upgrade to globi-libs v0.27.0

globalbioticinteractions · Nov 8, 2024 · fde6653 · fde6653
1 parent 3cd80e8
commit fde6653
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Showing 18 changed files with 188 additions and 88 deletions.
diff --git a/pom.xml b/pom.xml
@@ -9,7 +9,7 @@
     <description>Discover, access, and review, species interaction data</description>
 
     <properties>
-        <globi.version>0.26.6</globi.version>
+        <globi.version>0.27.0</globi.version>
         <preston.version>0.7.8</preston.version>
         <slf4j.version>1.7.30</slf4j.version>
         <picocli.version>4.6.3</picocli.version>

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdDatasets.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdDatasets.java
@@ -1,5 +1,6 @@
 package org.globalbioticinteractions.elton.cmd;
 
+
 import org.globalbioticinteractions.dataset.Dataset;
 import org.globalbioticinteractions.dataset.DatasetRegistry;
 import org.globalbioticinteractions.dataset.DatasetRegistryException;
@@ -51,7 +52,9 @@ void run(PrintStream out) {
         DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(
                 getCacheDir(),
                 getWorkDir(),
-                createInputStreamFactory());
+                createInputStreamFactory(),
+                getContentPathFactory(),
+                getProvenancePathFactory());
 
         try {
             CmdUtil.handleNamespaces(registry,

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdDefaultParams.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdDefaultParams.java
@@ -1,5 +1,9 @@
 package org.globalbioticinteractions.elton.cmd;
 
+import org.globalbioticinteractions.cache.ContentPathFactory;
+import org.globalbioticinteractions.cache.ContentPathFactoryDepth0;
+import org.globalbioticinteractions.cache.ProvenancePathFactory;
+import org.globalbioticinteractions.cache.ProvenancePathFactoryImpl;
 import org.globalbioticinteractions.elton.util.ProgressCursor;
 import org.globalbioticinteractions.elton.util.ProgressCursorFactory;
 import org.globalbioticinteractions.elton.util.ProgressCursorRotating;
@@ -13,36 +17,41 @@
 import java.util.List;
 
 abstract class CmdDefaultParams implements Runnable {
-    @CommandLine.Option (names = {"--cache-dir", "-c"},
+    @CommandLine.Option(names = {"--cache-dir", "-c"},
             description = "Cache directory"
     )
     private String cacheDir = "./datasets";
 
-    @CommandLine.Option (names = {"--work-dir", "-w"},
+    @CommandLine.Option(names = {"--work-dir", "-w"},
             description = "Work directory"
     )
     private String workDir = ".";
 
-    @CommandLine.Option (names = {"--no-progress"},
+    @CommandLine.Option(names = {"--no-progress"},
             description = "Do not show progress indicator"
     )
     private boolean noProgress = false;
 
+
     public void setNamespaces(List<String> namespaces) {
         this.namespaces = namespaces;
     }
 
-    @CommandLine.Parameters (
+    @CommandLine.Parameters(
             description = "[namespace1] [namespace2] ..."
     )
     private List<String> namespaces = new ArrayList<>();
 
+    private ContentPathFactory contentPathFactory = new ContentPathFactoryDepth0();
+    private ProvenancePathFactory provenancePathFactory = new ProvenancePathFactoryImpl();
+
     private PrintStream stderr = System.err;
     private PrintStream stdout = System.out;
     private InputStream stdin = System.in;
 
     final private ProgressCursorFactory cursorFactory = new ProgressCursorFactory() {
         private final ProgressCursor cursor = new ProgressCursorRotating(stderr);
+
         @Override
         public ProgressCursor createProgressCursor() {
             return cursor;
@@ -92,19 +101,29 @@ public void setCacheDir(String cacheDir) {
         this.cacheDir = cacheDir;
     }
 
+
+    public ContentPathFactory getContentPathFactory() {
+        return (this.contentPathFactory);
+    }
+
+
     public void setWorkDir(String workingDir) {
         this.workDir = workingDir;
     }
 
     public ProgressCursorFactory getProgressCursorFactory() {
         return noProgress
-                ? () -> () -> {}
-                 : cursorFactory;
+                ? () -> () -> {
+        }
+                : cursorFactory;
     }
 
     public InputStreamFactoryLogging createInputStreamFactory() {
         return new InputStreamFactoryLogging(getProgressCursorFactory());
     }
 
 
+    public ProvenancePathFactory getProvenancePathFactory() {
+        return provenancePathFactory;
+    }
 }
diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdGet.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdGet.java
@@ -1,43 +1,23 @@
 package org.globalbioticinteractions.elton.cmd;
 
