refactor: wrap methods for bulk data model

- wrap methods that we can change to another repository easier
Chinlinlee · Jan 16, 2024 · 92b67c0 · 92b67c0
1 parent a0b4299
commit 92b67c0
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Showing 4 changed files with 177 additions and 104 deletions.
diff --git a/api/dicom-web/controller/WADO-RS/bulkdata/service/bulkdata.js b/api/dicom-web/controller/WADO-RS/bulkdata/service/bulkdata.js
@@ -1,6 +1,6 @@
 const fs = require("fs");
 const path = require("path");
-const dicomBulkDataModel = require("@dbModels/dicomBulkData.model");
+const { DicomBulkDataModel } = require("@dbModels/dicomBulkData.model");
 const { MultipartWriter } = require("../../../../../../utils/multipartWriter");
 const { streamToBuffer } = require("@jorgeferrero/stream-to-buffer");
 const { raccoonConfig } = require("../../../../../../config-class");
@@ -15,7 +15,7 @@ class BulkDataService {
     constructor(req, res, bulkDataFactory) {
         this.request = req;
         this.response = res;
-        this.bulkDataFactory = new bulkDataFactory({...this.request.params});
+        this.bulkDataFactory = new bulkDataFactory({ ...this.request.params });
         this.multipartWriter = new MultipartWriter([], req, res);
         this.multipartWriter.setHeaderMultipartRelatedContentType("application/octet-stream");
     }
@@ -28,7 +28,7 @@ class BulkDataService {
     async writeBulkData(bulkData) {
         let absFilename;
         // is imagePathObj
-        if(bulkData.instancePath) {
+        if (bulkData.instancePath) {
             absFilename = bulkData.instancePath;
         } else {
             absFilename = path.join(raccoonConfig.dicomWebConfig.storeRootPath, bulkData.filename);
@@ -39,7 +39,7 @@ class BulkDataService {
         this.multipartWriter.writeBoundary();
         this.multipartWriter.writeContentType("application/octet-stream");
         this.multipartWriter.writeContentLength(fileBuffer.length);
-        
+
         let urlPath = `/dicom-web/studies/${bulkData.studyUID}/series/${bulkData.seriesUID}/instances/${bulkData.instanceUID}/bulkdata/${bulkData.binaryValuePath}`;
         if (bulkData.instancePath) {
             urlPath = `/dicom-web/studies/${bulkData.studyUID}/series/${bulkData.seriesUID}/instances/${bulkData.instanceUID}`;
@@ -51,7 +51,7 @@ class BulkDataService {
     async getBulkData() {
         return await this.bulkDataFactory.getBulkData();
     }
-    
+
 }
 
 class BulkDataFactory {
@@ -79,15 +79,7 @@ class StudyBulkDataFactory extends BulkDataFactory {
             studyUID
         } = this.uids;
 
-        let studyBulkDataArray = await dicomBulkDataModel.find({
-            $and: [
-                {
-                    studyUID
-                }
-            ]
-        }).exec();
-
-        return studyBulkDataArray;
+        return await DicomBulkDataModel.findStudyBulkData({ studyUID });
     }
 }
 
@@ -102,18 +94,11 @@ class SeriesBulkDataFactory extends BulkDataFactory {
             seriesUID
         } = this.uids;
 
-        let seriesBulkDataArray = await dicomBulkDataModel.find({
-            $and: [
-                {
-                    studyUID
-                },
-                {
-                    seriesUID
-                }
-            ]
-        }).exec();
-
-        return seriesBulkDataArray;
+        return await DicomBulkDataModel.findSeriesBulkData({
+            studyUID,
+            seriesUID
+        });
+
     }
 }
 
@@ -130,21 +115,11 @@ class InstanceBulkDataFactory extends BulkDataFactory {
             instanceUID
         } = this.uids;
 
-        let instanceBulkDataArray = await dicomBulkDataModel.find({
-            $and: [
-                {
-                    studyUID
-                },
-                {
-                    seriesUID
-                },
-                {
-                    instanceUID
-                }
-            ]
-        }).exec();
-
-        return instanceBulkDataArray;
+        return await DicomBulkDataModel.findInstanceBulkData({
+            studyUID,
+            seriesUID,
+            instanceUID
+        });
     }
 }
 
@@ -162,27 +137,13 @@ class SpecificBulkDataFactory extends BulkDataFactory {
             binaryValuePath
         } = this.uids;
 
