JDBC bindings (#5)

mlin · Sep 18, 2020 · 050940f · 050940f
1 parent 7298095
commit 050940f
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Showing 13 changed files with 754 additions and 30 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -18,6 +18,8 @@ jobs:
         sudo pip3 install --system pre-commit $PIP_DEPS black flake8 pylint
     - name: pre-commit
       run: pre-commit run --all-files
+    - name: mvn spotless:check
+      run: mvn spotless:check -B -f bindings/jdbc/genomicsqlite-jdbc/pom.xml
 
   test:
     runs-on: ubuntu-20.04
@@ -97,7 +99,7 @@ jobs:
         name: libgenomicsqlite.dylib
         path: libgenomicsqlite.dylib
 
-  combined-zip:
+  artifacts:
     runs-on: ubuntu-20.04
     needs: [linux-so, macOS-dylib]
     steps:
@@ -123,3 +125,11 @@ jobs:
           genomicsqlite.h
           libgenomicsqlite.so
           libgenomicsqlite.dylib
+    - name: build jar
+      run: |
+        cp libgenomicsqlite.so libgenomicsqlite.dylib bindings/jdbc/genomicsqlite-jdbc/src/main/resources/
+        mvn deploy -Drevision=${{ env.GIT_REVISION }} -B -f bindings/jdbc/genomicsqlite-jdbc/pom.xml
+    - uses: actions/upload-artifact@v2
+      with:
+        name: genomicsqlite-jdbc-${{ env.GIT_REVISION }}
+        path: bindings/jdbc/genomicsqlite-jdbc/target/mvn-repo
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -54,8 +54,9 @@ if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
     add_subdirectory(test)
     include(CTest)
     enable_testing()
-    set(GENOMICSQLITE_TEST_ENV env PYTHONPATH=${CMAKE_CURRENT_SOURCE_DIR}/bindings/python:${PYTHONPATH} LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}:${LD_LIBRARY_PATH} GENOMICSQLITE_SYSTEM_LIBRARY=1)
+    set(GENOMICSQLITE_TEST_ENV env PYTHONPATH=${CMAKE_CURRENT_SOURCE_DIR}/bindings/python:${PYTHONPATH} LIBGENOMICSQLITE=${CMAKE_BINARY_DIR}/libgenomicsqlite)
     add_test(NAME smoke_test COMMAND ${GENOMICSQLITE_TEST_ENV} python3 ${CMAKE_CURRENT_SOURCE_DIR}/test/genomicsqlite_smoke_test.py)
     add_test(NAME capi_smoke_test COMMAND ${GENOMICSQLITE_TEST_ENV} ${CMAKE_BINARY_DIR}/test/capi_smoke_test)
+    add_test(NAME JdbcTests COMMAND ${GENOMICSQLITE_TEST_ENV} mvn test -B -f ${CMAKE_CURRENT_SOURCE_DIR}/bindings/jdbc/genomicsqlite-jdbc/pom.xml)
     add_test(NAME pytest COMMAND ${GENOMICSQLITE_TEST_ENV} python3 -m pytest -xv -n 4 --tb=short ${CMAKE_CURRENT_SOURCE_DIR}/test)
 endif()
diff --git a/bindings/jdbc/genomicsqlite-jdbc/.gitignore b/bindings/jdbc/genomicsqlite-jdbc/.gitignore
@@ -0,0 +1,12 @@
+target/
+pom.xml.tag
+pom.xml.releaseBackup
+pom.xml.versionsBackup
+pom.xml.next
+release.properties
+dependency-reduced-pom.xml
+buildNumber.properties
+.mvn/timing.properties
+# https://github.com/takari/maven-wrapper#usage-without-binary-jar
+.mvn/wrapper/maven-wrapper.jar
+src/resources/libgenomicsqlite*
diff --git a/bindings/jdbc/genomicsqlite-jdbc/pom.xml b/bindings/jdbc/genomicsqlite-jdbc/pom.xml
@@ -0,0 +1,128 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <groupId>net.mlin</groupId>
+  <artifactId>genomicsqlite-jdbc</artifactId>
+  <version>${revision}</version>
+  <packaging>jar</packaging>
+
+  <name>genomicsqlite-jdbc</name>
+  <url>https://github.com/mlin/GenomicSQLite</url>
+
+  <licenses>
+    <license>
+      <name>The Apache Software License, Version 2.0</name>
+      <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
+    </license>
+  </licenses>
+
+  <developers>
+    <developer>
+      <name>Mike Lin</name>
+      <email>dna@mlin.net</email>
+      <organization>mlin.net LLC</organization>
+      <organizationUrl>https://www.mlin.net</organizationUrl>
+    </developer>
+  </developers>
+
+  <scm>
+    <connection>scm:git:git://github.com/mlin/GenomicSQLite.git</connection>
+    <developerConnection>scm:git:ssh://github.com:mlin/GenomicSQLite.git</developerConnection>
+    <url>https://github.com/mlin/GenomicSQLite/tree/main</url>
+  </scm>
+
+  <distributionManagement>
+    <repository>
+      <id>internal.repo</id>
+      <name>Temporary Staging Repository</name>
+      <url>file://${project.build.directory}/mvn-repo</url>
+    </repository>
+  </distributionManagement>
+
+  <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <maven.compiler.source>1.7</maven.compiler.source>
+    <maven.compiler.target>1.7</maven.compiler.target>
+  </properties>
+
+  <dependencies>
+    <dependency>
+      <groupId>org.xerial</groupId>
+      <artifactId>sqlite-jdbc</artifactId>
+      <version>[3.31.1,)</version>
+    </dependency>
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>4.11</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+
