コード例 #1
0
ファイル: metrics.py プロジェクト: v-makarenko/vtoolsmq
    def command(self):
        app = self.load_wsgi_app()
        storage = QLStorageSource(app.config)

        if len(self.args) < 2:
            print self.__class__.usage
            return

        for i in range(0,len(self.args)-1):
            plate_id = int(self.args[i])
            plate = dbplate_tree(plate_id)
            try:
                plate_path = storage.plate_path(plate)
            except Exception, e:
                print "Could not read plate: %s" % plate_id
                continue

            qlplate = get_plate(plate_path)
            if not qlplate:
                raise ValueError, "Could not read plate: %s" % plate_path
            else:
                print "Processing %s" % plate_path

            try:
                from qtools.lib.metrics import DEFAULT_CNV_CALC, compute_metric_foreach_qlwell
                plate_metrics = plate.metrics[0]
                compute_metric_foreach_qlwell(qlplate, plate_metrics, DEFAULT_CNV_CALC)
            except Exception, e:
                import sys, traceback
                traceback.print_exc(file=sys.stdout)
                Session.rollback()
                return
コード例 #2
0
ファイル: metrics.py プロジェクト: v-makarenko/vtoolsmq
    def command(self):
        app = self.load_wsgi_app()

        # enforce config.ini
        if len(self.args) < 2:
            raise ValueError, self.__class__.usage
        
        plate_id = int(self.args[0])

        plate = dbplate_tree(plate_id)
        if not plate:
            raise ValueError, "Invalid plate id: %s" % plate_id
        
        storage = QLStorageSource(app.config)

        # for now, no reprocessing.
        plate_path = storage.plate_path(plate)
                                        
        qlplate = get_plate(plate_path)
        if not qlplate:
            raise ValueError, "Could not read plate: %s" % plate_path
        
        try:
            plate_metrics = plate.metrics[0]
            self.process_plate( qlplate, plate_metrics)
        except Exception, e:
            import sys, traceback
            traceback.print_exc(file=sys.stdout)
            Session.rollback()
            return
コード例 #3
0
ファイル: template.py プロジェクト: v-makarenko/vtoolsmq
 def from_plate(self, id=None):
     if not id:
         abort(404)
     
     plate = Session.query(Plate).get(id)
     if not plate:
         abort(404)
     
     # ignore possibility of reprocess config for now
     storage = QLStorageSource(config)
     path = storage.plate_path(plate)
     factory = ExperimentMetadataObjectFactory()
     qlp = factory.parse_plate(path)
     c.wells = qlp.analyzed_wells
     c.original_source = plate.name
     c.plate_template_id = None
     c.plate_setup_id = None
     c.id = id
     return self.__display(rowcol_order=qlp.acquisition_order)
コード例 #4
0
ファイル: metrics.py プロジェクト: v-makarenko/vtoolsmq
    def process_plates(self, app, analysis_group, reprocess_config):
        storage = QLStorageSource(app.config)
        plates = analysis_group.plates
        for plate in plates:
            pms = [pm for pm in plate.metrics if pm.reprocess_config_id == reprocess_config.id]
            if not pms:
                print "Cannot find analysis group for plate %s" % plate.id
            else:
                pm = pms[0]
            dbplate = dbplate_tree(plate.id)

            if reprocess_config:
                data_root = app.config['qlb.reprocess_root']
                storage = QLPReprocessedFileSource(data_root, reprocess_config)
            else:
                storage = QLStorageSource(app.config)
            
            try:
                if reprocess_config:
                    plate_path = storage.full_path(analysis_group, dbplate)
                else:
                    plate_path = storage.plate_path(dbplate)
            except Exception, e:
                print "Could not read plate: %s" % plate.id
                continue
            
            qlplate = get_plate(plate_path)
            if not qlplate:
                raise ValueError, "Could not read plate: %s" % plate_path
            else:
                print "Processing %s" % plate_path
            
            try:
                self.backfill_plate(qlplate, pm)
                Session.commit()
            except Exception, e:
                print "Could not process plate %s" % dbplate.id
                import sys, traceback
                traceback.print_exc(file=sys.stdout)
                Session.rollback()
                continue
コード例 #5
0
ファイル: metrics.py プロジェクト: v-makarenko/vtoolsmq
    def command(self):
        app = self.load_wsgi_app()
        storage = QLStorageSource(app.config)

         # enforce config.ini
        if len(self.args) > 1:
            plate_id = int(self.args[0])
        else:
            plate_id = 1 ## default start....

        plate_metrics = Session.query(PlateMetric).filter(PlateMetric.plate_id >= plate_id)\
                               .options(joinedload(PlateMetric.plate, innerjoin=True))\
                               .options(joinedload(PlateMetric.reprocess_config))

        # TODO come up with version that takes care of reprocessed plates as well
        # (by iterating through analysis groups, most likely)
        for pm in plate_metrics:
            if pm.from_reprocessed:
                continue

            plate = dbplate_tree(pm.plate_id)
            try:
                plate_path = storage.plate_path(plate)
            except Exception:
                print "Could not read plate: %s" % pm.plate_id
                continue

            try:
                qlplate = get_plate(plate_path)
            except Exception:
                print  "Could not read plate: %s" % plate_path
                continue

            if not qlplate:
                print "Could not read plate: %s" % plate_path
                continue
            else:
                print "Processing %s: %s..." % (pm.plate_id, plate_path)

            self.process_plate(qlplate, pm)
コード例 #6
0
ファイル: metrics.py プロジェクト: v-makarenko/vtoolsmq
    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()