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lee-mcfaul2lee-mcfaul2
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Normally I would have opened a new branch. but this issue was causing this pull to fail it's build so I'm doing both in one fel swoop. I put the target files in the resource directory and manually copy them over before each test into the temporary working directory which is scanned before calling out in case the file is already there. this should fix the 429 errors in this class specifically.
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+1038
-14
lines changed

11 files changed

+1038
-14
lines changed

‎biojava-core/pom.xml‎

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@@ -44,6 +44,11 @@
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<artifactId>junit</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-io</artifactId>
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<version>1.3.2</version>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
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<dependency>
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<groupId>org.slf4j</groupId>

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java‎

Lines changed: 14 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,11 @@
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
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import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
35-
import org.biojava.nbio.core.sequence.features.*;
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import org.biojava.nbio.core.sequence.features.AbstractFeature;
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import org.biojava.nbio.core.sequence.features.DBReferenceInfo;
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import org.biojava.nbio.core.sequence.features.DatabaseReferenceInterface;
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import org.biojava.nbio.core.sequence.features.FeatureRetriever;
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import org.biojava.nbio.core.sequence.features.FeaturesKeyWordInterface;
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import org.biojava.nbio.core.sequence.io.GenbankSequenceParser;
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import org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser;
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import org.biojava.nbio.core.sequence.template.AbstractSequence;
@@ -41,7 +45,14 @@
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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44-
import java.io.*;
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import java.io.BufferedInputStream;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.net.URL;
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import java.net.URLConnection;
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import java.util.ArrayList;
@@ -54,7 +65,7 @@
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*/
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public class GenbankProxySequenceReader<C extends Compound> extends StringProxySequenceReader<C> implements FeaturesKeyWordInterface, DatabaseReferenceInterface, FeatureRetriever {
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private final static Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReader.class);
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private static final Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReader.class);
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private static final String eutilBaseURL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; //
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private String genbankDirectoryCache = null;

‎biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java‎

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Original file line numberDiff line numberDiff line change
@@ -20,25 +20,30 @@
2020
*/
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package org.biojava.nbio.core.sequence.loader;
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import org.apache.commons.io.IOUtils;
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import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
28+
import org.biojava.nbio.core.sequence.features.AbstractFeature;
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import org.biojava.nbio.core.sequence.features.FeatureInterface;
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import org.biojava.nbio.core.sequence.features.Qualifier;
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import org.biojava.nbio.core.sequence.template.AbstractSequence;
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import org.junit.Assert;
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import org.junit.Before;
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import org.junit.Test;
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import org.junit.runner.RunWith;
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import org.junit.runners.Parameterized;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
40-
import org.biojava.nbio.core.sequence.features.AbstractFeature;
41-
import org.biojava.nbio.core.sequence.features.Qualifier;
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/**
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* Testing example for issue #834
@@ -58,7 +63,7 @@ public GenbankProxySequenceReaderTest(String gi) {
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@Parameterized.Parameters
6065
public static Collection<String[]> getExamples() {
61-
String[][] out = new String[][]{
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String[][] accessorIds = new String[][]{
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{"399235158"},
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{"7525057"},
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{"379015144"},
@@ -69,9 +74,42 @@ public static Collection<String[]> getExamples() {
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{"254839678"}
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};
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72-
return Arrays.asList(out);
77+
return Arrays.asList(accessorIds);
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}
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/**
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* In {@link GenbankProxySequenceReader} there is a check to see if the requested files are already in the temp
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* directory before attemting to retrieve them from the remote server. so simply copying the test files to the temp
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* directory avoids calling out to the server and hitting a 429 status code from the server which fails the build.
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* @throws IOException
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*/
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@Before
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public void copyTestFiles() throws IOException {
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Collection<String[]> accessorIds = getExamples();
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for (String[] arr: accessorIds) {
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copyTestFileToWorkingDirectory(arr[0]+".gb");
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}
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}
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/**
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* Convenience method for {@link GenbankProxySequenceReaderTest#copyTestFiles()}
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* @param filename name of the file to copy from the resource folder
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* @throws IOException when something goes wrong with copying the files.
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*/
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private void copyTestFileToWorkingDirectory(String filename) throws IOException {
100+
String dest = System.getProperty("java.io.tmpdir") + filename;
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String src = "org/biojava/nbio/core/sequence/GenbankProxySequenceReader/" + filename;
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FileOutputStream destination = new FileOutputStream(new File(dest));
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InputStream source = this.getClass().getClassLoader().getResourceAsStream(src);
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106+
IOUtils.copy(source, destination);
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destination.close();
109+
source.close();
73110
}
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75113
@Test
76114
public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
77115
logger.info("run test for protein: {}", gi);
@@ -120,9 +158,6 @@ so it should be done here (manualy).
120158
Assert.assertTrue(!codedBy.isEmpty());
121159
logger.info("\t\tcoded_by: {}", codedBy);
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}
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124-
// genbank has limits on requests per second, we need to give it some time for next test or otherwise we get 429 http error codes - JD 2018-12-14
125-
Thread.sleep(500);
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}
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128163
@Test
@@ -161,9 +196,5 @@ public void testProteinSequenceFactoring() throws Exception {
161196
} else {
162197
logger.info("target {} has no CDS", gi);
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}
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// genbank has limits on requests per second, we need to give it some time for next test or otherwise we get 429 http error codes - JD 2018-12-14
166-
Thread.sleep(500);
167-
168199
}
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}

