Set up building self-contained JAR

PheMA · Jan 3, 2020 · 19c52c9 · 19c52c9
1 parent 645286b
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Showing 2 changed files with 29 additions and 2 deletions.
diff --git a/README.md b/README.md
@@ -37,7 +37,7 @@ are supported:
 |**Name**|**Description**|
 |---|---|
 |OMOP_BASE_URL| The base URL of the OHDSI WebAPI (should end with `WebAPI/`)|
-|INPUT_FILE_NAME| The name of the CQL library relative to `src/main/resources`|
+|INPUT_FILE_NAME| The path of the CQL library relative to `src/main/resources`|
 |VS_FILE_NAME| Name of the valueset CSV file relative to `src/main/resources`|
 |OUT_FILE_NAME| Output filename (will be created in `src/main/resources`) |
 |SOURCE|The OHDSI data source name |
@@ -58,6 +58,11 @@ Individual properties can also be overwritten on the command line as follows:
 mvn compile exec:java -Dexec.arguments="OMOP_BASE_URL=http://projectphema.org/WebAPI/ INPUT_FILE_NAME=autism/simple-dx-elm.xml"
 ```
 
+You can optionally build an executable JAR with all dependencies packaged (NOTE: this is a large file):
+```
+mvn clean package
+```
+
 ### Library
 
 To use the translator library, add the PhEMA Maven repo to your `pom.xml`:
@@ -153,4 +158,4 @@ can then be turned into one or more actual cohorts that exist in OHDSI. If no id
 to find any public definition (`<def accessLevel="Public">`) that is not used within another expression.  This will give
 us "top-level" expressions, which are most likely the phenotypes of interest.
 
-For further implementation considerations, see the [design document](docs/DESIGN.md).
+For further implementation considerations, see the [design document](docs/DESIGN.md).
diff --git a/pom.xml b/pom.xml
@@ -312,6 +312,28 @@
                     <doclint>none</doclint>
                 </configuration>
             </plugin>
+            <plugin>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <executions>
+                    <execution>
+                      <phase>package</phase>
+                      <goals>
+                        <goal>single</goal>
+                      </goals>
+                  </execution>
+                </executions>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <addClasspath>true</addClasspath>
+                            <mainClass>edu.phema.elm_to_omop.ElmToOmopConverter</mainClass>
+                        </manifest>
+                    </archive>
+                    <descriptorRefs>
+                        <descriptorRef>jar-with-dependencies</descriptorRef>
+                    </descriptorRefs>
+              </configuration>
+            </plugin>
         </plugins>
     </build>