bump to globi libs v0.12.1; add tests for empty access.tsv

pom.xml

@@ -9,7 +9,7 @@
     <description>Discover, cache and check species interaction data</description>
 
     <properties>
-        <globi.version>0.11.1</globi.version>
+        <globi.version>0.12.1</globi.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.build.resourceEncoding>UTF-8</project.build.resourceEncoding>
         <project.build.testResourceEncoding>UTF-8</project.build.testResourceEncoding>

src/test/java/org/globalbioticinteractions/elton/cmd/CmdInteractionsIT.java

@@ -0,0 +1,43 @@
+package org.globalbioticinteractions.elton.cmd;
+
+import com.beust.jcommander.JCommander;
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.io.ByteArrayOutputStream;
+import java.io.PrintStream;
+import java.net.URISyntaxException;
+
+import static org.hamcrest.CoreMatchers.is;
+import static org.hamcrest.core.IsCollectionContaining.hasItem;
+import static org.hamcrest.core.StringStartsWith.startsWith;
+import static org.junit.Assert.assertThat;
+
+public class CmdInteractionsIT {
+
+    @Test
+    public void interactions() throws URISyntaxException {
+        JCommander jc = new CmdLine().buildCommander();
+        jc.parse("interactions",
+                "--cache-dir=/home/jorrit/proj/parasite-tracker/tmp");
+
+        Assert.assertEquals(jc.getParsedCommand(), "interactions");
+
+        JCommander actual = jc.getCommands().get(jc.getParsedCommand());
+        Assert.assertEquals(actual.getObjects().size(), 1);
+        Object cmd = actual.getObjects().get(0);
+        Assert.assertEquals(cmd.getClass(), CmdInteractions.class);
+        CmdInteractions cmdInteractions = (CmdInteractions) actual.getObjects().get(0);
+        assertThat(cmdInteractions.getNamespaces().size(), is(1));
+//        assertThat(cmdInteractions.getNamespaces(), hasItem("globalbioticinteractions/template-dataset"));
+
+        if (actual.getObjects().get(0) instanceof Runnable) {
+            ByteArrayOutputStream out1 = new ByteArrayOutputStream();
+            PrintStream out = new PrintStream(out1);
+            ((CmdInteractions) actual.getObjects().get(0)).run(out);
+            assertThat(out1.toString(), startsWith("\tLeptoconchus incycloseris\t\t\t\t\thttp://purl.obolibrary.org/obo/RO_0002444\tparasiteOf\t\tFungia (Cycloseris) costulata\t\t\t\t\t\t\t\t\t\t10.1007/s13127-011-0039-1\thttps://doi.org/10.1007/s13127-011-0039-1\tGittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1\tglobalbioticinteractions/template-dataset\tJorrit H. Poelen. 2014. Species associations manually extracted from literature.\thttps://zenodo.org/record/207958/files/globalbioticinteractions/template-dataset-0.0.2.zip\t2017-09-19T17:01:39Z\t631d3777cf83e1abea848b59a6589c470cf0c7d0fd99682c4c104481ad9a543f\tdev\n"));
+        }
+    }
+
+
+}

src/test/java/org/globalbioticinteractions/elton/cmd/CmdNamesTest.java

@@ -64,5 +64,25 @@ public void namesWithHeader() throws URISyntaxException {
         }
     }
 
+    @Test
+    public void namesWithHeaderEmpty() throws URISyntaxException {
+        JCommander jc = new CmdLine().buildCommander();
+        jc.parse("names",
+                "--cache-dir=" + CmdTestUtil.cacheDirTestFor("/dataset-cache-empty/globalbioticinteractions/template-dataset/access.tsv"));
+
+        JCommander actual = jc.getCommands().get(jc.getParsedCommand());
+
+        if (actual.getObjects().get(0) instanceof Runnable) {
+            ByteArrayOutputStream out1 = new ByteArrayOutputStream();
+            PrintStream out = new PrintStream(out1);
+            ((CmdNames) actual.getObjects().get(0)).run(out);
+            String actualOutput = out1.toString();
+            String[] actualLines = StringUtils.splitByWholeSeparator(actualOutput, "\n");
+            assertThat(actualLines[0], is("taxonId\ttaxonName\ttaxonRank\ttaxonPath\ttaxonPathIds\ttaxonPathNames\tnamespace\tcitation\tarchiveURI\tlastSeenAt\tcontentHash\teltonVersion"));
+            assertThat(actualLines[1], is("\tLeptoconchus incycloseris\t\t\t\t\tglobalbioticinteractions/template-dataset\tJorrit H. Poelen. 2014. Species associations manually extracted from literature.\thttps://zenodo.org/record/207958/files/globalbioticinteractions/template-dataset-0.0.2.zip\t2017-09-19T17:01:39Z\t631d3777cf83e1abea848b59a6589c470cf0c7d0fd99682c4c104481ad9a543f\tdev"));
+            assertThat(actualLines[1].split("\t").length, is(actualLines[0].split("\t").length));
+        }
+    }
+
 
