From a99f04c934bc3c15ad4143564b86f9c5ef89ec36 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Tue, 19 Apr 2016 11:03:06 +0000
Subject: [PATCH] added some error handling when the values are not available
in the json file
SVN: 36226
---
.../2/dss/drop-boxes/read-json/read-json.py | 28 ++++++++++++++++---
1 file changed, 24 insertions(+), 4 deletions(-)
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
index d4873308a4d..dac56d3206c 100644
--- 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
@@ -48,16 +48,36 @@ def get_flowcell_id(json_string):
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())
+
+ flowcell = found_flow_cell[0]
+
+ get_flowcell_with_contained_samples = search_service.getSample(flowcell.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']
+
+ try:
+ aligned_mean = json_string['cluster_lane_dict'][str(lane_number)]['aligned'][0]['mean']
+ except KeyError:
+ print ("Problem occurred with aligned value for PhiX")
+ aligned_mean = -1
+
+ try:
+ cluster_density_mean = json_string['cluster_lane_dict'][str(lane_number)]['clusterDensity'][0]['mean']
+ except KeyError:
+ print ("Problem occurred with cluster density")
+ cluster_density_mean = -1
+
+ try:
+ error_rate_mean = json_string['error_metrics'][str(lane_number)]['mean']
+ except KeyError:
+ print ("Problem occurred with error rate")
+ error_rate_mean = -1
+
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))
--
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