Support for the Crate generated by onlly Sapporo

sapporo-wes · Sep 18, 2022 · 6a9dc11 · 6a9dc11
1 parent 4a98750
commit 6a9dc11
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Showing 3 changed files with 69 additions and 53 deletions.
diff --git a/src/crate.ts b/src/crate.ts
@@ -14,7 +14,7 @@ export interface CrateSummary {
   startTime: Date;
   endTime: Date;
   duration: ReturnType<typeof datetime.difference>;
-  exitCode: number;
+  exitCode: string;
   state: string;
   wfAttachments: string[];
   intermediateFiles: string[];
@@ -93,48 +93,45 @@ export class Crate {
   }
 
   summarize(): void {
+    const unknownToStr = (val: unknown) => {
+      return val == undefined ? "" : `${val}`;
+    };
+
     try {
       // General Metadata
-      const wfName = `${this.getValRecursively(this.mainWf, ["name"])}`;
-      const wfVersion = `${this.getValRecursively(this.mainWf, ["version"])}`;
-      const wfId = `${this.getValRecursively(this.mainWf, ["yevisId"])}`;
-      const wfType = `${
-        this.getValRecursively(this.mainWf, [
-          "programmingLanguage",
-          "name",
-        ])
-      }`;
-      const wfTypeVersion = `${
-        this.getValRecursively(this.mainWf, [
-          "programmingLanguage",
-          "version",
-        ])
-      }`;
-      const exitCode = this.getValRecursively(this.testResult, [
-        "exitCode",
-      ]);
-      if (typeof exitCode !== "number") {
-        throw new Error(`Invalid exit code ${exitCode}`);
-      }
-      const state = `${this.getValRecursively(this.testResult, ["state"])}`;
-      const testId = `${
-        this.getValRecursively(this.testDefinition, ["yevisTestId"])
-      }`;
-      const sapporoVersion = `${
-        this.getValRecursively(this.testInstance, ["version"])
-      }`;
-      const wfEngineName = `${
-        this.getValRecursively(this.testDefinition, [
-          "conformsTo",
-          "name",
-        ])
-      }`;
-      const wfEngineVersion = `${
-        this.getValRecursively(this.testDefinition, [
-          "conformsTo",
-          "version",
-        ])
-      }`;
+      const wfName = unknownToStr(
+        this.getValRecursively(this.mainWf, ["name"]),
+      );
+      const wfVersion = unknownToStr(
+        this.getValRecursively(this.mainWf, ["version"]),
+      );
+      const wfId = unknownToStr(
+        this.getValRecursively(this.mainWf, ["yevisId"]),
+      );
+      const wfType = unknownToStr(
+        this.getValRecursively(this.mainWf, ["programmingLanguage", "name"]),
+      );
+      const wfTypeVersion = unknownToStr(
+        this.getValRecursively(this.mainWf, ["programmingLanguage", "version"]),
+      );
+      const exitCode = unknownToStr(
+        this.getValRecursively(this.testResult, ["exitCode"]),
+      );
+      const state = unknownToStr(
+        this.getValRecursively(this.testResult, ["state"]),
+      );
+      const testId = unknownToStr(
+        this.getValRecursively(this.testDefinition, ["yevisTestId"]),
+      );
+      const sapporoVersion = unknownToStr(
+        this.getValRecursively(this.testInstance, ["runsOn", "version"]),
+      );
+      const wfEngineName = unknownToStr(
+        this.getValRecursively(this.testDefinition, ["conformsTo", "name"]),
+      );
+      const wfEngineVersion = unknownToStr(
+        this.getValRecursively(this.testDefinition, ["conformsTo", "version"]),
+      );
 
       // File IDs
       let wfAttachments: string[] = [];
@@ -158,22 +155,18 @@ export class Crate {
       const outputsWithEdam = this.filterHasEdam(outputs);
 
