[Git][java-team/ciftools-java][master] 5 commits: Fixing debian/watch (GitHub releases -> tags)
Andrius Merkys (@merkys)
gitlab at salsa.debian.org
Sun Dec 5 13:08:50 GMT 2021
Andrius Merkys pushed to branch master at Debian Java Maintainers / ciftools-java
Commits:
80deb401 by Andrius Merkys at 2021-12-05T07:29:00-05:00
Fixing debian/watch (GitHub releases -> tags)
- - - - -
6e9deed9 by Andrius Merkys at 2021-12-05T07:29:27-05:00
New upstream version 3.0.1
- - - - -
e9356470 by Andrius Merkys at 2021-12-05T07:29:38-05:00
Update upstream source from tag 'upstream/3.0.1'
Update to upstream version '3.0.1'
with Debian dir 8354586e33272ce5b8f7160f1be34d0a1566342b
- - - - -
79a73c0f by Andrius Merkys at 2021-12-05T07:32:17-05:00
Refreshing patches.
- - - - -
8f57eb67 by Andrius Merkys at 2021-12-05T07:32:34-05:00
Update changelog for 3.0.1-1 release
- - - - -
11 changed files:
- CHANGELOG.md
- README.md
- debian/changelog
- debian/patches/deactivate_tests_using_network.patch
- debian/watch
- pom.xml
- src/main/java/org/rcsb/cif/text/TokenizerState.java
- src/test/java/org/rcsb/cif/IntegrationTest.java
- src/test/java/org/rcsb/cif/ReaderTest.java
- + src/test/resources/cif/AF-O49373-F1-model_v1.cif
- + src/test/resources/cif/AF-Q76EI6-F1-model_v1.cif
Changes:
=====================================
CHANGELOG.md
=====================================
@@ -3,6 +3,11 @@ CIFTools Changelog
This project uses semantic versioning. Furthermore, this project provides code that was generated from schemata. Any schema change that introduces a breaking change in the generated code is considered as breaking for the whole project. Additional information is provided below when this occurs (named `Breaking schema changes`). Most of these occur in experimental categories and are unlikely to affect your code. `Breaking API changes` will be avoided starting with version 1.0.0.
+ciftools-java 3.0.1 - November 2021
+-------------
+### Bug fixes
+* proper handling of strings such as: `''cytochrome P450`
+
ciftools-java 3.0.0 - September 2021
-------------
### New features
=====================================
README.md
=====================================
@@ -15,7 +15,7 @@ CIFTools is distributed by maven. To get started, append your `pom.xml` by:
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>ciftools-java</artifactId>
- <version>2.0.2</version>
+ <version>3.0.0</version>
</dependency>
```
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+ciftools-java (3.0.1-1) unstable; urgency=medium
+
+ * New upstream version 3.0.1
+ * Fixing debian/watch (GitHub releases -> tags)
+ * Refreshing patches.
+
+ -- Andrius Merkys <merkys at debian.org> Sun, 05 Dec 2021 07:32:27 -0500
+
ciftools-java (3.0.0-2) unstable; urgency=medium
* Source-only upload
=====================================
debian/patches/deactivate_tests_using_network.patch
=====================================
@@ -85,7 +85,7 @@ Last-Update: 2021-10-17
import org.junit.jupiter.api.Test;
import org.rcsb.cif.model.Category;
import org.rcsb.cif.model.CifFile;
-@@ -313,6 +314,7 @@
+@@ -311,6 +312,7 @@
/**
* BinaryCIF might slightly violate the schema and lead to a ClassCastException if not handled.
*/
@@ -93,7 +93,7 @@ Last-Update: 2021-10-17
@Test
public void readRcsbAndEbiGeneric() throws IOException {
CifFile rcsb = CifIO.readById("1acj");
-@@ -329,6 +331,7 @@
+@@ -327,6 +329,7 @@
assertEquals(83, ebiNdbSeqNum.getRowCount());
}
@@ -101,11 +101,3 @@ Last-Update: 2021-10-17
@Test
public void readRcsbAndEbiWithSchema() throws IOException {
MmCifFile rcsb = CifIO.readById("1acj").as(StandardSchemata.MMCIF);
-@@ -346,6 +349,7 @@
- assertEquals(83, ebiNdbSeqNum.getRowCount());
- }
-
-+ @Disabled("Attempts to use the network")
- @Test
- public void whenReadingAlphaFoldData_thenConfidenceScoresAvailable() throws IOException {
- String id = "AF-Q76EI6-F1-model_v1";
=====================================
debian/watch
=====================================
@@ -1,3 +1,2 @@
version=4
-
-https://github.com/rcsb/ciftools-java/releases (?:.*?)?@PACKAGE at -(\d[\d.]*)\.tar\.gz
+https://github.com/rcsb/ciftools-java/tags (?:.*?)?@PACKAGE at -(\d[\d.]*)\.tar\.gz
=====================================
pom.xml
=====================================
@@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.rcsb</groupId>
<artifactId>ciftools-java</artifactId>
- <version>3.0.0</version>
+ <version>3.0.1</version>
<packaging>jar</packaging>
<description>
A Java library for handling text and binary CIF files.
