Merge branch 'develop' into 532-support-drug-interactions-2

data-loader/data/v2/config_items.csv

@@ -0,0 +1,109 @@
+Forms,Immediate packaging,Routes
+Bar,Aerosol,Buccal
+Block,Ampoule,Inhalation
+Capsule,Applicator,Intramuscular
+Capsule (enteric coated),Bag,Intrathecal
+Capsule (hard),Blister pack,Intratracheal
+Capsule (modified release),Bottle,Intrauterine
+Cement,Can,Intraperitoneal
+Chewing gum,Carton,Intravenous
+Collodion,Cartridge,Nasal
+Cream,Chamber,Ocular
+Cream (modified),Device,Oral
+Cream (vaginal),Dry powder inhaler,Otic
+Drug delivery system (intrauterine),Inhaler,Rectal
+Drug delivery system (vaginal),Metered dose inhaler,Subcutaneous
+Ear drop,Nebule,Subdermal
+Ear/eye drop,Pre-filled syringe,Sublingual
+Enema,Pump actuated aerosol,Topical
+Eye drop,Sachet,Transdermal
+Eye drop (gel forming),Spray,Vaginal
+Eye gel,Tube,
+Eye ointment,Vial,
+Eye solution,,
+Eye/ear ointment,,
+Foam,,
+Gas,,
+Gel,,
+Gel (intestinal),,
+Gel (modified release),,
+Granules,,
+Granules (effervescent),,
+Granules (modified release),,
+Implant,,
+Infusion,,
+Infusion (powder for),,
+Inhalation,,
+Inhalation (breath activated),,
+Inhalation (powder for),,
+Inhalation (pressurised),,
+Inhalation (solution),,
+Injection,,
+Injection (concentrated),,
+Injection (emulsion),,
+Injection (intra-ocular),,
+Injection (intrathecal),,
+Injection (modified release),,
+Injection (powder for),,
+Injection (suspension),,
+Injection (solution),,
+Jelly (lubricating),,
+Liniment,,
+Liquid,,
+Lotion,,
+Lozenge,,
+Mouth wash,,
+Nasal drop,,
+Nasal spray,,
+Nsal gel,,
+Oil,,
+Oil (bath),,
+Ointment,,
+Ointment (modified),,
+Oral application,,
+Oral gel,,
+Oral liquid,,
+Oral liquid (powder for),,
+Oral spray,,
+Paint,,
+Paste,,
+Paste (oromucosal),,
+Pastille,,
+Pessary,,
+Pessary (modified release),,
+Powder,,
+Powder (oral),,
+Shampoo,,
+Soap,,
+Solution,,
+Solution (concentrated dialysis),,
+Solution (dialysis),,
+Solution (irrigation),,
+Solution (peritoneal dialysis),,
+Solution (powder for dialysis),,
+Solution (powder for),,
+Spray,,
+Spray (pressurised),,
+Stick,,
+Strip (diagnostic),,
+Suppository,,
+Suspension,,
+Swab,,
+Tablet,,
+Tablet (buccal),,
+Tablet (chewable),,
+Tablet (compound diagnostic),,
+Tablet (dispersible),,
+Tablet (effervescent),,
+Tablet (enteric coated),,
+Tablet (gelatine coated),,
+Tablet (modified release),,
+Tablet (oral disintegrating),,
+Tablet (soluble),,
+Tablet (sublingual),,
+Tincture,,
+Toothpaste,,
+Topical application,,
+Topical liquid,,
+Transdermal patch,,
+Wafer,,

data-loader/src/main.ts

@@ -3,6 +3,7 @@ import path from 'path';
 import { DataLoader, DataParser, SchemaParser } from './v2';
 
 import propertyConfigItems from '../data/v2/properties.json';
+import { ConfigItemsDataParser } from './v2/ConfigItemsParser';
 
