SMILE refactoring

- refactored metadb references to smile - packages and class names updated - updated some prop names - updated mocked test data Signed-off-by: Angelica Ochoa <[email protected]>
mskcc · Mar 25, 2022 · ea94969 · ea94969
1 parent a18c2bc
commit ea94969
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Showing 27 changed files with 241 additions and 240 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -10,19 +10,19 @@ orbs:
 jobs:
   run_checkstyle:
     <<: *defaults
-    working_directory: /tmp/repos/cmo-metadb-label-generator
+    working_directory: /tmp/repos/smile-label-generator
     steps:
       - checkout
       - run:
-          name: Pull cmo metadb common code
+          name: Pull smile commons code
           command: |
-              export METADB_COMMON_VERSION=$(grep 'cmo_metadb_common\.version' pom.xml | head -1 | sed 's/<cmo_metadb_common\.version>//g' | sed 's|</cmo_metadb_common\.version>||' | tr -d '[:blank:]' | cut -f1) && \
-              export METADB_COMMON_ORG=$(grep 'cmo_metadb_common\.group' pom.xml | head -1 | sed 's/<cmo_metadb_common\.group>//g' | sed 's|</cmo_metadb_common\.group>||' | tr -d '[:blank:]' | cut -d. -f3) && \
+              export SMILE_COMMONS_VERSION=$(grep 'smile_commons\.version' pom.xml | head -1 | sed 's/<smile_commons\.version>//g' | sed 's|</smile_commons\.version>||' | tr -d '[:blank:]' | cut -f1) && \
+              export SMILE_COMMONS_ORG=$(grep 'smile_commons\.group' pom.xml | head -1 | sed 's/<smile_commons\.group>//g' | sed 's|</smile_commons\.group>||' | tr -d '[:blank:]' | cut -d. -f3) && \
               cd .. && \
-              git clone https://github.com/$METADB_COMMON_ORG/cmo-metadb-common.git && \
-              cd cmo-metadb-common && \
+              git clone https://github.com/$SMILE_COMMONS_ORG/smile-commons.git && \
+              cd smile-commons && \
               git fetch --tags && \
-              git checkout ${METADB_COMMON_VERSION}
+              git checkout ${SMILE_COMMONS_VERSION}
       - run:
           name: "Build project..."
           command: mvn clean install
@@ -31,9 +31,9 @@ jobs:
           command: mvn checkstyle:checkstyle
       - run:
           name: "Validating checkstyle plugin report..."
-          command: bash /tmp/repos/cmo-metadb-common/test/scripts/generate_checkstyle_report.sh /tmp/repos/cmo-metadb-label-generator
+          command: bash /tmp/repos/smile-commons/test/scripts/generate_checkstyle_report.sh /tmp/repos/smile-label-generator
       - store_artifacts:
-          path: /tmp/repos/cmo-metadb-label-generator/checkstyle_report_compiled.txt
+          path: /tmp/repos/smile-label-generator/checkstyle_report_compiled.txt
           destination: /checkstyle_report.txt
 
 workflows:

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -36,9 +36,10 @@ Please follow these checks if any changes were made to any classes in the web, s
 
 **Data checks:**
 Updates were made to the mocked incoming request data and/or mocked published request data:
-- [ ] [cmo-metadb test data](https://github.com/mskcc/cmo-metadb/tree/master/service/src/test/resources/data)
-- [ ] [cmo-metadb-common test data](https://github.com/mskcc/cmo-metadb-common/tree/master/src/test/resources/data)
-- [ ] [cmo-metadb-label-generator test data](https://github.com/mskcc/cmo-metadb-label-generator/tree/master/src/test/resources/data)
+
+- [ ] [smile-server test data](https://github.com/mskcc/smile-server/tree/master/service/src/test/resources/data)
+- [ ] [smile-commons test data](https://github.com/mskcc/smile-commons/tree/master/src/test/resources/data)
+- [ ] [smile-label-generator test data](https://github.com/mskcc/smile-label-generator/tree/master/src/test/resources/data)
 
 **Code checks:**
 - [ ] Unit tests were updated in relation to updates to the mocked test data.
@@ -56,8 +57,8 @@ Please describe how the workflow and messaging was tested/simulated:
 
 - NATS [local, local docker, dev server, production]
 - Neo4j [local, local docker, dev server, production]
-- MetaDB [local, local docker, dev server, production]
-- Message publishing simulation [nats cli, docker nats cli, metadb publisher tool, other (describe below)]
+- SMILE Server [local, local docker, dev server, production]
+- Message publishing simulation [nats cli, docker nats cli, smile publisher tool, other (describe below)]
 
