Merge branch 'release/0.9.0'

.gitignore

@@ -40,3 +40,4 @@ README.html
 application/.factorypath
 library/.factorypath
 qtakes/.factorypath
+graph/.factorypath

.vscode/settings.json

@@ -2,5 +2,8 @@
     "java.configuration.updateBuildConfiguration": "automatic",
     "cSpell.words": [
         "ESEARCH"
-    ]
+    ],
+    "licenser.license": "MPLv2",
+    "licenser.author": "Bell Eapen",
+    "licenser.projectName": "CKBLIB"
 }

application/pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 	<groupId>com.canehealth.ckblib</groupId>
 	<artifactId>ckblib-application</artifactId>
-	<version>0.2.0</version>
+	<version>0.9.0</version>
 	<name>ckblib-application</name>
 	<description>Demo project for Spring Boot</description>
 	<properties>
@@ -27,12 +27,30 @@
 			<artifactId>library</artifactId>
 			<version>${project.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>com.canehealth.ckblib</groupId>
+			<artifactId>qtakes</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>com.canehealth.ckblib</groupId>
+			<artifactId>graph</artifactId>
+			<version>${project.version}</version>
+		</dependency>
 		<dependency>
 			<groupId>org.projectlombok</groupId>
 			<artifactId>lombok</artifactId>
 			<version>${lombok.version}</version>
 			<scope>provided</scope>
 		</dependency>
+
+		<!-- https://stackoverflow.com/questions/62006284/noclassdeffounderror-org-w3c-dom-ls-documentls-issue-occurring-only-on-deploy -->
+		<dependency>
+			<groupId>xerces</groupId>
+			<artifactId>xercesImpl</artifactId>
+			<version>2.12.0</version>
+		</dependency>
+
 		<dependency>
 			<groupId>org.springframework.boot</groupId>
 			<artifactId>spring-boot-starter-test</artifactId>

application/src/main/java/com/canehealth/ckblib/application/DemoApplication.java

@@ -1,19 +1,83 @@
 package com.canehealth.ckblib.application;
 
 import com.canehealth.ckblib.library.service.MyService;
-import com.canehealth.ckblib.library.util.CkblibConstants;
+
+import java.util.List;
+import java.util.Random;
+import java.util.concurrent.TimeUnit;
+
+import com.canehealth.ckblib.graph.*;
+import com.canehealth.ckblib.graph.model.*;
+import com.canehealth.ckblib.library.model.BaseQuery;
+import com.canehealth.ckblib.library.model.EsearchResultRoot;
+import com.canehealth.ckblib.library.service.CkbEfetch;
+import com.canehealth.ckblib.library.service.CkbEsearch;
+import com.canehealth.ckblib.qtakes.service.QtakesService;
+import com.canehealth.ckblib.qtakes.model.ConceptMention;
+import com.canehealth.ckblib.qtakes.model.QtakesRoot;
+
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.data.neo4j.repository.config.EnableReactiveNeo4jRepositories;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.CommandLineRunner;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 @SpringBootApplication(scanBasePackages = "com.canehealth.ckblib")
+@EnableReactiveNeo4jRepositories(basePackages = "com.canehealth.ckblib.graph")
 public class DemoApplication implements CommandLineRunner {
 
 	private final MyService myService;
 	private static Logger LOG = LoggerFactory.getLogger(DemoApplication.class);
+	@Autowired
+	private BaseQuery baseQuery;
+
+	@Autowired
+	private CkbEsearch ckbEsearch;
+
+	@Autowired
+	private CkbEfetch ckbEfetch;
+
+	@Autowired
+	private QtakesService qtakesService;
+
+	@Autowired
+	JournalArticleService journalArticleService;
+
+	@Autowired
+	private JournalArticle journalArticle;
+
+	@Autowired
+	DiseaseDisorderService diseaseDisorderService;
+
+	@Autowired
+	private DiseaseDisorderMention diseaseDisorderMention;
+
+	@Autowired
+	SignSymptomService signSymptomService;
+
+	@Autowired
+	private SignSymptomMention signSymptomMention;
+
+	@Autowired
+	AnatomicalSiteService anatomicalSiteService;
+
+	@Autowired
+	private AnatomicalSiteMention anatomicalSiteMention;
+
+	@Autowired
+	MedicationService medicationService;
+
+	@Autowired
+	private MedicationMention medicationMention;
+
+	@Autowired
+	ProcedureService procedureService;
+
+	@Autowired
+	private ProcedureMention procedureMention;
 
 	public DemoApplication (MyService myService) {
 		this.myService = myService;
@@ -24,40 +88,215 @@ public static void main(String[] args) {
 	}
 