 const hostname = 'localhost';
 const port = '9080';
@@ -12,6 +13,7 @@ const schemaPath = 'v2/schema.gql';
 const drugDataPath = 'v2/drugs.csv';
 const consumableDataPath = 'v2/consumables.csv';
 const vaccineDataPath = 'v2/vaccines.csv';
+const configItemsDataPath = 'v2/config_items.csv';
 
 const schemaFile = path.resolve(__dirname, `${dirPath}/${schemaPath}`);
 const drugDataFile = path.resolve(__dirname, `${dirPath}/${drugDataPath}`);
@@ -23,6 +25,10 @@ const vaccineDataFile = path.resolve(
   __dirname,
   `${dirPath}/${vaccineDataPath}`
 );
+const configItemsDataFile = path.resolve(
+  __dirname,
+  `${dirPath}/${configItemsDataPath}`
+);
 
 const main = async () => {
   const schemaParser = new SchemaParser(schemaFile);
@@ -34,17 +40,21 @@ const main = async () => {
     vaccines: vaccineDataFile,
   });
 
+  const configItemsParser = new ConfigItemsDataParser(configItemsDataFile);
+
   await dataParser.parseData();
+  await configItemsParser.parseData();
 
   dataParser.buildGraph();
 
   if (dataParser.isValid()) {
     const schema = schemaParser.getSchema();
     const graph = dataParser.getGraph();
+    const configItems = configItemsParser.getItems();
 
     try {
       const loader = new DataLoader(hostname, port);
-      await loader.load(schema, graph, propertyConfigItems);
+      await loader.load(schema, graph, configItems, propertyConfigItems);
     } catch (err) {
       console.log(`Failed to load data due to following error: ${err}`);
     }

data-loader/src/v2/ConfigItemsParser.ts

@@ -0,0 +1,80 @@
+import * as fs from 'fs';
+import csv from 'csv-parser';
+import { ConfigItems } from './types';
+
+export class ConfigItemsDataParser {
+  public readonly path: fs.PathLike;
+
+  private data: ConfigItems;
+
+  private isParsed: boolean;
+  private isBuilt: boolean;
+
+  constructor(path: fs.PathLike) {
+    this.path = path;
+
+    this.isParsed = false;
+    this.isBuilt = false;
+
+    this.data = {
+      forms: [],
+      immediatePackaging: [],
+      routes: [],
+    };
+  }
+
+  public async parseData(): Promise<ConfigItems> {
+    if (this.isParsed) return this.data;
+
+    this.data = {
+      forms: [],
+      immediatePackaging: [],
+      routes: [],
+    };
+
+    const parseColumn = (column: string) => {
+      const REGEX = {
+        CR_LF: /[\r\n]/g,
+        BRACKETED_DESCRIPTION: / *\([^)]*\) */g,
+        SPACE: / /g,
+      };
+
+      return column
+        .trim()
+        .toLowerCase()
+        .replace(REGEX.CR_LF, '')
+        .replace(REGEX.BRACKETED_DESCRIPTION, '')
+        .replace(REGEX.SPACE, '_')
+        .split('_')
+        .map((word, index) =>
+          index === 0 ? word : word[0].toUpperCase() + word.slice(1)
+        )
+        .join('');
+    };
+
+    // Read data stream.
+    const stream = fs.createReadStream(this.path);
+    await new Promise(resolve => {
+      stream
+        .pipe(csv())
+        .on('data', (row: string) => {
+          Object.entries<string>(row).forEach(
+            ([column, value]: [string, string]) => {
+              if (value) {
+                const key = parseColumn(column);
+                this.data[key].push(value);
+              }
+            }
+          );
+        })
+        .on('end', () => resolve(null));
+    });
+
+    this.isParsed = true;
+    return this.data;
+  }
+
+  public getItems(): ConfigItems {
+    return this.data;
+  }
+}

data-loader/src/v2/DataLoader.ts

@@ -1,6 +1,11 @@
 import dgraph from 'dgraph-js';
 
