diff --git a/workflow/scripts/get_updated_rep_count.sh b/workflow/scripts/get_updated_rep_count.sh index dc81d513de9ea6494657ad4a5e4802465244d4a6..4d7a76bbdd762dfffaedf582a87a43a00d9d17a2 100644 --- a/workflow/scripts/get_updated_rep_count.sh +++ b/workflow/scripts/get_updated_rep_count.sh @@ -18,11 +18,11 @@ dev_success=0 dev_error=0 for rid in ${dev_workflow_RID} do - temp_total=$(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} + ${temp_total}) - temp_sucess=$(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} + ${temp_success}) - temp_error=$(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}) done staging_total=0 @@ -30,11 +30,11 @@ staging_success=0 staging_error=0 for rid in ${staging_workflow_RID} do - temp_total=$(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} + ${temp_total}) - temp_sucess=$(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} + ${temp_success}) - temp_error=$(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}) done prod_total=0 @@ -42,11 +42,11 @@ prod_success=0 prod_error=0 for rid in ${prod_workflow_RID} do - temp_total=$(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} + ${temp_total}) - temp_sucess=$(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} + ${temp_success}) - temp_error=$(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}) done