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bridgedb · Jul 24, 2019 · 7b2d90e · 7b2d90e
1 parent 6321eff
commit 7b2d90e
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Showing 68 changed files with 863,850 additions and 4,959 deletions.
diff --git a/bin/bridgedb b/bin/bridgedb
@@ -19,21 +19,21 @@ program
 
 program
   .command("datasource <input> [as]")
-    .description(
-      `If "as" not specified: identify the format used to specify a given xref data source.
+  .description(
+    `If "as" not specified: identify the format used to specify a given xref data source.
       If "as" specified: format an xref data source as specified.
 
     For example, Entrez Gene -> ncbigene
 
     The data comes from BridgeDb.
     `
-    )
+  )
   .action(function(input, as, options) {
     var serialize = ndjson.serialize();
     if (process.env.NODE_ENV === "development") {
       if (!process.env.MOCK_SERVER_WARNING_GIVEN) {
         console.warn("Using development mock server.");
-        process.env.MOCK_SERVER_WARNING_GIVEN = 'yes';
+        process.env.MOCK_SERVER_WARNING_GIVEN = "yes";
       }
       //*TODO: use this instance for testing:
       var bridgeDb = new BridgeDb({
@@ -58,25 +58,28 @@ program
     }
   })
   .on("--help", function() {
-    console.log(fs
-      .readFileSync(path.join(__dirname, "datasource.help.sh"), "utf8")
-      // We drop the shebang when displaying here as help
-      .replace(/^.*\n/, "")
-      // We also drop bash comment characters
-      .replace(/^#(\ )?/gm, "")
-      // and replace path to bridgedb with just bridgedb
-      .replace(/(\.\/)?bin\/(bridgedb)/gm, "\$2"));
+    console.log(
+      fs
+        .readFileSync(path.join(__dirname, "datasource.help.sh"), "utf8")
+        // We drop the shebang when displaying here as help
+        .replace(/^.*\n/, "")
+        // We also drop bash comment characters
+        .replace(/^#(\ )?/gm, "")
+        // and replace path to bridgedb with just bridgedb
+        .replace(/(\.\/)?bin\/(bridgedb)/gm, "$2")
+    );
   });
 
 createXrefsCLI(program);
 
-program
-  .command('*')
-  .action(function(cmd){
-    console.error("");
-    console.error('\ \ Unrecognized command "%s". Valid commands shown below:', cmd);
-    program.outputHelp();
-  });
+program.command("*").action(function(cmd) {
+  console.error("");
+  console.error(
+    '  Unrecognized command "%s". Valid commands shown below:',
+    cmd
+  );
+  program.outputHelp();
+});
 
 program.parse(process.argv);
 

diff --git a/bin/dsvXrefs.js b/bin/dsvXrefs.js
@@ -43,9 +43,8 @@ module.exports = function(
   var headersOption = options.hasOwnProperty("headers")
     ? Boolean(options.headers)
     : false;
-  var delimiterOption = options.format in delimiterFor
-    ? delimiterFor[options.format]
-    : "\t";
+  var delimiterOption =
+    options.format in delimiterFor ? delimiterFor[options.format] : "\t";
   var newlineOption = options.newline || "\n";
   var quoteOption = options.quote || '"';
   var commentOption = options.comment || "#";
@@ -54,19 +53,28 @@ module.exports = function(
   const xrefDataSourceArgType = argType(xrefDataSourceArg);
   const xrefIdentifierArgType = argType(xrefIdentifierArg);
 
-  var organismColumn = organismArgType === "auto"
-    ? 0
-    : organismArgType === "columnIndex" ? parseInt(organismArg) : organismArg;
+  var organismColumn =
+    organismArgType === "auto"
+      ? 0
+      : organismArgType === "columnIndex"
+      ? parseInt(organismArg)
+      : organismArg;
 
-  var xrefDataSourceColumn = xrefDataSourceArgType === "auto"
-    ? _.isFinite(parseInt(organismColumn)) ? organismColumn + 1 : 0
-    : xrefDataSourceArgType === "columnIndex"
+  var xrefDataSourceColumn =
+    xrefDataSourceArgType === "auto"
+      ? _.isFinite(parseInt(organismColumn))
+        ? organismColumn + 1
+        : 0
+      : xrefDataSourceArgType === "columnIndex"
       ? parseInt(xrefDataSourceArg)
       : xrefDataSourceArg;
 
