drop box for error rate of phix, error rate and density based on illuminate

SVN: 36052

deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/read-json/plugin.properties

+incoming-dir = ${incoming-root-dir}/read-json
+incoming-data-completeness-condition = marker-file
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+script-path = read-json.py
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+jython-version=2.7

deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/read-json/read-json.py

+'''
+@copyright:
+2016 ETH Zuerich, SIS
+    
+@license: 
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+    
+http://www.apache.org/licenses/LICENSE-2.0
+ 
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+@author:
+Manuel Kohler
+'''
+
+import re
+import glob
+import os
+from itertools import islice
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+
+# The following module is located in the path defined in the datastore_server.conf
+# Look for: -Dpython.path}
+from gfb_utils import *
+
+import json
+
+
+def get_json_from_file(file):
+    with open(file, 'r') as f:
+        read_json = f.read()
+    return json.loads(read_json)[0]
+
+def get_lane_count(json_string):
+    return int(json_string['lanecount'])
+
+
+def get_flowcell_id(json_string):
+    return json_string['name']
+
+
+def register_in_openbis(transaction, json_string):
+    lane_count = get_lane_count(json_string)
+    flowcell_id = get_flowcell_id(json_string)
+    found_flow_cell = search_unique_sample(transaction, flowcell_id)
+    search_service = transaction.getSearchService()
+    get_flowcell_with_contained_samples = search_service.getSample(found_flow_cell[0].getSampleIdentifier())
+    flowlanes = get_flowcell_with_contained_samples.getContainedSamples()
+    for lane in flowlanes:
+        mutable_lane = transaction.getSampleForUpdate(lane.getSampleIdentifier())
+        lane_number = lane.getCode().split(":")[-1]
+        aligned_mean = json_string['cluster_lane_dict'][str(lane_number)]['aligned'][0]['mean']
+        cluster_density_mean = json_string['cluster_lane_dict'][str(lane_number)]['clusterDensity'][0]['mean']
+        error_rate_mean = json_string['error_metrics'][str(lane_number)]['mean']
+        mutable_lane.setPropertyValue("PERC_PHIX_ALIGNED", str(aligned_mean))
+        mutable_lane.setPropertyValue("CLUSTER_DENSITY", str(cluster_density_mean))
+        mutable_lane.setPropertyValue("ERROR_RATE", str(error_rate_mean))
+
+
+def process(transaction):
+    incoming = transaction.getIncoming()
+    incoming_path = incoming.getAbsolutePath()
+    
+    json_file = glob.glob(os.path.join(incoming_path, "*.json"))
+    
+    if json_file:
+        json_string = get_json_from_file(json_file[0])
+        register_in_openbis(transaction, json_string)
+    else:
+        print("No json file found!")
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