Merge pull request #260 from veg/develop

Develop

.babelrc

@@ -0,0 +1,16 @@
+{
+  "plugins": [
+    "@babel/plugin-proposal-class-properties"
+  ],
+  "presets": [
+    "@babel/preset-env",
+    "@babel/preset-react"
+  ],
+  "env": {
+    "start": {
+      "presets": [
+        "@babel/preset-env"
+      ]
+    }
+  }
+}

README.md

@@ -4,7 +4,7 @@ datamonkey-js
 INSTALL
 ===========================
 ## System Dependencies
-* node >= 12
+* node >= 14
 * mongodb-server
 * redis
 

app/models/contrast-fel.js

@@ -0,0 +1,64 @@
+var mongoose = require("mongoose"),
+  extend = require("mongoose-schema-extend"),
+  path = require("path"),
+  Msa = require(__dirname + "/msa");
+
+var AnalysisSchema = require(__dirname + "/analysis");
+
+var ContrastFEL = AnalysisSchema.extend({
+  tagged_nwk_tree: String,
+  analysis_type: Number,
+  original_extension: String,
+  last_status_msg: String,
+  branch_sets: [String],
+  results: Object,
+  ds_variation: Number
+});
+
+ContrastFEL.virtual("pmid").get(function() {
+  return "22807683";
+});
+
+ContrastFEL.virtual("analysistype").get(function() {
+  return "cfel";
+});
+
+ContrastFEL.virtual("upload_redirect_path").get(function() {
+  return path.join("/contrast_fel/", String(this._id), "/select-foreground");
+});
+
+/**
+ * Complete file path for document's file upload
+ */
+ContrastFEL.virtual("filepath").get(function() {
+  return path.join(__dirname, "/../../uploads/msa/", this._id + ".fasta");
+});
+
+/**
+ * Original file path for document's file upload
+ */
+ContrastFEL.virtual("original_fn").get(function() {
+  return path.resolve(
+    __dirname +
+      "/../../uploads/msa/" +
+      this._id +
+      "-original." +
+      this.original_extension
+  );
+});
+
+/**
+ * Filename of document's file upload
+ */
+ContrastFEL.virtual("status_stack").get(function() {
+  return ["queue", "running", "completed"];
+});
+
+/**
+ * URL for a busted path
+ */
+ContrastFEL.virtual("url").get(function() {
+  return "http://" + setup.host + "/contrast_fel/" + this._id;
+});
+
+module.exports = mongoose.model("ContrastFEL", ContrastFEL);

app/models/gard.js

@@ -47,7 +47,7 @@ GARD.virtual("status_stack").get(function() {
 });
 
 /**
- * URL for a busted path
+ * URL for GARD path
  */
 GARD.virtual("url").get(function() {
   return "http://" + setup.host + "/gard/" + this._id;

app/models/hivtrace.js

@@ -5,9 +5,7 @@ path = require("path");
 var mongoose = require("mongoose"),
   moment = require("moment"),
   d3 = require("d3"),
-  check = require("validator").check,
   globals = require("../../config/globals.js"),
-  sanitize = require("validator").sanitize,
   fs = require("fs"),
   readline = require("readline"),
   spawn = require("child_process").spawn,

app/models/msa.js

@@ -1,9 +1,7 @@
 var mongoose = require("mongoose"),
   moment = require("moment"),
-  check = require("validator").check,
   globals = require("../../config/globals.js"),
   spawn = require("child_process").spawn,
-  sanitize = require("validator").sanitize,
   fs = require("fs"),
   winston = require("winston"),
   _ = require("lodash"),
@@ -66,7 +64,6 @@ var Msa = new Schema({
   visit_code: String,
   visit_date: Date,
   original_filename: String,
-  mailaddr: String,
   created: {
     type: Date,
     default: Date.now
@@ -193,16 +190,6 @@ Msa.statics.deliverFasta = function(filepath) {
 
 var MsaModel = mongoose.model("MsaModel", Msa);
 
-MsaModel.schema.path("mailaddr").validate(function(value) {
-  if (value) {
-    check(value)
-      .len(6, 64)
-      .isEmail();
-  } else {
-    return true;
-  }
-}, "Invalid email");
-
 Msa.methods.AnalysisCount = function(cb) {
   var type_counts = {};
   var c = 0;
@@ -397,7 +384,7 @@ Msa.statics.parseFile = function(fn, datatype, gencodeid, cb) {
     msa.gencodeid = file_info.gencodeid;
     msa.sites = file_info.sites;
     msa.sequences = file_info.sequences;
-    msa.timestamp = file_info.timestamp;
+    msa.timestamp = _.trim(file_info.timestamp);
     msa.goodtree = file_info.goodtree;
     msa.nj = file_info.nj;
     msa.usertree = fpi[0].usertree;

app/models/multihit.js

@@ -0,0 +1,49 @@
+var mongoose = require("mongoose"),
+  extend = require("mongoose-schema-extend"),
+  winston = require("winston"),
+  path = require("path"),
+  Msa = require(__dirname + "/msa");
+
+var AnalysisSchema = require(__dirname + "/analysis");
+
+var MULTIHIT = AnalysisSchema.extend({
+  last_status_msg: String,
+  results: Object,
+  triple_islands: String,
+  rate_classes: Number
+});
+
+MULTIHIT.virtual("analysistype").get(function() {
+  return "multihit";
+});
+
+MULTIHIT.virtual("pmid").get(function() {
+  return "TBD";
+});
+
+/**
+ * Filename of document's file upload
+ */
+MULTIHIT.virtual("status_stack").get(function() {
+  return ["queue", "running", "completed"];
+});
+
+MULTIHIT.virtual("upload_redirect_path").get(function() {
+  return path.join("/multihit/", String(this._id));
+});
+
+/**
+ * Complete file path for document's file upload
+ */
+MULTIHIT.virtual("filepath").get(function() {
+  return path.resolve(__dirname + "/../../uploads/msa/" + this._id + ".fasta");
+});
+
+/**
+ * URL for a multihit path
+ */
+MULTIHIT.virtual("url").get(function() {
+  return "http://" + setup.host + "/multihit/" + this._id;
+});
+
+module.exports = mongoose.model("MULTIHIT", MULTIHIT);

app/routes/analysis.js

@@ -11,11 +11,13 @@ var mongoose = require("mongoose"),
   Sequences = mongoose.model("Sequences"),
   PartitionInfo = mongoose.model("PartitionInfo"),
   FEL = mongoose.model("FEL"),
+  ContrastFEL = mongoose.model("ContrastFEL"),
   aBSREL = mongoose.model("aBSREL"),
   Busted = mongoose.model("Busted"),
   FUBAR = mongoose.model("FUBAR"),
   GARD = mongoose.model("GARD"),
   MEME = mongoose.model("MEME"),
+  MULTIHIT = mongoose.model("MULTIHIT"),
   Relax = mongoose.model("Relax"),
   HivTrace = mongoose.model("HivTrace"),
   Fade = mongoose.model("Fade"),
@@ -40,6 +42,7 @@ exports.getInfo = function(model_up, req, res) {
 };
 
 exports.getResults = function(model_up, req, res) {
+
   model_up.findOne({ _id: req.params.id }, function(err, model_var) {
     if (err || !model_var) {
       res.json(500, error.errorResponse("invalid id : " + req.params.id));