 }

src/test/java/org/globalbioticinteractions/elton/cmd/CmdTestUtil.java

@@ -10,7 +10,12 @@
 
 final class CmdTestUtil {
     static String cacheDirTest() throws URISyntaxException {
-        URL accessURL = CmdNamesTest.class.getResource("/dataset-cache-test/globalbioticinteractions/template-dataset/access.tsv");
+        String name = "/dataset-cache-test/globalbioticinteractions/template-dataset/access.tsv";
+        return cacheDirTestFor(name);
+    }
+
+    static String cacheDirTestFor(String name) throws URISyntaxException {
+        URL accessURL = CmdNamesTest.class.getResource(name);
         assertThat(accessURL, is(notNullValue()));
         return new File(accessURL.toURI()).getParentFile().getParentFile().getParentFile().getAbsolutePath();
     }

src/test/resources/dataset-cache-empty/globalbioticinteractions/template-dataset/1cc8eff62af0e6bb3e7771666e2e4109f351b7dfc6fc1dc8314e5671a8eecb80

@@ -0,0 +1,4 @@
+{ 
+  "_comment": "Sample GloBI dataset descriptor. See http://github.com/globalbioticinteractions for more information.",
+  "citation": "Jorrit H. Poelen. 2014. Species associations manually extracted from literature."
+}

src/test/resources/dataset-cache-empty/globalbioticinteractions/template-dataset/access.tsv

@@ -0,0 +1,4 @@
+globalbioticinteractions/template-dataset	https://zenodo.org/record/207958/files/globalbioticinteractions/template-dataset-0.0.2.zip		2017-09-19T17:01:39Z	application/globi
+globalbioticinteractions/template-dataset	https://zenodo.org/record/207958/files/globalbioticinteractions/template-dataset-0.0.2.zip	631d3777cf83e1abea848b59a6589c470cf0c7d0fd99682c4c104481ad9a543f	2017-09-19T17:01:39Z	
+globalbioticinteractions/template-dataset	jar:file:/home/jorrit/proj/globi/globinizer/./datasets/globalbioticinteractions/template-dataset/631d3777cf83e1abea848b59a6589c470cf0c7d0fd99682c4c104481ad9a543f!/globalbioticinteractions-template-dataset-e68f448/globi.json	1cc8eff62af0e6bb3e7771666e2e4109f351b7dfc6fc1dc8314e5671a8eecb80	2017-09-19T17:01:39Z	
+globalbioticinteractions/template-dataset	jar:file:/home/jorrit/proj/globi/globinizer/./datasets/globalbioticinteractions/template-dataset/631d3777cf83e1abea848b59a6589c470cf0c7d0fd99682c4c104481ad9a543f!/globalbioticinteractions-template-dataset-e68f448/interactions.tsv	c1b37add5ee5f30916f19811c59c2960e3b68ecf1a3846afe1776014c4c96271	2017-09-19T17:01:39Z	

src/test/resources/dataset-cache-empty/globalbioticinteractions/template-dataset/c1b37add5ee5f30916f19811c59c2960e3b68ecf1a3846afe1776014c4c96271

@@ -0,0 +1,12 @@
+sourceTaxonId	sourceTaxonName	interactionTypeId	interactionTypeName	targetTaxonId	targetTaxonName	localityId	localityName	decimalLatitude	decimalLongitude	observationDateTime	referenceDoi	referenceCitation
+	Leptoconchus incycloseris	RO:0002444	parasite of		Fungia (Cycloseris) costulata						doi:10.1007/s13127-011-0039-1	Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
+	Leptoconchus infungites	RO:0002444	parasite of		Fungia (Fungia) fungites						doi:10.1007/s13127-011-0039-1	Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
+	Leptoconchus ingrandifungi	RO:0002444	parasite of		Sandalolitha dentata						doi:10.1007/s13127-011-0039-1	Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
+	Leptoconchus ingranulosa	RO:0002444	parasite of		Fungia (Wellsofungia) granulosa						doi:10.1007/s13127-011-0039-1	Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
+	Leptoconchus inlimax	RO:0002444	parasite of		Herpolitha limax						doi:10.1007/s13127-011-0039-1	Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
+	Leptoconchus inpileus	RO:0002444	parasite of		Halomitra pileus						doi:10.1007/s13127-011-0039-1	Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
+	Leptoconchus inpleuractis	RO:0002444	parasite of		Fungia (Pleuractis) gravis						doi:10.1007/s13127-011-0039-1	Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
+	Leptoconchus inpleuractis	RO:0002444	parasite of		Fungia (Pleuractis) moluccensis						doi:10.1007/s13127-011-0039-1	Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
+	Leptoconchus inpleuractis	RO:0002444	parasite of		Fungia (Pleuractis) paumotensis						doi:10.1007/s13127-011-0039-1	Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
+	Leptoconchus massini	RO:0002444	parasite of		Fungia (Verrillofungia) concinna						doi:10.1007/s13127-011-0039-1	Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
+	Leptoconchus massini	RO:0002444	parasite of		Fungia (Verrillofungia) repanda						doi:10.1007/s13127-011-0039-1	Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1