scout-browser 4.82.2__py3-none-any.whl → 4.83__py3-none-any.whl

scout/load/case.py

@@ -1,36 +0,0 @@
-# -*- coding: utf-8 -*-
-import logging
-
-from scout.exceptions import IntegrityError
-
-logger = logging.getLogger(__name__)
-
-
-def load_case(adapter, case_obj, update=False):
-    """Load a case into the database
-
-    If the case already exists the function will exit.
-    If the user want to load a case that is already in the database
-    'update' has to be 'True'
-
-    Args:
-        adapter (MongoAdapter): connection to the database
-        case_obj (dict): case object to persist to the database
-        update(bool): If existing case should be updated
-
-    Returns:
-        case_obj(dict): A dictionary with the builded case
-    """
-    logger.info("Loading case {} into database".format(case_obj["display_name"]))
-
-    # Check if case exists in database
-    existing_case = adapter.case(case_obj["_id"])
-
-    if existing_case:
-        if update:
-            adapter.update_case(case_obj)
-        else:
-            raise IntegrityError("Case {0} already exists in database".format(case_obj["_id"]))
-    else:
-        adapter.add_case(case_obj)
-    return case_obj

scout/utils/cloud_resources.py

@@ -1,61 +0,0 @@
-# coding=UTF-8
-import logging
-
-LOG = logging.getLogger(__name__)
-
-REQUIRED_FIELDS = ["name", "type", "url"]
-TRACK_KEYS = ["name", "type", "format", "url", "indexURL"]
-
-
-class AlignTrackHandler:
-    """Class collecting external IGV tracks stored in the cloud"""
-
-    def init_app(self, app):
-        self.public_tracks = self.set_public_tracks(app.config["CLOUD_IGV_TRACKS"])
-
-    def track_template(self, track_info):
-        """Provides the template for a VCF track object"""
-        track = {}
-
-        for key in TRACK_KEYS:
-            if key in track_info:
-                track[key] = track_info[key]
-
-        # Save track only of it contains the minimal required keys
-        if all(track.get(key) for key in REQUIRED_FIELDS):
-            return track
-
-    def set_public_tracks(self, bucket_list):
-        """Return a list of public IGV tracks stored on the cloud
-
-        Args:
-            bucket_list(list): a list of cloud bucket dictionaries containing IGV tracks, can be public or private
-
-        Returns:
-            public_tracks(dict): a list of public access tracks stored on the cloud, where key is genome build
-        """
-        public_tracks = {}
-        # Loop over the bucket list and collect all public tracks
-        for bucket_obj in bucket_list:
-            if bucket_obj.get("access") == "private" or None:
-                continue
-            for track in bucket_obj.get("tracks", []):
-                build = track.get("build")
-                if build not in ["37", "38"]:
-                    LOG.warning(
-                        f"One or more IGV cloud public tracks could not be used, Please provide a genome build ('37', '38') for it."
-                    )
-                    continue
-                track_obj = self.track_template(track)
-                if track_obj is None:
-                    LOG.warning(
-                        f"One or more IGV cloud public tracks could not be used, Please provide all required keys:{REQUIRED_FIELDS}"
-                    )
-                    continue
-                if build in public_tracks:
-                    public_tracks[build].append(track_obj)
-                else:
-                    public_tracks[build] = [track_obj]
-
-        if public_tracks != {}:
-            return public_tracks