Merge pull request #89 from monarch-initiative/refactor

Refactor
monarch-initiative · Jan 29, 2019 · dfe74ba · dfe74ba
2 parents eabef03 + d250e5d
commit dfe74ba
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -118,7 +118,7 @@ Additional changes for this version
 
 * Prevent app from crashing when user's local HPO is outdated
 
-* Added classes to model patient phenopacket (phenotype only)
+* Added classes to appTempData patient phenopacket (phenotype only)
 * Refactored to use phenol 1.0.0
 
 ## v1.1.5
@@ -141,5 +141,5 @@ Additional changes for this version
 
 ## v1.1.7
 
-* Add algorithms to model patients
+* Add algorithms to appTempData patients
 
diff --git a/docs/source/Tutorial.rst b/docs/source/Tutorial.rst
@@ -24,7 +24,7 @@ Follow the steps to start the curation process.
 
 - Import LOINC codes. If you have configured the app properly, you should be able to see there are contents in the LOINC table. You can always click **"Initialize Loinc Table"** on the left upper corner to import Loinc codes from the Loinc Core Table file. Try using the "Search" function to select some Loinc codes, e.g. try searching for "10449-7" and then "glucose" (You will get one result for "10449-7" and many results for "glucose").
 
-- Import HPO. Click "Initialize HPO model" on the left upper corner to import all HPO terms to the app. If you configured the app properly, this will automatically run when you start the app.
+- Import HPO. Click "Initialize HPO appTempData" on the left upper corner to import all HPO terms to the app. If you configured the app properly, this will automatically run when you start the app.
 
 - After completing the above steps, you should be able to start annotating LOINC codes!
   - Go to the Loinc Table in the bottom half of the tab, and choose the LOINC code that you want to annotate. When you click the **"Auto Query"** button or double click on the LOINC code, the app will automatically find candidate HPO terms for you, listed from the most likely term to the least likely.

diff --git a/loinc2hpo-core/pom.xml b/loinc2hpo-core/pom.xml
@@ -23,21 +23,7 @@
 
 
     <dependencies>
-       <!--  <dependency>
-            <groupId>commons-io</groupId>
-            <artifactId>commons-io</artifactId>
-            <version>2.4</version>
-        </dependency>
-        <dependency>
-            <groupId>commons-net</groupId>
-            <artifactId>commons-net</artifactId>
-            <version>3.3</version>
-        </dependency>
-        <dependency>
-            <groupId>com.google.guava</groupId>
-            <artifactId>guava</artifactId>
-            <version>${guava.version}</version>
-        </dependency> -->
+
 
 
     </dependencies>
@@ -131,7 +117,7 @@
                         <!-- set useUniqueVersions=false in order that the classpath has the
                             SNAPSHOT instead of the build number prefixed to the dependency -->
                         <!--<useUniqueVersions>false</useUniqueVersions>-->
-                        <mainClass>org.monarchinitiative.loinc2hpo.Loinc2Hpo</mainClass>
+                        <!--<mainClass>org.monarchinitiative.loinc2hpo.Loinc2Hpo</mainClass>-->
                     </manifest>
                 </archive>
             </configuration>

diff --git a/loinc2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/Constants.java b/loinc2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/Constants.java
@@ -20,6 +20,9 @@ public class Constants {
     //folder for LOINC categories
     public static final String LOINCCategory = "LOINC CATEGORY";
 
+    //folder for Data folder
+    public static final String DATAFOLDER = "Data";
+
 
     public static final String LOINCSYSTEM = "http://loinc.org";
     //public static final String HAPIFHIRTESTSERVER = "http://fhirtest.uhn.ca/baseDstu3";

diff --git a/loinc2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/ResourceCollection.java b/loinc2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/ResourceCollection.java
@@ -10,20 +10,16 @@
 import org.monarchinitiative.loinc2hpo.loinc.LoincId;
 import org.monarchinitiative.loinc2hpo.loinc.LoincPanel;
 import org.monarchinitiative.phenol.base.PhenolException;
-import org.monarchinitiative.phenol.formats.hpo.HpoOntology;
-import org.monarchinitiative.phenol.io.obo.hpo.HpOboParser;
+import org.monarchinitiative.phenol.ontology.data.Ontology;
 import org.monarchinitiative.phenol.ontology.data.Term;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.stream.Collectors;
 
