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package org.rcsb.cif;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.rcsb.cif.binary.codec.MessagePackCodec;
import org.rcsb.cif.model.CifFile;
import org.rcsb.cif.model.binary.BinaryFile;
import org.rcsb.cif.model.text.TextFile;
import org.rcsb.cif.schema.StandardSchemata;
import org.rcsb.cif.schema.mm.AtomSite;
import org.rcsb.cif.schema.mm.MmCifFile;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.util.Map;
import java.util.zip.GZIPInputStream;
import static org.junit.jupiter.api.Assertions.*;
import static org.rcsb.cif.TestHelper.TEST_CASES;
class CifOptionsTest {
@Test
void testEncodingBehavior() throws IOException {
MmCifFile textCifFile = CifIO.readFromInputStream(TestHelper.getInputStream("cif/1acj.cif")).as(StandardSchemata.MMCIF);
byte[] binary1 = CifIO.writeBinary(textCifFile, CifOptions.builder()
.encodingStrategyHint(new String(TestHelper.getBytes("encoding-hint/hint1.json")))
.build());
// check that precision was honored
CifFile binaryCifFile1 = CifIO.readFromInputStream(new ByteArrayInputStream(binary1));
AtomSite atomSite1 = binaryCifFile1.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite();
atomSite1.getCartnX()
.values()
.map(d -> d * 10)
.forEach(d -> assertEquals(Math.round(d), d, TestHelper.ERROR_MARGIN));
atomSite1.getCartnY()
.values()
.map(d -> d * 100)
.forEach(d -> assertEquals(Math.round(d), d, TestHelper.ERROR_MARGIN));
atomSite1.getCartnZ()
.values()
.map(d -> d * 1000)
.forEach(d -> assertEquals(Math.round(d), d, TestHelper.ERROR_MARGIN));
byte[] binary2 = CifIO.writeBinary(textCifFile, CifOptions.builder()
.encodingStrategyHint(new String(TestHelper.getBytes("encoding-hint/hint2.json")))
.build());
// check that precision was honored
CifFile binaryCifFile2 = CifIO.readFromInputStream(new ByteArrayInputStream(binary2));
AtomSite atomSite2 = binaryCifFile2.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite();
atomSite2.getCartnX()
.values()
.map(d -> d * 10)
.forEach(d -> assertEquals(Math.round(d), d, TestHelper.ERROR_MARGIN));
atomSite2.getCartnY()
.values()
.map(d -> d * 1000)
.forEach(d -> assertEquals(Math.round(d), d, TestHelper.ERROR_MARGIN));
atomSite2.getCartnZ()
.values()
.map(d -> d * 100000)
.forEach(d -> assertEquals(Math.round(d), d, TestHelper.ERROR_MARGIN));
}
@Test
void testEncoder() throws IOException {
// the encoder name should be honored when specified
String encoderName = "yet-another-cif-encoder";
CifFile cifFile = CifIO.readFromInputStream(TestHelper.getInputStream("bcif/1acj.bcif"));
byte[] bytes = CifIO.writeBinary(cifFile,
CifOptions.builder().encoder(encoderName).build());
Map<String, Object> map = MessagePackCodec.decode(new ByteArrayInputStream(bytes));
assertEquals(encoderName, map.get("encoder"));
}
@Disabled("attempts to use the network")
@Test
void testFetchUrlText() throws IOException {
// by switching to RCSB cif files, the implementation type should be text
CifFile cifFile = CifIO.readById("1acj", CifOptions.builder()
.fetchUrl("https://files.rcsb.org/download/%s.cif").build());
assertTrue(cifFile instanceof TextFile);
}
@Disabled("attempts to use the network")
@Test
void testFetchUrlBinary() throws IOException {
// by switching to RCSB bcif files, the implementation type should be binary
CifFile cifFile = CifIO.readById("1acj", CifOptions.builder()
.fetchUrl("https://models.rcsb.org/%s.bcif").build());
assertTrue(cifFile instanceof BinaryFile);
}
@Test
void testFilteringBehavior() throws IOException {
for (String id : TEST_CASES.keySet()) {
testFilteringBehavior(id);
}
}
private static final CifOptions BLACKLIST_OPTIONS = CifOptions.builder()
.categoryBlacklist("entry")
.columnBlacklist("atom_site.Cartn_x")
.columnBlacklist("atom_site.Cartn_y")
.columnBlacklist("atom_site.Cartn_z")
.build();
private static final CifOptions WHITELIST_OPTIONS = CifOptions.builder()
.categoryWhitelist("entry")
.columnWhitelist("atom_site.Cartn_x")
.columnWhitelist("atom_site.Cartn_y")
.columnWhitelist("atom_site.Cartn_z")
.build();
private void testFilteringBehavior(String testCase) throws IOException {
// check that file was loaded correctly
CifFile file = CifIO.readFromInputStream(TestHelper.getInputStream("bcif/" + testCase + ".bcif"));
assertEquals(testCase.toUpperCase(), file.as(StandardSchemata.MMCIF).getFirstBlock().getEntry().getId().get(0));
// text file with some categories blacklisted
CifFile blacklistTextFile = CifIO.readFromInputStream(new ByteArrayInputStream(CifIO.writeText(file, BLACKLIST_OPTIONS)));
assertTrue(blacklistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getCategories().size() > 0);
