Merge pull request #131 from veg/develop

1.2.0

.gitignore

@@ -38,3 +38,8 @@ public/assets/js/datamonkey.css*
 public/assets/js/datamonkey.js*
 *vendor*
 *.aa
+dump.rdb
+
+.DS_Store
+.yalc/
+yalc.lock

.travis.yml

@@ -1,6 +1,6 @@
 language: node_js
 
-services: 
+services:
   - mongodb
   - redis-server
 
@@ -10,18 +10,19 @@ node_js:
 sudo: false
 
 notifications:
-    email:
-        recipients:
-            - spond@temple.edu
-            - steven@stevenweaver.org
-            - sshank@temple.edu
-        on_success: always
-        on_failure: always
+  email:
+    recipients:
+      - spond@temple.edu
+      - steven@stevenweaver.org
+      - sshank@temple.edu
+    on_success: always
+    on_failure: always
 
 branches:
   only:
-  - master
-  - develop
+    - master
+    - develop
+    - bootstrap4
 
 cache:
   yarn: true

Makefile

@@ -10,4 +10,4 @@ install:
 	@cd ./.tn93/ && cmake . && make && cd ../
 	@yarn install
 	@webpack
-	@mkdir -p ./uploads/msa ./uploads/hivtrace;
+	@mkdir -p ./uploads/msa ./uploads/hivtrace ./results/jobs/;

README.md

@@ -53,4 +53,4 @@ Start datamonkey.js
 
     node server.js
 
-Datamonkey should now be running at [localhost:4000](http://localhost:4000).
+Datamonkey should now be running at [localhost:4002](http://localhost:4002).

app/models/absrel.js

@@ -39,7 +39,13 @@ aBSREL.virtual("filepath").get(function() {
  * Original file path for document's file upload
  */
 aBSREL.virtual("original_fn").get(function() {
-  return path.resolve(__dirname + "/../../uploads/msa/" + this._id + "-original." + this.original_extension);
+  return path.resolve(
+    __dirname +
+      "/../../uploads/msa/" +
+      this._id +
+      "-original." +
+      this.original_extension
+  );
 });
 
 /**

app/models/analysis.js

@@ -1,17 +1,18 @@
 var mongoose = require("mongoose"),
   globals = require("../../config/globals.js"),
+  setup = require("./../../config/setup"),
   moment = require("moment"),
   _ = require("underscore"),
   winston = require("winston"),
   hpcsocket = require(__dirname + "/../../lib/hpcsocket.js"),
   Msa = require(__dirname + "/msa"),
   extend = require("mongoose-schema-extend");
 
-var redis = require('redis'),
+var redis = require("redis"),
   client = redis.createClient();
 
-var Schema = mongoose.Schema, ObjectId = Schema.ObjectId;
-
+var Schema = mongoose.Schema,
+  ObjectId = Schema.ObjectId;
 
 var AnalysisSchema = new Schema({
   msa: [Msa.MsaSchema],
@@ -39,10 +40,15 @@ AnalysisSchema.virtual("since_created").get(function() {
  * Original file path for document's file upload
  */
 AnalysisSchema.virtual("original_fn").get(function() {
-  return path.resolve(__dirname + "/../../uploads/msa/" + this._id + "-original." + this.original_extension);
+  return path.resolve(
+    __dirname +
+      "/../../uploads/msa/" +
+      this._id +
+      "-original." +
+      this.original_extension
+  );
 });
 
-
 AnalysisSchema.virtual("max_sites").get(function() {
   return 12000;
 });
@@ -77,13 +83,11 @@ AnalysisSchema.statics.pendingJobs = function(cb) {
 };
 
 AnalysisSchema.statics.submitJob = function(job, cb) {
-
   winston.info(
     "submitting " + job.analysistype + " : " + job._id + " to cluster"
   );
 
   var jobproxy = new hpcsocket.HPCSocket(
-
     {
       filepath: job.filepath,
       msa: job.msa,
@@ -94,7 +98,6 @@ AnalysisSchema.statics.submitJob = function(job, cb) {
     "spawn",
     cb
   );
-
 };
 
 AnalysisSchema.statics.subscribePendingJobs = function() {
@@ -114,10 +117,10 @@ AnalysisSchema.statics.usageStatistics = function(cb) {
     .sort({ created: -1 })
     .limit(1)
     .exec(function(err1, items1) {
-      if (err1 || items1.length == 0){
+      if (err1 || items1.length == 0) {
         cb(err1, null);
         return;
-      };
+      }
       self
         .find(
           {
@@ -134,12 +137,15 @@ AnalysisSchema.statics.usageStatistics = function(cb) {
           }
         )
         .exec(function(err, items) {
-          client.set(self.collection.name + "_job_stats", JSON.stringify(items), (err, reply) => {});
+          client.set(
+            setup.database_name + "_" + self.collection.name + "_job_stats",
+            JSON.stringify(items),
+            (err, reply) => {}
+          );
           cb(err, items);
-
-          });
-      });
-  };
+        });
+    });
+};
 /**
  * unix timestamp
  */
@@ -153,6 +159,12 @@ AnalysisSchema.virtual("generic_error_msg").get(function() {
   return error_msg;
 });
 
+AnalysisSchema.virtual("results_path").get(function() {
+  return path.resolve(
+    __dirname + "../../../results/jobs/" + this._id + "-results" + ".json"
+  );
+});
+
 AnalysisSchema.methods.resubscribe = function() {
   var jobproxy = new hpcsocket.HPCSocket(
     {
@@ -181,8 +193,7 @@ AnalysisSchema.methods.cancel = function(callback) {
 };
 
