v1.0.6: cBioPortal works

.gitmodules

@@ -16,3 +16,6 @@
 [submodule "webapp/packages/blobs"]
 	path = webapp/packages/blobs
 	url = https://github.com/UCSC-MedBook/blobs
+[submodule "webapp/packages/collaborations"]
+	path = webapp/packages/collaborations
+	url = https://github.com/UCSC-MedBook/collaborations

config/rb/run.sh

@@ -1,5 +1,4 @@
-if [ -z "$1" ]; then
-    MONGO_URL="mongodb://localhost:27017/MedBook" meteor --port 3003 --settings settings.json
-else
-    MONGO_URL="mongodb://localhost:27017/MedBook" meteor $1 --port 3003 --settings settings.json
-fi
+export MONGO_URL="mongodb://localhost:27017/MedBook"
+export MEDBOOK_FILESTORE=/tmp/filestore
+
+meteor --port 3003 --settings ../config/rb/settings.json

config/rb/settings.json

@@ -1,14 +1,20 @@
 {
-  "rscript": "Rscript",
-  "python": "python",
-  "limma_path": "/data/MedBook/External-Tools/limma/limma_ng.R",
-  "apply_signature_path" : "/data/MedBook/External-Tools/signature/apply_signature.py",
-  "viper_supervised_path": "/data/MedBook/UCSC_VIPER/bin/run-viper-supervised.R",
-  "viper_unsupervised_path": "/data/MedBook/UCSC_VIPER/bin/run-viper-unsupervised.R",
-  "viper_path": "/data/MedBook/UCSC_VIPER/bin/run-viper.R",
-  "marina_path": "/data/MedBook/UCSC_VIPER/bin/run-marina.R",
-  "gsea_path": "/data/MedBook/External-Tools/gsea/rgGSEA.py",
-  "boxplot_new_path": "/data/MedBook/Tools/MedBook-Adapters/boxplot//boxplot.new.R",
-  "boxplot_path": "/data/MedBook/Tools/MedBook-Adapters/boxplot//boxplot.R",
-  "violinplot_path": "/data/MedBook/Tools/MedBook-Adapters/boxplot//violinplot.R",
+ "sh": "/bin/sh",
+ "rscript": "Rscript",
+ "python": "python",
+ "limma_path": "/data/MedBook/MedBook-JobRunner/external-tools/limma/limma_ng.R",
+ "outlier_analysis": "/data/MedBook/MedBook-JobRunner/external-tools/OutlierAnalysis/outlier-analysis.sh",
+ "calculate_outlier_genes": "/data/MedBook/MedBook-JobRunner/external-tools/OutlierAnalysis/calculate_outlier_genes.R",
+ "genomic_expression_export": "/data/MedBook/MedBook-JobRunner/external-tools/exporters/genomic_expression_export.py",
+ "gene_set_collection_export": "/data/MedBook/MedBook-JobRunner/external-tools/exporters/gene_set_collection_export.py",
+ "limma_phenotype_export": "/data/MedBook/MedBook-JobRunner/external-tools/exporters/limma_phenotype_export.py",
+ "apply_signature_path" : "/data/MedBook/External-Tools/signature/apply_signature.py",
+ "viper_supervised_path": "/data/MedBook/UCSC_VIPER/bin/run-viper-supervised.R",
+ "viper_unsupervised_path": "/data/MedBook/UCSC_VIPER/bin/run-viper-unsupervised.R",
+ "viper_path": "/data/MedBook/UCSC_VIPER/bin/run-viper.R",
+ "marina_path": "/data/MedBook/UCSC_VIPER/bin/run-marina.R",
+ "gsea_path": "/data/MedBook/External-Tools/gsea/rgGSEA.py",
+ "boxplot_new_path": "/data/MedBook/Tools/MedBook-Adapters/boxplot//boxplot.new.R",
+ "boxplot_path": "/data/MedBook/Tools/MedBook-Adapters/boxplot//boxplot.R",
+ "violinplot_path": "/data/MedBook/Tools/MedBook-Adapters/boxplot//violinplot.R"
 }