 Other: [insert details on how messages were published or simulated for testing]
 

diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
@@ -1,5 +1,5 @@
 name-template: '$NEXT_PATCH_VERSION.RELEASE'
-tag-template: '- $TITLE @$AUTHOR (#$NUMBER)'
+tag-template: '$NEXT_PATCH_VERSION.RELEASE'
 categories:
   - title: 🚀 Features
     label: feature
@@ -14,4 +14,4 @@ template: |
 
   ## 🕵️ Full commit logs
 
-  https://github.com/mskcc/cmo-metadb-label-generator/compare/$PREVIOUS_TAG...$NEXT_PATCH_VERSION
+  https://github.com/mskcc/smile-label-generator/compare/$PREVIOUS_TAG...$NEXT_PATCH_VERSION.RELEASE
diff --git a/Dockerfile b/Dockerfile
@@ -7,5 +7,5 @@ RUN mvn clean install
 
 # copy jar and set entrypoint
 FROM openjdk:8-slim
-COPY --from=0 /label-generator/target/cmo_label_generator.jar /label-generator/cmo_label_generator.jar
+COPY --from=0 /label-generator/target/smile_label_generator.jar /label-generator/smile_label_generator.jar
 ENTRYPOINT ["java"]
diff --git a/README.md b/README.md
@@ -1,8 +1,8 @@
 # CMO Label Generator 🔍
 
-CMO Label Generator is a distributed microservices system. It receives messages from LIMS when a request is marked delivered. This message is processed and a unique CMO label Id is generated based on specifications that can be found in CMOPatientIDandSampleIDgeneration.pdf. Any new message is then published to downstream subscribers. The message published is a JSON reqpresentation of MetaDbRequest (more details can be found in cmo-metadb repository). 
+CMO Label Generator is a distributed microservices system. It receives messages from LIMS when a request is marked delivered. This message is processed and a unique CMO label Id is generated based on specifications that can be found in CMOPatientIDandSampleIDgeneration.pdf. Any new message is then published to downstream subscribers. The message published is a JSON reqpresentation of SmileRequest (more details can be found in smile-server repository). 
 
-Label Generator is dependent on MetaDb, Nats Jetstream and Nats RequestReply.
+Label Generator is dependent on SMILE, Nats Jetstream and Nats RequestReply.
 
 ## Run
 
@@ -12,7 +12,7 @@ Make an `application.properties` based on [application.properties.EXAMPLE](src/m
 
 Nats Pub/Sub topics:
 - `igo.cmo_label_generator_topic` : receives requests to process
-- `request_reply.patient_samples_topic` : used to patient samples set from MetaDB
+- `request_reply.patient_samples_topic` : used to patient samples set from SMILE Server
 - `igo.new_request_topic` : publishes the processed request to this topic
 
 All properties are required with the exception of some NATS connection-specific properties. The following are only required if `nats.tls_channel` is set to `true`:
@@ -40,7 +40,7 @@ mvn clean install
 Run with
 
 ```
-java -jar server/target/cmo_label_generator.jar
+java -jar server/target/smile_label_generator.jar
 ```
 
 ### With Docker
@@ -65,14 +65,14 @@ If the Docker image is built with the properties baked in then simply run with:
 
 ```
 docker run --name cmo-label-generator <repo>/<tag>:<version> \
-	-jar /cmo-label-generator/cmo_label_generator.jar
+	-jar /label-generator/smile_label_generator.jar
 ```
 
 Otherwise use a bind mount to make the local files available to the Docker image and add  `--spring.config.location` to the java arg
 
 ```
-docker run --mount type=bind,source=<local path to properties files>,target=/cmo-label-generator/src/main/resources \
-	--name cmo-label-generator <repo>/<tag>:<version> \
-	-jar /cmo-label-generator/cmo_label_generator.jar \
-	--spring.config.location=/cmo-label-generator/src/main/resources/application.properties
+docker run --mount type=bind,source=<local path to properties files>,target=/label-generator/src/main/resources \
+	--name label-generator <repo>/<tag>:<version> \
+	-jar /label-generator/smile_label_generator.jar \
+	--spring.config.location=/label-generator/src/main/resources/application.properties
 ```
diff --git a/pom.xml b/pom.xml
@@ -1,12 +1,12 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
   <modelVersion>4.0.0</modelVersion>
-  <groupId>org.mskcc.cmo.metadb</groupId>
+  <groupId>org.mskcc.smile</groupId>
   <artifactId>master</artifactId>
   <packaging>jar</packaging>
-  <name>MSKCC CMO MetaDB Label Generator</name>
+  <name>SMILE CMO Label Generator</name>
   <version>0.1.0</version>
   <description>master maven module</description>
-  <url>https://github.com/mskcc/cmo-metadb-label-generator</url>
+  <url>https://github.com/mskcc/smile-label-generator</url>
 
