Removed duplicate root specimens

Author: anthony-watkins

bsi/config.js

@@ -13,6 +13,7 @@ config.uri.vialReport = process.env.BSI_BASE_URL + 'VARI/reports/list?' +
     'display_fields=%2Bvial.mat_type&' +
     'display_fields=%2Bvial.study_id&' +
     'display_fields=%2Bvial.volume&' +
+    'display_fields=%2Bvial.volume_unit&' +
     'display_fields=%2Bvial.field_345&' +
     'display_fields=%2Bvial.field_342&' +
     'display_fields=%2Bvial.field_343&' +
@@ -104,7 +105,7 @@ config.receipts.fieldNameMap = {'shipment.date_modified': 'lastModified'};
 config.vials = {};
 config.vials.Metadata = [
     {'table': 'vial', 'fields': ['vial.bsi_id', 'vial.current_label', 'vial.parent_id', 'vial.date_entered', 
-    'vial.date_modified', 'vial.mat_type', 'vial.study_id', 'vial.volume', 'vial.field_345', 'vial.field_342', 'vial.field_343', 
+    'vial.date_modified', 'vial.mat_type', 'vial.study_id', 'vial.volume', 'vial.volume_unit', 'vial.field_345', 'vial.field_342', 'vial.field_343', 
     'vial.field_344', 'vial.field_348', 'vial.field_339', 'vial.field_397', 'vial.field_398', 'vial.field_399', 
     'vial.field_356', 'vial.field_366', 'vial.field_336']},
     {'table': 'sample', 'fields': ['sample.date_last_modified', 'sample.tumor_type']},

bsi/parse.js

@@ -187,22 +187,22 @@ const bsiParseModule = (() => {
 
         buildRna: (vial) => {
             return {
-                specimenIDs: vial.rootSpecimens.map(root => ({specimenID: root})),
+                specimenIDs: vial.rootSpecimens.filter((value, index, self) => self.indexOf(value) === index).map(root => ({specimenID: root})),
                 analyteID: vial.bsiId,
                 dateOfExtraction: vial.dateEntered,
                 volume: vial.initialVolume ? parseFloat(vial.initialVolume) : null,
                 rinValue: vial.rin ? parseFloat(vial.rin) : null,
                 nanoDrop: {
                     concentration: vial.concentrationByNanodropNgL ? parseFloat(vial.concentrationByNanodropNgL) : null,
                     a260OverA280: vial['260280'] ? parseFloat(vial['260280']) : null,
-                    a260OverA230: vial['260280'] ? parseFloat(vial['260230']) : null
+                    a260OverA230: vial['260230'] ? parseFloat(vial['260230']) : null
                 }
             }
         },
 
         buildDna: (vial) => {
             return {
-                specimenIDs: vial.rootSpecimens.map(root => ({specimenID: root})),
+                specimenIDs: vial.rootSpecimens.filter((value, index, self) => self.indexOf(value) === index).map(root => ({specimenID: root})),
                 analyteID: vial.bsiId,
                 dateOfExtraction: vial.dateEntered,
                 volume: vial.initialVolume ? parseFloat(vial.initialVolume) : null,
@@ -265,6 +265,7 @@ const bsiParseModule = (() => {
                         }
                     }
                 });
+                console.log(protein);
 
                 return protein;
             }
@@ -291,21 +292,21 @@ const bsiParseModule = (() => {
 
         buildProtein: (vial) => {
             return {
-                specimenIDs: vial.rootSpecimens.map(root => ({specimenID: root})),
+                specimenIDs: vial.rootSpecimens.filter((value, index, self) => self.indexOf(value) === index).map(root => ({specimenID: root})),
                 aliquotID: "",
-                analyteID: vial.bsiId,
+                analyteID: vial.currentLabel,
                 processingDate: new Date(vial.dateEntered.replace(' ', 'T')).toISOString(),
                 materialType: vial.materialType,
                 volume: vial.volume ? parseFloat(vial.volume) : null,
-                volumeUnit: "mg"
+                volumeUnit: vial.volumeUnit
             }
         },
 
         buildAmlProtein: (vial) => {
             return {
-                specimenIDs: vial.rootSpecimens.map(root => ({specimenID: root})),
+                specimenIDs: vial.rootSpecimens.filter((value, index, self) => self.indexOf(value) === index).map(root => ({specimenID: root})),
                 aliquotID: "",
-                analyteID: vial.bsiId,
+                analyteID: vial.currentLabel,
                 processingDate: "",
                 materialType: vial.materialType,
                 volume: vial.cellCount ? parseFloat(vial.cellCount) : null,
@@ -493,12 +494,14 @@ const bsiParseModule = (() => {
 
         proteins: {
             parseReport: (results) => {
-                Promise.all([cases.vials.parse(results[0]), cases.pooledTasks.parse(results[1])])
-                .then(async (reports) => {
-                    var vials = reports[0];
-                    vials = await cases.vials.buildLineage(vials, reports[1]);
-                    var protien = proteins.build(vials);
-                    resolve(protien);
+                return new Promise((resolve, reject) => {
+                    Promise.all([cases.vials.parse(results[0]), cases.pooledTasks.parse(results[1])])
+                    .then(async (reports) => {
+                        var vials = reports[0];
+                        vials = await cases.vials.buildLineage(vials, reports[1]);
+                        var protien = proteins.build(vials);
+                        resolve(protien);
+                    });
                 });
             }
         }

proteins.js

@@ -16,14 +16,14 @@ var proteinsModule = (() => {
         });
     }
 
-    function createCdrRequest(protiens) {
+    function createCdrRequest(proteins) {
         return new Promise((resolve, reject) => {
             getCdrSecrets().then(data => {
                 var secrets = JSON.parse(data.SecretString);
                 request({
                     uri: process.env.CDR_BASE_URL + 'proteinEvent/',
                     method: 'POST',
-                    body: protiens,
+                    body: proteins,
                     json: true,
                     auth: {
                         'user': secrets.username,
@@ -45,14 +45,14 @@ var proteinsModule = (() => {
                 var bsiCases = await bsi.cases.getUpdated(lastUpdated.lastModified);
 
                 for (let index = 0; index < bsiCases.length; index++) {
-                    var protein = await bsi.protiens.get(bsiCases[index]);
+                    var protein = await bsi.proteins.get(bsiCases[index]);
                     if (protein) {
-                        await dynamo.protiens.update(protein);
+                        await dynamo.proteins.update(protein);
                     }
                 }
 
                 await dynamo.updateLatest(lastUpdated);
-                await bsi.logoff();
+                // await bsi.logoff();
                 resolve();
             });
         },