Merge branch 'master' of github.com:veg/datamonkey-js

app/models/fel.js

@@ -15,6 +15,16 @@ var FEL = mongoose.Schema({
   resample: Number,
   ci: Boolean,
   bootstrap: Boolean,
+  multiple_hits: {
+    type: String,
+    enum: ["None", "Double", "Double+Triple"],
+    default: "None",
+  },
+  site_multihit: {
+    type: String,
+    enum: ["Estimate", "Global"],
+    default: "Estimate",
+  },
 });
 
 FEL.add(AnalysisSchema);
@@ -47,7 +57,7 @@ FEL.virtual("original_fn").get(function () {
       "/../../uploads/msa/" +
       this._id +
       "-original." +
-      this.original_extension
+      this.original_extension,
   );
 });
 
@@ -123,7 +133,7 @@ FEL.statics.spawn = function (fn, options, callback) {
         } else {
           var move = Msa.removeTreeFromFile(
             fel_result.filepath,
-            fel_result.filepath
+            fel_result.filepath,
           );
           move.then(
             (val) => {
@@ -137,7 +147,7 @@ FEL.statics.spawn = function (fn, options, callback) {
             },
             (reason) => {
               callback(err, "issue removing tree from file");
-            }
+            },
           );
         }
       }

app/models/meme.js

@@ -12,6 +12,10 @@ var MEME = mongoose.Schema({
   results: Object,
   resample: Number,
   bootstrap: Boolean,
+  multiple_hits: String,
+  site_multihit: String,
+  rates: Number,
+  impute_states: String,
 });
 
 MEME.add(AnalysisSchema);
@@ -49,50 +53,41 @@ MEME.virtual("url").get(function () {
   return "http://" + setup.host + "/meme/" + this._id;
 });
 
-/**
- * Shared API / Web request job spawn
- */
+
 MEME.statics.spawn = function (fn, options, callback) {
   const Msa = mongoose.model("Msa");
-  var meme = new this();
+  const meme = new this();
 
-  let gencodeid = options.gencodeid,
-    datatype = options.datatype;
-
-  meme.mail = options.mail;
+  // Dynamically add all options to the meme object
+  Object.keys(options).forEach((key) => {
+    meme[key] = options[key];
+  });
 
   // Check advanced options
-  if (!_.isNaN(options.resample)) {
-    meme.resample = options.resample;
-    meme.bootstrap = true;
-  } else {
-    meme.bootstrap = false;
-  }
+  meme.bootstrap = !_.isNaN(options.resample);
 
   const connect_callback = function (data) {
-    if (data == "connected") {
+    if (data === "connected") {
       logger.log("connected");
     }
   };
 
-  Msa.parseFile(fn, datatype, gencodeid, (err, msa) => {
+  Msa.parseFile(fn, options.datatype, options.gencodeid, (err, msa) => {
     if (err) {
       callback(err);
       return;
     }
+
     // Check if msa exceeds limitations
     if (msa.sites > meme.max_sites) {
-      const error =
-        "Site limit exceeded! Sites must be less than " + meme.max_sites;
+      const error = `Site limit exceeded! Sites must be less than ${meme.max_sites}`;
       logger.error(error);
       callback(error);
       return;
     }
 
     if (msa.sequences > meme.max_sequences) {
-      var error =
-        "Sequence limit exceeded! Sequences must be less than " +
-        meme.max_sequences;
+      const error = `Sequence limit exceeded! Sequences must be less than ${meme.max_sequences}`;
       logger.error(error);
       callback(error);
       return;
@@ -108,32 +103,24 @@ MEME.statics.spawn = function (fn, options, callback) {
         return;
       }
 
-      function move_cb(err, result) {
+      function move_cb(err) {
         if (err) {
           logger.error(
-            "meme rename failed" +
-              " Errored on line 113~ within models/meme.js :: move_cb " +
-              err
+            `meme rename failed. Error on line 113~ within models/meme.js :: move_cb ${err}`,
           );
           callback(err, null);
         } else {
-          var move = Msa.removeTreeFromFile(
-            meme_result.filepath,
-            meme_result.filepath
-          );
-          move.then(
-            (val) => {
-              let to_send = meme;
-              to_send.upload_redirect_path = meme.upload_redirect_path;
+          Msa.removeTreeFromFile(meme_result.filepath, meme_result.filepath)
+            .then(() => {
               this.submitJob(meme_result, connect_callback);
               callback(null, meme);
-            },
-            (reason) => {
-              res.json(500, { error: "issue removing tree from file" });
-            }
-          );
+            })
+            .catch(() => {
+              callback(new Error("issue removing tree from file"));
+            });
         }
       }
+
       helpers.moveSafely(fn, meme_result.filepath, move_cb.bind(this));
     });
   });

app/models/msa.js

@@ -65,12 +65,12 @@ Msa.virtual("genetic_code").get(function () {
 });
 