 /**
  * This class manages all resources that are required for this app. Whenever a new resource is required, just call a getter to retrieve it.
@@ -39,7 +35,7 @@ public class ResourceCollection {
     private String loincPanelPath;
     //private String loincPanelAnnotationPath;
     private HpoOntologyParser hpoOntologyParser;
-    private HpoOntology hpo;
+    private Ontology hpo;
     private Map<TermId, Term> termidTermMap;
     private Map<String, Term> termnameTermMap;
     private ImmutableMap<LoincId, LoincEntry> loincEntryMap;
@@ -152,7 +148,7 @@ private void addLoincPanelAnnotation(String loincPanelAnnotationPath, Map<LoincI
 
     }
 
-    public HpoOntology getHPO() throws PhenolException, FileNotFoundException {
+    public Ontology getHPO() throws PhenolException, FileNotFoundException {
         if (this.hpo != null) {
             return this.hpo;
         }
@@ -164,4 +160,23 @@ public HpoOntology getHPO() throws PhenolException, FileNotFoundException {
         return this.hpo;
     }
 
+    public String getLoincEntryPath() {
+        return loincEntryPath;
+    }
+
+    public String getHpoOboPath() {
+        return hpoOboPath;
+    }
+
+    public String getHpoOwlPath() {
+        return hpoOwlPath;
+    }
+
+    public String getAnnotationMapPath() {
+        return annotationMapPath;
+    }
+
+    public String getLoincPanelPath() {
+        return loincPanelPath;
+    }
 }
diff --git a/loinc2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/io/HpOwlParser.java b/loinc2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/io/HpOwlParser.java
@@ -1,18 +1,11 @@
 package org.monarchinitiative.loinc2hpo.io;
 
-import com.google.common.collect.ImmutableMap;
-import com.google.common.collect.ImmutableSortedMap;
-import org.monarchinitiative.phenol.base.PhenolException;
-import org.monarchinitiative.phenol.formats.hpo.HpoOntology;
-import org.monarchinitiative.phenol.io.owl.OwlOntologyLoader;
-import org.monarchinitiative.phenol.ontology.data.*;
-
 import java.io.File;
 
 /**
  * This class parses the Human Phenotype Ontology in the owl format.
  */
-
+@Deprecated
 public class HpOwlParser {
 
     private final File owlFile;
@@ -28,28 +21,28 @@ public HpOwlParser(File owlFile) {
         this(owlFile,false);
     }
 
-    public HpoOntology parse() throws PhenolException {
-        Ontology ontology;
-
-        //final OwlImmutableOntologyLoader loader = new OwlImmutableOntologyLoader(owlFile);
-        OwlOntologyLoader loader = new OwlOntologyLoader(owlFile);
-        ontology = loader.load();
-        if (debug) {
-            System.err.println(String.format("Parsed a total of %d HP terms",ontology.countAllTerms()));
-        }
-
-        // hpo root termid
-        //TermId hpoRoot = new TermId(new TermPrefix("HP"), "0000001");
-        TermId hpoRoot = TermId.of("HP", "0000001");
-
-        return new HpoOntology(
-                (ImmutableSortedMap<String, String>) ontology.getMetaInfo(),
-                ontology.getGraph(),
-                hpoRoot,
-                ontology.getNonObsoleteTermIds(),
-                ontology.getObsoleteTermIds(),
-                (ImmutableMap<TermId, Term>) ontology.getTermMap(),
-                (ImmutableMap<Integer, Relationship>) ontology.getRelationMap());
-    }
+//    public HpoOntology parse() throws PhenolException {
+//        Ontology ontology;
+//
+//        //final OwlImmutableOntologyLoader loader = new OwlImmutableOntologyLoader(owlFile);
+//        OwlOntologyLoader loader = new OwlOntologyLoader(owlFile);
+//        ontology = loader.load();
+//        if (debug) {
+//            System.err.println(String.format("Parsed a total of %d HP terms",ontology.countAllTerms()));
+//        }
+//
+//        // hpo root termid
+//        //TermId hpoRoot = new TermId(new TermPrefix("HP"), "0000001");
+//        TermId hpoRoot = TermId.of("HP", "0000001");
+//
+//        return new HpoOntology(
+//                (ImmutableSortedMap<String, String>) ontology.getMetaInfo(),
+//                ontology.getGraph(),
+//                hpoRoot,
+//                ontology.getNonObsoleteTermIds(),
+//                ontology.getObsoleteTermIds(),
+//                (ImmutableMap<TermId, Term>) ontology.getTermMap(),
+//                (ImmutableMap<Integer, Relationship>) ontology.getRelationMap());
+//    }
 
