Changed the code to use version specified dependencies

episphere · Oct 27, 2023 · 7f7e35b · 7f7e35b
1 parent 5bd780b
commit 7f7e35b
Show file tree

Hide file tree

Showing 2 changed files with 46 additions and 40 deletions.
diff --git a/mSigSDKScripts/mSigPortalAPIs.js b/mSigSDKScripts/mSigPortalAPIs.js
@@ -1,10 +1,8 @@
-import {
-  fetchURLAndCache,
-} from "./utils.js";
-
- //#region Mutational Signatures
+import { fetchURLAndCache } from "./utils.js";
 
-  /**
+//#region Mutational Signatures
+
+/**
 
 Retrieves the mutational signature options from the specified API endpoint.
 @async
@@ -45,14 +43,13 @@ export async function getMutationalSignaturesData(
   genomeDataType = "WGS",
   signatureSetName = "COSMIC_v3_Signatures_GRCh37_SBS96",
   mutationType = "SBS",
+  matrix = 96,
   numberofResults = 10
 ) {
   const url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/mutational_signature?
-  source=Reference_signatures&strategy=${genomeDataType}&profile=${mutationType}&matrix=96&signatureSetName=${signatureSetName}&limit=${numberofResults}&offset=0`;
+  source=Reference_signatures&strategy=${genomeDataType}&profile=${mutationType}&matrix=${matrix}&signatureSetName=${signatureSetName}&limit=${numberofResults}&offset=0`;
   const cacheName = "getMutationalSignaturesData";
-  const unformattedData = await (
-    await fetchURLAndCache(cacheName, url)
-  ).json();
+  const unformattedData = await (await fetchURLAndCache(cacheName, url)).json();
   // const formattedData = extractMutationalSpectra(
   //   unformattedData,
   //   "signatureName"
@@ -138,22 +135,36 @@ export async function getMutationalSpectrumData(
   const promises = [];
   let urls = [];
 
-  if (cancerType == null) {
+  if (cancerType == '') {
     let url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/mutational_spectrum?study=${study}&strategy=${genomeDataType}&profile=${mutationType}&matrix=${matrixSize}&offset=0`;
 
-    let unformattedData = await (
-      await fetchURLAndCache(cacheName, url)
-    ).json();
+    let unformattedData = await (await fetchURLAndCache(cacheName, url)).json();
 
     return unformattedData;
   }
 
   if (samples === null) {
-    let url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/mutational_spectrum?study=${study}&cancer=${cancerType}&strategy=${genomeDataType}&profile=${mutationType}&matrix=${matrixSize}&offset=0`;
+    let url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/mutational_spectrum?study=${study}`;
+
+    if (cancerType !== null) {
+      url += `&cancer=${cancerType}`;
+    }
+
+    if (genomeDataType !== null) {
+      url += `&strategy=${genomeDataType}`;
+    }
+
+    if (mutationType !== null) {
+      url += `&profile=${mutationType}`;
+    }
 
-    let unformattedData = await (
-      await fetchURLAndCache(cacheName, url)
-    ).json();
+    if (matrixSize !== null) {
+      url += `&matrix=${matrixSize}`;
+    }
+
+    url += `&offset=0`;
+
+    let unformattedData = await (await fetchURLAndCache(cacheName, url)).json();
     // let formattedData = extractMutationalSpectra(unformattedData, "sample");
     return unformattedData;
   } else {
@@ -300,13 +311,11 @@ export async function getMutationalSignatureActivityData(
   cancerType = "",
   numberOfResults = 10
 ) {
-  let url = '';
+  let url = "";
   if (cancerType == "") {
     url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_activity?study=${study}&strategy=${genomeDataType}&signatureSetName=${signatureSetName}&limit=${numberOfResults}&offset=0`;
-
-  }else{
+  } else {
     url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_activity?study=${study}&strategy=${genomeDataType}&signatureSetName=${signatureSetName}&limit=${numberOfResults}&cancer=${cancerType}&offset=0`;
-
   }
 
   const cacheName = "getMutationalSignatureActivityData";
@@ -333,11 +342,10 @@ export async function getMutationalSignatureLandscapeData(
   signatureSetName = "COSMIC_v3_Signatures_GRCh37_SBS96",
   numberOfResults = 10
 ) {
-  let url = '';
+  let url = "";
   if (cancerType == "") {
     url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_activity?study=${study}&strategy=${genomeDataType}&signatureSetName=${signatureSetName}&limit=${numberOfResults}&offset=0`;
-
-  }else{
+  } else {
     url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_activity?study=${study}&strategy=${genomeDataType}&signatureSetName=${signatureSetName}&limit=${numberOfResults}&cancer=${cancerType}&offset=0`;
   }
   const cacheName = "getMutationalSignatureLandscapeData";
@@ -375,24 +383,24 @@ export async function getMutationalSignatureEtiologyOptions(
   cancerType = "",
   numberOfResults = 10
 ) {
-
   // Pass the arguments into the url of the api call only if they are not empty strings
-
-  let url = "https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology_options?"
+
+  let url =
+    "https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology_options?";
 
   if (category != "") {
-    url += `category=${category}&`
+    url += `category=${category}&`;
   }
   if (etiology != "") {
-    url += `etiology=${etiology}&`
+    url += `etiology=${etiology}&`;
   }
   if (signatureName != "") {
-    url += `signature=${signatureName}&`
+    url += `signature=${signatureName}&`;
   }
   if (cancerType != "") {
-    url += `cancer=${cancerType}&`
+    url += `cancer=${cancerType}&`;
   }
-  url += `limit=${numberOfResults}&offset=0`
+  url += `limit=${numberOfResults}&offset=0`;
 
   const cacheName = "getMutationalSignatureEtiologyOptions";
   return await (await fetchURLAndCache(cacheName, url)).json();
@@ -418,15 +426,13 @@ export async function getMutationalSignatureEtiologyData(
   cancerType = "",
   numberOfResults = 10
 ) {
-  let url = '';
-
+  let url = "";
 
   if (cancerType == "") {
     url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&limit=${numberOfResults}&offset=0`;
-  }
-  else{
+  } else {
     url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&cancer=${cancerType}&limit=${numberOfResults}&offset=0`;
-  }  
+  }
 
   const cacheName = "getMutationalSignatureEtiologyData";
   return await (await fetchURLAndCache(cacheName, url)).json();

diff --git a/mSigSDKScripts/machineLearning.js b/mSigSDKScripts/machineLearning.js
@@ -1,6 +1,6 @@
-import * as MLR from "https://cdn.jsdelivr.net/npm/ml-regression-multivariate-linear/+esm";
+import * as MLR from "https://esm.sh/ml-regression-multivariate-linear@2.0.4";
 
-import * as CV from "https://cdn.jsdelivr.net/npm/ml-cross-validation/+esm";
+import * as CV from "https://esm.sh/ml-cross-validation@1.3.0";
 
 import { groupBy } from "./utils.js";