-import bio.guoda.preston.HashType;
-import bio.guoda.preston.Hasher;
-import bio.guoda.preston.RefNodeConstants;
 import bio.guoda.preston.RefNodeFactory;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.rdf.api.IRI;
-import org.apache.commons.rdf.api.Quad;
-import org.eol.globi.data.NodeFactory;
-import org.eol.globi.service.CacheService;
-import org.eol.globi.service.ResourceService;
-import org.eol.globi.tool.NullImportLogger;
-import org.globalbioticinteractions.dataset.Dataset;
-import org.globalbioticinteractions.dataset.DatasetProxy;
+
 import org.globalbioticinteractions.dataset.DatasetRegistry;
 import org.globalbioticinteractions.dataset.DatasetRegistryException;
-import org.globalbioticinteractions.dataset.DatasetRegistryProxy;
 import org.globalbioticinteractions.elton.util.DatasetRegistryUtil;
-import org.globalbioticinteractions.elton.util.NamespaceHandler;
-import org.globalbioticinteractions.elton.util.NodeFactoryNull;
-import org.nanopub.Run;
 import picocli.CommandLine;
 
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.PrintStream;
-import java.net.URI;
-import java.security.DigestInputStream;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.List;
-import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -61,7 +41,9 @@ void run(PrintStream out) {
         DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(
                 getCacheDir(),
                 getWorkDir(),
-                createInputStreamFactory()
+                createInputStreamFactory(),
+                getContentPathFactory(),
+                getProvenancePathFactory()
         );
 
         final List<String> actualNamespaces = new ArrayList<>();

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdInteractions.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdInteractions.java
@@ -3,6 +3,7 @@
 import org.eol.globi.data.ImportLogger;
 import org.eol.globi.data.NodeFactory;
 import org.eol.globi.domain.LogContext;
+
 import org.globalbioticinteractions.dataset.DatasetRegistry;
 import org.globalbioticinteractions.elton.util.DatasetRegistryUtil;
 import org.globalbioticinteractions.elton.util.ProgressUtil;
@@ -29,7 +30,9 @@ void run(PrintStream out) {
         DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(
                 getCacheDir(),
                 getWorkDir(),
-                createInputStreamFactory());
+                createInputStreamFactory(),
+                getContentPathFactory(),
+                getProvenancePathFactory());
 
         NodeFactory nodeFactory = WriterUtil.nodeFactoryForInteractionWriting(!shouldSkipHeader(), out);
 

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdList.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdList.java
@@ -1,6 +1,7 @@
 package org.globalbioticinteractions.elton.cmd;
 
 import org.eol.globi.util.ResourceServiceRemote;
+
 import org.globalbioticinteractions.dataset.DatasetRegistry;
 import org.globalbioticinteractions.dataset.DatasetRegistryException;
 import org.globalbioticinteractions.dataset.DatasetRegistryGitHubArchive;
@@ -28,7 +29,7 @@ public void run() {
 
     public void run(PrintStream out) {
         InputStreamFactoryLogging inputStreamFactory = createInputStreamFactory();
-        DatasetRegistry registryLocal = DatasetRegistryUtil.forCacheDirOrLocalDir(getCacheDir(), getWorkDir(), inputStreamFactory);
+        DatasetRegistry registryLocal = DatasetRegistryUtil.forCacheDirOrLocalDir(getCacheDir(), getWorkDir(), inputStreamFactory, getContentPathFactory(), getProvenancePathFactory());
 
         File cacheDir = new File(getCacheDir());
         List<DatasetRegistry> registries =

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdLog.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdLog.java
@@ -9,6 +9,7 @@
 import org.eol.globi.data.NodeFactory;
 import org.eol.globi.service.ResourceService;
 import org.eol.globi.tool.NullImportLogger;
+
 import org.globalbioticinteractions.dataset.Dataset;
 import org.globalbioticinteractions.dataset.DatasetProxy;
 import org.globalbioticinteractions.dataset.DatasetRegistry;
@@ -47,7 +48,8 @@ public void run() {
         DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(
                 getCacheDir(),
                 getWorkDir(),
-                createInputStreamFactory()
+                createInputStreamFactory(),
+                getContentPathFactory(), getProvenancePathFactory()
         );
 
         IRI softwareAgent = RefNodeFactory.toIRI("https://zenodo.org/doi/10.5281/zenodo.998263");

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdNames.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdNames.java
@@ -2,6 +2,7 @@
 
 import org.eol.globi.data.NodeFactory;
 import org.eol.globi.tool.NullImportLogger;
+
 import org.globalbioticinteractions.dataset.DatasetRegistry;
 import org.globalbioticinteractions.elton.util.DatasetRegistryUtil;
 import picocli.CommandLine;
@@ -23,7 +24,7 @@ public void run() {
 
     void run(PrintStream out) {
 
-        DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(getCacheDir(), getWorkDir(), createInputStreamFactory());
+        DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(getCacheDir(), getWorkDir(), createInputStreamFactory(), getContentPathFactory(), getProvenancePathFactory());
 
