Merge pull request #465 from monarch-initiative/release-v2.1.1

Release v2.1.1

CHANGELOG.rst

@@ -2,9 +2,11 @@
 Changelog
 =========
 
-------
-latest
-------
+-----
+2.1.1
+-----
+
+- add *Past medical history* to `Aspect` enum
 
 -----
 2.1.0

README.md

@@ -14,7 +14,6 @@ associate phenotype annotation files.
 
 - **Language/Platform:** Java >=11
 - **License:** BSD 3-Clause Clear
-- **Version:** 2.1.0
 - **Authors:**
     - Sebastian Bauer
     - Peter N. Robinson
@@ -34,25 +33,25 @@ associate phenotype annotation files.
     - `phenol-cli` for performing empirical score distribution computation as a stand-alone program.
 
 ## Usage
-We recommend indicating the phenol version in the `properties` section of the pom file of the application.
+We recommend importing the `phenol` modules that are needed for your application.
 
-```
-<properties>
-  (...)
-  <phenol.version>2.1.0</phenol.version>
-</properties>
-```
+For instance:
 
-Then import the phenol modules that are needed for your application.
 ```xml
 <dependency>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol-core</artifactId>
     <version>${phenol.version}</version>
 </dependency>
+<dependency>
+  <groupId>org.monarchinitiative.phenol</groupId>
+  <artifactId>phenol-io</artifactId>
+<version>${phenol.version}</version>
+</dependency>
 <!-- ... and other modules -->
 ```
 
+where `${phenol.version}` corresponds to the desired version, such as `2.1.0`.
 
 ## History
 Phenol was initially forked from [ontolib]([https://github.com/Phenomics/ontolib) in February 2018, but was

docs/conf.py

@@ -12,7 +12,7 @@
 # The short X.Y version.
 version = '2.1'
 # The full version, including alpha/beta/rc tags.
-release = '2.1.0'
+release = '2.1.1'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

phenol-analysis/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.1.0</version>
+    <version>2.1.1</version>
   </parent>
 
   <artifactId>phenol-analysis</artifactId>

phenol-annotations/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.1.0</version>
+    <version>2.1.1</version>
   </parent>
 
   <artifactId>phenol-annotations</artifactId>

phenol-annotations/src/main/java/org/monarchinitiative/phenol/annotations/constants/hpo/HpoSubOntologyRootTermIds.java

@@ -25,5 +25,7 @@ public final class HpoSubOntologyRootTermIds {
   /** {@link TermId} of sub ontology "mode of inheritance" (<code>HP:0000005</code>). */
   public static final TermId MODE_OF_INHERITANCE = TermId.of("HP:0000005");
 
+  /** {@link TermId} of sub ontology Past medical history (<code>HP:0032443</code>). */
+  public static final TermId PAST_MEDICAL_HISTORY = TermId.of("HP:0032443");
   private HpoSubOntologyRootTermIds(){}
 }

phenol-annotations/src/main/java/org/monarchinitiative/phenol/annotations/io/hpo/Aspect.java

@@ -1,16 +1,39 @@
 package org.monarchinitiative.phenol.annotations.io.hpo;
 
+import org.monarchinitiative.phenol.ontology.data.TermId;
+
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Optional;
 
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoClinicalModifierTermIds.CLINICAL_COURSE;
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoModeOfInheritanceTermIds.INHERITANCE_ROOT;
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoSubOntologyRootTermIds.*;
+
 /**
  * An enum for aspect column of {@link HpoAnnotationLine}.
  */
 public enum Aspect {
 
-  P,
-  I,
-  C,
-  M;
+  P(PHENOTYPIC_ABNORMALITY),
+  I(INHERITANCE_ROOT),
+  C(CLINICAL_COURSE),
+  M(CLINICAL_MODIFIER),
+  H(PAST_MEDICAL_HISTORY);
+
+  private final TermId termId;
+  private static final Map<TermId, Aspect> BY_TERMID = new HashMap<>();
+
+
+  static {
+    for (Aspect e: values()) {
+      BY_TERMID.put(e.termId, e);
+    }
+  }
+
+  Aspect(TermId termId) {
+    this.termId = termId;
+  }
 
   public static Optional<Aspect> parse(String aspect) {
     switch (aspect.toUpperCase()) {
@@ -22,8 +45,15 @@ public static Optional<Aspect> parse(String aspect) {
         return Optional.of(Aspect.C);
       case "M":
         return Optional.of(Aspect.M);
+      case "H":
+        return Optional.of(Aspect.H);
       default:
         return Optional.empty();
     }
   }
+
+  public static Optional<Aspect> fromTermId(TermId termId) {
+    return Optional.ofNullable(BY_TERMID.get(termId));
+  }
+
 }

phenol-annotations/src/test/java/org/monarchinitiative/phenol/annotations/io/hpo/AspectTest.java

@@ -0,0 +1,24 @@
+package org.monarchinitiative.phenol.annotations.io.hpo;
+
+import org.junit.jupiter.api.Test;
+import org.monarchinitiative.phenol.ontology.data.TermId;
+
+import static org.hamcrest.MatcherAssert.*;
+import static org.hamcrest.Matchers.*;
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoClinicalModifierTermIds.CLINICAL_COURSE;
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoModeOfInheritanceTermIds.INHERITANCE_ROOT;
+import static org.monarchinitiative.phenol.annotations.constants.hpo.HpoSubOntologyRootTermIds.*;
+
+public class AspectTest {
+
+  @Test
+  public void test_aspect_from_termId() {
+    assertThat(Aspect.fromTermId(PHENOTYPIC_ABNORMALITY).get(), equalTo(Aspect.P));
+    assertThat(Aspect.fromTermId(INHERITANCE_ROOT).get(), equalTo(Aspect.I));
+    assertThat(Aspect.fromTermId(CLINICAL_COURSE).get(), equalTo(Aspect.C));
+    assertThat(Aspect.fromTermId(CLINICAL_MODIFIER).get(), equalTo(Aspect.M));
+    assertThat(Aspect.fromTermId(PAST_MEDICAL_HISTORY).get(), equalTo(Aspect.H));
+    assertThat(Aspect.fromTermId(TermId.of("HP:0000000")).isEmpty(), equalTo(true));
+    assertThat(Aspect.H.toString(), equalTo("H"));
+  }
+}

phenol-cli/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.1.0</version>
+    <version>2.1.1</version>
   </parent>
 
   <artifactId>phenol-cli</artifactId>

phenol-core/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.1.0</version>
+    <version>2.1.1</version>
   </parent>
 
   <artifactId>phenol-core</artifactId>

phenol-io/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.1.0</version>
+    <version>2.1.1</version>
   </parent>
 
   <artifactId>phenol-io</artifactId>

pom.xml

@@ -5,7 +5,7 @@
   <groupId>org.monarchinitiative.phenol</groupId>
   <artifactId>phenol</artifactId>
   <packaging>pom</packaging>
-  <version>2.1.0</version>
+  <version>2.1.1</version>
 
   <name>Phenol</name>