‎biojava-core/src/test/resources/org/biojava/nbio/core/sequence/GenbankProxySequenceReader/152970917.gb‎

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LOCUS YP_001336026 324 aa linear CON 16-DEC-2014
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DEFINITION lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase
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[Klebsiella pneumoniae subsp. pneumoniae MGH 78578].
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ACCESSION YP_001336026
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VERSION YP_001336026.1
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DBLINK BioProject: PRJNA57619
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DBSOURCE REFSEQ: accession NC_009648.1
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KEYWORDS RefSeq.
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SOURCE Klebsiella pneumoniae subsp. pneumoniae MGH 78578
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ORGANISM Klebsiella pneumoniae subsp. pneumoniae MGH 78578
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Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
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Enterobacteriaceae; Klebsiella.
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REFERENCE 1 (residues 1 to 324)
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CONSRTM NCBI Genome Project
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TITLE Direct Submission
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JOURNAL Submitted (09-JUL-2007) National Center for Biotechnology
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Information, NIH, Bethesda, MD 20894, USA
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REFERENCE 2 (residues 1 to 324)
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AUTHORS McClelland,M., Sanderson,E.K., Spieth,J., Clifton,W.S.,
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Latreille,P., Sabo,A., Pepin,K., Bhonagiri,V., Porwollik,S., Ali,J.
21+
and Wilson,R.K.
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CONSRTM The Klebsiella pneumonia Genome Sequencing Project
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TITLE Direct Submission
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JOURNAL Submitted (06-SEP-2006) Genetics, Genome Sequencing Center, 4444
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Forest Park Parkway, St. Louis, MO 63108, USA
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COMMENT VALIDATED REFSEQ: This record has undergone validation or
27+
preliminary review. The reference sequence was derived from
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ABR77796.
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Method: conceptual translation.
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FEATURES Location/Qualifiers
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source 1..324
32+
/organism="Klebsiella pneumoniae subsp. pneumoniae MGH
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78578"
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/strain="ATCC 700721; MGH 78578"
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/sub_species="pneumoniae"
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/db_xref="ATCC:700721"
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/db_xref="taxon:272620"
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Protein 1..324
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/product="lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA
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acyltransferase"
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/calculated_mol_wt=37353
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Region 1..310
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/region_name="PRK08943"
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/note="lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA
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acyltransferase; Validated"
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/db_xref="CDD:236355"
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Site order(139,142,144,161..164,210..212)
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/site_type="other"
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/note="putative acyl-acceptor binding pocket"
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/db_xref="CDD:153246"
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CDS 1..324
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/gene="msbB"
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/locus_tag="KPN_02370"
54+
/coded_by="complement(NC_009648.1:2595658..2596632)"
55+
/inference="ab initio prediction:Genemark:2.0"
56+
/inference="protein motif:Pfam:IPR004960"
57+
/note="Transfers myristate or laurate, activated on ACP,
58+
to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA"
59+
/transl_table=11
60+
/db_xref="GeneID:5340071"
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CONTIG join(WP_002911442.1:1..324)
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ORIGIN
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1 metkknnief ipkfeksfll prywgawlgv fafagialtp psfrdpllgk lgrlvgrlak
64+
61 ssrrraqinl lycfpeksey ereaiidamy asapqamvmm aelglrdpqk ilarvdwqgk
65+
121 aiidemqrnn ekviflvpha wgvdipamlm asggqkmaam fhnqgnpvfd yvwntvrrrf
66+
181 ggrmharndg ikpfiqsvrq gywgyylpdq dhgaehsefv dffatykatl paigrlmkvc
67+
241 rarvvplfpv ydskthrltv lvrppmddll daddttiarr mneevevfvk phteqytwil
68+
301 kllktrkpge iepykrkelf pkkk
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//
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‎biojava-core/src/test/resources/org/biojava/nbio/core/sequence/GenbankProxySequenceReader/254839678.gb‎

