Merge pull request #11 from nlpsandbox/ymnliu-develop

Update API to version 0.2.2

.github/dependabot.yml

@@ -7,8 +7,8 @@ updates:
       interval: "monthly"
     target-branch: "develop"
 
-  - package-ecosystem: "pip"
-    directory: "/server"
+  - package-ecosystem: "npm"
+    directory: "/"
     schedule:
       interval: "monthly"
-    target-branch: "develop"
+    target-branch: "develop"

.github/workflows/ci.yml

@@ -11,6 +11,10 @@ on:
       - '*.*.*'
   pull_request:
 
+
+env:
+  docker_repository: nlpsandbox/person-name-annotator-example
+
 jobs:
   lint:
     runs-on: ubuntu-latest
@@ -38,7 +42,7 @@ jobs:
     - name: Prepare
       id: prep
       run: |
-        DOCKER_IMAGE=nlpsandbox/date-annotator-example-java
+        DOCKER_IMAGE=${{ env.docker_repository }}
         VERSION=noop
         PUSH=false
         if [ "${{ github.event_name }}" = "schedule" ]; then
@@ -99,4 +103,4 @@ jobs:
       with:
         username: ${{ secrets.DOCKERHUB_USERNAME }}
         password: ${{ secrets.DOCKERHUB_PASSWORD }}
-        repository: nlpsandbox/date-annotator-example-java
+        repository: ${{ env.docker_repository }}

.gitignore

@@ -1,3 +1,5 @@
 node_modules
 .idea
-venv
+venv
+dist.yaml
+openapi.yaml

README.md

@@ -9,8 +9,8 @@ An example implementation of the [NLP Sandbox Date Annotator] using Java Spring
 
 ## Specification
 
-- Annotates date strings in clinical notes using simple regular expressions
 - Implements the [NLP Sandbox Date Annotator OpenAPI specification]
+- Annotates date strings in clinical notes using simple regular expressions
 
 ## Usage
 
@@ -26,7 +26,7 @@ Build and start the Date Annotator.
 
     cd server/
     mvn package
-    java -jar target/openapi-spring-0.1.6.jar
+    java -jar target/openapi-spring-0.2.2.jar
 
 ## Interactive documentation
 

docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.8"
 
 services:
   date-annotator:
-    image: nlpsandbox/date-annotator-example-java:edge
+    image: nlpsandbox/date-annotator-example-java:latest
     build:
       context: server
       dockerfile: Dockerfile

package.json

@@ -0,0 +1,11 @@
+{
+    "name": "date-annotator-example-java",
+    "version": "0.2.2",
+    "license": "Apache-2.0",
+    "devDependencies": {
+        "@openapitools/openapi-generator-cli": "^1.0.18-4.3.1"
+    },
+    "scripts": {
+        "generate:server": "openapi-generator generate -g spring -o server -i $npm_config_spec"
+    }
+}

server/.openapi-generator-ignore

@@ -21,3 +21,5 @@
 #docs/*.md
 # Then explicitly reverse the ignore rule for a single file:
 #!docs/README.md
+
+Dockerfile

server/.openapi-generator/FILES

@@ -0,0 +1,20 @@
+README.md
+pom.xml
+src/main/java/org/openapitools/OpenAPI2SpringBoot.java
+src/main/java/org/openapitools/RFC3339DateFormat.java
+src/main/java/org/openapitools/api/ApiUtil.java
+src/main/java/org/openapitools/api/ServiceApi.java
+src/main/java/org/openapitools/api/ServiceApiController.java
+src/main/java/org/openapitools/api/TextDateAnnotationsApi.java
+src/main/java/org/openapitools/api/TextDateAnnotationsApiController.java
+src/main/java/org/openapitools/configuration/HomeController.java
+src/main/java/org/openapitools/configuration/OpenAPIDocumentationConfig.java
+src/main/java/org/openapitools/model/Error.java
+src/main/java/org/openapitools/model/Note.java
+src/main/java/org/openapitools/model/Service.java
+src/main/java/org/openapitools/model/TextAnnotation.java
+src/main/java/org/openapitools/model/TextDateAnnotation.java
+src/main/java/org/openapitools/model/TextDateAnnotationAllOf.java
+src/main/java/org/openapitools/model/TextDateAnnotationRequest.java
+src/main/java/org/openapitools/model/TextDateAnnotations.java
+src/main/resources/application.properties

