bsh script

patch.bsh

import org.openscience.cdk.Molecule;
import org.openscience.cdk.io.CDKSourceCodeWriter;
import org.openscience.cdk.io.MDLReader;
import org.eclipse.jgit.api.*;
import org.eclipse.jgit.lib.*;
import org.eclipse.jgit.storage.file.*;

element = bsh.args[0];
FileRepositoryBuilder builder = new FileRepositoryBuilder();
Repository repository = builder.readEnvironment().findGitDir().build();
Git git = new Git(repository);
status = git.status().call();
molFilePaths = status.getAdded();

// convert the molfiles to cdk calls
codeFrags = new HashMap();
for (molFilePath : molFilePaths) {
    molFile = new File(molFilePath);
    mdlReader = new MDLReader(new FileReader(molFile));
    mol = mdlReader.read(new Molecule());
    mdlReader.close();
    name = new File(molFilePath).getName();
    name = name.substring(0, name.indexOf("."));
    print(molFilePath);
    sw = new StringWriter();
    sourceWriter = new CDKSourceCodeWriter(sw);
    sourceWriter.getIOSettings()[0].setSetting("false");
    sourceWriter.write(mol);
    sourceWriter.close();
    //print(sw.toString());
    String code = sw.toString();
    code = code.replace("}", "");
    code = code.replace("\n", "\n      ");
    code = "\n    @Test\n    public void test_" + name + "() throws Exception " + code;
    codeFrags.put(name, code);
    molFile.delete();
}

// read in the test class
testClass = new File("src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java");
javaFileReader = new BufferedReader(new FileReader(testClass));
String line;
buffer = new ArrayList();
inFix = false;
seenFix = false;
molName = "";
while ((line = javaFileReader.readLine()) != null) {
    if (line.contains("fix_" + element) && !inFix) {
        buffer.remove(buffer.size() - 1);   // remove the @Test line
        inFix = true;
    } else if (inFix && line.contains("String[] expectedTypes")) {
        buffer.add(codeFrags.get(molName));
        buffer.add(line.replaceFirst("\\s(expectedTypes.*)=", " expectedTypes ="));
    } else if (inFix && line.contains("assertAtomTypes")) {
        buffer.add(line.replaceFirst("\\s(expectedTypes.*),", " expectedTypes,")
                       .replaceFirst("\\s(mol.*)\\)", " mol\\)"));
        buffer.add("    }\n");
    } else if (inFix && line.contains("}")) {
        inFix = false;
        seenFix = true;
    } else if (inFix && line.contains("String molName")) {
        molName = line.substring(line.indexOf("\"") + 1, line.lastIndexOf("\""));
    } else if (seenFix) {
        buffer.add(line);
    } else if (!inFix) {
        buffer.add(line);
    }
}
javaFileReader.close();

testClass.delete();

// print out the modified test file
fileWriter = new BufferedWriter(new FileWriter(testClass));
for (String l : buffer) {
    fileWriter.write(l);
    if (!l.endsWith("\n")) {
        fileWriter.newLine();
    }
}
fileWriter.close();