 AnalysisSchema.statics.cachePath = function() {
-   return this.collection.name + "_job_stats";
-  };
-
+  return setup.database_name + "_" + this.collection.name + "_job_stats";
+};
 
 module.exports = AnalysisSchema;

app/models/busted.js

@@ -27,6 +27,10 @@ Busted.virtual("status_stack").get(function() {
   return ["queue", "running", "completed"];
 });
 
+Busted.virtual("upload_redirect_path").get(function() {
+  return path.join("/busted/", String(this._id), "/select-foreground");
+});
+
 /**
  * Complete file path for document's file upload
  */

app/models/fel.js

@@ -37,7 +37,13 @@ FEL.virtual("filepath").get(function() {
  * Original file path for document's file upload
  */
 FEL.virtual("original_fn").get(function() {
-  return path.resolve(__dirname + "/../../uploads/msa/" + this._id + "-original." + this.original_extension);
+  return path.resolve(
+    __dirname +
+      "/../../uploads/msa/" +
+      this._id +
+      "-original." +
+      this.original_extension
+  );
 });
 
 /**

app/models/flea.js

@@ -80,8 +80,6 @@ Flea.virtual("pdb_structure").get(function() {
   return __dirname + "/../../public/assets/flea/pdbs/env_structure.pdb";
 });
 
-
-
 /**
  * URL for a envmonkey path
  */

app/models/gard.js

@@ -33,13 +33,12 @@ GARD.virtual("filepath").get(function() {
 });
 
 /**
- * Result NEXUS file 
+ * Result NEXUS file
  */
 GARD.virtual("result_nexus_fn").get(function() {
   return __dirname + "/../../uploads/msa/" + this._id + ".gard.result.nex";
 });
 
-
 /**
  * Filename of document's file upload
  */

app/models/hivtrace.js

@@ -29,7 +29,8 @@ var error_codes = {
   FAILED_ASSIGNMENT: 1
 };
 
-var Schema = mongoose.Schema, ObjectId = Schema.ObjectId;
+var Schema = mongoose.Schema,
+  ObjectId = Schema.ObjectId;
 
 function notEmptyValidator(val) {
   return val !== null;
@@ -107,7 +108,7 @@ var HivTrace = new Schema({
     validate: [notEmptyValidator, "Ambiguity Handling field is empty"]
   },
   sequence_length: Number,
-  job_started : { type: Boolean, default:false },
+  job_started: { type: Boolean, default: false },
   status_stack: Array,
   status: {
     type: String
@@ -208,29 +209,29 @@ HivTrace.virtual("analysistype").get(function() {
 });
 
 /**
-* file path for aligned document
-*/
+ * file path for aligned document
+ */
 HivTrace.virtual("aligned_fasta_fn").get(function() {
   return __dirname + "/../../uploads/hivtrace/" + this._id + ".aligned.fa";
 });
 
 /**
-* file path for trace results
-*/
+ * file path for trace results
+ */
 HivTrace.virtual("trace_results").get(function() {
   return __dirname + "/../../uploads/hivtrace/" + this._id + ".trace.json";
 });
 
 /**
-* file path for trace results
-*/
+ * file path for trace results
+ */
 HivTrace.virtual("rel_trace_results").get(function() {
   return this._id + ".trace.json";
 });
 
 /**
-* relative file path for aligned document
-*/
+ * relative file path for aligned document
+ */
 HivTrace.virtual("rel_aligned_fasta_fn").get(function() {
   return this._id + ".aligned.fa";
 });
@@ -257,7 +258,7 @@ HivTrace.virtual("status_index").get(function() {
  * Percentage of job complete
  */
 HivTrace.virtual("percentage_complete").get(function() {
-  return (this.status_index + 1) / this.status_stack.length * 100 + "%";
+  return ((this.status_index + 1) / this.status_stack.length) * 100 + "%";
 });
 
 /**
@@ -275,7 +276,6 @@ HivTrace.virtual("url").get(function() {
 });
 
 HivTrace.methods.saveAttributes = function(cb) {
-
   var self = this;
 
   // Once annotations are configured, save the mapped attributes so that we
@@ -290,19 +290,16 @@ HivTrace.methods.saveAttributes = function(cb) {
   });
 
   var patient_attributes = _.map(headers, function(d) {
-
     var attrs = d.split(delimiter);
     var key_val = _.object(annotations, attrs);
     key_val["header"] = d;
     return key_val;
-
   });
 
   // save attributes for each patient
   self.patient_attributes = patient_attributes;
 
   cb(null, self);
-
 };
 
 HivTrace.methods.addAttributesToResults = function(cb) {
@@ -312,9 +309,9 @@ HivTrace.methods.addAttributesToResults = function(cb) {
   var attr_keys = _.keys(attributes[0]);
 
   var category_map = {
-    "categorical" : "String",
-    "individual" : "String",
-    "temporal" : "Date"
+    categorical: "String",
+    individual: "String",
+    temporal: "Date"
   };
 
   // transform attributes to be a dictionary
@@ -337,6 +334,7 @@ HivTrace.methods.addAttributesToResults = function(cb) {
 
   // read from trace results
   fs.readFile(self.trace_results, function(err, results) {
+    //fs.readFile(path.resolve(__dirname + "../../../results/jobs/" + this._id + "-results" + ".json"), function(err, results) {
     if (err) {
       cb(err, null);
       return;
@@ -456,10 +454,10 @@ HivTrace.statics.usageStatistics = function(cb) {
     .sort({ created: -1 })
     .limit(1)
     .exec(function(err1, items1) {
-      if (err1 || items1.length == 0){
+      if (err1 || items1.length == 0) {
         cb(err1, null);
         return;
-      };
+      }
       self
         .find(
           {