Fixed mSigPortal APIs

episphere · Oct 27, 2023 · 6729a8a · 6729a8a
1 parent fe5c2ac
commit 6729a8a
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Showing 3 changed files with 50 additions and 8 deletions.
diff --git a/bundle.js b/bundle.js
@@ -8360,7 +8360,13 @@ async function getMutationalSignatureLandscapeData(
   signatureSetName = "COSMIC_v3_Signatures_GRCh37_SBS96",
   numberOfResults = 10
 ) {
-  const url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_activity?study=${study}&strategy=${genomeDataType}&signatureSetName=${signatureSetName}&cancer=${cancerType}&limit=${numberOfResults}&offset=0`;
+  let url = '';
+  if (cancerType == "") {
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_activity?study=${study}&strategy=${genomeDataType}&signatureSetName=${signatureSetName}&limit=${numberOfResults}&offset=0`;
+
+  }else {
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_activity?study=${study}&strategy=${genomeDataType}&signatureSetName=${signatureSetName}&limit=${numberOfResults}&cancer=${cancerType}&offset=0`;
+  }
   const cacheName = "getMutationalSignatureLandscapeData";
   return await (await fetchURLAndCache(cacheName, url)).json();
 }
@@ -8396,7 +8402,14 @@ async function getMutationalSignatureEtiologyOptions(
   cancerType = "",
   numberOfResults = 10
 ) {
-  const url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology_options?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&cancer=${cancerType}&limit=${numberOfResults}&offset=0`;
+  let url = '';
+
+  if (cancerType == "") {
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology_options?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&limit=${numberOfResults}&offset=0`;
+  }else {
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology_options?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&cancer=${cancerType}&limit=${numberOfResults}&offset=0`;
+  }
+
   const cacheName = "getMutationalSignatureEtiologyOptions";
   return await (await fetchURLAndCache(cacheName, url)).json();
 }
@@ -8421,7 +8434,15 @@ async function getMutationalSignatureEtiologyData(
   cancerType = "",
   numberOfResults = 10
 ) {
-  const url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&cancer=${cancerType}&limit=${numberOfResults}&offset=0`;
+  let url = '';
+
+  if (cancerType == "") {
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&limit=${numberOfResults}&offset=0`;
+  }
+  else {
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology?study=${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/mSigPortalAPIs.js b/mSigSDKScripts/mSigPortalAPIs.js
@@ -333,7 +333,13 @@ export async function getMutationalSignatureLandscapeData(
   signatureSetName = "COSMIC_v3_Signatures_GRCh37_SBS96",
   numberOfResults = 10
 ) {
-  const url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_activity?study=${study}&strategy=${genomeDataType}&signatureSetName=${signatureSetName}&cancer=${cancerType}&limit=${numberOfResults}&offset=0`;
+  let url = '';
+  if (cancerType == "") {
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_activity?study=${study}&strategy=${genomeDataType}&signatureSetName=${signatureSetName}&limit=${numberOfResults}&offset=0`;
+
+  }else{
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_activity?study=${study}&strategy=${genomeDataType}&signatureSetName=${signatureSetName}&limit=${numberOfResults}&cancer=${cancerType}&offset=0`;
+  }
   const cacheName = "getMutationalSignatureLandscapeData";
   return await (await fetchURLAndCache(cacheName, url)).json();
 }
@@ -369,7 +375,14 @@ export async function getMutationalSignatureEtiologyOptions(
   cancerType = "",
   numberOfResults = 10
 ) {
-  const url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology_options?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&cancer=${cancerType}&limit=${numberOfResults}&offset=0`;
+  let url = '';
+
+  if (cancerType == "") {
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology_options?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&limit=${numberOfResults}&offset=0`;
+  }else{
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology_options?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&cancer=${cancerType}&limit=${numberOfResults}&offset=0`;
+  }
+
   const cacheName = "getMutationalSignatureEtiologyOptions";
   return await (await fetchURLAndCache(cacheName, url)).json();
 }
@@ -394,7 +407,15 @@ export async function getMutationalSignatureEtiologyData(
   cancerType = "",
   numberOfResults = 10
 ) {
-  const url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&cancer=${cancerType}&limit=${numberOfResults}&offset=0`;
+  let url = '';
+
+  if (cancerType == "") {
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&limit=${numberOfResults}&offset=0`;
+  }
+  else{
+    url = `https://analysistools-dev.cancer.gov/mutational-signatures/api/signature_etiology?study=${study}&strategy=${genomeDataType}&signatureName=${signatureName}&cancer=${cancerType}&limit=${numberOfResults}&offset=0`;
+  }  
+
   const cacheName = "getMutationalSignatureEtiologyData";
   return await (await fetchURLAndCache(cacheName, url)).json();
 }

diff --git a/test.js b/test.js
@@ -32,5 +32,5 @@ await fetch("https://api.gdc.cancer.gov/data/0b3d2db3-8ae3-4d39-bd9b-9d1e7a133b6
 
 // Testing UMAP
 mSigSDK = await (await import("./main.js")).mSigSDK;
-cancerType = "Lung-AdenoCA"
-data = await mSigSDK.mSigPortal.mSigPortalData.getMutationalSignatureActivityData('PCAWG','WGS','COSMIC_v3_Signatures_GRCh37_SBS96','',10)
+// cancerType = "Lung-AdenoCA"
+getMutationalSignatureEtiologyOptions = mSigSDK.mSigPortal.mSigPortalData.getMutationalSignatureEtiologyOptions()