   <parent>
     <groupId>org.springframework.boot</groupId>
@@ -35,35 +35,35 @@
     <spring.boot.version>2.3.3.RELEASE</spring.boot.version>
     <slf4j.version>1.7.30</slf4j.version>
     <jackson.version>2.11.2</jackson.version>
-    <!-- metadb messaging -->
-    <cmo_metadb_messaging_java.group>com.github.mskcc</cmo_metadb_messaging_java.group>
-    <cmo_metadb_messaging_java.version>1.2.2.RELEASE</cmo_metadb_messaging_java.version>
-    <!-- metadb common centralized config properties -->
-    <cmo_metadb_common.group>com.github.mskcc</cmo_metadb_common.group>
-    <cmo_metadb_common.version>1.2.2.RELEASE</cmo_metadb_common.version>
-    <!-- metadb server model module -->
-    <cmo_metadb_server.group>com.github.mskcc.cmo-metadb</cmo_metadb_server.group>
-    <cmo_metadb_server.version>1.2.3.RELEASE</cmo_metadb_server.version>
+    <!-- smile messaging and shared entities dependency versions -->
+    <smile_messaging_java.group>com.github.mskcc</smile_messaging_java.group>
+    <smile_messaging_java.version>1.3.1.RELEASE</smile_messaging_java.version>
+    <!-- smile commons centralized config properties -->
+    <smile_commons.group>com.github.mskcc</smile_commons.group>
+    <smile_commons.version>1.3.1.RELEASE</smile_commons.version>
+    <!-- smile server model module -->
+    <smile_server.group>com.github.mskcc.smile-server</smile_server.group>
+    <smile_server.version>1.3.0.RELEASE</smile_server.version>
   </properties>
 
   <dependencies>
-      <!-- cmo messaging library -->
+      <!-- smile messaging library -->
     <dependency>
-      <groupId>${cmo_metadb_messaging_java.group}</groupId>
-      <artifactId>cmo-messaging-java</artifactId>
-      <version>${cmo_metadb_messaging_java.version}</version>
+      <groupId>${smile_messaging_java.group}</groupId>
+      <artifactId>smile-messaging-java</artifactId>
+      <version>${smile_messaging_java.version}</version>
     </dependency>
-    <!-- cmo metadb common -->
+    <!-- smile commons -->
     <dependency>
-      <groupId>${cmo_metadb_common.group}</groupId>
-      <artifactId>cmo-metadb-common</artifactId>
-      <version>${cmo_metadb_common.version}</version>
+      <groupId>${smile_commons.group}</groupId>
+      <artifactId>smile-commons</artifactId>
+      <version>${smile_commons.version}</version>
     </dependency>
-    <!-- cmo metadb server model -->
+    <!-- smile server model -->
     <dependency>
-      <groupId>${cmo_metadb_server.group}</groupId>
+      <groupId>${smile_server.group}</groupId>
       <artifactId>model</artifactId>
-      <version>${cmo_metadb_server.version}</version>
+      <version>${smile_server.version}</version>
     </dependency>
     <!-- spring -->
     <dependency>
@@ -116,7 +116,7 @@
   </dependencies>
 
   <build>
-    <finalName>cmo_label_generator</finalName>
+    <finalName>smile_label_generator</finalName>
     <resources>
       <resource>
         <directory>src/main/resources</directory>
@@ -158,9 +158,9 @@
         <version>3.1.1</version>
         <dependencies>
           <dependency>
-            <groupId>${cmo_metadb_common.group}</groupId>
-            <artifactId>cmo-metadb-common</artifactId>
-            <version>${cmo_metadb_common.version}</version>
+            <groupId>${smile_commons.group}</groupId>
+            <artifactId>smile-commons</artifactId>
+            <version>${smile_commons.version}</version>
           </dependency>
         </dependencies>
         <configuration>
@@ -187,7 +187,7 @@
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-maven-plugin</artifactId>
         <configuration>
-          <mainClass>org.mskcc.cmo.metadb.CmoLabelGeneratorApp</mainClass>
+          <mainClass>org.mskcc.smile.CmoLabelGeneratorApp</mainClass>
         </configuration>
       </plugin>
     </plugins>

