diff --git a/workflow/scripts/get_updated_rep_count.sh b/workflow/scripts/get_updated_rep_count.sh index be054ea1a8531cb2166436f21aab2e42a09065f4..daeb0575d08f2126b40f2db089ae82af4f01ed0c 100644 --- a/workflow/scripts/get_updated_rep_count.sh +++ b/workflow/scripts/get_updated_rep_count.sh @@ -3,19 +3,34 @@ echo "collecting stats for badges" latest_release_tag=$(git tag --sort=-committerdate -l *.*.* | head -1) current_pipeline_version=$(git show ${latest_release_tag}:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')") +current_pipeline_versionMajor=$(echo ${current_pipeline_version} | cut -f1 -d".") +current_pipeline_versionMajor=$(echo ${current_pipeline_versionMajor}".") +echo "Major pipeline version for search: "${current_pipeline_versionMajor} echo "collecting workflow RIDs from servers" -dev_workflow_RID=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Workflow/Version=${current_pipeline_version} | grep -o '\"RID\":\".*\",\"RCT') -dev_workflow_RID=${dev_workflow_RID:7:-6} -staging_workflow_RID=$(curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Workflow/Version=${current_pipeline_version} | grep -o '\"RID\":\".*\",\"RCT') -staging_workflow_RID=${staging_workflow_RID:7:-6} -prod_workflow_RID=$(curl -s https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Workflow/Version=${current_pipeline_version} | grep -o '\"RID\":\".*\",\"RCT') -prod_workflow_RID=${prod_workflow_RID:7:-6} +dev_workflow_RID=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Workflow/Version::ciregexp::%5E${current_pipeline_versionMajor} | grep -o '\"RID\":\".*\",\"RCT' | cut -f4 -d"\"") +staging_workflow_RID=$(curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Workflow/Version::ciregexp::%5E${current_pipeline_versionMajor} | grep -o '\"RID\":\".*\",\"RCT' | cut -f4 -d"\"") +prod_workflow_RID=$(curl -s https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Workflow/Version::ciregexp::%5E${current_pipeline_versionMajor} | grep -o '\"RID\":\".*\",\"RCT' | cut -f4 -d"\"") echo "collecting unique replicates with successful execution runs" -dev_count=$(curl -s https://dev.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Execution_Status=Success/Workflow=${dev_workflow_RID} | grep -o \"Replicate\".*,\"Workflow | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Workflow)" | sort | uniq | wc -l) -staging_count=$(curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Execution_Status=Success/Workflow=${staging_workflow_RID} | grep -o \"Replicate\".*,\"Workflow | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Workflow)" | sort | uniq | wc -l) -prod_count=$(curl -s https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Execution_Status=Success/Workflow=${prod_workflow_RID} | grep -o \"Replicate\".*,\"Workflow | grep -oP "(?<=\"Replicate\":\").*(?=\",\"Workflow)" | sort | uniq | wc -l) +dev_count=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}) +done +staging_count=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}) +done +prod_count=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}) +done echo "collecting badges" mkdir -p ./badges/counts