V0.19.0

README.md

@@ -50,6 +50,13 @@ Database:
 - `DB_PASS` : password if the db uses auth (undefined by default)
 - `DB_CERT` : local file path to certificate (cert) file if the db uses ssl (undefined by default)
 
+Downloads:
+
+- `BULK_DOWNLOADS_PATH` : relative path to bulk downloads
+- `BIOPAX_DOWNLOADS_PATH` : relative path to biopax downloads
+- `BIOPAX_IDMAP_DOWNLOADS_PATH` : relative path to id-mapped biopax downloads
+- `EXPORT_BULK_DELAY_HOURS` : period to delay (batch) export tasks
+
 Services:
 
 - `DEFAULT_CACHE_SIZE` : default max number of entries in each cache

package.json

@@ -133,5 +133,5 @@
   "engines": {
     "node": ">=10.0.0"
   },
-  "version": "0.18.0"
+  "version": "0.19.0"
 }

src/config.js

@@ -56,6 +56,12 @@ export const DB_USER = env('DB_USER', undefined); // username if db uses auth
 export const DB_PASS = env('DB_PASS', undefined); // password if db uses auth
 export const DB_CERT = env('DB_CERT', undefined);  // path to a certificate (cert) file if db uses ssl
 
+// Downloads
+export const BULK_DOWNLOADS_PATH = env('BULK_DOWNLOADS_PATH', 'download/factoid_bulk.zip');
+export const BIOPAX_DOWNLOADS_PATH = env('BIOPAX_DOWNLOADS_PATH', 'download/factoid_biopax.zip');
+export const BIOPAX_IDMAP_DOWNLOADS_PATH = env('BIOPAX_IDMAP_DOWNLOADS_PATH', 'download/factoid_biopax_with_id_mapping.zip');
+export const EXPORT_BULK_DELAY_HOURS = env('EXPORT_BULK_DELAY_HOURS', 0.25);
+
 // Services
 export const PC_URL = env('PC_URL', 'https://apps.pathwaycommons.org/');
 export const REACH_URL = env('REACH_URL', 'http://reach.baderlab.org/api/uploadFile');
@@ -65,7 +71,7 @@ export const NCBI_EUTILS_BASE_URL = env('NCBI_EUTILS_BASE_URL', 'https://eutils.
 export const NCBI_EUTILS_API_KEY = env('NCBI_EUTILS_API_KEY', 'b99e10ebe0f90d815a7a99f18403aab08008');
 export const INDRA_DB_BASE_URL = env('INDRA_DB_BASE_URL', 'https://db.indra.bio/latest/');
 export const INDRA_ENGLISH_ASSEMBLER_URL = env('INDRA_ENGLISH_ASSEMBLER_URL', 'http://api.indra.bio:8000/assemblers/english');
-export const SEMANTIC_SEARCH_BASE_URL = env('SEMANTIC_SEARCH_BASE_URL', 'https://semanticsearch.baderlab.org/');
+export const SEMANTIC_SEARCH_BASE_URL = env('SEMANTIC_SEARCH_BASE_URL', 'https://main.semanticsearch.baderlab.org/');
 
 // Links
 export const UNIPROT_LINK_BASE_URL = env('UNIPROT_LINK_BASE_URL', 'http://www.uniprot.org/uniprot/');

src/server/db.js

@@ -86,7 +86,26 @@ let db = {
         table: table
       };
     } );
+  },
+
+  guaranteeIndex: function( tableName, secondaryKey ){
+    let t, c, r;
+    return this.accessTable( tableName )
+      .then( ({ table, conn, rethink }) => {
+        t = table;
+        c = conn;
+        r = rethink;
+      })
+      .then( () => {
+        return r.branch(
+           t.indexList().contains( secondaryKey ).not(),
+           t.indexCreate( secondaryKey ),
+           null
+        ).run( c );
+      })
+      .then( () => t.indexWait( secondaryKey ).run( c ) );
   }
+
 };
 
 export default db;

src/server/index.js

@@ -20,6 +20,7 @@ import cron from 'node-cron';
 import updateCron from './update-cron';
 import { Appsignal } from '@appsignal/nodejs';
 import { expressMiddleware as asExpressMiddleware, expressErrorHandler as asExpressErrorHandler } from '@appsignal/express';
+import { initExportTasks } from './routes/api/document/export';
 
 let app = express();
 let server = http.createServer(app);
@@ -144,18 +145,24 @@ tryPromise( () => {
       .then( log('Accessed table "%s"', name) )
       .then( t => synch( t, name ) )
       .then( log('Set up synching for "%s"', name) )
+      .then( () => db.guaranteeIndex( 'document', 'createdDate' ) )
+      .then( log('Set up index for document') )
     ;
   };
 
