A hematoxylin & eosin (H&E) stain was applied to this biopsy slide. The H&E stain is a good general stain for studying the overall structure of the kidney, especially cells from the renal tubule. It is typically the first stain a pathologist will review.
" +},{ + "_id": { + "$oid": "5c05744a0056482794321e5d" + }, + "type": "pas", + "title": "Periodic Acid-Schiff (PAS) Stain", + "description": "A periodic acid-Schiff (PAS) stain was applied to this biopsy slide. In this stain certain areas of the kidney are stained purple, and the staining allows pathologists to get a good understanding of the amount and thickness of certain cells.
" +},{ + "_id": { + "$oid": "5c05744a0056482794321e5f" + }, + "type": "tri", + "title": "Trichrome Stain", + "description": "A Masson’s trichrome stain was applied to this biopsy slide. It is called a trichrome stain because it typically shows kidney features in three different colors.
This stain is very helpful for detecting scarring (also called fibrosis), among other things. Scarring shows up as a blue color on the images.
" +},{ + "_id": { + "$oid": "5c05744a0056482794321e5e" + }, + "type": "silver", + "title": "Silver Methenamine Stain", + "description": "A silver methenamine stain, sometimes called a Jones' stain, was applied to this biopsy slide. This stain is commonly used in analyzing kidney diseases because it makes it easy to see an important part of the kidney called the glomerular basement membrane.
" +},{ + "_id": { + "$oid": "5dd56f4f6d8ef3c60f5a0b68" + }, + "type": "tol", + "title": "tol", + "description": "tol" +},{ + "_id": { + "$oid": "5dd56f436d8ef3c60f5a0b67" + }, + "type": "frz", + "title": "frz", + "description": "frz" +},{ + "_id": { + "$oid": "5f983de8b4f594e1f53ca9e5" + }, + "type": "cr", + "title": "cr", + "description": "cr" +}] \ No newline at end of file diff --git a/scripts/generateDPRCommands.js b/scripts/generateDPRCommands.js new file mode 100644 index 0000000..54f0a0c --- /dev/null +++ b/scripts/generateDPRCommands.js @@ -0,0 +1,56 @@ +const MongoClient = require('mongodb').MongoClient; +const assert = require('assert'); +const { SlowBuffer } = require('buffer'); +const fs = require('fs'); + +const url = 'mongodb://localhost:27017'; +const dbName = 'dataLake'; +const slideTypeMap = { 'PAS':'pas', 'FRZ': 'frz', 'HE': 'he', 'SIL': 'silver', + 'TOL': 'tol', 'TRI': 'tri', 'CR': 'cr', 'IHC': 'ihc'} + +let dprCommands = []; + +let packageIds = process.argv.slice(2); + +// Give usage command if no packageIds provided + +MongoClient.connect(url, function(err, client) { + assert.strictEqual(null, err); + console.log("successfully connected to server"); + + const db = client.db(dbName); + var packageCollection = db.collection('packages'); + + + + for(i=0; i< packageIds.length; i++) { + let packageId = packageIds[i] + packageCollection.findOne({ _id: packageId }, function(err, document) { + assert.strictEqual(null, err); + + let updateCommands = '#/bin/sh\n'; + let kpmpId = document.subjectId; + + document.files.forEach(fileInfo => { + let fileName = fileInfo.fileName.replace(/\.svs/g, ''); + let stainType = ''; + for(const key in slideTypeMap) { + if (fileName.includes(key)) { + stainType = slideTypeMap[key]; + } + } + updateCommands = updateCommands.concat('\n', './run-wsi-worker.sh ' + kpmpId + ' ' + fileName + ' ' + fileInfo._id + ' ' + stainType ); + }); + + fs.writeFile('dprUpdate_' + packageId + '.sh', updateCommands, { flag: 'a'}, function(err) { + if (err) { + return console.log(err); + } + + }); + }); + + } + client.close(); +}); + diff --git a/scripts/package-lock.json b/scripts/package-lock.json new file mode 100644 index 0000000..4acf6be --- /dev/null +++ b/scripts/package-lock.json @@ -0,0 +1,434 @@ +{ + "requires": true, + "lockfileVersion": 