 	@Override
-	public void run(String... args) {
+	public void run(String... args) throws InterruptedException {
 		LOG.info("EXECUTING : " + myService.message());
 
-		String _function = "";
-		String _source = "";
-		String _destination = "";
+		String _term = "";
+		String mainCui = "";
+
 		try {
 			if (args[0].toLowerCase().equals("help")) {
-				System.out.println(CkblibConstants.HELP_STRING);
+				LOG.info(myService.message());
 			} else {
 				for (int i = 0; i < args.length; ++i) {
 					LOG.debug("args[{}]: {}", i, args[i]);
-					_function = args[0];
-					_source = args[1];
-					_destination = args[2];
+					_term = args[0];
 				}
 			}
+			baseQuery.setTerm(_term);
+			baseQuery.setRetmax(3);
+
+			// Check and adjust for total count of articles
+			ckbEsearch.setBaseQuery(baseQuery);
+			ckbEsearch.get();
+			TimeUnit.SECONDS.sleep(1);
+			EsearchResultRoot esearchResultRoot = ckbEsearch.getResults().get(0);
+			LOG.info("Count: " + esearchResultRoot.esearchresult.count);
+			int ct = Integer.parseInt(esearchResultRoot.esearchresult.count);
+			Random random = new Random();
+			if(ct>3){
+				baseQuery.setRetstart(random.nextInt(ct));
+			}
+
+
+			ckbEfetch.setBaseQuery(baseQuery);
+			TimeUnit.SECONDS.sleep(3);
+			ckbEfetch.get();
+			TimeUnit.SECONDS.sleep(5);
+
+			// Fails if disease not known, Try again after adding concepts
+			try {
+				mainCui = diseaseDisorderService.getDiseasesByName(_term).block().getCui();
+			} catch (Exception e) {
+			}
+
+			LOG.info("MainCUI: " + mainCui + "\n");
+
+			List<String> abstracts = ckbEfetch.getPath("//Abstract");
+			List<String> pmids = ckbEfetch.getPath("//PMID");
+			List<String> titles = ckbEfetch.getPath("//ArticleTitle");
+
+			qtakesService.setQtakesUrl("http://127.0.0.1:8093");
+
+			for (int i = 0; i < abstracts.size(); i++) {
+				LOG.info(pmids.get(i) + " : " + titles.get(i));
+				String pmid = pmids.get(i);
 
-			if (_function.equals("tofhirbundle")) {
+				// Chech if pmid processed
+				try{
+					JournalArticle processed = journalArticleService.getSymptomByPmid(pmid).block();
+					if(processed.getPmid().equals(pmid)){
+						LOG.info(pmid + " known.");
+						break;
+					}
+				}catch (Exception e) {
+					LOG.info("Processing: " + pmid);
+				}
+
+				journalArticle.setPmid(pmid);
+				journalArticle.setName(titles.get(i));
+				qtakesService.post(abstracts.get(i));
 				try {
+					// Should fail if already created
+					journalArticleService.saveArticle(journalArticle).block();
 
 				} catch (Exception e) {
-					System.out.println(CkblibConstants.HELP_STRING);
+
 				}
-			} else if (_function.equals("tofhirserver")) {
-				System.out.println("To FHIR SERVER not implemented yet");
-			} else if (_function.equals("toomop")) {
+				TimeUnit.SECONDS.sleep(3);
+				QtakesRoot r = qtakesService.getQtakesResults();
 
