Merge pull request #760 from veg/mongoose-5-migration

mongoose 5 migration
veg · Nov 20, 2024 · 4977e66 · 4977e66
2 parents 441e3e8 + 4f48820
commit 4977e66
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Showing 20 changed files with 228 additions and 173 deletions.
diff --git a/app/models/absrel.js b/app/models/absrel.js
@@ -3,17 +3,18 @@ var mongoose = require("mongoose"),
   logger = require("../../lib/logger"),
   helpers = require(__dirname + "/../../lib/helpers.js");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var aBSREL = AnalysisSchema.extend({
+var aBSREL = new mongoose.Schema({
   tagged_nwk_tree: String,
   analysis_type: Number,
   last_status_msg: String,
   results: Object,
 });
 
+// Inherit fields from BaseSchema
+aBSREL.add(AnalysisSchema);
+
 aBSREL.virtual("max_sequences").get(function () {
   return 75;
 });

diff --git a/app/models/bgm.js b/app/models/bgm.js
@@ -3,11 +3,9 @@ var mongoose = require("mongoose"),
   logger = require("../../lib/logger"),
   helpers = require(__dirname + "/../../lib/helpers.js");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var BGM = AnalysisSchema.extend({
+var BGM = new mongoose.Schema({
   analysis_type: Number,
   substitution_model: Number,
   last_status_msg: String,
@@ -19,6 +17,8 @@ var BGM = AnalysisSchema.extend({
   results: Object,
 });
 
+BGM.add(AnalysisSchema);
+
 BGM.virtual("pmid").get(function () {
   return "18562270";
 });

diff --git a/app/models/busted.js b/app/models/busted.js
@@ -7,14 +7,16 @@ require("mongoose-schema-extend");
 
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var Busted = AnalysisSchema.extend({
+var Busted = new mongoose.Schema({
   tagged_nwk_tree: String,
   last_status_msg: String,
   multihit: String,
   results: Object,
   ds_variation: Number,
 });
 
+Busted.add(AnalysisSchema);
+
 Busted.virtual("analysistype").get(function () {
   return "busted";
 });

diff --git a/app/models/contrast-fel.js b/app/models/contrast-fel.js
@@ -2,11 +2,9 @@ var mongoose = require("mongoose"),
   path = require("path"),
   helpers = require("../../lib/helpers");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var ContrastFEL = AnalysisSchema.extend({
+var ContrastFEL = mongoose.Schema({
   tagged_nwk_tree: String,
   analysis_type: Number,
   original_extension: String,
@@ -16,6 +14,8 @@ var ContrastFEL = AnalysisSchema.extend({
   ds_variation: Number,
 });
 
+ContrastFEL.add(AnalysisSchema);
+
 ContrastFEL.virtual("pmid").get(function () {
   return "22807683";
 });

diff --git a/app/models/fade.js b/app/models/fade.js
@@ -3,11 +3,9 @@ var mongoose = require("mongoose"),
   logger = require("../../lib/logger"),
   helpers = require(__dirname + "/../../lib/helpers.js");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var Fade = AnalysisSchema.extend({
+var Fade = mongoose.Schema({
   analysis_type: Number,
   last_status_msg: String,
   results: Object,
@@ -21,6 +19,8 @@ var Fade = AnalysisSchema.extend({
   posterior_estimation_method: Number,
 });
 
+Fade.add(AnalysisSchema);
+
 Fade.virtual("pmid").get(function () {
   return "22807683";
 });

diff --git a/app/models/fel.js b/app/models/fel.js
@@ -3,11 +3,9 @@ var mongoose = require("mongoose"),
   logger = require("../../lib/logger"),
   helpers = require("../../lib/helpers");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var FEL = AnalysisSchema.extend({
+var FEL = mongoose.Schema({
   tagged_nwk_tree: String,
   analysis_type: Number,
   original_extension: String,
@@ -19,6 +17,8 @@ var FEL = AnalysisSchema.extend({
   bootstrap: Boolean,
 });
 