assertFalse(blacklistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getEntry().isDefined());
assertTrue(blacklistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().isDefined());
assertTrue(blacklistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getGroupPDB().isDefined());
assertFalse(blacklistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnX().isDefined());
assertFalse(blacklistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnY().isDefined());
assertFalse(blacklistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnZ().isDefined());
// text file with only some categories whitelisted
CifFile whitelistTextFile = CifIO.readFromInputStream(new ByteArrayInputStream(CifIO.writeText(file, WHITELIST_OPTIONS)));
assertTrue(whitelistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getCategories().size() > 0);
assertTrue(whitelistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getEntry().isDefined());
assertTrue(whitelistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().isDefined());
assertFalse(whitelistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getGroupPDB().isDefined());
assertTrue(whitelistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnX().isDefined());
assertTrue(whitelistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnY().isDefined());
assertTrue(whitelistTextFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnZ().isDefined());
// binary file with some categories blacklisted
CifFile blacklistBinaryFile = CifIO.readFromInputStream(new ByteArrayInputStream(CifIO.writeBinary(file, BLACKLIST_OPTIONS)));
assertTrue(blacklistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getCategories().size() > 0);
assertFalse(blacklistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getEntry().isDefined());
assertTrue(blacklistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().isDefined());
assertTrue(blacklistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getGroupPDB().isDefined());
assertFalse(blacklistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnX().isDefined());
assertFalse(blacklistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnY().isDefined());
assertFalse(blacklistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnZ().isDefined());
// binary file with only some categories whitelisted
CifFile whitelistBinaryFile = CifIO.readFromInputStream(new ByteArrayInputStream(CifIO.writeBinary(file, WHITELIST_OPTIONS)));
assertTrue(whitelistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getCategories().size() > 0);
assertTrue(whitelistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getEntry().isDefined());
assertTrue(whitelistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().isDefined());
assertFalse(whitelistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getGroupPDB().isDefined());
assertTrue(whitelistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnX().isDefined());
assertTrue(whitelistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnY().isDefined());
assertTrue(whitelistBinaryFile.as(StandardSchemata.MMCIF).getFirstBlock().getAtomSite().getCartnZ().isDefined());
}
@Test
void testGzipWritingBehavior() throws IOException {
// should wrap output in gzip if requested
for (String id : TEST_CASES.keySet()) {
testGzipWritingBehavior(id);
}
}
private void testGzipWritingBehavior(String testCase) throws IOException {
// check that file was loaded correctly
CifFile file = CifIO.readFromInputStream(TestHelper.getInputStream("bcif/" + testCase + ".bcif"));
assertEquals(testCase.toUpperCase(), file.as(StandardSchemata.MMCIF).getFirstBlock().getEntry().getId().get(0));
// write text text with downstream gzip
byte[] binaryGz = CifIO.writeText(file, CifOptions.builder().gzip(true).build());
// magic number must be gzip
assertEquals(GZIPInputStream.GZIP_MAGIC, (binaryGz[0] & 0xff | ((binaryGz[1] << 8) & 0xff00)));
// write text text
byte[] binary = CifIO.writeText(file, CifOptions.builder().gzip(false).build());
// magic number must not be gzip
assertNotEquals(GZIPInputStream.GZIP_MAGIC, (binary[0] & 0xff | ((binary[1] << 8) & 0xff00)));
// write text text with downstream gzip
byte[] textGz = CifIO.writeText(file, CifOptions.builder().gzip(true).build());
// magic number must be gzip
assertEquals(GZIPInputStream.GZIP_MAGIC, (textGz[0] & 0xff | ((textGz[1] << 8) & 0xff00)));
// write text text
byte[] text = CifIO.writeText(file, CifOptions.builder().gzip(false).build());
// magic number must not be gzip
assertNotEquals(GZIPInputStream.GZIP_MAGIC, (text[0] & 0xff | ((text[1] << 8) & 0xff00)));
}
}
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