1, + "dependencies": { + "array-filter": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/array-filter/-/array-filter-1.0.0.tgz", + "integrity": "sha1-uveeYubvTCpMC4MSMtr/7CUfnYM=" + }, + "assert": { + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/assert/-/assert-2.0.0.tgz", + "integrity": "sha512-se5Cd+js9dXJnu6Ag2JFc00t+HmHOen+8Q+L7O9zI0PqQXr20uk2J0XQqMxZEeo5U50o8Nvmmx7dZrl+Ufr35A==", + "requires": { + "es6-object-assign": "^1.1.0", + "is-nan": "^1.2.1", + "object-is": "^1.0.1", + "util": "^0.12.0" + } + }, + "available-typed-arrays": { + "version": "1.0.2", + "resolved": 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org.springframework.data.mongodb.core.mapping.Document; + +@Document(collection = "patients") +public class Aperio { + + private String OriginalHeight; + + private String OriginalWidth; + + public String getOriginalHeight() { + return OriginalHeight; + } + + public void setOriginalHeight(String OriginalHeight) { + this.OriginalHeight = OriginalHeight; + } + + public String getOriginalWidth() { + return OriginalWidth; + } + + public void setOriginalWidth(String OriginalWidth) { + this.OriginalWidth = OriginalWidth; + } + + +} diff --git a/src/main/java/org/kpmp/slides/Metadata.java b/src/main/java/org/kpmp/slides/Metadata.java new file mode 100644 index 0000000..ab6be73 --- /dev/null +++ b/src/main/java/org/kpmp/slides/Metadata.java @@ -0,0 +1,29 @@ +package org.kpmp.slides; + +import org.springframework.data.mongodb.core.mapping.Document; + +@Document(collection = "patients") +public class Metadata { + + // @Field("aperio") + private Aperio aperio; + private OpenSlide openslide; + + public Aperio getAperio() { + return aperio; + } + + public void setAperio(Aperio aperio) { + this.aperio = aperio; + } + + public OpenSlide getOpenSlide() { + return openslide; + } + + public void setOpenSlide(OpenSlide openslide) { + this.openslide = openslide; + } + + +} diff --git a/src/main/java/org/kpmp/slides/OpenSlide.java b/src/main/java/org/kpmp/slides/OpenSlide.java new file mode 100644 index 0000000..0a6d3a7 --- /dev/null +++ b/src/main/java/org/kpmp/slides/OpenSlide.java @@ -0,0 +1,27 @@ +package org.kpmp.slides; + +import org.springframework.data.mongodb.core.mapping.Document; + +@Document(collection = "patients") +public class OpenSlide { + + private String mpp_x; + private String mpp_y; + + public String getMpp_x() { + return mpp_x; + } + + public void setMpp_x(String mpp_x) { + this.mpp_x = mpp_x; + } + + public String getMpp_y() { + return mpp_y; + } + + public void setMpp_y(String mpp_y) { + this.mpp_y = mpp_y; + } + +} diff --git a/src/main/java/org/kpmp/slides/Slide.java b/src/main/java/org/kpmp/slides/Slide.java index 726fe7c..bf5d465 100644 --- a/src/main/java/org/kpmp/slides/Slide.java +++ b/src/main/java/org/kpmp/slides/Slide.java @@ -11,6 +11,9 @@ public class Slide { private String id; private String slideName; + @Field("metadata") + private Metadata metadata; + @Field("stain") private Stain stain; @@ -30,6 +33,14 @@ public void setSlideName(String slideName) { this.slideName = slideName; } + public Metadata getMetadata() { + return metadata; + } + + public void setMetadata(Metadata metadata) { + this.metadata = metadata; + } + public String getId() { return id; } diff --git a/src/test/java/org/kpmp/slides/SlideTest.java b/src/test/java/org/kpmp/slides/SlideTest.java index 88c9a7d..830c445 100644 --- a/src/test/java/org/kpmp/slides/SlideTest.java +++ b/src/test/java/org/kpmp/slides/SlideTest.java @@ -42,4 +42,29 @@ public void testSetId() { assertEquals("54354", slide.getId()); } + @Test + public void testSetMetadata() { + Metadata metadata = new Metadata(); + slide.setMetadata(metadata); + + assertEquals(metadata, slide.getMetadata()); + } + + @Test + public void testSetAperio() { + Aperio aperio = new Aperio(); + Metadata metadata = new Metadata(); + metadata.setAperio(aperio); + + assertEquals(aperio, metadata.getAperio()); + } + + @Test + public void testSetOpenSlide() { + OpenSlide openSlide = new OpenSlide(); + Metadata metadata = new Metadata(); + metadata.setOpenSlide(openSlide); + + assertEquals(openSlide, metadata.getOpenSlide()); + } }