diff --git a/...skcc/cmo/metadb/CmoLabelGeneratorApp.java → ...org/mskcc/smile/CmoLabelGeneratorApp.java b/...skcc/cmo/metadb/CmoLabelGeneratorApp.java → ...org/mskcc/smile/CmoLabelGeneratorApp.java
@@ -1,18 +1,18 @@
-package org.mskcc.cmo.metadb;
+package org.mskcc.smile;
 
 import java.util.concurrent.CountDownLatch;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.mskcc.cmo.messaging.Gateway;
-import org.mskcc.cmo.metadb.service.MessageHandlingService;
-import org.mskcc.cmo.metadb.service.RequestReplyHandlingService;
+import org.mskcc.smile.service.MessageHandlingService;
+import org.mskcc.smile.service.RequestReplyHandlingService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.CommandLineRunner;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 
 @SpringBootApplication(scanBasePackages = {"org.mskcc.cmo.messaging",
-        "org.mskcc.cmo.common.*", "org.mskcc.cmo.metadb.*"})
+        "org.mskcc.smile.commons.*", "org.mskcc.smile.*"})
 public class CmoLabelGeneratorApp implements CommandLineRunner {
     private static final Log LOG = LogFactory.getLog(CmoLabelGeneratorApp.class);
 

diff --git a/...adb/service/CmoLabelGeneratorService.java → ...ile/service/CmoLabelGeneratorService.java b/...adb/service/CmoLabelGeneratorService.java → ...ile/service/CmoLabelGeneratorService.java
@@ -1,8 +1,8 @@
-package org.mskcc.cmo.metadb.service;
+package org.mskcc.smile.service;
 
 import java.util.List;
-import org.mskcc.cmo.metadb.model.SampleMetadata;
-import org.mskcc.cmo.metadb.model.igo.IgoSampleManifest;
+import org.mskcc.smile.model.SampleMetadata;
+import org.mskcc.smile.model.igo.IgoSampleManifest;
 
 /**
  *

diff --git a/...etadb/service/MessageHandlingService.java → ...smile/service/MessageHandlingService.java b/...etadb/service/MessageHandlingService.java → ...smile/service/MessageHandlingService.java
@@ -1,7 +1,7 @@
-package org.mskcc.cmo.metadb.service;
+package org.mskcc.smile.service;
 
 import org.mskcc.cmo.messaging.Gateway;
-import org.mskcc.cmo.metadb.model.SampleMetadata;
+import org.mskcc.smile.model.SampleMetadata;
 
 public interface MessageHandlingService {
     void initialize(Gateway gateway) throws Exception;

diff --git a/.../service/RequestReplyHandlingService.java → .../service/RequestReplyHandlingService.java b/.../service/RequestReplyHandlingService.java → .../service/RequestReplyHandlingService.java
@@ -1,4 +1,4 @@
-package org.mskcc.cmo.metadb.service;
+package org.mskcc.smile.service;
 
 import org.mskcc.cmo.messaging.Gateway;
 

diff --git a/...ce/impl/CmoLabelGeneratorServiceImpl.java → ...ce/impl/CmoLabelGeneratorServiceImpl.java b/...ce/impl/CmoLabelGeneratorServiceImpl.java → ...ce/impl/CmoLabelGeneratorServiceImpl.java
@@ -1,4 +1,4 @@
-package org.mskcc.cmo.metadb.service.impl;
+package org.mskcc.smile.service.impl;
 
 import java.util.Arrays;
 import java.util.HashMap;
@@ -9,14 +9,14 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.mskcc.cmo.common.enums.CmoSampleClass;
-import org.mskcc.cmo.common.enums.NucleicAcid;
-import org.mskcc.cmo.common.enums.SampleOrigin;
-import org.mskcc.cmo.common.enums.SampleType;
-import org.mskcc.cmo.common.enums.SpecimenType;
-import org.mskcc.cmo.metadb.model.SampleMetadata;
-import org.mskcc.cmo.metadb.model.igo.IgoSampleManifest;
-import org.mskcc.cmo.metadb.service.CmoLabelGeneratorService;
+import org.mskcc.smile.commons.enums.CmoSampleClass;
+import org.mskcc.smile.commons.enums.NucleicAcid;
+import org.mskcc.smile.commons.enums.SampleOrigin;
+import org.mskcc.smile.commons.enums.SampleType;
+import org.mskcc.smile.commons.enums.SpecimenType;
+import org.mskcc.smile.model.SampleMetadata;
+import org.mskcc.smile.model.igo.IgoSampleManifest;
+import org.mskcc.smile.service.CmoLabelGeneratorService;
 import org.springframework.stereotype.Service;
 