+FEL.add(AnalysisSchema);
+
 FEL.virtual("pmid").get(function () {
   return "22807683";
 });

diff --git a/app/models/flea.js b/app/models/flea.js
@@ -6,17 +6,17 @@ var mongoose = require("mongoose"),
   winston = require("winston"),
   Msa = require(__dirname + "/msa");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var Flea = AnalysisSchema.extend({
+var Flea = mongoose.Schema({
   msas: [Msa.MsaSchema],
   last_status_msg: String,
   mail: String,
   results: Object,
 });
 
+Flea.add(AnalysisSchema);
+
 Flea.virtual("analysistype").get(function () {
   return "flea";
 });

diff --git a/app/models/fubar.js b/app/models/fubar.js
@@ -2,18 +2,18 @@ var mongoose = require("mongoose"),
   path = require("path"),
   helpers = require("../../lib/helpers");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var FUBAR = AnalysisSchema.extend({
+var FUBAR = mongoose.Schema({
   analysis_type: Number,
   last_status_msg: String,
   results: Object,
   number_of_grid_points: Number,
   concentration_of_dirichlet_prior: Number,
 });
 
+FUBAR.add(AnalysisSchema);
+
 FUBAR.virtual("pmid").get(function () {
   return "22807683";
 });

diff --git a/app/models/gard.js b/app/models/gard.js
@@ -3,11 +3,9 @@ var mongoose = require("mongoose"),
   logger = require("../../lib/logger"),
   helpers = require("../../lib/helpers");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var GARD = AnalysisSchema.extend({
+var GARD = mongoose.Schema({
   analysis_type: Number,
   datatype: String,
   run_mode: String,
@@ -17,6 +15,8 @@ var GARD = AnalysisSchema.extend({
   rate_classes: Number,
 });
 
+GARD.add(AnalysisSchema);
+
 GARD.virtual("pmid").get(function () {
   return "22807683";
 });

diff --git a/app/models/hivtrace.js b/app/models/hivtrace.js
@@ -11,8 +11,6 @@ const mongoose = require("mongoose"),
   mailer = require(path.join(__dirname, "/../../lib/mailer.js")),
   winston = require("winston");
 
-require("mongoose-schema-extend");
-
 const Schema = mongoose.Schema;
 
 function notEmptyValidator(val) {
@@ -325,9 +323,8 @@ HivTrace.methods.addAttributesToResults = function (cb) {
     try {
       let json_results = JSON.parse(results);
 
-      json_results["trace_results"][
-        "patient_attribute_schema"
-      ] = patient_schema;
+      json_results["trace_results"]["patient_attribute_schema"] =
+        patient_schema;
 
       // annotate each node with the attributes
       _.each(json_results["trace_results"].Nodes, function (node) {
@@ -362,22 +359,24 @@ HivTrace.methods.onComplete = function (data, publisher, channel) {
   if (data) {
     // save results to file
     //self.results = data.results;
-    fs.writeFile(self.trace_results, JSON.stringify(data.results), function (
-      err
-    ) {
-      if (err) throw err;
-      winston.info("saved results file");
-
-      if (self.mail) {
-        mailer.sendJobComplete(self);
-      }
-
-      //Update the status for the analysis
-      self.save(function (err, result) {
+    fs.writeFile(
+      self.trace_results,
+      JSON.stringify(data.results),
+      function (err) {
         if (err) throw err;
-        publisher.publish(channel, JSON.stringify(redis_packet));
-      });
-    });
+        winston.info("saved results file");
+
+        if (self.mail) {
+          mailer.sendJobComplete(self);
+        }
+
+        //Update the status for the analysis
+        self.save(function (err, result) {
+          if (err) throw err;
+          publisher.publish(channel, JSON.stringify(redis_packet));
+        });
+      }
+    );
     winston.info("job complete; got results");
   } else {
     winston.error("job complete, but no data received");

diff --git a/app/models/meme.js b/app/models/meme.js
@@ -4,18 +4,18 @@ var mongoose = require("mongoose"),
   logger = require("../../lib/logger"),
   helpers = require("../../lib/helpers");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var MEME = AnalysisSchema.extend({
+var MEME = mongoose.Schema({
   analysis_type: Number,
   last_status_msg: String,
   results: Object,
   resample: Number,
   bootstrap: Boolean,
 });
 