-			} else if (_function.toLowerCase().equals("help")) {
-				System.out.println(CkblibConstants.HELP_STRING);
+				// Diseases
+				List<ConceptMention>concepts = r.getDiseaseDisorderMention();
+				for(ConceptMention concept : concepts){
+					String name = concept.getText();
+					int polarity = 1;
+					if(concept.getPolarity()<0) polarity = concept.getPolarity();
+					String cui = concept.getConceptAttributes().get(0).cui;
+					diseaseDisorderMention.setCui(cui);
+					diseaseDisorderMention.setName(name);
+					try {
+						diseaseDisorderService.saveDisease(diseaseDisorderMention).block();
+					} catch (Exception e) {
+						LOG.info(name + " known.");
+					}
+					journalArticleService.addEvidence(cui, pmid).block();
+
+					if (!"".equals(mainCui) && !mainCui.equals(cui)) {
+						LOG.info("Adding DDs");
+						diseaseDisorderService.addDifferential(mainCui, cui, polarity, 0, 0);
+					}
+				}
+				// Disease should exist now
+				if("".equals(mainCui)){
+					try {
+						mainCui = diseaseDisorderService.getDiseasesByName(_term).block().getCui();
+					} catch (Exception e) {
+						LOG.error(mainCui + " unknown.");
+					}
+				}
+
+				// Signs and symptoms
+				concepts = r.getSignSymptomMention();
+				for (ConceptMention concept : concepts) {
+					String name = concept.getText();
+					int polarity = 1;
+					if (concept.getPolarity() < 0)
+						polarity = concept.getPolarity();
+					String cui = concept.getConceptAttributes().get(0).cui;
+					signSymptomMention.setCui(cui);
+					signSymptomMention.setName(name);
+					try {
+						signSymptomService.saveSymptom(signSymptomMention).block();
+					} catch (Exception e) {
+						LOG.info(name + " known.");
+					}
+					LOG.info("Disease: " + mainCui + " Contept: " + cui + "\n");
+					signSymptomService.addRelation(mainCui, cui, polarity, 0, 0).block();
+					journalArticleService.addEvidence(cui, pmid).block();
+				}
+
+				// Anatomy
+				concepts = r.getAnatomicalSiteMention();
+				for (ConceptMention concept : concepts) {
+					String name = concept.getText();
+					int polarity = 1;
+					if (concept.getPolarity() < 0)
+						polarity = concept.getPolarity();
+					String cui = concept.getConceptAttributes().get(0).cui;
+					anatomicalSiteMention.setCui(cui);
+					anatomicalSiteMention.setName(name);
+					try {
+						anatomicalSiteService.saveSymptom(anatomicalSiteMention).block();
+					} catch (Exception e) {
+						LOG.info(name + " known.");
+					}
+					LOG.info("Disease: " + mainCui + " Contept: " + cui + "\n");
+					anatomicalSiteService.addRelation(mainCui, cui, polarity, 0, 0).block();
+					journalArticleService.addEvidence(cui, pmid).block();
+				}
+
+				// Medication
+				concepts = r.getMedicationMention();
+				for (ConceptMention concept : concepts) {
+					String name = concept.getText();
+					int polarity = 1;
+					if (concept.getPolarity() < 0)
+						polarity = concept.getPolarity();
+					String cui = concept.getConceptAttributes().get(0).cui;
+					medicationMention.setCui(cui);
+					medicationMention.setName(name);
+					try {
+						medicationService.saveSymptom(medicationMention).block();
+					} catch (Exception e) {
+						LOG.info(name + " known.");
+					}
+					LOG.info("Disease: " + mainCui + " Contept: " + cui + "\n");
+					medicationService.addRelation(mainCui, cui, polarity, 0, 0).block();
+					journalArticleService.addEvidence(cui, pmid).block();
+				}
+
+				// Procedure
+				concepts = r.getProcedureMention();
+				for (ConceptMention concept : concepts) {
+					String name = concept.getText();
+					int polarity = 1;
+					if (concept.getPolarity() < 0)
+						polarity = concept.getPolarity();
+					String cui = concept.getConceptAttributes().get(0).cui;
+					procedureMention.setCui(cui);
+					procedureMention.setName(name);
+					try {
+						procedureService.saveSymptom(procedureMention).block();
+					} catch (Exception e) {
+						LOG.info(name + " known.");
+					}
+					LOG.info("Disease: " + mainCui + " Contept: " + cui + "\n");
+					procedureService.addRelation(mainCui, cui, polarity, 0, 0).block();
+					journalArticleService.addEvidence(cui, pmid).block();
+				}
+				//System.out.println(r);
 			}
+
 		} catch (Exception e) {
-			System.out.println(CkblibConstants.HELP_STRING);
+			LOG.error(e.getLocalizedMessage());
 		}
+		// String myPublications = ckbEfetch.getPath("//Abstract").get(0);
+		// String myPMID = ckbEfetch.getPath("//PMID").get(0);
+		// System.out.print(myPublications);
+		// System.out.print(myPMID);
+
+		// qtakesService.setQtakesUrl("http://127.0.0.1:8093");
+		// qtakesService.post(myPublications);
+		// TimeUnit.SECONDS.sleep(3);
+		// QtakesRoot r = qtakesService.getQtakesResults();
+		// System.out.print(r.toString());
+		// String s = ckbEfetch.getChain(baseQuery).block();
+		// List<String> abstracts = ckbEfetch.getPathFromString("//Abstract", s);
+		// for (String abs : abstracts){
+		// 	System.out.println(abs);
+		// }
+
 	}
 
 }