 /**

diff --git a/...l/LabelGenMessageHandlingServiceImpl.java → ...l/LabelGenMessageHandlingServiceImpl.java b/...l/LabelGenMessageHandlingServiceImpl.java → ...l/LabelGenMessageHandlingServiceImpl.java
@@ -1,4 +1,4 @@
-package org.mskcc.cmo.metadb.service.impl;
+package org.mskcc.smile.service.impl;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -20,11 +20,11 @@
 import org.apache.commons.logging.LogFactory;
 import org.mskcc.cmo.messaging.Gateway;
 import org.mskcc.cmo.messaging.MessageConsumer;
-import org.mskcc.cmo.metadb.model.SampleMetadata;
-import org.mskcc.cmo.metadb.model.igo.IgoSampleManifest;
-import org.mskcc.cmo.metadb.service.CmoLabelGeneratorService;
-import org.mskcc.cmo.metadb.service.MessageHandlingService;
-import org.mskcc.cmo.metadb.service.util.RequestStatusLogger;
+import org.mskcc.smile.model.SampleMetadata;
+import org.mskcc.smile.model.igo.IgoSampleManifest;
+import org.mskcc.smile.service.CmoLabelGeneratorService;
+import org.mskcc.smile.service.MessageHandlingService;
+import org.mskcc.smile.service.util.RequestStatusLogger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
@@ -45,7 +45,7 @@ public class LabelGenMessageHandlingServiceImpl implements MessageHandlingServic
     @Value("${igo.cmo_sample_label_update_topic}")
     private String CMO_LABEL_UPDATE_TOPIC;
 
-    @Value("${metadb.sample_update_topic}")
+    @Value("${smile.sample_update_topic}")
     private String IGO_SAMPLE_UPDATE_TOPIC;
 
     @Value("${num.new_request_handler_threads}")

diff --git a/...impl/RequestReplyHandlingServiceImpl.java → ...impl/RequestReplyHandlingServiceImpl.java b/...impl/RequestReplyHandlingServiceImpl.java → ...impl/RequestReplyHandlingServiceImpl.java
@@ -1,4 +1,4 @@
-package org.mskcc.cmo.metadb.service.impl;
+package org.mskcc.smile.service.impl;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import io.nats.client.Message;
@@ -17,9 +17,9 @@
 import org.apache.commons.logging.LogFactory;
 import org.mskcc.cmo.messaging.Gateway;
 import org.mskcc.cmo.messaging.MessageConsumer;
-import org.mskcc.cmo.metadb.model.SampleMetadata;
-import org.mskcc.cmo.metadb.service.CmoLabelGeneratorService;
-import org.mskcc.cmo.metadb.service.RequestReplyHandlingService;
+import org.mskcc.smile.model.SampleMetadata;
+import org.mskcc.smile.service.CmoLabelGeneratorService;
+import org.mskcc.smile.service.RequestReplyHandlingService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;

diff --git a/...adb/service/util/RequestStatusLogger.java → ...ile/service/util/RequestStatusLogger.java b/...adb/service/util/RequestStatusLogger.java → ...ile/service/util/RequestStatusLogger.java
@@ -1,11 +1,11 @@
-package org.mskcc.cmo.metadb.service.util;
+package org.mskcc.smile.service.util;
 
 import java.io.File;
 import java.io.IOException;
 import java.time.LocalDate;
 import java.time.format.DateTimeFormatter;
 import org.apache.commons.lang3.StringUtils;
-import org.mskcc.cmo.common.FileUtil;
+import org.mskcc.smile.commons.FileUtil;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Component;
@@ -34,7 +34,7 @@ public class RequestStatusLogger {
      * - CMO_REQUEST_MISSING_REQ_FIELDS: a CMO request with sample metadata
      *        that is missing required fields (cmoPatientId, baitSet)
      * - REQUEST_PARSING_ERROR: json parsing exception thrown
-     * - CMO_REQUEST_FILTER_SKIPPED_REQUEST: applies if metadb server is running
+     * - CMO_REQUEST_FILTER_SKIPPED_REQUEST: applies if smile server is running
      *        with the cmoRequestFilter enabled and a non-cmo request is encountered
      * - REQUEST_WITH_FAILED_CMO_LABEL_GENERATION: request contains samples for which a
      *        CMO label was not successfully generated