+MEME.add(AnalysisSchema);
+
 MEME.virtual("pmid").get(function () {
   return "22807683";
 });

diff --git a/app/models/multihit.js b/app/models/multihit.js
@@ -3,17 +3,17 @@ var mongoose = require("mongoose"),
   logger = require("../../lib/logger"),
   helpers = require(__dirname + "/../../lib/helpers.js");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var MULTIHIT = AnalysisSchema.extend({
+var MULTIHIT = mongoose.Schema({
   last_status_msg: String,
   results: Object,
   triple_islands: String,
   rate_classes: Number,
 });
 
+MULTIHIT.add(AnalysisSchema);
+
 MULTIHIT.virtual("analysistype").get(function () {
   return "multihit";
 });

diff --git a/app/models/nrm.js b/app/models/nrm.js
@@ -3,15 +3,15 @@ var mongoose = require("mongoose"),
   logger = require("../../lib/logger"),
   helpers = require(__dirname + "/../../lib/helpers.js");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var NRM = AnalysisSchema.extend({
+var NRM = mongoose.Schema({
   last_status_msg: String,
   results: Object,
 });
 
+NRM.add(AnalysisSchema);
+
 NRM.virtual("analysistype").get(function () {
   return "nrm";
 });

diff --git a/app/models/prime.js b/app/models/prime.js
@@ -1,16 +1,16 @@
 var mongoose = require("mongoose"),
   Msa = require(__dirname + "/msa");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var PRIME = AnalysisSchema.extend({
+var PRIME = mongoose.Schema({
   analysis_type: Number,
   last_status_msg: String,
   results: Object,
 });
 
+PRIME.add(AnalysisSchema);
+
 PRIME.virtual("pmid").get(function () {
   return "22807683";
 });

diff --git a/app/models/relax.js b/app/models/relax.js
@@ -3,18 +3,18 @@ var mongoose = require("mongoose"),
   logger = require("../../lib/logger"),
   helpers = require(__dirname + "/../../lib/helpers.js");
 
-require("mongoose-schema-extend");
-
 var AnalysisSchema = require(__dirname + "/analysis");
 
-var Relax = AnalysisSchema.extend({
+var Relax = mongoose.Schema({
   tagged_nwk_tree: String,
   analysis_type: Number,
   original_extension: String,
   last_status_msg: String,
   results: Object,
 });
 
+Relax.add(AnalysisSchema);
+
 Relax.virtual("analysistype").get(function () {
   return "relax";
 });

diff --git a/app/models/slac.js b/app/models/slac.js
@@ -2,16 +2,16 @@ const mongoose = require("mongoose"),
   path = require("path"),
   helpers = require("../../lib/helpers");
 
-require("mongoose-schema-extend");
-
 const AnalysisSchema = require(__dirname + "/analysis");
 
-const SLAC = AnalysisSchema.extend({
+const SLAC = mongoose.Schema({
   analysis_type: Number,
   last_status_msg: String,
   results: Object,
 });
 
+SLAC.add(AnalysisSchema);
+
 SLAC.virtual("pmid").get(function () {
   return "22807683";
 });

diff --git a/app/routes/absrel.js b/app/routes/absrel.js
@@ -66,6 +66,7 @@ exports.uploadFile = function (req, res) {
     absrel.save(function (err, absrel_result) {
       if (err) {
         logger.error("absrel save failed");
+        console.log(err);
         res.json(500, { error: err });
         return;
       }

diff --git a/package.json b/package.json
@@ -48,8 +48,7 @@
     "main-bower-files": "^2.9.0",
     "moment": "^2.29.4",
     "mongodb": "^2.0.0",
-    "mongoose": "^4.11.7",
-    "mongoose-schema-extend": "^0.1.0",
+    "mongoose": "5",
     "morgan": "x.x.x",
     "multer": "^1.3.0",
     "nodemailer": "^1.0.0",