+  <build>
+    <pluginManagement><!-- lock down plugins versions to avoid using Maven defaults (may be moved to parent pom) -->
+      <plugins>
+        <!-- clean lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#clean_Lifecycle -->
+        <plugin>
+          <artifactId>maven-clean-plugin</artifactId>
+          <version>3.1.0</version>
+        </plugin>
+        <!-- default lifecycle, jar packaging: see https://maven.apache.org/ref/current/maven-core/default-bindings.html#Plugin_bindings_for_jar_packaging -->
+        <plugin>
+          <artifactId>maven-resources-plugin</artifactId>
+          <version>3.0.2</version>
+        </plugin>
+        <plugin>
+          <artifactId>maven-compiler-plugin</artifactId>
+          <version>3.8.0</version>
+        </plugin>
+        <plugin>
+          <artifactId>maven-surefire-plugin</artifactId>
+          <version>2.22.2</version>
+          <configuration>
+            <trimStackTrace>false</trimStackTrace>
+          </configuration>
+        </plugin>
+        <plugin>
+          <artifactId>maven-jar-plugin</artifactId>
+          <version>3.0.2</version>
+        </plugin>
+        <plugin>
+          <artifactId>maven-install-plugin</artifactId>
+          <version>2.5.2</version>
+        </plugin>
+        <plugin>
+          <artifactId>maven-deploy-plugin</artifactId>
+          <version>2.8.2</version>
+        </plugin>
+        <!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
+        <plugin>
+          <artifactId>maven-site-plugin</artifactId>
+          <version>3.7.1</version>
+        </plugin>
+        <plugin>
+          <artifactId>maven-project-info-reports-plugin</artifactId>
+          <version>3.0.0</version>
+        </plugin>
+        <plugin>
+          <groupId>com.diffplug.spotless</groupId>
+          <artifactId>spotless-maven-plugin</artifactId>
+          <version>2.3.1</version>
+          <configuration>
+            <java>
+              <includes>
+                <include>src/**/*.java</include>
+              </includes>
+              <importOrder/>
+              <removeUnusedImports/>
+              <googleJavaFormat/>
+            </java>
+          </configuration>
+        </plugin>
+      </plugins>
+    </pluginManagement>
+  </build>
+</project>
diff --git a/bindings/jdbc/genomicsqlite-jdbc/src/main/java/net/mlin/genomicsqlite/GenomicSQLite.java b/bindings/jdbc/genomicsqlite-jdbc/src/main/java/net/mlin/genomicsqlite/GenomicSQLite.java
@@ -0,0 +1,191 @@
+package net.mlin.genomicsqlite;
+
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.HashMap;
+
+public class GenomicSQLite {
+  public static String version(Connection conn) throws SQLException {
+    ResultSet row = conn.createStatement().executeQuery("SELECT genomicsqlite_version()");
+    row.next();
+    return row.getString(1);
+  }
+
+  public static String attachSQL(
+      Connection conn, String dbFileName, String schemaName, String configJson)
+      throws SQLException {
+    PreparedStatement stmt = conn.prepareStatement("SELECT genomicsqlite_attach_sql(?,?,?)");
+    stmt.setString(1, dbFileName);
+    stmt.setString(2, schemaName);
+    stmt.setString(3, configJson);
+    ResultSet row = stmt.executeQuery();
+    row.next();
+    return row.getString(1);
+  }
+
+  public static String attachSQL(Connection conn, String dbFileName, String schemaName)
+      throws SQLException {
+    return attachSQL(conn, dbFileName, schemaName, "{}");
+  }
+
+  public static String vacuumIntoSQL(Connection conn, String destFileName, String configJson)
+      throws SQLException {
+    PreparedStatement stmt = conn.prepareStatement("SELECT genomicsqlite_vacuum_into_sql(?,?)");
+    stmt.setString(1, destFileName);
+    stmt.setString(2, configJson);
+    ResultSet row = stmt.executeQuery();
+    row.next();
+    return row.getString(1);
+  }
+
+  public static String vacuumIntoSQL(Connection conn, String destFileName) throws SQLException {
+    return vacuumIntoSQL(conn, destFileName, "{}");
+  }
+
+  public static String createGenomicRangeIndexSQL(
+      Connection conn,
+      String tableName,
+      String rid,
+      String beginPosition,
+      String endPosition,
+      int floor)
+      throws SQLException {
+    PreparedStatement stmt =
+        conn.prepareStatement("SELECT create_genomic_range_index_sql(?,?,?,?,?)");
+    stmt.setString(1, tableName);
+    stmt.setString(2, rid);
+    stmt.setString(3, beginPosition);
+    stmt.setString(4, endPosition);
+    stmt.setInt(5, floor);
+    ResultSet row = stmt.executeQuery();
+    row.next();
+    return row.getString(1);
