delete existing files on new zenodo deposit version; related to #304

bio-guoda · Sep 9, 2024 · cc33b09 · cc33b09
1 parent c46025e
commit cc33b09
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Showing 23 changed files with 527 additions and 6 deletions.
diff --git a/preston-cmd/src/main/java/bio/guoda/preston/zenodo/CmdZenodoEnabled.java b/preston-cmd/src/main/java/bio/guoda/preston/zenodo/CmdZenodoEnabled.java
@@ -30,6 +30,10 @@ public abstract class CmdZenodoEnabled extends LoggingPersisting implements Runn
     )
     private String apiEndpoint = EnvUtil.getEnvironmentVariable(ZENODO_ENDPOINT, "https://zenodo.org");
 
+    public void setCreateNewVersionForExisting(Boolean createNewVersionForExisting) {
+        this.createNewVersionForExisting = createNewVersionForExisting;
+    }
+
     @CommandLine.Option(
             names = {"--new-version"},
             description = "create new version if a Zenodo deposit with matching identifiers already exists"

diff --git a/preston-cmd/src/main/java/bio/guoda/preston/zenodo/ZenodoUtils.java b/preston-cmd/src/main/java/bio/guoda/preston/zenodo/ZenodoUtils.java
@@ -28,6 +28,7 @@
 import java.io.InputStream;
 import java.net.URI;
 import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.TreeSet;
@@ -69,16 +70,25 @@ static ObjectMapper getObjectMapper() {
 
     public static void delete(ZenodoContext ctx) throws IOException {
         String deleteRequestURI = ctx.getEndpoint() + "/api/deposit/depositions/" + ctx.getDepositId();
-        try (InputStream inputStream = ResourcesHTTP.asInputStream(
-                RefNodeFactory.toIRI(deleteRequestURI),
-                new HttpDelete(URI.create(deleteRequestURI)),
-                ignoreProgress(),
-                ignoreNone()
-        )) {
+        try (InputStream inputStream = delete(deleteRequestURI)) {
             updateContext(ctx, inputStream);
         }
     }
 
+    public static InputStream delete(String deleteRequestURI) throws IOException {
+        IRI dataURI = RefNodeFactory.toIRI(deleteRequestURI);
+        return delete(dataURI);
+    }
+
+    public static InputStream delete(IRI dataURI) throws IOException {
+        return ResourcesHTTP.asInputStream(
+                dataURI,
+                new HttpDelete(dataURI.getIRIString()),
+                ignoreProgress(),
+                ignoreNone()
+        );
+    }
+
     public static ZenodoContext update(ZenodoContext ctx, String metadata) throws IOException {
         String requestURI = ctx.getEndpoint() + "/api/deposit/depositions/" + ctx.getDepositId();
         IRI dataURI = RefNodeFactory.toIRI(requestURI);
@@ -287,4 +297,20 @@ private static void executeQueryAndCollectIds(Collection<Pair<Long, String>> fou
     private static IRI getQuery(String apiEndpoint, String filter, String method) {
         return RefNodeFactory.toIRI((apiEndpoint + method) + "?" + filter);
     }
+
+    public static List<IRI> getFileEndpoints(ZenodoContext ctx) {
+        JsonNode metadata = ctx.getMetadata();
+        JsonNode files = metadata == null ? new ObjectMapper().createArrayNode() : metadata.at("/files");
+        List<String> ids = new ArrayList<>();
+        for (JsonNode file : files) {
+            JsonNode at = file.at("/id");
+            if (!at.isMissingNode()) {
+                ids.add(at.asText());
+            }
+        }
+        return ids
+                .stream()
+                .map(id -> ctx.getEndpoint() + "/api/deposit/depositions/" + ctx.getDepositId() + "/files/" + id)
+                .map(RefNodeFactory::toIRI).collect(Collectors.toList());
+    }
 }
diff --git a/preston-zenodo/src/main/java/bio/guoda/preston/zenodo/ZenodoMetadataFileStreamHandler.java b/preston-zenodo/src/main/java/bio/guoda/preston/zenodo/ZenodoMetadataFileStreamHandler.java
@@ -11,6 +11,9 @@
 import bio.guoda.preston.stream.ContentStreamHandler;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.sun.xml.internal.ws.policy.privateutil.PolicyUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.output.NullOutputStream;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.apache.commons.rdf.api.IRI;
@@ -28,6 +31,7 @@
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.stream.Collectors;
 