 }
diff --git a/loinc2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/io/HpoOntologyParser.java b/loinc2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/io/HpoOntologyParser.java
@@ -4,8 +4,7 @@
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.monarchinitiative.phenol.base.PhenolException;
-import org.monarchinitiative.phenol.formats.hpo.HpoOntology;
-import org.monarchinitiative.phenol.io.obo.hpo.HpOboParser;
+import org.monarchinitiative.phenol.io.OntologyLoader;
 import org.monarchinitiative.phenol.ontology.data.*;
 
 import java.io.File;
@@ -23,7 +22,7 @@ public class HpoOntologyParser {
     private String hpoOboPath =null;
     private String hpoOwlPath = null;
     private boolean isObo = false;
-    private HpoOntology hpoOntology;
+    private Ontology hpoOntology;
 
 
     /** Map of all of the Phenotypic abnormality terms (i.e., not the inheritance terms). */
@@ -45,14 +44,8 @@ public HpoOntologyParser(String path){
      * @throws PhenolException, OWLOntologyCreationException
      */
     public void parseOntology() throws PhenolException, FileNotFoundException {
-        if (isObo) {
-            HpOboParser hpoOboParser = new HpOboParser(new File(hpoOboPath));
-            logger.debug("ontology path: " + hpoOboPath);
-            this.hpoOntology = hpoOboParser.parse();
-        } else {
-            HpOwlParser hpoOwlParser = new HpOwlParser(new File(hpoOwlPath));
-            this.hpoOntology = hpoOwlParser.parse();
-        }
+        logger.debug("ontology path: " + hpoOboPath);
+        this.hpoOntology = OntologyLoader.loadOntology(new File(hpoOboPath));
     }
 
     private void initTermMaps() {
@@ -64,7 +57,7 @@ private void initTermMaps() {
         }
     }
 
-    public HpoOntology getOntology() {
+    public Ontology getOntology() {
 
         return this.hpoOntology;
 

diff --git a/...2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/io/LoincAnnotationSerializer.java b/...2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/io/LoincAnnotationSerializer.java
@@ -3,9 +3,6 @@
 import org.monarchinitiative.loinc2hpo.loinc.LOINC2HpoAnnotationImpl;
 import org.monarchinitiative.loinc2hpo.loinc.LoincId;
 import org.monarchinitiative.phenol.ontology.data.TermId;
-//import org.monarchinitiative.phenol.ontology.data.ImmutableTermId;
-import org.monarchinitiative.phenol.ontology.data.TermPrefix;
-//import org.monarchinitiative.phenol.ontology.data.ImmutableTermPrefix;
 
 import java.io.IOException;
 import java.util.Map;
@@ -17,8 +14,8 @@ public interface LoincAnnotationSerializer {
     Map<LoincId, LOINC2HpoAnnotationImpl> parse(String filepath) throws Exception;
 
     default TermId convertToTermID(String record) {
-        TermPrefix prefix = new TermPrefix("HP");
-        if (!record.startsWith(prefix.getValue()) || record.length() <= 3) {
+        String prefix = "HP";
+        if (!record.startsWith(prefix) || record.length() <= 3) {
             return null;
         }
         String id = record.substring(3);