   const tables = ['element', 'document'];
   return tables.reduce( ( p, name ) => p.then( () => setup( name ) ), Promise.resolve() );
-} ).then( () => {
+} )
+.then( () => {
   cron.schedule( config.CRON_SCHEDULE, () => {
     updateCron();
   });
-} ).then( () => {
+} )
+.then( () => {
   server.listen(port);
-} );
+} )
+.then( initExportTasks )
+;
 
 function normalizePort(val) {
   let port = parseInt(val, 10);

src/server/routes/api/document/export.js

@@ -1,16 +1,21 @@
-import fetch from 'node-fetch';
 import JSZip from 'jszip';
 import _ from 'lodash';
 import fs from 'fs';
-import logger from '../../../logger';
+import util from 'util';
+import addMilliseconds from 'date-fns/addMilliseconds';
+import formatDistance from 'date-fns/formatDistance';
 
+import logger from '../../../logger';
+import db from '../../../db';
 import Document from '../../../../model/document';
-
-import { convertDocumentToBiopax,
-        convertDocumentToJson,
-        convertDocumentToSbgn } from '../../../document-util';
-
-import { checkHTTPStatus } from '../../../../util';
+import { getBioPAX, getSBGN, getDocuments, getDocumentJson } from './index';
+import {
+  BULK_DOWNLOADS_PATH,
+  BIOPAX_DOWNLOADS_PATH,
+  EXPORT_BULK_DELAY_HOURS,
+  BIOPAX_IDMAP_DOWNLOADS_PATH,
+  NODE_ENV
+} from '../../../../config';
 
 const DOCUMENT_STATUS_FIELDS = Document.statusFields();
 const CHUNK_SIZE = 20;
@@ -20,20 +25,21 @@ const EXPORT_TYPES = Object.freeze({
   'SBGN': 'sbgn'
 });
 
-const exportToZip = (baseUrl, zipPath, types, biopaxIdMapping) => {
+const exportToZip = (zipPath, types, biopaxIdMapping) => {
   let offset = 0;
   let zip = new JSZip();
 
   const processNext = () => {
-    return fetch(`${baseUrl}/api/document?limit=${CHUNK_SIZE}&offset=${offset}`)
-      .then( checkHTTPStatus )
-      .then( res => res.json() )
-      .then( res => {
-        offset += res.length;
-        if ( res.length > 0 ) {
-          const includedStatuses = [DOCUMENT_STATUS_FIELDS.PUBLIC];
-          const shouldInclude = doc => _.includes(includedStatuses, doc.status);
-          let ids = res.filter( shouldInclude ).map( doc => doc.id );
+
+    return getDocuments({
+        limit: CHUNK_SIZE,
+        offset,
+        status: [DOCUMENT_STATUS_FIELDS.PUBLIC]
+      })
+      .then( ({ results }) => {
+        offset += results.length;
+        if ( results.length > 0 ) {
+          let ids = results.map( doc => doc.id );
           return addToZip( ids, biopaxIdMapping ).then( processNext );
         }
 
@@ -50,11 +56,12 @@ const exportToZip = (baseUrl, zipPath, types, biopaxIdMapping) => {
   };
 
   const addToZip = ( ids, biopaxIdMapping ) => {
-    let _convertDocumentToBiopax = ( id, baseUrl ) => convertDocumentToBiopax( id, baseUrl, biopaxIdMapping );
+    let _getBioPAX = id => getBioPAX( id, biopaxIdMapping );
+    let _getDocumentJson = id => getDocumentJson( id ).then( r => JSON.stringify( r ) );
     let typeToConverter = {
-      [EXPORT_TYPES.JSON]: convertDocumentToJson,
-      [EXPORT_TYPES.BP]: _convertDocumentToBiopax,
-      [EXPORT_TYPES.SBGN]: convertDocumentToSbgn
+      [EXPORT_TYPES.JSON]: _getDocumentJson,
+      [EXPORT_TYPES.BP]: _getBioPAX,
+      [EXPORT_TYPES.SBGN]: getSBGN
     };
 
     let typeToExt = {
@@ -69,7 +76,7 @@ const exportToZip = (baseUrl, zipPath, types, biopaxIdMapping) => {
     }
 
     const idToFiles = id => types.map( t => {
-      return typeToConverter[ t ]( id, baseUrl )
+      return typeToConverter[ t ]( id )
               .catch( () => {
                 logger.error(`Error in export: cannot convert the document ${id} into ${t}`);
                 return null;
@@ -99,4 +106,112 @@ const exportToZip = (baseUrl, zipPath, types, biopaxIdMapping) => {
   return processNext();
 };
 