+  }
+
+  public static String createGenomicRangeIndexSQL(
+      Connection conn, String tableName, String rid, String beginPosition, String endPosition)
+      throws SQLException {
+    return createGenomicRangeIndexSQL(conn, tableName, rid, beginPosition, endPosition, -1);
+  }
+
+  public static String putReferenceAssemblySQL(Connection conn, String assembly)
+      throws SQLException {
+    PreparedStatement stmt = conn.prepareStatement("SELECT put_genomic_reference_assembly_sql(?)");
+    stmt.setString(1, assembly);
+    ResultSet row = stmt.executeQuery();
+    row.next();
+    return row.getString(1);
+  }
+
+  public static String putReferenceSequenceSQL(
+      Connection conn,
+      String name,
+      long length,
+      String assembly,
+      String refget_id,
+      String meta_json,
+      long rid)
+      throws SQLException {
+    PreparedStatement stmt =
+        conn.prepareStatement("SELECT put_genomic_reference_sequence_sql(?,?,?,?,?,?)");
+    stmt.setString(1, name);
+    stmt.setLong(2, length);
+    stmt.setString(3, assembly);
+    stmt.setString(4, refget_id);
+    stmt.setString(5, meta_json);
+    stmt.setLong(6, rid);
+    ResultSet row = stmt.executeQuery();
+    row.next();
+    return row.getString(1);
+  }
+
+  public static String putReferenceSequenceSQL(
+      Connection conn,
+      String name,
+      long length,
+      String assembly,
+      String refget_id,
+      String meta_json)
+      throws SQLException {
+    PreparedStatement stmt =
+        conn.prepareStatement("SELECT put_genomic_reference_sequence_sql(?,?,?,?,?)");
+    stmt.setString(1, name);
+    stmt.setLong(2, length);
+    if (assembly != null) stmt.setString(3, assembly);
+    if (refget_id != null) stmt.setString(4, refget_id);
+    if (meta_json != null) stmt.setString(5, meta_json);
+    ResultSet row = stmt.executeQuery();
+    row.next();
+    return row.getString(1);
+  }
+
+  public static String putReferenceSequenceSQL(
+      Connection conn, String name, long length, String assembly, String refget_id)
+      throws SQLException {
+    return putReferenceSequenceSQL(conn, name, length, assembly, refget_id, null);
+  }
+
+  public static String putReferenceSequenceSQL(
+      Connection conn, String name, long length, String assembly) throws SQLException {
+    return putReferenceSequenceSQL(conn, name, length, assembly, null, null);
+  }
+
+  public static String putReferenceSequenceSQL(Connection conn, String name, long length)
+      throws SQLException {
+    return putReferenceSequenceSQL(conn, name, length, null, null, null);
+  }
+
+  public static HashMap<Long, ReferenceSequence> getReferenceSequencesByRid(
+      Connection conn, String assembly) throws SQLException {
+    String sql =
+        "SELECT _gri_rid, gri_refseq_name, gri_refseq_length, gri_assembly, gri_refget_id, gri_refseq_meta_json FROM _gri_refseq";
+    PreparedStatement stmt;
+    if (assembly != null) {
+      stmt = conn.prepareStatement(sql + " WHERE gri_assembly = ?");
+      stmt.setString(1, assembly);
+    } else {
+      stmt = conn.prepareStatement(sql);
+    }
+    ResultSet row = stmt.executeQuery();
+    HashMap<Long, ReferenceSequence> ans = new HashMap<Long, ReferenceSequence>();
+    while (row.next()) {
+      ReferenceSequence grs =
+          new ReferenceSequence(
+              row.getLong(1),
+              row.getString(2),
+              row.getLong(3),
+              row.getString(4),
+              row.getString(5),
+              row.getString(6));
+      ans.put(grs.rid, grs);
+    }
+    return ans;
+  }
+
+  public static HashMap<Long, ReferenceSequence> getReferenceSequencesByRid(Connection conn)
+      throws SQLException {
+    return getReferenceSequencesByRid(conn, null);
+  }
+
+  public static HashMap<String, ReferenceSequence> getReferenceSequencesByName(
+      Connection conn, String assembly) throws SQLException {
+    HashMap<String, ReferenceSequence> ans = new HashMap<String, ReferenceSequence>();
+    for (HashMap.Entry<Long, ReferenceSequence> entry :
+        getReferenceSequencesByRid(conn, assembly).entrySet()) {
+      ReferenceSequence grs = entry.getValue();
+      if (ans.containsKey(grs.name)) {
+        throw new RuntimeException(
+            "GenomicSQLite.getReferenceSequencesByName: duplicate name; try filtering by assembly");
+      }
+      ans.put(grs.name, grs);
+    }
+    return ans;
+  }
+
+  public static HashMap<String, ReferenceSequence> getReferenceSequencesByName(Connection conn)
+      throws SQLException {
+    return getReferenceSequencesByName(conn, null);
+  }
+}