From 65d7b70ce9788fd1680a5e81b1eaae30126b8ed2 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 23 May 2016 11:07:16 +0100 Subject: [PATCH 1/1] JAL-2113 EBIFetchClient refactor / unit tests / remove unused fields and parameters --- src/MCview/PDBViewer.java | 2 +- src/jalview/ws/dbsources/EmblXmlSource.java | 1 - src/jalview/ws/dbsources/Pdb.java | 2 +- src/jalview/ws/dbsources/Uniprot.java | 2 +- src/jalview/ws/ebi/EBIFetchClient.java | 150 ++++++++++++++------------- test/jalview/ws/ebi/EBIFetchClientTest.java | 113 ++++++++++++++++++++ 6 files changed, 193 insertions(+), 77 deletions(-) create mode 100644 test/jalview/ws/ebi/EBIFetchClientTest.java diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java index e032c7a..d5f0d0b 100755 --- a/src/MCview/PDBViewer.java +++ b/src/MCview/PDBViewer.java @@ -151,7 +151,7 @@ public class PDBViewer extends JInternalFrame implements Runnable { EBIFetchClient ebi = new EBIFetchClient(); String query = "pdb:" + pdbentry.getId(); - pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw", ".xml") + pdbentry.setFile(ebi.fetchDataAsFile(query, "default", ".xml") .getAbsolutePath()); if (pdbentry.getFile() != null) diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java index b71f032..2049766 100644 --- a/src/jalview/ws/dbsources/EmblXmlSource.java +++ b/src/jalview/ws/dbsources/EmblXmlSource.java @@ -64,7 +64,6 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy { reply = dbFetch.fetchDataAsFile( emprefx.toLowerCase() + ":" + query.trim(), "display=xml", - null, ".xml"); } catch (Exception e) { diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java index 4a089f7..0d590b0 100644 --- a/src/jalview/ws/dbsources/Pdb.java +++ b/src/jalview/ws/dbsources/Pdb.java @@ -136,7 +136,7 @@ public class Pdb extends EbiFileRetrievedProxy : ".xml"; EBIFetchClient ebi = new EBIFetchClient(); file = ebi.fetchDataAsFile("pdb:" + id, - getCurrentDefaultFomart().toLowerCase(), "raw", ext) + getCurrentDefaultFomart().toLowerCase(), ext) .getAbsolutePath(); stopQuery(); if (file == null) diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index 17f1842..8cc0ce4 100644 --- a/src/jalview/ws/dbsources/Uniprot.java +++ b/src/jalview/ws/dbsources/Uniprot.java @@ -165,7 +165,7 @@ public class Uniprot extends DbSourceProxyImpl // uniprotxml parameter required since december 2007 // uniprotkb dbname changed introduced december 2008 File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml", - null, ".xml"); + ".xml"); Vector entries = getUniprotEntries(new FileReader(file)); if (entries != null) diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java index f55aad4..dd3cc16 100644 --- a/src/jalview/ws/ebi/EBIFetchClient.java +++ b/src/jalview/ws/ebi/EBIFetchClient.java @@ -42,9 +42,6 @@ import java.util.StringTokenizer; */ public class EBIFetchClient { - String format = "default"; - - String style = "raw"; /** * Creates a new EBIFetchClient object. @@ -93,14 +90,13 @@ public class EBIFetchClient * the query formatted as db:query1;query2;query3 * @param format * the format wanted - * @param s - * - unused parameter + * @param extension + * for the temporary file to hold response * @return the file holding the response * @throws OutOfMemoryError */ - public File fetchDataAsFile(String ids, String format, String s, - String ext) + public File fetchDataAsFile(String ids, String format, String ext) throws OutOfMemoryError { File outFile = null; @@ -108,7 +104,7 @@ public class EBIFetchClient { outFile = File.createTempFile("jalview", ext); outFile.deleteOnExit(); - fetchData(ids, format, s, outFile); + fetchData(ids, format, outFile); if (outFile.length() == 0) { outFile.delete(); @@ -120,61 +116,19 @@ public class EBIFetchClient return outFile; } - /** - * Single DB multiple record retrieval - * - * @param ids - * db:query1;query2;query3 - * @param format - * raw/xml - * @param s - * not used - remove? - * - * @return Raw string array result of query set - */ - public String[] fetchData(String ids, String format, String s) - throws OutOfMemoryError - { - return fetchData(ids, format, s, null); - } - - String[] fetchData(String ids, String f, String s, File outFile) + String[] fetchData(String ids, String f, File outFile) throws OutOfMemoryError { - // Need to split - // ids of the form uniprot:25KD_SARPE;ADHR_DROPS; String[] rslts = new String[0]; - StringTokenizer queries = new StringTokenizer(ids, ";"); - String db = null; - StringBuffer querystring = null; - int nq = 0; - while (queries.hasMoreTokens()) - { - String query = queries.nextToken(); - int p; - if ((p = query.indexOf(':')) > -1) - { - db = query.substring(0, p); - query = query.substring(p + 1); - } - if (querystring == null) - { - querystring = new StringBuffer(query); - nq++; - } - else - { - querystring.append("," + query); - nq++; - } - } + StringBuilder querystring = new StringBuilder(ids.length()); + String db = parseIds(ids, querystring); if (db == null) { - System.err.println("Invalid Query string : '" + ids - + "'\nShould be of form 'dbname:q1;q2;q3;q4'"); + System.err.println("Invalid Query string : '" + ids + "'"); + System.err.println("Should be of form 'dbname:q1;q2;q3;q4'"); return null; } - String[] rslt = fetchBatch(querystring.toString(), db, f, s, outFile); + String[] rslt = fetchBatch(querystring.toString(), db, f, outFile); if (rslt != null) { String[] nrslts = new String[rslt.length + rslts.length]; @@ -186,26 +140,50 @@ public class EBIFetchClient return (rslts.length == 0 ? null : rslts); } - public String[] fetchBatch(String ids, String dbPath, String format, String s, - File outFile) throws OutOfMemoryError + /** + * Parses ids formatted as dbname:q1;q2;q3, returns the dbname and adds + * queries as comma-separated items to the querystring. dbname must be + * specified for at least one queryId. Returns null if a mixture of different + * dbnames is found (ignoring case). + * + * @param ids + * @param queryString + * @return + */ + static String parseIds(String ids, StringBuilder queryString) { - // long time = System.currentTimeMillis(); - /* - * JAL-1855 dbfetch from ena_sequence, ena_coding - */ - String url; - if (dbPath.equalsIgnoreCase(DBRefSource.EMBL) - || dbPath.equalsIgnoreCase(DBRefSource.EMBLCDS)) - { - url = "http://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase() - + (format != null ? "&" + format : ""); - } - else + String database = null; + StringTokenizer queries = new StringTokenizer(ids, ";"); + boolean appending = queryString.length() > 0; + while (queries.hasMoreTokens()) { - url = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/" - + dbPath.toLowerCase() + "/" + ids.toLowerCase() - + (format != null ? "/" + format : ""); + String query = queries.nextToken(); + int p = query.indexOf(':'); + if (p > -1) + { + String db = query.substring(0, p); + if (database != null && !db.equalsIgnoreCase(database)) + { + /* + * different databases mixed in together - invalid + */ + return null; + } + database = db; + query = query.substring(p + 1); + } + queryString.append(appending ? "," : ""); + queryString.append(query); + appending = true; } + return database; + } + + String[] fetchBatch(String ids, String dbPath, String format, + File outFile) throws OutOfMemoryError + { + // long time = System.currentTimeMillis(); + String url = buildUrl(ids, dbPath, format); try { @@ -260,4 +238,30 @@ public class