         NodeFactory nodeFactory = WriterUtil.nodeFactoryForTaxonWriting(!shouldSkipHeader(), out);
 

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdNanoPubs.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdNanoPubs.java
@@ -1,6 +1,7 @@
 package org.globalbioticinteractions.elton.cmd;
 
 import org.eol.globi.tool.NullImportLogger;
+
 import org.globalbioticinteractions.dataset.DatasetRegistry;
 import org.globalbioticinteractions.elton.util.DatasetRegistryUtil;
 import org.globalbioticinteractions.elton.util.IdGenerator;
@@ -43,7 +44,8 @@ void run(PrintStream out) {
         DatasetRegistry registry = DatasetRegistryUtil.forCacheDirOrLocalDir(
                 getCacheDir(),
                 getWorkDir(),
-                createInputStreamFactory());
+                createInputStreamFactory(),
+                getContentPathFactory(), getProvenancePathFactory());
 
         InteractionWriter serializer = createSerializer(out);
 

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdReview.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdReview.java
@@ -25,6 +25,7 @@
 import org.eol.globi.util.InputStreamFactory;
 import org.eol.globi.util.ResourceServiceLocal;
 import org.eol.globi.util.ResourceServiceLocalAndRemote;
+
 import org.globalbioticinteractions.dataset.CitationUtil;
 import org.globalbioticinteractions.dataset.Dataset;
 import org.globalbioticinteractions.dataset.DatasetConstant;
@@ -87,6 +88,7 @@ public class CmdReview extends CmdTabularWriterParams {
     private String reviewId = UUID.randomUUID().toString();
 
 
+
     @Override
     public void run() {
         try {
@@ -111,7 +113,8 @@ public void run() {
                 DatasetRegistry registryLocal = DatasetRegistryUtil.forLocalDir(
                         localNamespace,
                         getCacheDir(),
-                        new ResourceServiceLocalAndRemote(factory, new File(getCacheDir()))
+                        new ResourceServiceLocalAndRemote(factory, new File(getCacheDir())),
+                        getContentPathFactory()
                 );
 
                 review(DatasetRegistryUtil.NAMESPACE_LOCAL, registryLocal, factory, shouldSkipHeader());
@@ -129,7 +132,9 @@ private void reviewCachedOrRemote(List<String> namespaces, InputStreamFactory in
             review(namespace,
                     DatasetRegistryUtil.forCacheDir(
                             getCacheDir(),
-                            new ResourceServiceLocal(inputStreamFactory)
+                            new ResourceServiceLocal(inputStreamFactory),
+                            getContentPathFactory(),
+                            getProvenancePathFactory()
                     ),
                     inputStreamFactory,
                     shouldSkipHeader()

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdStream.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdStream.java
@@ -11,6 +11,7 @@
 import org.eol.globi.data.NodeFactory;
 import org.eol.globi.domain.LogContext;
 import org.eol.globi.tool.NullImportLogger;
+
 import org.globalbioticinteractions.elton.util.DatasetRegistryUtil;
 import org.globalbioticinteractions.elton.util.ProgressCursor;
 import org.globalbioticinteractions.elton.util.ProgressCursorFactory;
@@ -69,7 +70,9 @@ public void run() {
                                     this.getStderr(),
                                     this.createInputStreamFactory(),
                                     new NodeFactoryFactoryImpl(shouldWriteHeader, recordType, loggerFactory.createImportLogger()),
-                                    loggerFactory
+                                    loggerFactory,
+                                    getContentPathFactory(),
+                                    getProvenancePathFactory()
                             );
                             namespaceHandler.onNamespace(namespace);
                             isFirst.set(false);

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdUpdate.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdUpdate.java
@@ -3,6 +3,7 @@
 import org.eol.globi.data.NodeFactory;
 import org.eol.globi.data.StudyImporterException;
 import org.eol.globi.util.DatasetImportUtil;
+
 import org.globalbioticinteractions.dataset.Dataset;
 import org.globalbioticinteractions.dataset.DatasetFactory;
 import org.globalbioticinteractions.dataset.DatasetRegistry;
@@ -65,11 +66,15 @@ public void run() {
                     registryProxy,
                     namespace,
                     getCacheDir(),
-                    inputStreamFactory);
+                    inputStreamFactory,
+                    getContentPathFactory(),
+                    getProvenancePathFactory()
+            );
 
             Dataset dataset =
                     new DatasetFactory(registry, createInputStreamFactory())
                             .datasetFor(namespace);
+
             NodeFactory factory = new NodeFactoryNull();
             factory.getOrCreateDataset(dataset);
             try {