server/.openapi-generator/VERSION

@@ -1 +1 @@
-4.3.1
+5.0.0-beta2

server/Dockerfile

@@ -1,8 +1,7 @@
 FROM python:3.8.5-slim-buster
 
-ENV PIP_NO_CACHE_DIR=off
 ENV APP_DIR=/opt/app
-ENV APP_VERSION="0.1.6"
+ENV APP_VERSION="0.2.2"
 
 # Safer bash scripts with 'set -euxo pipefail'
 SHELL ["/bin/bash", "-euxo", "pipefail", "-c"]
@@ -14,11 +13,8 @@ RUN mkdir -p /usr/share/man/man1
 # hadolint ignore=DL3008
 RUN apt-get update -qq -y \
     && apt-get install --no-install-recommends -qq -y \
-        build-essential \
+        # build-essential \
         gosu \
-        libpcre3 \
-        libpcre3-dev \
-        # Java
         default-jre \
         maven \
     && apt-get -y autoclean \
@@ -27,13 +23,10 @@ RUN apt-get update -qq -y \
 
 # Copy server files
 COPY src ${APP_DIR}/src
-COPY requirements.txt pom.xml app.ini ${APP_DIR}/
+COPY pom.xml ${APP_DIR}/
 COPY docker-entrypoint.sh /
 RUN chmod +x /docker-entrypoint.sh
 
-# Install dependencies
-RUN pip install -r ${APP_DIR}/requirements.txt
-
 # Build app
 WORKDIR ${APP_DIR}
 RUN mvn package \
@@ -43,6 +36,4 @@ RUN mvn package \
 EXPOSE 8080
 
 # Set the entrypoint script and the default command run by the container
-ENTRYPOINT ["java", "-jar", "target/app.jar"]
-# ENTRYPOINT ["/docker-entrypoint.sh"]
-# CMD ["uwsgi", "--ini", "app.ini", "--http-socket", ":8080"]
+ENTRYPOINT ["java", "-jar", "target/app.jar"]

server/docker-entrypoint.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 set -e
 
-if [ "$1" = 'uwsgi' ]; then
+if [ "$1" = 'java' ]; then
     cd ${APP_DIR}
     exec gosu www-data "$@"
 fi

server/pom.xml

@@ -4,17 +4,17 @@
     <artifactId>openapi-spring</artifactId>
     <packaging>jar</packaging>
     <name>openapi-spring</name>
-    <version>0.1.6</version>
+    <version>0.2.2</version>
     <properties>
         <java.version>1.8</java.version>
         <maven.compiler.source>${java.version}</maven.compiler.source>
         <maven.compiler.target>${java.version}</maven.compiler.target>
-        <springfox-version>2.8.0</springfox-version>
+        <springfox-version>2.9.2</springfox-version>
     </properties>
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.3.5.RELEASE</version>
+        <version>2.3.3.RELEASE</version>
     </parent>
     <build>
         <sourceDirectory>src/main/java</sourceDirectory>

