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Commit d11c1942 authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Add excapes

parent 9806f48c
2 merge requests!77Docs,!76Develop
Pipeline #9213 passed with stages
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workflow/scripts/get_updated_rep_count.sh
+ 9
− 9
View file @ d11c1942
...@@ -18,11 +18,11 @@ dev_success=0 ...@@ -18,11 +18,11 @@ dev_success=0
dev_error=0 dev_error=0
for rid in ${dev_workflow_RID} for rid in ${dev_workflow_RID}
do do
temp_total=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l) temp_total=$(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} + ${temp_total}) dev_total=$(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=${rid}/Execution_Status=Success/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l) temp_sucess=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=\(Execution_Run\)=\(RNASeq:Execution_Run:RID\)/Workflow=${rid}/Execution_Status=Success/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
dev_success=$(expr ${dev_success} + ${temp_success}) dev_success=$(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=${rid}/Execution_Status=Error/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l) temp_error=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=\(Execution_Run\)=\(RNASeq:Execution_Run:RID\)/Workflow=${rid}/Execution_Status=Error/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
dev_error=$(expr ${dev_error} + ${temp_error}) dev_error=$(expr ${dev_error} + ${temp_error})
done done
staging_total=0 staging_total=0
...@@ -30,11 +30,11 @@ staging_success=0 ...@@ -30,11 +30,11 @@ staging_success=0
staging_error=0 staging_error=0
for rid in ${staging_workflow_RID} for rid in ${staging_workflow_RID}
do do
temp_total=$(curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l) temp_total=$(curl -s https://staging.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} + ${temp_total}) staging_total=$(expr ${staging_total} + ${temp_total})
temp_sucess=$(curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/Execution_Status=Success/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l) temp_sucess=$(curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=\(Execution_Run\)=\(RNASeq:Execution_Run:RID\)/Workflow=${rid}/Execution_Status=Success/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
staging_success=$(expr ${staging_success} + ${temp_success}) staging_success=$(expr ${staging_success} + ${temp_success})
temp_error=$(curl -s https://dstagingev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/Execution_Status=Error/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l) temp_error=$(curl -s https://dstagingev.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=\(Execution_Run\)=\(RNASeq:Execution_Run:RID\)/Workflow=${rid}/Execution_Status=Error/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
staging_error=$(expr ${staging_error} + ${temp_error}) staging_error=$(expr ${staging_error} + ${temp_error})
done done
prod_total=0 prod_total=0
...@@ -42,11 +42,11 @@ prod_success=0 ...@@ -42,11 +42,11 @@ prod_success=0
prod_error=0 prod_error=0
for rid in ${prod_workflow_RID} for rid in ${prod_workflow_RID}
do do
temp_total=$(curl -s https://www.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/!Execution_Status=In-progress/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l) temp_total=$(curl -s https://www.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} + ${temp_total}) prod_total=$(expr ${prod_total} + ${temp_total})
temp_sucess=$(curl -s https://www.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/Execution_Status=Success/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l) temp_sucess=$(curl -s https://www.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=\(Execution_Run\)=\(RNASeq:Execution_Run:RID\)/Workflow=${rid}/Execution_Status=Success/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
prod_success=$(expr ${prod_success} + ${temp_success}) prod_success=$(expr ${prod_success} + ${temp_success})
temp_error=$(curl -s https://www.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=(Execution_Run)=(RNASeq:Execution_Run:RID)/Workflow=${rid}/Execution_Status=Error/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l) temp_error=$(curl -s https://www.gudmap.org/ermrest/catalog/2/entity/Q:=RNASeq:mRNA_QC/E:=\(Execution_Run\)=\(RNASeq:Execution_Run:RID\)/Workflow=${rid}/Execution_Status=Error/\$Q | grep -o \"Replicate\".*,\"Paired_End | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Paired_End)" | sort | uniq | wc -l)
prod_error=$(expr ${prod_error} + ${temp_error}) prod_error=$(expr ${prod_error} + ${temp_error})
done done
......
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