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LOCUS 3IAN_A 321 aa linear BCT 24-NOV-2018
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DEFINITION Chain A, Chitinase.
3+
ACCESSION 3IAN_A
4+
VERSION 3IAN_A
5+
DBSOURCE pdb: molecule 3IAN, chain 65, release Nov 21, 2018;
6+
deposition: Jul 14, 2009;
7+
class: HYDROLASE;
8+
source: Mmdb_id: 999999, Pdb_id 1: 3IAN;
9+
Exp. method: X-ray Diffraction.
10+
KEYWORDS .
11+
SOURCE Lactococcus lactis subsp. lactis
12+
ORGANISM Lactococcus lactis subsp. lactis
13+
Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
14+
Lactococcus.
15+
REFERENCE 1 (residues 1 to 321)
16+
AUTHORS Bonanno,J.B., Rutter,M., Bain,K.T., Miller,S., Ozyurt,S.,
17+
Sauder,J.M., Burley,S.K. and Almo,S.C.
18+
TITLE Crystal structure of a chitinase from Lactococcus lactis subsp.
19+
lactis
20+
JOURNAL Unpublished
21+
REFERENCE 2 (residues 1 to 321)
22+
AUTHORS Bonanno,J.B., Rutter,M., Bain,K.T., Miller,S., Ozyurt,S.,
23+
Sauder,J.M., Burley,S.K., Almo,S.C. and New York SGX Research
24+
Center for Structural Genomics (NYSGXRC).
25+
TITLE Direct Submission
26+
JOURNAL Submitted (14-JUL-2009)
27+
COMMENT Crystal structure of a chitinase from Lactococcus lactis subsp.
28+
lactis.
29+
FEATURES Location/Qualifiers
30+
source 1..321
31+
/organism="Lactococcus lactis subsp. lactis"
32+
/sub_species="lactis"
33+
/db_xref="taxon:1360"
34+
Het join(bond(115),bond(117),bond(76))
35+
/heterogen="(NA,2572)"
36+
Region 4..313
37+
/region_name="Chi1"
38+
/note="Chitinase [Carbohydrate transport and metabolism];
39+
COG3469"
40+
/db_xref="CDD:226000"
41+
Region 5..288
42+
/region_name="Glyco_hydro_18"
43+
/note="Glycosyl hydrolases family 18; pfam00704"
44+
/db_xref="CDD:279094"
45+
SecStr 5..12
46+
/sec_str_type="sheet"
47+
/note="strand 1"
48+
Site order(10,46,122,124,189,191,283)
49+
/site_type="active"
50+
/note="putative active site [active]"
51+
/db_xref="CDD:119350"
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SecStr 24..28
53+
/sec_str_type="sheet"
54+
/note="strand 2"
55+
SecStr 40..45
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/sec_str_type="sheet"
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/note="strand 3"
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SecStr 65..78
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/sec_str_type="helix"
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/note="helix 1"
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SecStr 80..89
62+
/sec_str_type="sheet"
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/note="strand 4"
64+
SecStr 100..114
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/sec_str_type="helix"
66+
/note="helix 2"
67+
SecStr 117..124
68+
/sec_str_type="sheet"
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/note="strand 5"
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SecStr 133..151
71+
/sec_str_type="helix"
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/note="helix 3"
73+
SecStr 155..163
74+
/sec_str_type="sheet"
75+
/note="strand 6"
76+
SecStr 172..180
77+
/sec_str_type="helix"
78+
/note="helix 4"
79+
SecStr 184..190
80+
/sec_str_type="sheet"
81+
/note="strand 7"
82+
SecStr 196..201
83+
/sec_str_type="sheet"
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/note="strand 8"
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SecStr 204..209
86+
/sec_str_type="sheet"
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/note="strand 9"
88+
SecStr 215..228
89+
/sec_str_type="helix"
90+
/note="helix 5"
91+
SecStr 240..246
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/sec_str_type="sheet"
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/note="strand 10"
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SecStr 261..273
95+
/sec_str_type="helix"
96+
/note="helix 6"
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SecStr 278..283
98+
/sec_str_type="sheet"
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/note="strand 11"
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SecStr 289..293
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/sec_str_type="sheet"
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/note="strand 12"
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SecStr 300..307
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/sec_str_type="helix"
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/note="helix 7"
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ORIGIN
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1 msldkvlvgy whnwkstgkd gykggssadf nlsstqegyn vinvsfmktp egqtlptfkp
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61 ynktdtefra eisklnaegk svlialggad ahielkksqe sdfvneiirl vdtygfdgld
109+
121 idleqaaiea adnqtvipsa lkkvkdhyrk dgknfmitma pefpyltssg kyapyinnld
110+
181 syydfinpqy ynqggdgfwd sdlnmwisqs ndekkedfly gltqrlvtgt dgfikipask
111+
241 fviglpsnnd aaatgyvkdp navknalnrl kasgneikgl mtwsvnwdag tnsngekynn
112+
301 tfvntyapml fnneghhhhh h
113+
//
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