Move scripts out of java jar

Author: ruslan-forostianov

.gitignore

@@ -23,6 +23,8 @@
 hs_err_pid*
 replay_pid*
 /target/
+# the final jar artifact is placed in the root of the project
+/core-*.jar
 .DS_Store
 .project
 /.settings/
@@ -31,3 +33,14 @@ replay_pid*
 
 .idea
 /dependency-reduced-pom.xml
+
+# python
+__pycache__/
+*.pyc
+.venv/
+
+# test html reports
+*.html~
+
+# app properties that contains credentials
+/application.properties

README.md

@@ -0,0 +1,5 @@
+spring.datasource.url=jdbc:mysql://localhost:3306/cbioportal?useSSL=false
+spring.datasource.username=cbio
+spring.datasource.password=P@ssword1
+spring.datasource.driver-class-name=com.mysql.jdbc.Driver
+spring.jpa.database-platform=org.hibernate.dialect.MySQL5InnoDBDialect

application.properties.example

@@ -323,6 +323,13 @@
 					</execution>
 				</executions>
 			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-jar-plugin</artifactId>
+				<configuration>
+					<outputDirectory>${project.basedir}</outputDirectory>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 

pom.xml

@@ -39,18 +39,18 @@
 }
 
 # Set up Classpath to use the scripts jar
-sub locate_src_root {
+sub locate_root {
     # isolate the directory this code file is in
     my ($volume, $script_dir, undef) = File::Spec->splitpath(__FILE__);
-    # go up from cbioportal/core/src/main/scripts/ to cbioportal/
-    my $src_root_dir = File::Spec->catdir($script_dir, (File::Spec->updir()) x 4);
+    # go up one level
+    my $root_dir = File::Spec->catdir($script_dir, File::Spec->updir());
     # reassamble the path and resolve updirs (/../)
-    return abs_path(File::Spec->catpath($volume, $src_root_dir));
+    return abs_path(File::Spec->catpath($volume, $root_dir));
 }
-$src_root = locate_src_root();
-@jar_files = glob("$src_root/scripts/target/scripts-*.jar");
+$root_dir = locate_root();
+@jar_files = glob("$root_dir/core-*.jar");
 if (scalar @jar_files != 1) {
-    die "Expected to find 1 scripts-*.jar, but found: " . scalar @jar_files;
+    die "Expected to find 1 core-*.jar, but found: " . scalar @jar_files;
 }
 $cp = pop @jar_files;
 

src/main/resources/scripts/addCaseList.pl renamed to scripts/addCaseList.pl

@@ -34,18 +34,18 @@
 }
 
 # Set up Classpath to use the scripts jar
-sub locate_src_root {
+sub locate_root {
     # isolate the directory this code file is in
     my ($volume, $script_dir, undef) = File::Spec->splitpath(__FILE__);
-    # go up from cbioportal/core/src/main/scripts/ to cbioportal/
-    my $src_root_dir = File::Spec->catdir($script_dir, (File::Spec->updir()) x 1);
+    # go up one level
+    my $root_dir = File::Spec->catdir($script_dir, File::Spec->updir());
     # reassamble the path and resolve updirs (/../)
-    return abs_path(File::Spec->catpath($volume, $src_root_dir));
+    return abs_path(File::Spec->catpath($volume, $root_dir));
 }
-$src_root = locate_src_root();
-@jar_files = glob("$src_root/core-*.jar");
+$root_dir = locate_root();
+@jar_files = glob("$root_dir/core-*.jar");
 if (scalar @jar_files != 1) {
-    die "Expected to find 1 scripts-*.jar, but found: " . scalar @jar_files;
+    die "Expected to find 1 core-*.jar, but found: " . scalar @jar_files;
 }
 $cp = pop @jar_files;
 

src/main/resources/scripts/all-breast-su2c.sh renamed to scripts/all-breast-su2c.sh

@@ -498,10 +498,11 @@ def locate_jar():
     """
     # get the directory name of the currently running script,
     # resolving any symlinks
-    script_dir = Path(__file__).resolve().parent
-    # go up from core/scripts/importer/ to core/
-    src_root = script_dir.parent.parent
-    jars = list((src_root ).glob('core-*.jar'))
+    this_file = Path(__file__).resolve()
+    importer_dir = this_file.parent
+    scripts_dir = importer_dir.parent
+    root_dir = scripts_dir.parent
+    jars = list((root_dir).glob('core-*.jar'))
     if len(jars) != 1:
         raise FileNotFoundError(
             'Expected to find 1 scripts-*.jar, but found ' + str(len(jars)))

src/main/resources/scripts/all-coadread-public.sh renamed to scripts/all-coadread-public.sh

@@ -997,7 +997,9 @@ def run_java(*args):
         java_command = os.path.join(java_home, 'bin', 'java')
     else:
         java_command = 'java'
-    process = Popen([java_command] + list(args), stdout=PIPE, stderr=STDOUT,
+    full_cmd = [java_command] + list(args)
+    print(">", " ".join(full_cmd))
+    process = Popen(full_cmd, stdout=PIPE, stderr=STDOUT,
                     universal_newlines=True)
     ret = []
     while process.poll() is None:

src/main/resources/scripts/all-gbm-public.sh renamed to scripts/all-gbm-public.sh

@@ -0,0 +1 @@
+pushd tests/; PYTHONPATH=../scripts:$PYTHONPATH python -m unittest *.py; popd