From 23d3afca728a5e12d20327853751061cffcd4b22 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Thu, 31 Mar 2016 12:23:19 +0000
Subject: [PATCH] drop box for error rate of phix, error rate and density
based on illuminate
SVN: 36052
---
.../drop-boxes/read-json/plugin.properties | 6 ++
.../2/dss/drop-boxes/read-json/read-json.py | 76 +++++++++++++++++++
2 files changed, 82 insertions(+)
create mode 100644 deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/read-json/plugin.properties
create mode 100644 deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/read-json/read-json.py
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/read-json/plugin.properties b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/read-json/plugin.properties
new file mode 100644
index 00000000000..98a7c8ff001
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/read-json/plugin.properties
@@ -0,0 +1,6 @@
+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
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/read-json/read-json.py b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/read-json/read-json.py
new file mode 100644
index 00000000000..d4873308a4d
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/2/dss/drop-boxes/read-json/read-json.py
@@ -0,0 +1,76 @@
+'''
+@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!")
\ No newline at end of file
--
GitLab