Revert "Revert "Feature/45 lecter integration""

.env.example

@@ -2,8 +2,10 @@ CLINICAL_DB_URL=mongodb://localhost:27017/clinical
 # has to be lower case
 LOG_LEVEL=debug
 INITIAL_SCHEMA_VERSION=1.0
-SCHEMA_NAME=ARGO Dictionary
+SCHEMA_NAME=ARGO Clinical Submission
 JWT_TOKEN_PUBLIC_KEY_URL=
 # optional, if this is set, it will take precedence over fetching from the url
 # if you provide the url instead this env key will be set in the process env from the url
-JWT_TOKEN_PUBLIC_KEY=
+JWT_TOKEN_PUBLIC_KEY=
+# you can use file url for testing  : file:///path/to/test/schema/stub-schema.json
+LECTERN_URL=

Dockerfile

@@ -15,5 +15,9 @@ FROM node:12.5.0-alpine
 WORKDIR /app
 COPY --from=builder /app/dist ./dist
 COPY --from=builder /app/node_modules ./node_modules
+ARG COMMIT_ID
+ENV CLINICAL_COMMIT_ID=${COMMIT_ID}
+ARG VERSION
+ENV CLINICAL_VERSION=${VERSION}
 EXPOSE 3000
 CMD ["node", "dist/src/server.js"]

Jenkinsfile.groovy

@@ -78,7 +78,7 @@ spec:
 
                     // the network=host needed to download dependencies using the host network (since we are inside 'docker'
                     // container)
-                    sh "docker build --network=host -f Dockerfile . -t icgcargo/clinical:edge -t icgcargo/clinical:${version}-${commit}"
+                    sh "docker build --build-arg COMMIT_ID=${commit} --build-arg VERSION=${version} --network=host -f Dockerfile . -t icgcargo/clinical:edge -t icgcargo/clinical:${version}-${commit}"
                     sh "docker push icgcargo/clinical:${version}-${commit}"
                     sh "docker push icgcargo/clinical:edge"
                }
@@ -110,7 +110,7 @@ spec:
                   withCredentials([usernamePassword(credentialsId:'argoDockerHub', usernameVariable: 'USERNAME', passwordVariable: 'PASSWORD')]) {
                       sh 'docker login -u $USERNAME -p $PASSWORD'
                   }
-                  sh "docker  build --network=host -f Dockerfile . -t icgcargo/clinical:latest -t icgcargo/clinical:${version}"
+                  sh "docker  build --build-arg COMMIT_ID=${commit} --build-arg VERSION=${version} --network=host -f Dockerfile . -t icgcargo/clinical:latest -t icgcargo/clinical:${version}"
                   sh "docker push icgcargo/clinical:${version}"
                   sh "docker push icgcargo/clinical:latest"
              }

README.md

@@ -1,5 +1,7 @@
 # Argo clinical
 
+[![Build Status](https://jenkins.qa.cancercollaboratory.org/buildStatus/icon?job=ARGO%2Fargo-clinical%2Fmaster)](https://jenkins.qa.cancercollaboratory.org/job/ARGO/job/argo-clinical/job/master/)
+
 ## Requirements:
 
 - node 12+

package.json

@@ -97,6 +97,7 @@
     "multer": "^1.4.1",
     "node-fetch": "^2.6.0",
     "nodemailer": "^6.2.1",
+    "promise-tools": "^2.1.0",
     "swagger-ui-express": "^4.0.7",
     "winston": "^3.2.1",
     "yamljs": "^0.3.0"

