Merge pull request #416 from microbiomedata/update-bulk-submission-template

Update bulk submission template

Author: mflynn-lanl

data/docs/bulk-submissions/NMDC-EDGE-Metagenomics-ReadsQC-bulk-submission.xlsx

@@ -65,7 +65,7 @@ const bulkSubmissionMonitor = async () => {
       let submission = {};
       let dataSource = cols[2] ? cols[2].trim() : 'Uploaded File';
       currRow++;
-      if(cols.length < 6) {
+      if(cols.length < 5) {
         validInput = false;
         errMsg += `ERROR: Row ${currRow}: Invalid input.\n`;
         continue;
@@ -79,20 +79,20 @@ const bulkSubmissionMonitor = async () => {
         submission['proj_desc'] = cols[1];
       }
       //get Sequencing Platform, default is Illumina
-      if (cols[6] && cols[6] === 'PacBio') {
+      if (cols[3] && cols[3] === 'PacBio') {
         submission['platform'] = 'PacBio';
         submission['shortRead'] = false;
       } else {
         submission['platform'] = 'Illumina';
         submission['shortRead'] = true;
       }
 
-      if (cols[3] && cols[3].trim()) {
+      if (cols[4] && cols[4].trim()) {
         // validate Interleaved or Single-end Illumina/PacBio fastq and ignore the Illumina Pair-1/paire-2
         submission['interleaved'] = true;
         let fastqs = [];
         let fastqs_display = [];
-        const fqs = cols[3].split(/,/);
+        const fqs = cols[4].split(/,/);
         for (fq of fqs) {
           fq = fq.trim();
           if (dataSource === 'HTTP(s) URL') {
@@ -106,14 +106,14 @@ const bulkSubmissionMonitor = async () => {
               fastqs_display.push(`sradata/${accession}/${fq}`);
             } else {
               validInput = false;
-              errMsg += `ERROR: Row ${currRow}: Interleaved or Single-end Illumina/PacBio FASTQ ${fq} not found.\n`;
+              errMsg += `ERROR: Row ${currRow}: ${dataSource}: Interleaved or Single-end Illumina/PacBio FASTQ: ${fq} not found.\n`;
             }
           } else {
             // it's uploaded file
             const file = await Upload.findOne({ name: { $eq: fq }, status: { $ne: 'delete' } });
             if (!file) {
               validInput = false;
-              errMsg += `ERROR: Row ${currRow}: Interleaved or Single-end Illumina/PacBio FASTQ ${fq} not found.\n`;
+              errMsg += `ERROR: Row ${currRow}: ${dataSource}: Interleaved or Single-end Illumina/PacBio FASTQ: ${fq} not found.\n`;
             } else {
               fastqs.push(`${config.IO.UPLOADED_FILES_DIR}/${file.code}`);
               fastqs_display.push(`uploads/${file.owner}/${fq}`);
@@ -135,11 +135,11 @@ const bulkSubmissionMonitor = async () => {
           let fq1s = null;
           let fq2s = null;
           // validate the Illumina Pair-1/paire-2
-          if (!(cols[4] && cols[4].trim())) {
+          if (!(cols[5] && cols[5].trim())) {
             validInput = false;
             errMsg += `ERROR: Row ${currRow}: Illumina Paired-end R1 required.\n`;
           } else {
-            fq1s = cols[4].split(/,/);
+            fq1s = cols[5].split(/,/);
             for (fq of fq1s) {
               fq = fq.trim();
               if (dataSource === 'HTTP(s) URL') {
@@ -153,14 +153,14 @@ const bulkSubmissionMonitor = async () => {
                   pairFq1_display.push(`sradata/${accession}/${fq}`);
                 } else {
                   validInput = false;
-                  errMsg += `ERROR: Row ${currRow}: Interleaved or Single-end Illumina/PacBio FASTQ ${fq} not found.\n`;
+                  errMsg += `ERROR: Row ${currRow}: ${dataSource}: Illumina Paired-end R1 FASTQ: ${fq} not found.\n`;
                 }
               } else {
                 // it's uploaded file
                 const file = await Upload.findOne({ name: { $eq: fq }, status: { $ne: 'delete' } });
                 if (!file) {
                   validInput = false;
-                  errMsg += `ERROR: Row ${currRow}: Illumina Paired-end R1 ${fq} not found.\n`;
+                  errMsg += `ERROR: Row ${currRow}: ${dataSource}: Illumina Paired-end R1 FASTQ: ${fq} not found.\n`;
                 } else {
                   pairFq1.push(`${config.IO.UPLOADED_FILES_DIR}/${file.code}`);
                   pairFq1_display.push(`uploads/${file.owner}/${fq}`);
@@ -169,11 +169,11 @@ const bulkSubmissionMonitor = async () => {
             };
           }
 
-          if (!(cols[5] && cols[5].trim())) {
+          if (!(cols[6] && cols[6].trim())) {
             validInput = false;
             errMsg += `ERROR: Row ${currRow}: Illumina Paired-end R2 required.\n`;
           } else {
-            fq2s = cols[5].split(/,/);
+            fq2s = cols[6].split(/,/);
             for (fq of fq2s) {
               fq = fq.trim();
               if (dataSource === 'HTTP(s) URL') {
@@ -187,14 +187,14 @@ const bulkSubmissionMonitor = async () => {
                   pairFq2_display.push(`sradata/${accession}/${fq}`);
                 } else {
                   validInput = false;
-                  errMsg += `ERROR: Row ${currRow}: Interleaved or Single-end Illumina/PacBio FASTQ ${fq} not found.\n`;
+                  errMsg += `ERROR: Row ${currRow}: ${dataSource}: Illumina Paired-end R2 FASTQ: ${fq} not found.\n`;
                 }
               } else {
                 // it's uploaded file
                 const file = await Upload.findOne({ name: { $eq: fq }, status: { $ne: 'delete' } });
                 if (!file) {
                   validInput = false;
-                  errMsg += `ERROR: Row ${currRow}: Illumina Paired-end R2 ${fq} not found.\n`;
+                  errMsg += `ERROR: Row ${currRow}: ${dataSource}: Illumina Paired-end R2 FASTQ: ${fq} not found.\n`;
                 } else {
                   pairFq2.push(`${config.IO.UPLOADED_FILES_DIR}/${file.code}`);
                   pairFq2_display.push(`uploads/${file.owner}/${fq}`);
@@ -224,7 +224,7 @@ const bulkSubmissionMonitor = async () => {
       // submit projects
       const workflowSettings = { ...workflowlist, ...pipelinelist };
       let projects = [];
-
+      let submission = null;
       for (submission of submissions) {
         //console.log(submission)
         let code = randomize('Aa0', 16);