Merge pull request #4602 from solgenomics/topic/solgs/fix-slurm-jobs-…

…check Topic/solgs/fix slurm jobs check
solgenomics · Jul 30, 2023 · d35a4e3 · d35a4e3
2 parents 89aad62 + 318573f
commit d35a4e3
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Showing 12 changed files with 399 additions and 408 deletions.
diff --git a/R/solGS/gs.r b/R/solGS/gs.r
@@ -88,7 +88,7 @@ markerFile  <- grep('marker_effects', outputFiles, value = TRUE)
 modelPhenoFile <- grep('model_phenodata', outputFiles, value = TRUE)
 message('model input trait pheno file ', modelPhenoFile)
 modelGenoFile <- grep('model_genodata', outputFiles, value = TRUE)
-message('model input trait geno file ', modelPhenoFile)
+message('model input trait geno file ', modelGenoFile)
 traitRawPhenoFile <- grep('trait_raw_phenodata', outputFiles, value = TRUE)
 varianceComponentsFile <- grep("variance_components", outputFiles, value = TRUE)
 analysisReportFile <- grep("_report_", outputFiles, value = TRUE)
@@ -105,7 +105,7 @@ if (is.null(genoFile)) {
 }
 
 if (file.info(genoFile)$size == 0) {
-  stop("genotype data file is empty.")
+  stop(paste0("genotype data file ", genoFile, " is empty."))
 }
 
 readfilteredTrainingGenoData <- c()
@@ -187,7 +187,8 @@ if (length(formattedPhenoFile) != 0 && file.info(formattedPhenoFile)$size != 0)
     }
 
     if (file.info(phenoFile)$size == 0) {
-        stop("phenotype data file is empty.")
+       stop(paste0("phenotype data file ", phenoFile, " is empty."))
+
     }
 
     phenoData <- data.frame(fread(phenoFile,

diff --git a/js/source/legacy/solGS/cluster.js b/js/source/legacy/solGS/cluster.js
@@ -1176,8 +1176,8 @@ jQuery(document).ready(function () {
             jQuery(jobSubmit).appendTo("body");
 
             jQuery("#cluster_submit").dialog({
-              height: 200,
-              width: 400,
+              height: "auto",
+              width: "auto",
               modal: true,
               title: "cluster job submission",
               buttons: {

diff --git a/js/source/legacy/solGS/kinship.js b/js/source/legacy/solGS/kinship.js
@@ -239,7 +239,6 @@ solGS.kinship = {
   },
 
   addDowloandLinks: function (res) {
-    console.log(`adddownloadlinks res: ${JSON.stringify(res)}`);
     var popName = res.kinship_pop_name;
     var kinFileId = res.kinship_file_id;
     var kinshipFile = res.kinship_table_file;
@@ -366,8 +365,8 @@ jQuery(document).ready(function () {
             jQuery(jobSubmit).appendTo("body");
 
             jQuery("#kinship_submit").dialog({
-              height: 200,
-              width: 400,
+              height: "auto",
+              width: "auto",
               modal: true,
               title: "Kinship job submission",
               buttons: {

diff --git a/js/source/legacy/solGS/pca.js b/js/source/legacy/solGS/pca.js
@@ -1008,8 +1008,8 @@ jQuery(document).ready(function () {
             jQuery(jobSubmit).appendTo("body");
 
             jQuery("#pca_submit").dialog({
-              height: 200,
-              width: 400,
+              height: "auto",
+              width: "auto",
               modal: true,
               title: "pca job submission",
               buttons: {

diff --git a/js/source/legacy/solGS/solGS.js b/js/source/legacy/solGS/solGS.js
@@ -364,6 +364,9 @@ solGS.submitJob = {
     args["analysis_name"] = analysisName;
     args["analysis_page"] = page;
 
+    var hostname = `${location.protocol}//${location.hostname}`;
+    args['hostname'] = hostname;
+
     args = JSON.stringify(args);
 
     var analysisProfile = {