 Msa.virtual("day_created_on").get(function () {
-  var time = moment(this.timestamp);
+  var time = moment.unix(this.timestamp);
   return time.format("YYYY-MMM-DD");
 });
 
 Msa.virtual("time_created_on").get(function () {
-  var time = moment(this.timestamp);
+  var time = moment.unix(this.timestamp);
   return time.format("HH:mm");
 });
 

app/routes/fel.js

@@ -25,6 +25,7 @@ exports.uploadFile = function (req, res) {
     }
   };
 
+
   var fn = req.files.files.file,
     fel = new FEL(),
     postdata = req.body,
@@ -33,9 +34,12 @@ exports.uploadFile = function (req, res) {
     ds_variation = postdata.ds_variation,
     resample = parseInt(postdata.resample);
 
+
   fel.original_extension = path.basename(fn).split(".")[1];
   fel.mail = postdata.mail;
   fel.ci = postdata.confidence_interval == "true";
+  fel.multiple_hits = postdata.multiple_hits;
+  fel.site_multihit = postdata.site_multihit;
 
   // Check advanced options
   if (!_.isNaN(resample)) {
@@ -87,7 +91,7 @@ exports.uploadFile = function (req, res) {
         } else {
           var move = Msa.removeTreeFromFile(
             fel_result.filepath,
-            fel_result.filepath
+            fel_result.filepath,
           );
           move.then(
             (val) => {
@@ -98,7 +102,7 @@ exports.uploadFile = function (req, res) {
             },
             (reason) => {
               res.json(500, { error: "issue removing tree from file" });
-            }
+            },
           );
         }
       }
@@ -116,7 +120,7 @@ exports.uploadFile = function (req, res) {
           helpers.moveSafely(
             req.files.files.file,
             fel_result.filepath,
-            move_cb
+            move_cb,
           );
         });
       });

app/routes/meme.js

@@ -18,12 +18,16 @@ exports.form = function (req, res) {
 exports.invoke = function (req, res) {
   var fn = req.files.files.file;
   let postdata = req.body;
-  //let resample = parseInt(postdata.resample);
 
   let options = {
     datatype: 0,
     gencodeid: postdata.gencodeid,
     mail: postdata.mail,
+    multiple_hits: postdata.multiple_hits,
+    site_multihit: postdata.site_multihit,
+    rates: parseInt(postdata.rates),
+    resample: parseInt(postdata.resample || 0),
+    impute_states: postdata.impute_states,
   };
 
   //// Check advanced options

app/templates/fel/msa_form.ejs

@@ -88,6 +88,22 @@
         </select>
       </div>
 
+      <div class="form-group">
+        <label for="multiple-hits">Multiple Hits</label>
+        <select name="multiple_hits" id="multiple-hits">
+          <option value="None">None (Single mutations only)</option>
+          <option value="Double">Double (Branch-specific rates for double substitutions)</option>
+          <option value="Double+Triple">Double+Triple (Branch-specific rates for double and triple substitutions)</option>
+        </select>
+      </div>
+
+      <div class="form-group">
+        <label for="estimated-rates">Site Multihit</label>
+        <select name="site_multihit" id="site-multihit">
+          <option value="Estimate">Estimate (Branch-specific rates for substitutions based on model fit)</option>
+          <option value="Global">Global (Rates derived from global model fit)</option>
+        </select>
+      </div>
 
       <div class="form-group <%if (typeof errors != "undefined" && typeof errors.mail != "undefined") { %>has-error<% } %>">
         <label id="datatype-content" class="control-label">Notify When Completed?</label>

app/templates/meme/form.ejs

@@ -1,7 +1,7 @@
 <%- include("../includes/header.ejs") %>
 <div id="container" class="container">
   <%- include("header.ejs") %>
-  <%- include("../partials/msa/form.ejs") %>
+  <%- include("./msa_form.ejs") %>
   <%- include("../includes/modal.ejs") %>
 </div>
 <%- include("../includes/footer.ejs") %>