server/src/main/java/org/nlpsandbox/DateExtractor.java

@@ -0,0 +1,82 @@
+package org.nlpsandbox;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.openapitools.model.TextDateAnnotation;
+
+public class DateExtractor {
+
+    class NamedPattern{
+        public String name;
+        public Pattern pattern;
+
+        public NamedPattern(String name, Pattern pattern){
+            this.name = name;
+            this.pattern = pattern;
+        }
+    }
+
+    class Span{
+        int begin;
+        int end;
+        int length;
+
+        public Span(int begin, int end){
+            this.begin = begin;
+            this.end = end;
+            this.length = end - begin;
+        }
+    }
+
+    static List<NamedPattern> datePatterns;
+
+    public DateExtractor(){
+        datePatterns = new ArrayList<>();
+        datePatterns.add(new NamedPattern("DD/MM/YYYY",
+                Pattern.compile(
+                    "\\b([1-9]|0[1-9]|1[0-9]|2[0-9]|3[0-1])(/)([1-9]|0[1-9]|1[0-2])(/)(19[0-9][0-9]|20[0-9][0-9])")));
+
+        datePatterns.add(new NamedPattern("MM/DD/YYYY",
+                Pattern.compile(
+                    "\\b([1-9]|0[1-9]|1[0-2])(/)([1-9]|0[1-9]|1[0-9]|2[0-9]|3[0-1])(/)(19[0-9][0-9]|20[0-9][0-9])")));
+
+        datePatterns.add(new NamedPattern("MM-DD-YYYY",
+                Pattern.compile(
+                    "\\b([1-9]|0[1-9]|1[0-2])(-)([1-9]|0[1-9]|1[0-9]|2[0-9]|3[0-1])(-)(19[0-9][0-9]|20[0-9][0-9])")));
+
+        datePatterns.add(new NamedPattern("MMMM",
+                Pattern.compile("\\b(January|February|March|April|May|June|" +
+                    "July|August|September|October|November|" +
+                    "December)")));
+    }
+
+    public List<TextDateAnnotation> findDatesFromString(String sentence){
+
+        List<TextDateAnnotation> annotations = new ArrayList<>();
+        for (NamedPattern np: datePatterns) {
+            // Now create matcher object.
+            Matcher m = np.pattern.matcher(sentence);
+            while (m.find()) {
+                annotations.add(new TextDateAnnotation()
+                        .start(m.start(0))
+                        .length(m.group(0).length())
+                        .text(m.group(0))
+                        .dateFormat(np.name)
+                        .confidence(92.5f));
+            }
+        }
+        return annotations;
+    }
+
+    public static void main(String[] args) {
+        DateExtractor de = new DateExtractor();
+        String str1 = "Today is 10/26/2020, and yesterday is 10/25/2020. ";
+        de.findDatesFromString(str1);
+
+        String str2 = "Today is 26/11/2020. ";
+        de.findDatesFromString(str2);
+    }
+}

server/src/main/java/org/openapitools/RFC3339DateFormat.java

@@ -1,22 +1,38 @@
 package org.openapitools;
 
-import com.fasterxml.jackson.databind.util.ISO8601DateFormat;
-import com.fasterxml.jackson.databind.util.ISO8601Utils;
+import com.fasterxml.jackson.databind.util.StdDateFormat;
 
+import java.text.DateFormat;
 import java.text.FieldPosition;
+import java.text.ParsePosition;
 import java.util.Date;
+import java.util.GregorianCalendar;
+import java.util.TimeZone;
 
+public class RFC3339DateFormat extends DateFormat {
+  private static final long serialVersionUID = 1L;
+  private static final TimeZone TIMEZONE_Z = TimeZone.getTimeZone("UTC");
 
-public class RFC3339DateFormat extends ISO8601DateFormat {
+  private final StdDateFormat fmt = new StdDateFormat()
+          .withTimeZone(TIMEZONE_Z)
+          .withColonInTimeZone(true);
 
-  private static final long serialVersionUID = 1L;
+  public RFC3339DateFormat() {
+    this.calendar = new GregorianCalendar();
+  }
+
+  @Override
+  public Date parse(String source, ParsePosition pos) {
+    return fmt.parse(source, pos);
+  }
 
-  // Same as ISO8601DateFormat but serializing milliseconds.
   @Override
   public StringBuffer format(Date date, StringBuffer toAppendTo, FieldPosition fieldPosition) {
-    String value = ISO8601Utils.format(date, true);
-    toAppendTo.append(value);
-    return toAppendTo;
+    return fmt.format(date, toAppendTo, fieldPosition);
   }
 
+  @Override
+  public Object clone() {
+    return this;
+  }
 }