diff --git a/...ain/java/org/monarchinitiative/loinc2hpo/io/LoincAnnotationSerializerToTSVSingleFile.java b/...ain/java/org/monarchinitiative/loinc2hpo/io/LoincAnnotationSerializerToTSVSingleFile.java
@@ -45,7 +45,7 @@ public LoincAnnotationSerializerToTSVSingleFile(Map<TermId, Term> hpoTermMap) {
     @Override
     public void serialize(Map<LoincId, LOINC2HpoAnnotationImpl> annotationmap, String filepath) throws IOException {
 
-
+        logger.info("file path: " + filepath);
 
         BufferedWriter writer = new BufferedWriter(new FileWriter(filepath));
         writer.write(header);
@@ -68,7 +68,8 @@ public Map<LoincId, LOINC2HpoAnnotationImpl> parse(String filepath) throws FileN
         Map<LoincId, LOINC2HpoAnnotationImpl> deserializedMap = new LinkedHashMap<>();
         Map<LoincId, LOINC2HpoAnnotationImpl.Builder> builders = new LinkedHashMap<>();
         BufferedReader reader = new BufferedReader(new FileReader(filepath));
-        reader.lines().forEach(serialized -> {
+
+        reader.lines().filter(l -> !l.isEmpty()).forEach(serialized -> {
             String[] elements = serialized.split("\\t");
             if (elements.length == 13 && !serialized.startsWith("loincId")) {
                 try {

diff --git a/loinc2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/io/WriteToFile.java b/loinc2hpo-core/src/main/java/org/monarchinitiative/loinc2hpo/io/WriteToFile.java
@@ -4,7 +4,6 @@
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.monarchinitiative.phenol.ontology.data.TermId;
-import org.monarchinitiative.phenol.ontology.data.TermPrefix;
 
 
 import java.io.*;
@@ -69,8 +68,8 @@ public static <K extends Serializable, V extends Serializable> Map<K, V> deseria
 
 
     public static TermId convertToTermID(String record) {
-        TermPrefix prefix = new TermPrefix("HP");
-        if (!record.startsWith(prefix.getValue()) || record.length() <= 3) {
+        String prefix = "HP";
+        if (!record.startsWith(prefix) || record.length() <= 3) {
             logger.error("Non HPO termId is detected from TSV: " + record);
             return null;
         }

diff --git a/...-core/src/test/java/org/monarchinitiative/loinc2hpo/fhir/FhirObservationAnalyzerTest.java b/...-core/src/test/java/org/monarchinitiative/loinc2hpo/fhir/FhirObservationAnalyzerTest.java
@@ -10,14 +10,12 @@
 import org.monarchinitiative.loinc2hpo.codesystems.Loinc2HPOCodedValue;
 import org.monarchinitiative.loinc2hpo.loinc.*;
 import org.monarchinitiative.loinc2hpo.testresult.LabTestOutcome;
-import org.monarchinitiative.phenol.base.PhenolException;
-import org.monarchinitiative.phenol.formats.hpo.HpoOntology;
-import org.monarchinitiative.phenol.io.obo.hpo.HpOboParser;
+import org.monarchinitiative.phenol.io.OntologyLoader;
+import org.monarchinitiative.phenol.ontology.data.Ontology;
 import org.monarchinitiative.phenol.ontology.data.Term;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
 import java.io.File;
-import java.io.IOException;
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -34,13 +32,7 @@ public static void setup() throws Exception{
         observation = FhirResourceRetriever.parseJsonFile2Observation(path);
 
