Convert Avro -> proto3.

ga4gh · Apr 16, 2016 · 0ff95ff · 0ff95ff
1 parent f421d6e
commit 0ff95ff
Show file tree

Hide file tree

Showing 18 changed files with 1,667 additions and 2,432 deletions.
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -118,54 +118,12 @@ Syntax Style and Conventions
 
 The current code conventions for the source files are as follows:
 
+- Follow the `protocol buffers style guide
+  <https://developers.google.com/protocol-buffers/docs/style>`__
 - Use two-space indentation, and no tabs.
 - Hard-wrap code to 80 characters per line.
-- Use ``UpperCamelCase`` for object or record names.
-- Use ``lowerCamelCase`` for attribute or method names.
-- Use ``CONSTANT_CASE`` for global and constant values.
-- Comments:
-
-  - Comments should be indented at the same level as the surrounding
-    code.
-  - Comments should precede the code that they make a comment on.
-    Documentation comments will not work otherwise.
-  - Documentation comments, which are intended to be processed by
-    avrodoc and displayed in the user-facing API documentation, must use
-    the ``/** ... */`` style, and must not have a leading ``*`` on each
-    internal line:
-
-    ::
-
-       /**
-       This documentation comment will be
-       processed correctly by avrodoc.
-       */
-
-    ::
-
-       /**
-       * This documentation comment will have a
-       * bullet point at the start of every line
-       * when processed by avrodoc.
-       */
-
-  - Block and multi-line non-documentation comments, intended for schema
-    developers only, must use the ``/* ... */`` style.
-
-    ::
-
-       /*
-       This multi-line comment will not appear in the
-       avrodoc documentation and is intended for
-       schema developers.
-       */
-
-  - All multi-line comments should have the comment text at the same
-    indent level as the comment delimeters.
-  - One-line non-documentation comments, intended for schema developers
-    only, must use the ``// ...`` style.
-  - Comments may use `reStructuredText
-    <http://docutils.sourceforge.net/rst.html>`__ mark up.
+- Comments may use `reStructuredText
+  <http://docutils.sourceforge.net/rst.html>`__ mark up.
 
 Documentation
 @@@@@@@@@@@@@

diff --git a/README.rst b/README.rst
@@ -31,8 +31,8 @@ primary data collected from sequencing machines.
 The team will deliver:
 
 #. Data model. An abstract, mathematically complete and precise model of
-   the data that is manipulated by the API. See the `Avro
-   directory <src/main/resources/avro>`__ for our in-progress work on
+   the data that is manipulated by the API. See the `Proto
+   directory <src/main/proto>`__ for our in-progress work on
    defining v0.5 of the data model.
 
 #. API Specification. A human-readable document introducing and

diff --git a/pom.xml b/pom.xml
@@ -35,21 +35,44 @@
   </developers>
 
   <properties>
-    <avro.version>1.7.7</avro.version>
+    <proto.version>3.0.0-beta-2</proto.version>
     <maven.enforcer.jdk-version>[1.6,)</maven.enforcer.jdk-version>
     <maven.enforcer.maven-version>[3.0.4,)</maven.enforcer.maven-version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.build.targetEncoding>UTF-8</project.build.targetEncoding>
   </properties>
 
+  <!-- pluginRepositories can be removed entirely once
+       https://github.com/sergei-ivanov/maven-protoc-plugin/issues/11 is
+       resolved. -->
+  <pluginRepositories>
+    <pluginRepository>
+        <releases>
+            <updatePolicy>never</updatePolicy>
+        </releases>
+        <snapshots>
+            <enabled>false</enabled>
+        </snapshots>
+        <id>central</id>
+        <name>Central Repository</name>
+        <url>https://repo.maven.apache.org/maven2</url>
+    </pluginRepository>
+    <pluginRepository>
+        <id>protoc-plugin</id>
+        <url>https://dl.bintray.com/sergei-ivanov/maven/</url>
+    </pluginRepository>
+  </pluginRepositories>
+
   <build>
+    <extensions>
+      <extension>
+        <groupId>kr.motd.maven</groupId>
+        <artifactId>os-maven-plugin</artifactId>
+        <version>1.4.0.Final</version>
+      </extension>
+    </extensions>
     <pluginManagement>
       <plugins>
-        <plugin>
-          <groupId>org.apache.avro</groupId>
-          <artifactId>avro-maven-plugin</artifactId>
-          <version>${avro.version}</version>
-        </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-clean-plugin</artifactId>
@@ -125,21 +148,18 @@
     </pluginManagement>
     <plugins>
       <plugin>
-        <groupId>org.apache.avro</groupId>
-        <artifactId>avro-maven-plugin</artifactId>
+        <groupId>com.google.protobuf.tools</groupId>
+        <artifactId>maven-protoc-plugin</artifactId>
+        <version>0.4.4</version>
+        <configuration>
+          <protocArtifact>com.google.protobuf:protoc:${proto.version}:exe:${os.detected.classifier}</protocArtifact>
+        </configuration>
         <executions>
           <execution>
-            <id>schemas</id>
-            <phase>generate-sources</phase>
             <goals>
-              <goal>schema</goal>
-              <goal>protocol</goal>
-              <goal>idl-protocol</goal>
+              <goal>compile</goal>
+              <goal>compile-python</goal>
             </goals>
-            <configuration>
-              <sourceDirectory>${project.basedir}/src/main/resources/avro</sourceDirectory>
-              <stringType>String</stringType>
-            </configuration>
           </execution>
         </executions>
       </plugin>
@@ -165,7 +185,8 @@
           </execution>
         </executions>
       </plugin>
-      <plugin>
+<!-- FIXME: Doc generation temporarily disabled due to dependency on avro.
+     <plugin>
         <groupId>org.codehaus.mojo</groupId>
         <artifactId>exec-maven-plugin</artifactId>
         <version>1.4.0</version>
@@ -184,33 +205,14 @@
 	    <argument>docs</argument>
 	  </arguments>
         </configuration>
-      </plugin>
+      </plugin> -->
     </plugins>
   </build>
-  <dependencyManagement>
-    <dependencies>
-      <dependency>
-        <groupId>org.apache.avro</groupId>
-        <artifactId>avro</artifactId>
-        <version>${avro.version}</version>
-      </dependency>
-      <dependency>
-        <groupId>org.apache.avro</groupId>
-        <artifactId>avro-ipc</artifactId>
-        <version>${avro.version}</version>
-      </dependency>
-    </dependencies>
-  </dependencyManagement>
   <dependencies>
     <dependency>
-      <groupId>org.apache.avro</groupId>
-      <artifactId>avro</artifactId>
-      <scope>compile</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.apache.avro</groupId>
-      <artifactId>avro-ipc</artifactId>
-      <scope>compile</scope>
+      <groupId>com.google.protobuf</groupId>
+      <artifactId>protobuf-java</artifactId>
+      <version>${proto.version}</version>
     </dependency>
   </dependencies>
   <distributionManagement>