sampleFiles/sample-schema.json

@@ -0,0 +1,142 @@
+{
+  "schemas": [
+    {
+      "name": "registration",
+      "description": "TSV for Registration of Donor-Specimen-Sample",
+      "key": "submitter_donor_id",
+      "fields": [
+        {
+          "name": "program_id",
+          "valueType": "string",
+          "description": "Unique identifier for program",
+          "meta": {
+            "key": true
+          },
+          "restrictions": {
+            "required": true,
+            "regex": "^[A-Z1-9][-_A-Z1-9]{2,7}(-[A-Z][A-Z])$"
+          }
+        },
+        {
+          "name": "submitter_donor_id",
+          "valueType": "string",
+          "description": "Unique identifier for donor, assigned by the data provider.",
+          "meta": {
+            "key": true
+          },
+          "restrictions": {
+            "required": true,
+            "regex": "^(?!(DO|do)).+"
+          }
+        },
+        {
+          "name": "gender",
+          "valueType": "string",
+          "description": "The gender of the patient",
+          "restrictions": {
+            "required": true,
+            "codeList": ["Male", "Female", "Other"]
+          }
+        },
+        {
+          "name": "submitter_specimen_id",
+          "valueType": "string",
+          "description": "Submitter assigned specimen id",
+          "meta": {
+            "key": true
+          },
+          "restrictions": {
+            "required": true,
+            "regex": "^(?!(SP|sp)).+"
+          }
+        },
+        {
+          "name": "specimen_type",
+          "valueType": "string",
+          "description": "Indicate the tissue source of the biospecimen",
+          "meta": {
+            "default": "Other"
+          },
+          "restrictions": {
+            "required": true,
+            "codeList": [
+              "Blood derived",
+              "Blood derived - bone marrow",
+              "Blood derived - peripheral blood",
+              "Bone marrow",
+              "Buccal cell",
+              "Lymph node",
+              "Solid tissue",
+              "Plasma",
+              "Serum",
+              "Urine",
+              "Cerebrospinal fluid",
+              "Sputum",
+              "NOS (Not otherwise specified)",
+              "Other",
+              "FFPE",
+              "Pleural effusion",
+              "Mononuclear cells from bone marrow",
+              "Saliva",
+              "Skin"
+            ]
+          }
+        },
+        {
+          "name": "tumour_normal_designation",
+          "valueType": "string",
+          "description": "Indicate whether specimen is tumour or normal type",
+          "restrictions": {
+            "required": true,
+            "codeList": [
+              "Normal",
+              "Normal - tissue adjacent to primary tumour",
+              "Primary tumour",
+              "Primary tumour - adjacent to normal",
+              "Primary tumour - additional new primary",
+              "Recurrent tumour",
+              "Metastatic tumour",
+              "Metastatic tumour - metastasis local to lymph node",
+              "Metastatic tumour - metastasis to distant location",
+              "Metastatic tumour - additional metastatic",
+              "Xenograft - derived from primary tumour",
+              "Xenograft - derived from tumour cell line",
+              "Cell line - derived from xenograft tissue",
+              "Cell line - derived from tumour",
+              "Cell line - derived from normal"
+            ]
+          }
+        },
+        {
+          "name": "submitter_sample_id",
+          "valueType": "string",
+          "description": "Submitter assigned sample id",
+          "restrictions": {
+            "required": true,
+            "regex": "^(?!(SA|sa)).+"
+          }
+        },
+        {
+          "name": "sample_type",
+          "valueType": "string",
+          "description": "Specimen Type",
+          "restrictions": {
+            "required": true,
+            "codeList": [
+              "Total DNA",
+              "Amplified DNA",
+              "ctDNA",
+              "other DNA enrichments",
+              "Total RNA",
+              "Ribo-Zero RNA",
+              "polyA+ RNA",
+              "other RNA fractions"
+            ]
+          }
+        }
+      ]
+    }
+  ],
+  "name": "ARGO Clinical Submission",
+  "version": "1.0"
+}

src/app-health.ts

@@ -0,0 +1,45 @@
+export type AppHealth = {
+  all: ComponentStatus;
+  db: ComponentStatus;
+  schema: ComponentStatus;
+  egoPublicKey: ComponentStatus;
+};
+
+export type ComponentStatus = {
+  status: "GREEN" | "RED" | "UNKNOWN";
+  info?: any;
+};
+
+const health: AppHealth = {
+  all: {
+    status: "UNKNOWN"
+  },
+  db: {
+    status: "UNKNOWN"
+  },
+  schema: {
+    status: "UNKNOWN"
+  },
+  egoPublicKey: {
+    status: "UNKNOWN"
+  }
+};
+
+export function setStatus(component: keyof AppHealth, status: ComponentStatus) {
+  health[component] = status;
+  for (const k in health) {
+    const key = k as keyof AppHealth;
+    if (key == "all") {
+      continue;
+    }
+    if (health[key].status !== "GREEN") {
+      health["all"].status = "RED";
+      return;
+    }
+  }
+  health["all"].status = "GREEN";
+}
+
+export function getHealth(): AppHealth {
+  return health;
+}

src/app.ts

@@ -3,13 +3,14 @@ import errorHandler from "errorhandler";
 import bodyParser from "body-parser";
 import path from "path";
 import submissionAPI from "./submission/submission-api";
-import * as schemaApi from "./lectern-client/schema-api";
+import * as schemaApi from "./submission/schema-api";
 import * as middleware from "./middleware";
 import * as swaggerUi from "swagger-ui-express";
 import yaml from "yamljs";
 import multer from "multer";
 import { loggerFor } from "./logger";
 import { findDonors, deleteDonors } from "./clinical/clinical-api";
+import { getHealth } from "./app-health";
 
 const L = loggerFor(__filename);
 
@@ -28,6 +29,17 @@ app.use(
 app.set("port", process.env.PORT || 3000);
 
 app.get("/", (req, res) => res.sendFile(path.join(__dirname, "./resources/working.gif")));
+app.get("/health", (req, res) => {
+  const health = getHealth();
+  const resBody = {
+    version: `${process.env.CLINICAL_VERSION} - ${process.env.CLINICAL_COMMIT_ID}`,
+    health: health
+  };
+  if (health.all.status == "GREEN") {
+    return res.status(200).send(resBody);
+  }
+  return res.status(500).send(resBody);
+});
 app.get(
   "/submission/program/:programId/registration",
   middleware.wrapAsync(submissionAPI.getRegistrationByProgramId)
@@ -61,7 +73,7 @@ app.delete("/clinical/donors", middleware.wrapAsync(deleteDonors));
 // this has to be defined after all routes for it to work for these paths.
 app.use(middleware.errorHandler);
 app.use(
-  "/swagger",
+  "/api-docs",
   swaggerUi.serve,
   swaggerUi.setup(yaml.load(path.join(__dirname, "./resources/swagger.yaml")))
 );