-        let bulkData = await dicomBulkDataModel.findOne({
-            $and: [
-                {
-                    studyUID
-                },
-                {
-                    seriesUID
-                },
-                {
-                    instanceUID
-                },
-                {
-                    binaryValuePath: {
-                        $regex: `^${binaryValuePath}`,
-                        $options: "m"
-                    }
-                }
-            ]
-        }).exec();
-
-        return bulkData;
+        return await DicomBulkDataModel.findSpecificBulkData({
+            studyUID,
+            seriesUID,
+            instanceUID,
+            binaryValuePath
+        });
+
     }
 }
 

diff --git a/api/dicom-web/controller/WADO-RS/service/rendered.service.js b/api/dicom-web/controller/WADO-RS/service/rendered.service.js
@@ -13,6 +13,7 @@ const errorResponse = require("../../../../../utils/errorResponse/errorResponseM
 const { logger } = require("../../../../../utils/logs/log");
 
 const { raccoonConfig } = require("../../../../../config-class");
+const { DicomBulkDataModel } = require("@dbModels/dicomBulkData.model");
 
 class RenderedImageProcessParameterHandler {
     #params;
@@ -40,15 +41,9 @@ class RenderedImageProcessParameterHandler {
         let iccProfileAction = {
             "no": async () => { },
             "yes": async () => {
-                let iccProfileBinaryFile = await mongoose.model("dicomBulkData").findOne({
-                    $and: [
-                        {
-                            binaryValuePath: "00480105.Value.0.00282000.InlineBinary"
-                        },
-                        {
-                            instanceUID: instanceID
-                        }
-                    ]
+                let iccProfileBinaryFile = await DicomBulkDataModel.findOneBulkData({
+                    binaryValuePath: "00480105.Value.0.00282000.InlineBinary",
+                    instanceUID: instanceID
                 });
                 if (!iccProfileBinaryFile) throw new Error("The Image dose not have icc profile tag");
                 let iccProfileSrc = path.join(raccoonConfig.dicomWebConfig.storeRootPath, iccProfileBinaryFile.filename);

diff --git a/models/DICOM/dicom-json-model.js b/models/DICOM/dicom-json-model.js
@@ -23,7 +23,7 @@ const { dictionary } = require("./dicom-tags-dic");
  * *Remove tags when processing that not use them.
  */
 const BIG_VALUE_TAGS = [
-    "52009230", 
+    "52009230",
     "00480200"
 ];
 
@@ -35,7 +35,7 @@ class BaseDicomJson {
      */
     constructor(dicomJson, ...selection) {
         this.dicomJson = dicomJson;
-        if(selection.length > 0) {
+        if (selection.length > 0) {
             this.initSelectionJson(selection);
         }
     }
@@ -46,7 +46,7 @@ class BaseDicomJson {
      */
     initSelectionJson(selection) {
         let selectionJson = {};
-        for(let i = 0; i < selection.length; i++) {
+        for (let i = 0; i < selection.length; i++) {
             let tag = selection[i];
             let item = this.getItem(tag);
             if (item) {
@@ -86,7 +86,7 @@ class BaseDicomJson {
         return _.get(dictionary.tag, `${tag}`);
     }
 
-    static getTagOfKeyword(keyword)  {
+    static getTagOfKeyword(keyword) {
         return _.get(dictionary.keyword, `${keyword}`);
     }
 
@@ -158,7 +158,7 @@ class DicomJsonModel {
                 this.storeSeriesCollection(dbJson),
                 this.storePatientCollection(dbJson)
             ]);
-        } catch(e) {
+        } catch (e) {
             throw e;
         }
     }
@@ -346,7 +346,7 @@ class DicomJsonModel {
         } else {
             startedDate = moment(startedDate, "YYYYMMDDhhmmss").toISOString();
         }
-        
+
         return startedDate;
     }
 
@@ -360,14 +360,14 @@ class DicomJsonModel {
         };
     }
 
-    getPatientDicomJson(dicomJson=undefined) {
+    getPatientDicomJson(dicomJson = undefined) {
         if (!dicomJson) dicomJson = this.dicomJson;
 
         let patientDicomJson = {
             patientID: dicomJson.patientID
         };
 
-        for(let tag in tagsNeedStore.Patient) {
+        for (let tag in tagsNeedStore.Patient) {
             let value = _.get(dicomJson, tag);
             if (value)
                 _.set(patientDicomJson, tag, value);
@@ -376,7 +376,7 @@ class DicomJsonModel {
         return patientDicomJson;
     }
 
-    getStudyDicomJson(dicomJson=undefined) {
+    getStudyDicomJson(dicomJson = undefined) {
 
         if (!dicomJson) dicomJson = this.dicomJson;
 