config/teo/settings.json

@@ -1,12 +1,12 @@
 {
   "sh": "/bin/sh",
   "rscript": "Rscript",
-  "limma_path": "/Users/mokolodi1/work/medbook/next/MedBook-JobRunner/external-tools/limma/limma_ng.R",
-  "outlier_analysis": "/Users/mokolodi1/work/medbook/next/MedBook-JobRunner/external-tools/OutlierAnalysis/outlier-analysis.sh",
-  "calculate_outlier_genes": "/Users/mokolodi1/work/medbook/next/MedBook-JobRunner/external-tools/OutlierAnalysis/calculate_outlier_genes.R",
-  "genomic_expression_export": "/Users/mokolodi1/work/medbook/next/MedBook-JobRunner/external-tools/exporters/genomic_expression_export.py",
-  "gene_set_collection_export": "/Users/mokolodi1/work/medbook/next/MedBook-JobRunner/external-tools/exporters/gene_set_collection_export.py",
-  "limma_phenotype_export": "/Users/mokolodi1/work/medbook/next/MedBook-JobRunner/external-tools/exporters/limma_phenotype_export.py",
-  "gsea_path": "/Users/mokolodi1/work/medbook/next/MedBook-JobRunner/external-tools/gsea/rgGSEA.py",
-  "gsea_jar_path": "/Users/mokolodi1/work/medbook/next/MedBook-JobRunner/external-tools/gsea/gsea2-2.2.2.jar"
+  "limma_path": "/Users/mokolodi1/work/medbook/medbook/MedBook-JobRunner/external-tools/limma/limma_ng.R",
+  "outlier_analysis": "/Users/mokolodi1/work/medbook/medbook/MedBook-JobRunner/external-tools/OutlierAnalysis/outlier-analysis.sh",
+  "calculate_outlier_genes": "/Users/mokolodi1/work/medbook/medbook/MedBook-JobRunner/external-tools/OutlierAnalysis/calculate_outlier_genes.R",
+  "genomic_expression_export": "/Users/mokolodi1/work/medbook/medbook/MedBook-JobRunner/external-tools/exporters/genomic_expression_export.py",
+  "gene_set_collection_export": "/Users/mokolodi1/work/medbook/medbook/MedBook-JobRunner/external-tools/exporters/gene_set_collection_export.py",
+  "limma_phenotype_export": "/Users/mokolodi1/work/medbook/medbook/MedBook-JobRunner/external-tools/exporters/limma_phenotype_export.py",
+  "gsea_path": "/Users/mokolodi1/work/medbook/medbook/MedBook-JobRunner/external-tools/gsea/rgGSEA.py",
+  "gsea_jar_path": "/Users/mokolodi1/work/medbook/medbook/MedBook-JobRunner/external-tools/gsea/gsea2-2.2.2.jar"
 }

webapp/.meteor/packages

@@ -26,3 +26,4 @@ mokolodi1:[email protected]
 medbook:adapters
 medbook:namespace
 medbook:blobs
+medbook:collaborations

webapp/.meteor/versions

@@ -31,6 +31,7 @@ [email protected]
 [email protected]
 [email protected]
 [email protected]
+erasaur:[email protected]
 [email protected]
 [email protected]
 [email protected]
@@ -47,6 +48,7 @@ [email protected]
 matb33:[email protected]
 medbook:[email protected]
 medbook:[email protected]
+medbook:[email protected]
 medbook:[email protected]
 medbook:[email protected]
 medbook:[email protected]

webapp/packages.json

@@ -5,5 +5,6 @@
   "q": "1.4.1",
   "xlsx": "0.8.0",
 	"mime": "1.2.11",
-  "docker-run": "2.4.0"
+  "docker-run": "2.4.0",
+  "mysql": "2.11.1"
 }