-import { IEntityNode, IEntityGraph, PropertyConfigItem } from './types';
+import {
+  IEntityNode,
+  IEntityGraph,
+  PropertyConfigItem,
+  ConfigItems,
+} from './types';
 
 export class DgraphClient {
   public readonly host: string;
@@ -83,6 +88,7 @@ export class DataLoader {
   public async load(
     schema: string,
     graph: IEntityGraph,
+    configItems: ConfigItems,
     propertyConfigItems: PropertyConfigItem[]
   ): Promise<boolean> {
     // Delete all existing data.
@@ -100,11 +106,6 @@ export class DataLoader {
 
     console.log(`INFO: Extracted entity nodes`);
 
-    const routes = new Set();
-    const forms = new Set();
-    const formQualifiers = new Set();
-    const immediatePackagings = new Set();
-
     // Load individual entities.
     for await (const entity of entities) {
       const query = `
@@ -131,18 +132,6 @@ export class DataLoader {
       } else {
         console.log(`WARNING: Failed to load entity with code ${entity.code}`);
       }
-      if (entity.type === 'Route') routes.add(entity.name.trim());
-      if (entity.type === 'Form') forms.add(entity.name.trim());
-      if (
-        entity.type === 'FormQualifier' &&
-        entity.name &&
-        entity.name.trim() &&
-        entity.name.trim().length < 20
-      ) {
-        formQualifiers.add(entity.name.trim());
-      }
-      if (entity.type === 'PackImmediate')
-        immediatePackagings.add(entity.name.trim());
     }
 
     // Link parent entities to children.
@@ -199,7 +188,7 @@ export class DataLoader {
     }
 
     // Create routes.
-    for await (const route of routes) {
+    for await (const route of configItems.routes) {
       if (!route) continue;
       const nQuads = `
         _:route <name> "${route}" .
@@ -216,7 +205,7 @@ export class DataLoader {
     }
 
     // Create forms.
-    for await (const form of forms) {
+    for await (const form of configItems.forms) {
       if (!form) continue;
       const nQuads = `
         _:form <name> "${form}" .
@@ -230,41 +219,10 @@ export class DataLoader {
       } else {
         console.log(`WARNING: Failed to load form with name ${form}`);
       }
-
-      // Look to see if the form and qualifier combination exists in a entity description...
-      // If so we need to create a form with the qualifier attached
-
-      for await (const formQualifier of formQualifiers) {
-        if (!formQualifier) continue;
-        for await (const entity of entities) {
-          if (
-            entity.description &&
-            entity.description.includes(`${form} ${formQualifier}`)
-          ) {
-            const nQuads = `
-              _:form <name> "${form} (${formQualifier})" .
-              _:form <code> "${form} (${formQualifier})" .
-              _:form <type> "Form" .
-              _:form <dgraph.type> "ConfigurationItem" .
-            `;
-
-            if (await this.dgraph.mutate(nQuads)) {
-              console.log(
-                `INFO: Loaded form qualifier with name ${formQualifier}`
-              );
-            } else {
-              console.log(
-                `WARNING: Failed to load form qualifier with name ${formQualifier}`
-              );
-            }
-            break;
-          }
-        }
-      }
     }
 
     // Create immediate packagings.
-    for await (const immediatePackaging of immediatePackagings) {
+    for await (const immediatePackaging of configItems.immediatePackaging) {
       if (!immediatePackaging) continue;
       const nQuads = `
         _:pack <name> "${immediatePackaging}" .

data-loader/src/v2/types/ConfigItems.ts

@@ -0,0 +1,5 @@
+export interface ConfigItems {
+  forms: string[];
+  immediatePackaging: string[];
+  routes: string[];
+}

data-loader/src/v2/types/index.ts

@@ -5,3 +5,4 @@ export * from './EntityGraph';
 export * from './EntityNode';
 export * from './ParserOptions';
 export * from './PropertyConfigItem';
+export * from './ConfigItems';