@@ -385,7 +385,7 @@ class DicomJsonModel {
             studyPath: dicomJson.studyPath
         };
 
-        for(let tag in tagsNeedStore.Study) {
+        for (let tag in tagsNeedStore.Study) {
             let value = _.get(dicomJson, tag);
             if (value)
                 _.set(studyDicomJson, tag, value);
@@ -399,7 +399,7 @@ class DicomJsonModel {
         };
     }
 
-    getSeriesDicomJson(dicomJson=undefined) {
+    getSeriesDicomJson(dicomJson = undefined) {
         if (!dicomJson) dicomJson = this.dicomJson;
 
         let seriesDicomJson = {
@@ -408,9 +408,9 @@ class DicomJsonModel {
             seriesPath: dicomJson.seriesPath
         };
 
-        for(let tag in tagsNeedStore.Series) {
+        for (let tag in tagsNeedStore.Series) {
             let value = _.get(dicomJson, tag);
-            if(value)
+            if (value)
                 _.set(seriesDicomJson, tag, value);
         }
 
@@ -426,7 +426,7 @@ class DicomJsonModel {
 
 
 class DicomJsonBinaryDataModel {
-    constructor(dicomJsonModel, bulkDataModelClass=BulkData) {
+    constructor(dicomJsonModel, bulkDataModelClass = BulkData) {
 
         /** @type {DicomJsonModel} */
         this.dicomJsonModel = dicomJsonModel;
@@ -455,7 +455,7 @@ class DicomJsonBinaryDataModel {
     getPathGroupOfBinaryProperties_() {
         let pathGroupOfBinaryProperties = [];
 
-        for(let binaryKey of this.binaryKeys) {
+        for (let binaryKey of this.binaryKeys) {
 
             if (_.get(this.dicomJsonModel.dicomJson, `${binaryKey}.Value.0`)) {
                 pathGroupOfBinaryProperties.push(`${binaryKey}.Value.0`);
@@ -476,7 +476,7 @@ class DicomJsonBinaryDataModel {
             sopInstanceUID
         } = this.dicomJsonModel.uidObj;
 
-        for(let i = 0; i < this.binaryKeys.length ; i++) {
+        for (let i = 0; i < this.binaryKeys.length; i++) {
             let binaryKey = this.binaryKeys[i];
 
             // Reset VR to UR, because BulkDataURI is URI
@@ -493,7 +493,7 @@ class DicomJsonBinaryDataModel {
                 `${binaryKey}.BulkDataURI`,
                 `/studies/${studyUID}/series/${seriesUID}/instances/${sopInstanceUID}/bulkdata/${pathOfBinaryProperty}`
             );
-            
+
             _.unset(this.dicomJsonModel.dicomJson, `${binaryKey}.InlineBinary`);
         }
 
@@ -510,14 +510,14 @@ class DicomJsonBinaryDataModel {
 
         let shortInstanceUID = shortHash(sopInstanceUID);
 
-        
-        for(let i = 0; i < this.pathGroupOfBinaryProperties.length ; i++) {
+
+        for (let i = 0; i < this.pathGroupOfBinaryProperties.length; i++) {
             let relativeFilename = `files/bulkData/${shortInstanceUID}/`;
             let pathOfBinaryProperty = this.pathGroupOfBinaryProperties[i];
 
             let binaryData = _.get(this.dicomJsonModel.dicomJson, pathOfBinaryProperty);
 
-            if(binaryData) {
+            if (binaryData) {
                 relativeFilename += `${pathOfBinaryProperty}.raw`;
                 let filename = path.join(
                     raccoonConfig.dicomWebConfig.storeRootPath,
@@ -561,26 +561,17 @@ class BulkData {
             binaryValuePath: this.pathOfBinaryProperty
         };
 
-        await dicomBulkDataModel.updateOne(
+        await dicomBulkDataModel.createOrUpdateBulkData(
             {
-                $and: [
-                    {
-                        instanceUID: this.uidObj.sopInstanceUID
-                    },
-                    {
-                        binaryValuePath: this.pathOfBinaryProperty
-                    }
-                ]
+                instanceUID: this.uidObj.sopInstanceUID,
+                binaryValuePath: this.pathOfBinaryProperty
             },
             {
                 studyUID: this.uidObj.studyUID,
                 seriesUID: this.uidObj.seriesUID,
                 instanceUID: this.uidObj.sopInstanceUID,
                 filename: this.filename,
                 binaryValuePath: this.pathOfBinaryProperty
-            },
-            {
-                upsert: true
             }
         );
         logger.info(`[STOW-RS] [Store bulkdata ${JSON.stringify(item)} successful]`);