webapp/server/classes/UpdateCbioSecurity.js

@@ -0,0 +1,144 @@
+function UpdateCbioSecurity (job_id) {
+  Job.call(this, job_id);
+}
+UpdateCbioSecurity.prototype = Object.create(Job.prototype);
+UpdateCbioSecurity.prototype.constructor = UpdateCbioSecurity;
+
+var mysql = Meteor.npmRequire('mysql');
+
+UpdateCbioSecurity.prototype.run = function () {
+  var connection = mysql.createConnection({
+    host     : "mysql",
+    user     : "cbio",
+    password : "P@ssword1",
+    database : "cbioportal"
+  });
+
+  connection.connect();
+
+  // Collect this information out here so that it runs in the Meteor
+  // environment, which we'll lose in the promise code below
+  var allNamesAndEmails = _.map(this.job.args.collab_names, function (name) {
+    var collab = Collaborations.findOne({ name: name });
+
+    if (!collab) {
+      throw new Error("collaboration name invalid: " + name);
+    }
+
+    return {
+      name: name,
+      emails: collab.getUserEmails(),
+    };
+  });
+
+  var self = this;
+  var jobDeferred = Q.defer();
+
+  // This 5 was chosen arbitrarily because I don't know how to start with a
+  // .then. I like it better when all the logic code is in .thens because
+  // I find it easier to read.
+  Q.when(5)
+    // NOTE: Q.nfcall doesn't work here for some reason
+    .then(function () {
+      var deferred = Q.defer();
+
+      connection.query("DELETE FROM users", function (error, result) {
+        if (error) { deferred.reject(error); }
+        else { deferred.resolve(result); }
+      });
+
+      return deferred.promise;
+    })
+    .then(function () {
+      var deferred = Q.defer();
+
+      connection.query("DELETE FROM authorities", function (error, result) {
+        if (error) { deferred.reject(error); }
+        else { deferred.resolve(result); }
+      });
+
+      return deferred.promise;
+    })
+    .then(function () {
+      var deferred = Q.defer();
+      var allPromises = [];
+
+      // For each email insert into the users table and the authorities
+      // table. Wait until every command is done running before continuing.
+      _.each(allNamesAndEmails, function (nameAndEmails) {
+        _.each(nameAndEmails.emails, function (email) {
+          // insert into the users table
+          var usersDeferred = Q.defer();
+          connection.query('INSERT INTO users SET ?', {
+            name: email,
+            email: email,
+            enabled: 1
+          }, function (err, result) {
+            if (err) { usersDeferred.reject(err); }
+            else { usersDeferred.resolve(result); }
+          });
+          allPromises.push(usersDeferred.promise);
+
+          // insert into the authorities table
+          var authoritiesDeferred = Q.defer();
+          connection.query('INSERT INTO authorities SET ?', {
+            email: email,
+
+            // TODO: change to `cbioportal:${nameAndEmails.name}`
+            authority: 'cbioportal:ALL',
+          }, function (err, result) {
+            if (err) { authoritiesDeferred.reject(err); }
+            else { authoritiesDeferred.resolve(result); }
+          });
+          allPromises.push(authoritiesDeferred.promise);
+        });
+
+        console.log("added " + nameAndEmails.emails.length + " users to " +
+            "cbioportal:ALL");
+      });
+
+      // wait for all the promises to resolve and then continue
+      Q.all(allPromises)
+        .then(deferred.resolve)
+        .catch(deferred.reject);
+
+      return deferred.promise;
+    })
+    .then(function () {
+      connection.end();
+
+      jobDeferred.resolve();
+    })
+    .catch(function (error) {
+      jobDeferred.reject(error);
+    });
+
+  return jobDeferred.promise;
+}
+
+Meteor.startup(function () {
+  var newJobBlueprint = {
+    name: "UpdateCbioSecurity",
+    user_id: "admin",
+    args: {
+      collab_names: [ "WCDT" ]
+    }
+  };
+
+  // set up a cron job to execute every so often
+  SyncedCron.add({
+    name: "update-cbio-security",
+    schedule: function(parser) {
+      // parser is a later.parse object
+      return parser.text('every 12 hours');
+    },
+    job: function () {
+      Jobs.insert(newJobBlueprint);
+    },
+  });
+
+  // also execute immediately
+  Jobs.insert(newJobBlueprint);
+});
+
+JobClasses.UpdateCbioSecurity = UpdateCbioSecurity;