@@ -35,7 +35,7 @@
<connection>scm:git:git://github.com/rcsb/ciftools-java.git</connection>
<developerConnection>scm:git:git at github.com:rcsb/ciftools-java.git</developerConnection>
<url>https://github.com/rcsb/ciftools-java</url>
- <tag>ciftools-java-3.0.0</tag>
+ <tag>ciftools-java-3.0.1</tag>
</scm>
<dependencies>
@@ -110,7 +110,7 @@
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
- <autoReleaseAfterClose>false</autoReleaseAfterClose>
+ <autoReleaseAfterClose>true</autoReleaseAfterClose>
</configuration>
</plugin>
=====================================
src/main/java/org/rcsb/cif/text/TokenizerState.java
=====================================
@@ -343,7 +343,7 @@ class TokenizerState {
tokenType = CifTokenType.COMMENT;
break;
case '"': case '\'':
- if (isTripleQuoteAtPosition()) {
+ if (c == '\'' && isTripleQuoteAtPosition()) {
eatTripleQuote();
tokenType = CifTokenType.VALUE;
break;
=====================================
src/test/java/org/rcsb/cif/IntegrationTest.java
=====================================
@@ -19,9 +19,7 @@ import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.lang.reflect.Array;
-import java.net.URL;
import java.nio.charset.StandardCharsets;
-import java.util.OptionalDouble;
import static org.junit.jupiter.api.Assertions.*;
import static org.rcsb.cif.TestHelper.TEST_CASES;
@@ -345,19 +343,4 @@ public class IntegrationTest {
.getNdbSeqNum();
assertEquals(83, ebiNdbSeqNum.getRowCount());
}
-
- @Test
- public void whenReadingAlphaFoldData_thenConfidenceScoresAvailable() throws IOException {
- String id = "AF-Q76EI6-F1-model_v1";
- URL url = new URL("https://alphafold.ebi.ac.uk/files/" + id + ".cif");
- MmCifFile cifFile = CifIO.readFromURL(url).as(StandardSchemata.MMCIF);
-
- OptionalDouble averageLocal = cifFile.getFirstBlock()
- .getMaQaMetricLocal()
- .getMetricValue()
- .values()
- .average();
-
- assertTrue(averageLocal.isPresent());
- }
}
=====================================
src/test/java/org/rcsb/cif/ReaderTest.java
=====================================
@@ -6,14 +6,16 @@ import org.rcsb.cif.model.IntColumn;
import org.rcsb.cif.schema.StandardSchemata;
import org.rcsb.cif.schema.mm.AtomSite;
import org.rcsb.cif.schema.mm.MmCifBlock;
+import org.rcsb.cif.schema.mm.MmCifFile;
import java.io.IOException;
import java.io.InputStream;
import java.util.List;
import java.util.Map;
+import java.util.OptionalDouble;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.rcsb.cif.TestHelper.ERROR_MARGIN;
import static org.rcsb.cif.TestHelper.TEST_CASES;
@@ -101,4 +103,30 @@ public class ReaderTest {
);
}
+
+
+ @Test
+ public void whenReadingAlphaFoldData_thenConfidenceScoresAvailable() throws IOException {
+ String id = "AF-Q76EI6-F1-model_v1";
+ InputStream inputStream = TestHelper.getInputStream("cif/" + id + ".cif");
+ MmCifFile cifFile = CifIO.readFromInputStream(inputStream).as(StandardSchemata.MMCIF);
+
+ OptionalDouble averageLocal = cifFile.getFirstBlock()
+ .getMaQaMetricLocal()
+ .getMetricValue()
+ .values()
+ .average();
+
+ assertTrue(averageLocal.isPresent());
+ }
+
+ @Test
+ public void whenReadingStringWithEmptyQuotation_thenValueAvailable() throws IOException {
+ String id = "AF-O49373-F1-model_v1";
+ InputStream inputStream = TestHelper.getInputStream("cif/" + id + ".cif");
+ MmCifFile cifFile = CifIO.readFromInputStream(inputStream).as(StandardSchemata.MMCIF);
+
+ String gene = cifFile.getFirstBlock().getCategory("af_target_ref_db_details").getColumn("gene").getStringData(0);
+ assertEquals("''cytochrome P450", gene, "Gene name with additional quotes not parsed correctly");
+ }
}
\ No newline at end of file
=====================================
src/test/resources/cif/AF-O49373-F1-model_v1.cif
=====================================
The diff for this file was not included because it is too large.
=====================================
src/test/resources/cif/AF-Q76EI6-F1-model_v1.cif
=====================================
The diff for this file was not included because it is too large.
View it on GitLab: https://salsa.debian.org/java-team/ciftools-java/-/compare/ca8a71c1e5425a2a558110c3a11255985e370623...8f57eb67c24993f76c5b56184a9d526622a253c8
--
View it on GitLab: https://salsa.debian.org/java-team/ciftools-java/-/compare/ca8a71c1e5425a2a558110c3a11255985e370623...8f57eb67c24993f76c5b56184a9d526622a253c8
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