Add new badges for execution run success/error

workflow/scripts/get_updated_rep_count.sh

@@ -13,27 +13,52 @@ staging_workflow_RID=$(curl -s https://staging.gudmap.org/ermrest/catalog/2/enti
 prod_workflow_RID=$(curl -s https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Workflow/Version::ciregexp::%5E${current_pipeline_versionMajor} | grep -o '\"RID\":\".*\",\"RCT' | cut -f4 -d"\"")
 
 echo "collecting unique replicates with successful execution runs"
-dev_count=0
+dev_total=0
+dev_success=0
+dev_error=0
 for rid in ${dev_workflow_RID}
 do
-    temp_count=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Execution_Status=Success/Workflow=${rid} | grep -o \"Replicate\".*,\"Workflow | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Workflow)" | sort | uniq | wc -l)
-    dev_count=$(expr ${dev_count} + ${temp_count})
+    temp_total=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
+    dev_total=$(expr ${dev_total} + ${temp_total})
+    temp_sucess=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
+    dev_success=$(expr ${dev_success} + ${temp_success})
+    temp_error=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
+    dev_error=$(expr ${dev_error} + ${temp_error})
 done
-staging_count=0
+staging_total=0
+staging_success=0
+staging_error=0
 for rid in ${staging_workflow_RID}
 do
-    temp_count=$(curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Execution_Status=Success/Workflow=${rid} | grep -o \"Replicate\".*,\"Workflow | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Workflow)" | sort | uniq | wc -l)
-    staging_count=$(expr ${staging_count} + ${temp_count})
+    temp_total=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
+    staging_total=$(expr ${staging_total} + ${temp_total})
+    temp_sucess=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
+    staging_success=$(expr ${staging_success} + ${temp_success})
+    temp_error=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
+    staging_error=$(expr ${staging_error} + ${temp_error})
 done
-prod_count=0
+prod_total=0
+prod_success=0
+prod_error=0
 for rid in ${prod_workflow_RID}
 do
-    temp_count=$(curl -s https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Execution_Status=Success/Workflow=${rid} | grep -o \"Replicate\".*,\"Workflow | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Workflow)" | sort | uniq | wc -l)
-    prod_count=$(expr ${prod_count} + ${temp_count})
+    temp_total=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
+    prod_total=$(expr ${prod_total} + ${temp_total})
+    temp_sucess=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
+    prod_success=$(expr ${prod_success} + ${temp_success})
+    temp_error=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
+    prod_error=$(expr ${prod_error} + ${temp_error})
 done
 
 echo "collecting badges"
 mkdir -p ./badges/counts
-curl --request GET https://img.shields.io/badge/Development%20Replicate%20Count-${dev_count}-lightgrey?style=flat > ./badges/counts/dev_counts.svg
-curl --request GET https://img.shields.io/badge/Staging%20Replicate%20Count-${staging_count}-lightgrey?style=flat > ./badges/counts/staging_counts.svg
-curl --request GET https://img.shields.io/badge/Production%20Replicate%20Count-${prod_count}-lightgrey?style=flat > ./badges/counts/prod_counts.svg
+curl --request GET https://img.shields.io/badge/Development%20Replicate%20Count-${dev_success}/${dev_total}-green?style=flat > ./badges/counts/dev_success.svg
+curl --request GET https://img.shields.io/badge/Development%20Replicate%20Count-${dev_error}/${dev_total}-green?style=flat > ./badges/counts/dev_error.svg
+curl --request GET https://img.shields.io/badge/Development%20Replicate%20Count-${staging_success}/${staging_total}-green?style=flat > ./badges/counts/staging_success.svg
+curl --request GET https://img.shields.io/badge/Development%20Replicate%20Count-${staging_error}/${staging_total}-green?style=flat > ./badges/counts/staging_error.svg
+curl --request GET https://img.shields.io/badge/Development%20Replicate%20Count-${prod_success}/${prod_total}-green?style=flat > ./badges/counts/prod_success.svg
+curl --request GET https://img.shields.io/badge/Development%20Replicate%20Count-${prod_error}/${prod_total}-green?style=flat > ./badges/counts/prod_error.svg
+
+curl --request GET https://img.shields.io/badge/Development%20Replicate%20Count-${dev_success}-lightgrey?style=flat > ./badges/counts/dev_counts.svg
+curl --request GET https://img.shields.io/badge/Staging%20Replicate%20Count-${staging_success}-lightgrey?style=flat > ./badges/counts/staging_counts.svg
+curl --request GET https://img.shields.io/badge/Production%20Replicate%20Count-${prod_success}-lightgrey?style=flat > ./badges/counts/prod_counts.svg