-  var xrefIdentifierColumn = xrefIdentifierArgType === "auto"
-    ? _.isFinite(parseInt(xrefDataSourceColumn)) ? xrefDataSourceColumn + 1 : 0
-    : xrefIdentifierArgType === "columnIndex"
+  var xrefIdentifierColumn =
+    xrefIdentifierArgType === "auto"
+      ? _.isFinite(parseInt(xrefDataSourceColumn))
+        ? xrefDataSourceColumn + 1
+        : 0
+      : xrefIdentifierArgType === "columnIndex"
       ? parseInt(xrefIdentifierArg)
       : xrefIdentifierArg;
 
@@ -93,13 +101,12 @@ module.exports = function(
     `^${commentOption}.*$[${newlineOption}]?`,
     "gm"
   );
-  Rx.Observable
-    .fromNodeReadableStream(
-      hl(process.stdin)
-        // Ignore comments
-        .through(replaceStream(commentLineRe, ""))
-        .through(parser)
-    )
+  Rx.Observable.fromNodeReadableStream(
+    hl(process.stdin)
+      // Ignore comments
+      .through(replaceStream(commentLineRe, ""))
+      .through(parser)
+  )
     .mergeMap(function(row) {
       const organism = organismField(row);
       const xrefDataSource = xrefDataSourceField(row);
@@ -149,9 +156,10 @@ module.exports = function(
       } else {
         // long format
         return mappedXrefs$.mergeMap(function(xrefs) {
-          const firstColumn = typeof xrefDataSourceOption !== "undefined"
-            ? xrefIdentifier
-            : [xrefDataSource, xrefIdentifier].join(delimiterOption);
+          const firstColumn =
+            typeof xrefDataSourceOption !== "undefined"
+              ? xrefIdentifier
+              : [xrefDataSource, xrefIdentifier].join(delimiterOption);
 
           return Rx.Observable.from(xrefs).map(xref => {
             return [

diff --git a/bin/jsonXrefs.js b/bin/jsonXrefs.js
@@ -28,13 +28,14 @@ ensembl ncbigene uniprot wikidata
 // ...
 
 function parseJQPath(path) {
-  return path.replace(/^\./, "")
+  return path
+    .replace(/^\./, "")
     .split(".")
     .reduce((acc, s) => {
       (s.match(/(\w+)?(\[\w*\])?/) || [])
         .slice(1)
         .filter(_.negate(_.isUndefined))
-        .map(s => s === "[]" ? true : s.replace(/\[(\w+)\]/, "\1"))
+        .map(s => (s === "[]" ? true : s.replace(/\[(\w+)\]/, "\1")))
         //.map(s => s.replace(/\[(\w+)\]/, "\1").replace(/\[\]/, true))
         .forEach(function(s) {
           acc.push(s);
@@ -59,20 +60,20 @@ function resolveJQPath(base, relativePath) {
  */
 function getByParsedPath(value, path) {
   if (path.length > 0) {
-    return _.get(
-      value,
-      path
-    );
+    return _.get(value, path);
   } else {
     return value;
   }
 }
 
 module.exports = function(
-    bridgeDb, organism,
-    pathToXrefDataSource, pathToXrefIdentifier,
-    desiredXrefDataSources,
-    { base, format, insertionPoint }) {
+  bridgeDb,
+  organism,
+  pathToXrefDataSource,
+  pathToXrefIdentifier,
+  desiredXrefDataSources,
+  { base, format, insertionPoint }
+) {
   var pathToInsertionPoint = insertionPoint;
 
   var { common, relPaths } = _.zip
@@ -210,9 +211,8 @@ module.exports = function(
       }
       var valuesByKey = acc.valuesByKey;
 
-      var entityKey = lastCommonKey !== true
-        ? lastCommonKey
-        : path.slice(-1)[0];
+      var entityKey =
+        lastCommonKey !== true ? lastCommonKey : path.slice(-1)[0];
 
       var entityPathRelToValue = common
         .slice(JSONStreamPath.length)
@@ -428,9 +428,10 @@ it's not a string or array. Skipping addition of ${xrefIdentifier}.`);
               return {
                 event: "data",
                 path: JSONStreamParentPath,
-                value: NEST0_OBJECT_KEY in valuesByKey
-                  ? valuesByKey[NEST0_OBJECT_KEY]
-                  : valuesByKey
+                value:
+                  NEST0_OBJECT_KEY in valuesByKey
+                    ? valuesByKey[NEST0_OBJECT_KEY]
+                    : valuesByKey
               };
             });
         });
@@ -453,11 +454,13 @@ it's not a string or array. Skipping addition of ${xrefIdentifier}.`);
   var i = 0;
 
