added OPAVER_WEB_DIR to replace hard-coded path to opaver_web_path

microbiomedata · Feb 26, 2025 · d9574db · d9574db
1 parent f2b0a42
commit d9574db
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Showing 7 changed files with 9 additions and 3 deletions.
diff --git a/data/workflow/templates/metaAnnotation_inputs.tmpl b/data/workflow/templates/metaAnnotation_inputs.tmpl
@@ -1,3 +1,4 @@
     "main_workflow.<WORKFLOW>_input_file": <INPUT_FILE>,
     "main_workflow.<WORKFLOW>_imgap_project_id": <PROJID>,
-    "main_workflow.<WORKFLOW>_outdir": <OUTDIR>
+    "main_workflow.<WORKFLOW>_outdir": <OUTDIR>,
+    "main_workflow.<WORKFLOW>_opaver_web_path":<OPAVER_WEB_DIR>,
diff --git a/data/workflow/templates/metaAnnotation_wdl.tmpl b/data/workflow/templates/metaAnnotation_wdl.tmpl
@@ -4,7 +4,7 @@ input {
     String  <WORKFLOW>_outdir
     Int     <WORKFLOW>_additional_threads=42
     String  <WORKFLOW>_database_location="/refdata/img/"
-    String  <WORKFLOW>_opaver_web_path="/expanse/projects/nmdc/edge_app/nmdc-edge/io/opaver_web/data"
+    String  <WORKFLOW>_opaver_web_path
 }
 call <WORKFLOW>.annotation as <ALIAS> {
     input: 

diff --git a/data/workflow/templates/metagenome_pipeline_inputs.tmpl b/data/workflow/templates/metagenome_pipeline_inputs.tmpl
@@ -12,6 +12,7 @@
    "main_workflow.virusPlasmid_outdir":<VIRUSPLASMID_OUTDIR>,
    "main_workflow.metaAnnotation_outdir":<METAANNOTATION_OUTDIR>,
    "main_workflow.metaAnnotation_imgap_project_id":<PREFIX>,
+   "main_workflow.metaAnnotation_opaver_web_path":<OPAVER_WEB_DIR>,
    "main_workflow.metaMAGs_outdir":<METAMAGS_OUTDIR>,
    "main_workflow.metaMAGs_proj":<PREFIX>,
    "main_workflow.metaMAGs_map_file":<METAMAGS_MAP_FILE>,

diff --git a/data/workflow/templates/metagenome_pipeline_wdl.tmpl b/data/workflow/templates/metagenome_pipeline_wdl.tmpl
@@ -65,7 +65,7 @@ workflow main_workflow {
         Int     metaAnnotation_additional_threads=8
         String  metaAnnotation_database_location="/refdata/img/"
         String  metaAnnotation_outdir
-        String  metaAnnotation_opaver_web_path="/expanse/projects/nmdc/edge_app/nmdc-edge/io/opaver_web/data"
+        String  metaAnnotation_opaver_web_path
         # metaMAGS
         String  metaMAGs_proj
         File    metaMAGs_contig_file = metaAnnotation_call.renamed_fasta

diff --git a/webapp/server/config.js b/webapp/server/config.js
@@ -173,6 +173,8 @@ const config = {
         UPLOADED_FILES_TEMP_DIR: process.env.UPLOADED_FILES_TEMP_DIR || path.join(IO_BASE_DIR, "upload/tmp"),
         // Maximum rows to pass to UI data table
         MAX_DATATABLE_ROWS: process.env.MAX_DATATABLE_ROWS || 300000,
+        // opaver_web_path
+        OPAVER_WEB_DIR: process.env.OPAVER_WEB_DIR || path.join(__dirname, "../../io/opaver_web/data"),
     },
     // Parameters that influence the behavior of `Winston.js`, a logging library.
     // Reference: https://github.com/winstonjs/winston-daily-rotate-file#options

diff --git a/webapp/server/crons/pipelineMonitor.js b/webapp/server/crons/pipelineMonitor.js
@@ -248,6 +248,7 @@ async function generateInputs(proj_home, conf, proj) {
             templInputs = templInputs.replace(/<VIRUSPLASMID_OUTDIR>/, '"' + proj_home + "/" + workflowSettings['outdir'] + '"');
         } else if (workflow.name === 'MetaAnnotation') {
             templInputs = templInputs.replace(/<DOANNOTATION>/, workflow.paramsOn);
+            templInputs = templInputs.replace(/<OPAVER_WEB_DIR>/, config.IO.OPAVER_WEB_DIR);
             templInputs = templInputs.replace(/<METAANNOTATION_OUTDIR>/, '"' + proj_home + "/" + workflowSettings['outdir'] + '"');
         } else if (workflow.name === 'MetaMAGs') {
             templInputs = templInputs.replace(/<DOMETAMAGS>/, workflow.paramsOn);

diff --git a/webapp/server/crons/workflowMonitor.js b/webapp/server/crons/workflowMonitor.js
@@ -343,6 +343,7 @@ async function generateInputs(proj_home, workflow, proj) {
         let input_fasta = workflow['input_fasta'];
         templInputs = templInputs.replace(/<INPUT_FILE>/, '"' + input_fasta + '"');
         templInputs = templInputs.replace(/<PROJID>/, '"' + proj.name + '"');
+        templInputs = templInputs.replace(/<OPAVER_WEB_DIR>/, config.IO.OPAVER_WEB_DIR);
         templInputs = templInputs.replace(/<OUTDIR>/, '"' + proj_home + "/" + workflowSettings['outdir'] + '"');
 
     } else if (workflow.name === 'MetaMAGs') {