbplate_tree(id)
# TODO: right abstraction?
plate_path = file_source.full_path(analysis_group, dbplate)
print "Reading/updating metrics for %s" % plate_path
qlplate = get_plate(plate_path)
if not qlplate:
print "Could not read plate: %s" % plate_path
continue
plate_metrics = get_beta_plate_metrics(dbplate, qlplate, reprocess_config)
Session.add(plate_metrics)
del qlplate
Session.commit()