-export { exportToZip, EXPORT_TYPES };
+/**
+ * scheduleTask
+ * Schedule a task in 'delay' ms. Ignore additional requests while scheduled.
+ *
+ * @param {object} task The task to execute
+ * @param {number} delay ms delay for task execution (default 0)
+ * @param {object} next The callback to run after a task is initiated
+ */
+const taskScheduler = ( task, delay = 0, next = () => {} ) => {
+  let taskScheduled = false;
+  let taskTime = null;
+  const resetTaskSchedule = () => { taskScheduled = false; taskTime = null; };
+
+  return (() => {
+    const setTimeoutPromise = util.promisify( setTimeout );
+    let now = new Date();
+    logger.info( `A task request has been received` );
+
+    if( taskScheduled ){
+      logger.info( `A task has already been scheduled for ${taskTime} (${formatDistance( now, taskTime )})` );
+
+    } else {
+      taskTime = addMilliseconds( new Date(), delay );
+      logger.info( `A task was scheduled for ${taskTime} (${formatDistance( now, taskTime )})` );
+      taskScheduled = true;
+
+      setTimeoutPromise( delay )
+        .then( task )
+        .then( next )
+        .catch( () => {} ) // swallow
+        .finally( resetTaskSchedule ); // allow another backup request
+    }
+
+    return Promise.resolve();
+  });
+};
+
+// Configure Changefeeds for the document table
+const setupChangefeeds = async ({ rethink: r, conn, table }) => {
+  const docOpts = {
+    includeTypes: true,
+    squash: true
+   };
+
+  // Database restore of doc with public status
+  const toPublicStatusFromNull = r.row( 'new_val' )( 'status' ).eq( 'public' )
+    .and( r.row( 'old_val' ).eq( null ) );
+  // Status changed to 'public'
+  const toPublicStatusFromOtherStatus = r.row( 'new_val' )( 'status' ).eq( 'public' )
+    .and( r.row( 'old_val' )( 'status' ).ne( 'public' ) );
+  // Status is changed from 'public'
+  const toOtherStatusFromPublicStatus = r.row( 'new_val' )( 'status' ).ne( 'public' )
+    .and( r.row( 'old_val' )( 'status' ).eq( 'public' ) );
+
+  const docFilter = toPublicStatusFromNull.or( toPublicStatusFromOtherStatus ).or( toOtherStatusFromPublicStatus );
+  const cursor = await table.changes( docOpts )
+   .filter( docFilter )
+   .run( conn );
+  return cursor;
+};
+
+/**
+* initExportTasks
+* Initialize the export tasks
+*/
+const initExportTasks = async () => {
+  const MS_PER_SEC = 1000;
+  const SEC_PER_MIN = 60;
+  const MIN_PER_HOUR = 60;
+
+  const loadTable = name => db.accessTable( name );
+  const dbTable = await loadTable( 'document' );
+  const cursor = await setupChangefeeds( dbTable );
+
+  let export_delay = MS_PER_SEC * SEC_PER_MIN * MIN_PER_HOUR * EXPORT_BULK_DELAY_HOURS;
+
+  const exportTask = () => exportToZip( BULK_DOWNLOADS_PATH );
+  const doExport = taskScheduler( exportTask, export_delay );
+
+  const exportBiopaxTask = () => exportToZip( BIOPAX_DOWNLOADS_PATH, [ EXPORT_TYPES.BP ], false );
+  const doExportBiopax = taskScheduler( exportBiopaxTask, export_delay );
+  const exportBiopaxIdMapTask = () => exportToZip( BIOPAX_IDMAP_DOWNLOADS_PATH, [ EXPORT_TYPES.BP ], true );
+  const doExportBiopaxIdMap = taskScheduler( exportBiopaxIdMapTask, export_delay );
+
+  let taskList = [ exportTask, exportBiopaxTask, exportBiopaxIdMapTask ];
+  let scheduledTaskList = [ doExport, doExportBiopax, doExportBiopaxIdMap ];
+
+  const doTasks = tasks => Promise.all( tasks.map( t => t() ) );
+
+  cursor.each( async err => {
+    if( err ){
+      logger.error( `Error in Changefeed: ${err}` );
+      return;
+    }
+    await doTasks( scheduledTaskList );
+  });
+
+  const isProduction = NODE_ENV == 'production';
+  const exportIsMissing = [
+    BULK_DOWNLOADS_PATH,
+    BIOPAX_DOWNLOADS_PATH,
+    BIOPAX_IDMAP_DOWNLOADS_PATH
+  ].some( p => !fs.existsSync( p ) );
+
+  if ( isProduction || exportIsMissing ) await doTasks( taskList );
+};
+
+
+export { exportToZip, EXPORT_TYPES, initExportTasks };