EBIFetchClient } return null; } + + /** + * Constructs the URL to fetch from + * + * @param ids + * @param database + * @param format + * @return + */ + static String buildUrl(String ids, String database, String format) + { + String url; + if (database.equalsIgnoreCase(DBRefSource.EMBL) + || database.equalsIgnoreCase(DBRefSource.EMBLCDS)) + { + url = "http://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase() + + (format != null ? "&" + format : ""); + } + else + { + url = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/" + + database.toLowerCase() + "/" + ids.toLowerCase() + + (format != null ? "/" + format : ""); + } + return url; + } } diff --git a/test/jalview/ws/ebi/EBIFetchClientTest.java b/test/jalview/ws/ebi/EBIFetchClientTest.java new file mode 100644 index 0000000..4eaa5b1 --- /dev/null +++ b/test/jalview/ws/ebi/EBIFetchClientTest.java @@ -0,0 +1,113 @@ +package jalview.ws.ebi; + +import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertNull; + +import org.testng.annotations.Test; + +public class EBIFetchClientTest +{ + /** + * Test method that constructs URL to fetch from + */ + @Test(groups = "Functional") + public void testBuildUrl() + { + /* + * EMBL + */ + assertEquals("http://www.ebi.ac.uk/ena/data/view/x53838&display=xml", + EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml")); + + /* + * EMBLCDS + */ + assertEquals("http://www.ebi.ac.uk/ena/data/view/caa37824&display=xml", + EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml")); + + /* + * Uniprot + */ + assertEquals( + "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/uniprot/p00340/uniprotxml", + EBIFetchClient.buildUrl("P00340", "UNIPROT", "uniprotxml")); + + /* + * PDB / pdb + */ + assertEquals("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/pdb", + EBIFetchClient.buildUrl("3A6S", "PDB", "pdb")); + + /* + * PDB / mmCIF + */ + assertEquals( + "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/pdb/3a6s/mmCIF", + EBIFetchClient.buildUrl("3A6S", "PDB", "mmCIF")); + } + + /** + * Test method that parses db:id;id;id + */ + @Test(groups = "Functional") + public void testParseIds() + { + /* + * pdb, two accessions + */ + StringBuilder queries = new StringBuilder(); + String db = EBIFetchClient.parseIds("pdb:3a6s;1A70", queries); + assertEquals("pdb", db); + assertEquals("3a6s,1A70", queries.toString()); + + /* + * pdb specified on second accession + */ + queries.setLength(0); + queries = new StringBuilder(); + db = EBIFetchClient.parseIds("3a6s;pdb:1A70", queries); + assertEquals("pdb", db); + assertEquals("3a6s,1A70", queries.toString()); + + /* + * uniprot, one accession + */ + queries.setLength(0); + db = EBIFetchClient.parseIds("uniprot:P00340", queries); + assertEquals("uniprot", db); + assertEquals("P00340", queries.toString()); + + /* + * uniprot, one accession, appending to existing queries + */ + queries.setLength(0); + queries.append("P30419"); + db = EBIFetchClient.parseIds("uniprot:P00340", queries); + assertEquals("uniprot", db); + assertEquals("P30419,P00340", queries.toString()); + + /* + * pdb and uniprot mixed - rejected + */ + queries.setLength(0); + db = EBIFetchClient.parseIds("pdb:3a6s;1a70;uniprot:P00340", queries); + assertNull(db); + assertEquals("3a6s,1a70", queries.toString()); + + /* + * pdb and PDB mixed - ok + */ + queries.setLength(0); + db = EBIFetchClient.parseIds("pdb:3a6s;pdb:1a70;PDB:1QIP", queries); + assertEquals("PDB", db); + assertEquals("3a6s,1a70,1QIP", queries.toString()); + + /* + * no database (improper format) + */ + queries.setLength(0); + db = EBIFetchClient.parseIds("P00340", queries); + assertNull(db); + assertEquals("P00340", queries.toString()); + } +} -- 1.7.10.2