       // Time
-      const startTimeStr = `${
-        this.getValRecursively(this.testResult, [
-          "startTime",
-        ])
-      }`;
+      const startTimeStr = unknownToStr(
+        this.getValRecursively(this.testResult, ["startTime"]),
+      );
       let startTime: Date;
       try {
         startTime = utils.parseDatetime(startTimeStr);
       } catch (_) {
         throw new Error(`Invalid start time ${startTimeStr}`);
       }
-      const endTimeStr = `${
-        this.getValRecursively(this.testResult, [
-          "endTime",
-        ])
-      }`;
+      const endTimeStr = unknownToStr(
+        this.getValRecursively(this.testResult, ["endTime"]),
+      );
       let endTime: Date;
       try {
         endTime = utils.parseDatetime(endTimeStr);

diff --git a/tests/README.md b/tests/README.md
@@ -35,6 +35,9 @@ $ deno test -A ./tests/rnaseq_v3.6_test.ts
 # RNA-seq (Linux, 1st) <-> RNA-seq (Linux, small)
 $ deno test -A ./tests/rnaseq_small_test.ts
 
+# RNA-seq (Linux, with yevis) <-> RNA-seq (Linux, only sapporo)
+$ deno test -A ./tests/rnaseq_only_sapporo_test.ts
+
 # Trimming (Linux) <-> Trimming (Mac)
 $ deno test -A ./tests/trimming_mac_test.ts
 ```
@@ -54,6 +57,7 @@ example_crate/
 ├── rnaseq_1st.json
 ├── rnaseq_2nd.json
 ├── rnaseq_mac.json
+├── rnaseq_only_sapporo.json
 ├── rnaseq_small.json
 ├── rnaseq_v3.6.json
 ├── trimming.json
@@ -72,8 +76,8 @@ About the environment in which the crate was generated.
 | CPU Architecture        | `x86_64`                                   | `arm64`               |
 | Memory                  | `24.0 GiB`                                 | `64.0 GiB`            |
 | Docker version          | `20.10.8`                                  | `20.10.16`            |
-| Sapporo-service version | `1.4.6`                                    | `1.4.6`               |
-| Yevis-cli version       | `0.5.3`                                    | `0.5.3`               |
+| Sapporo-service version | `1.4.8`                                    | `1.4.8`               |
+| Yevis-cli version       | `0.5.4`                                    | `0.5.4`               |
 
 ### GATK
 
@@ -107,6 +111,10 @@ $ yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/test
   - [`rnaseq_v3.6.json`](./example_crate/rnaseq_v3.6.json)
     - Crate generated on `Linux` environment.
     - Using `nf-core/rnaseq` version is `3.6`. (Normal one is `3.7`)
+  - [`rnaseq_only_sapporo.json`](./example_crate/rnaseq_only_sapporo.json)
+    - Crate generated on `Linux` environment.
+    - Using `nf-core/rnaseq` version is `3.7`.
+    - Using `Sapporo` only. (Not using `Yevis`)
 
 See https://github.com/sapporo-wes/test-workflow#nf-corernaseq for more details about the executed workflow.
 

diff --git a/tests/rnaseq_only_sapporo_test.ts b/tests/rnaseq_only_sapporo_test.ts
@@ -0,0 +1,15 @@
+import { args, compare, crate } from "../src/mod.ts";
+
+const CRATE_DIR = `${new URL(".", import.meta.url).pathname}example_crate`;
+
+Deno.test("RNA-seq using only Sapporo test", async () => {
+  const loc1 = `${CRATE_DIR}/rnaseq_1st.json`;
+  const loc2 = `${CRATE_DIR}/rnaseq_only_sapporo.json`;
+
+  const parsedArgs = await args.parseArgs([loc1, loc2]);
+  const crate1 = new crate.Crate(parsedArgs.loc1);
+  await crate1.initialize();
+  const crate2 = new crate.Crate(parsedArgs.loc2);
+  await crate2.initialize();
+  compare.compare(crate1, crate2, parsedArgs.all, parsedArgs.threshold);
+});