   if (pathToInsertionPoint === "none") {
-    return parsedDataStream
-      .flatMap(x => hl(x[0].xrefs))
-      //.through(JSONStream.stringify(false))
-      .through(ndjson.serialize())
-      .pipe(process.stdout);
+    return (
+      parsedDataStream
+        .flatMap(x => hl(x[0].xrefs))
+        //.through(JSONStream.stringify(false))
+        .through(ndjson.serialize())
+        .pipe(process.stdout)
+    );
   }
 
   return hl([headerStream, parsedDataStream, footerStream])
@@ -483,8 +486,8 @@ it's not a string or array. Skipping addition of ${xrefIdentifier}.`);
               typeof nsValue === "undefined"
                 ? value
                 : _.isArray(nsValue)
-                  ? nsValue.concat(value)
-                  : _.assign(nsValue, value),
+                ? nsValue.concat(value)
+                : _.assign(nsValue, value),
             (nsValue, key, nsObject) =>
               nsValue || _.isFinite(parseInt(key)) ? Array : Object
           );
@@ -512,7 +515,9 @@ it's not a string or array. Skipping addition of ${xrefIdentifier}.`);
       return acc;
     })
     .flatMap(function(s) {
-      return hl(_.isArray(s) ? s : [s]).through(stringifier).concat(hl(["\n"]));
+      return hl(_.isArray(s) ? s : [s])
+        .through(stringifier)
+        .concat(hl(["\n"]));
     })
     .pipe(process.stdout);
 };
diff --git a/bin/noneXrefs.js b/bin/noneXrefs.js
@@ -17,11 +17,10 @@ module.exports = function(
     .xrefs(organism, xrefDataSource, xrefIdentifier, desiredXrefDataSources)
     //.throughNodeStream(serialize)
     .mergeMap(function(xrefs) {
-      return Rx.Observable
-        .from(xrefs)
-        .map(({ xrefDataSource, xrefIdentifier }) =>
+      return Rx.Observable.from(xrefs).map(
+        ({ xrefDataSource, xrefIdentifier }) =>
           [xrefDataSource, xrefIdentifier].join("\t")
-        );
+      );
     })
     .map(line => line + "\n")
     .pipeToStdout();

diff --git a/karma-ui-combo.conf.js b/karma-ui-combo.conf.js
@@ -1,44 +1,39 @@
-var bridgeDbDefaultConfig = require('./lib/config.js');
+var bridgeDbDefaultConfig = require("./lib/config.js");
 //require('./test/mockserver.js');
 
 module.exports = function(config) {
   var options = {
-    basePath: '',
-    frameworks: ['mocha', 'chai', 'browserify'],
-    browsers: [
-      'Chrome',
-      'Firefox'
-    ],
-    files: ['test/unit/ui-components/ui-combo.test.js'],
+    basePath: "",
+    frameworks: ["mocha", "chai", "browserify"],
+    browsers: ["Chrome", "Firefox"],
+    files: ["test/unit/ui-components/ui-combo.test.js"],
     preprocessors: {
-      'test/unit/ui-components/ui-combo.test.js': 'browserify'
+      "test/unit/ui-components/ui-combo.test.js": "browserify"
     },
     browserify: {
       debug: true,
-      transform: ['brfs']
+      transform: ["brfs"]
     },
     colors: true,
-    reporters: [
-      'coverage',
-      'mocha',
-    ],
+    reporters: ["coverage", "mocha"],
     browserDisconnectTimeout: 60000,
     browserNoActivityTimeout: 60000,
     client: {
       mocha: {
-        timeout: 59000,
-      },
-    },
+        timeout: 59000
+      }
+    }
   };
 
   process.env.MOCKSERVER_PORT = 4522;
   var proxies = {};
   proxies[bridgeDbDefaultConfig.baseIri] = {
-    target: 'http://localhost:' + process.env.MOCKSERVER_PORT + '/',
+    target: "http://localhost:" + process.env.MOCKSERVER_PORT + "/",
     changeOrigin: true
   };
   proxies[bridgeDbDefaultConfig.datasetsMetadataIri] = {
-    target: 'http://localhost:' + process.env.MOCKSERVER_PORT + '/datasources.txt',
+    target:
+      "http://localhost:" + process.env.MOCKSERVER_PORT + "/datasources.txt",
     changeOrigin: true
   };
   options.proxies = proxies;
@@ -48,7 +43,7 @@ module.exports = function(config) {
   }
 
   if (process.env.GROWL) {
-    options.reporters.push('growl');
+    options.reporters.push("growl");
   }
 
   config.set(options);