         String hpo_obo = FhirObservationAnalyzerTest.class.getClassLoader().getResource("obo/hp.obo").getPath();
-        HpOboParser hpoOboParser = new HpOboParser(new File(hpo_obo));
-        HpoOntology hpo = null;
-        try {
-            hpo = hpoOboParser.parse();
-        } catch (PhenolException e) {
-            e.printStackTrace();
-        }
+        Ontology hpo = OntologyLoader.loadOntology(new File(hpo_obo));
         ImmutableMap.Builder<String,Term> termmap = new ImmutableMap.Builder<>();
         if (hpo !=null) {
             List<Term> res = hpo.getTermMap().values().stream().distinct()

diff --git a/...est/java/org/monarchinitiative/loinc2hpo/fhir/ObservationAnalysisFromCodedValuesTest.java b/...est/java/org/monarchinitiative/loinc2hpo/fhir/ObservationAnalysisFromCodedValuesTest.java
@@ -9,9 +9,8 @@
 import org.monarchinitiative.loinc2hpo.exception.MalformedLoincCodeException;
 import org.monarchinitiative.loinc2hpo.exception.UnrecognizedCodeException;
 import org.monarchinitiative.loinc2hpo.loinc.*;
-import org.monarchinitiative.phenol.base.PhenolException;
-import org.monarchinitiative.phenol.formats.hpo.HpoOntology;
-import org.monarchinitiative.phenol.io.obo.hpo.HpOboParser;
+import org.monarchinitiative.phenol.io.OntologyLoader;
+import org.monarchinitiative.phenol.ontology.data.Ontology;
 import org.monarchinitiative.phenol.ontology.data.Term;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
@@ -50,13 +49,8 @@ public static void setup() throws MalformedLoincCodeException, DataFormatExcepti
 
 
         String hpo_obo = FhirObservationAnalyzerTest.class.getClassLoader().getResource("obo/hp.obo").getPath();
-        HpOboParser hpoOboParser = new HpOboParser(new File(hpo_obo));
-        HpoOntology hpo = null;
-        try {
-            hpo = hpoOboParser.parse();
-        } catch (PhenolException e) {
-            e.printStackTrace();
-        }
+        Ontology hpo = OntologyLoader.loadOntology(new File(hpo_obo));
+
         ImmutableMap.Builder<String,Term> termmap = new ImmutableMap.Builder<>();
         ImmutableMap.Builder<TermId,Term> termmap2 = new ImmutableMap.Builder<>();
         if (hpo !=null) {

diff --git a/.../java/org/monarchinitiative/loinc2hpo/fhir/ObservationAnalysisFromInterpretationTest.java b/.../java/org/monarchinitiative/loinc2hpo/fhir/ObservationAnalysisFromInterpretationTest.java
@@ -9,9 +9,8 @@
 import org.monarchinitiative.loinc2hpo.exception.AmbiguousResultsFoundException;
 import org.monarchinitiative.loinc2hpo.exception.MalformedLoincCodeException;
 import org.monarchinitiative.loinc2hpo.loinc.*;
-import org.monarchinitiative.phenol.base.PhenolException;
-import org.monarchinitiative.phenol.formats.hpo.HpoOntology;
-import org.monarchinitiative.phenol.io.obo.hpo.HpOboParser;
+import org.monarchinitiative.phenol.io.OntologyLoader;
+import org.monarchinitiative.phenol.ontology.data.Ontology;
 import org.monarchinitiative.phenol.ontology.data.Term;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
@@ -42,13 +41,7 @@ public static void setup() throws MalformedLoincCodeException, IOException, Data
         observations[1] = observation2;
 
         String hpo_obo = FhirObservationAnalyzerTest.class.getClassLoader().getResource("obo/hp.obo").getPath();
-        HpOboParser hpoOboParser = new HpOboParser(new File(hpo_obo));
-        HpoOntology hpo = null;
-        try {
-            hpo = hpoOboParser.parse();
-        } catch (PhenolException e) {
-            e.printStackTrace();
-        }
+        Ontology hpo = OntologyLoader.loadOntology(new File(hpo_obo));
         ImmutableMap.Builder<String,Term> termmap = new ImmutableMap.Builder<>();
         ImmutableMap.Builder<TermId,Term> termmap2 = new ImmutableMap.Builder<>();
         if (hpo !=null) {