+import static bio.guoda.preston.zenodo.ZenodoUtils.delete;
 import static bio.guoda.preston.zenodo.ZenodoUtils.getObjectMapper;
 
 public class ZenodoMetadataFileStreamHandler implements ContentStreamHandler {
@@ -186,6 +190,7 @@ private void createNewVersion(IRI coordinate, JsonNode zenodoMetadata, List<Stri
             } else if (existingIds.size() == 1 && ctx.createNewVersionForExisting()) {
                 ctxLocal.setDepositId(existingIds.get(0));
                 ctxLocal = ZenodoUtils.createNewVersion(ctxLocal);
+                deleteExistingContentIfPresent(ctxLocal);
                 String input = getObjectMapper().writer().writeValueAsString(zenodoMetadata);
                 ZenodoUtils.update(ctxLocal, input);
                 uploadContentAndPublish(zenodoMetadata, contentIds, ctxLocal);
@@ -208,6 +213,17 @@ private void createNewVersion(IRI coordinate, JsonNode zenodoMetadata, List<Stri
         }
     }
 
+    private void deleteExistingContentIfPresent(ZenodoContext ctxLocal) throws IOException {
+        List<IRI> fileEndpoints = ZenodoUtils.getFileEndpoints(ctxLocal);
+        for (IRI fileEndpoint : fileEndpoints) {
+            try (InputStream inputStream = delete(fileEndpoint)) {
+                IOUtils.copy(inputStream, NullOutputStream.INSTANCE);
+            } catch (IOException e) {
+                throw new IOException("failed to delete existing file [" + fileEndpoint.getIRIString() + "] for deposition [" + ctxLocal.getMetadata() + "]", e);
+            }
+        }
+    }
+
     public static boolean hasAllowedPublicationDate(JsonNode zenodoMetadata, ZenodoConfig ctx) {
         return !zenodoMetadata.at("/metadata/publication_date").isMissingNode()
                 || ctx.shouldAllowEmptyPublicationDate();

diff --git a/preston-zenodo/src/test/java/bio/guoda/preston/zenodo/CmdZenodoIT.java b/preston-zenodo/src/test/java/bio/guoda/preston/zenodo/CmdZenodoIT.java
@@ -1,5 +1,6 @@
 package bio.guoda.preston.zenodo;
 
+import bio.guoda.preston.HashType;
 import bio.guoda.preston.RefNodeFactory;
 import bio.guoda.preston.ResourcesHTTP;
 import bio.guoda.preston.cmd.ZenodoMetaUtil;
@@ -22,6 +23,7 @@
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
 import java.util.Arrays;
+import java.util.List;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.regex.Matcher;
@@ -30,6 +32,7 @@
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.greaterThan;
+import static org.hamcrest.Matchers.is;
 import static org.hamcrest.Matchers.startsWith;
 
 
@@ -122,6 +125,79 @@ public void createDepositAndUpdateToRestrict() throws URISyntaxException, IOExce
 
     }
 
+    @Test
+    public void createDepositAndCreateNewVersionWithDifferentFile() throws URISyntaxException, IOException {
+        ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+        String resourceOld = "darktaxon-delete/29/cc/29ccb90cb281069a23b4e07ec10583c8";
+        String fileChecksumOld = "md5:d3b07384d113edec49eaa6238ad5ff00";
+        publishNewVersionOfResource(outputStream, resourceOld);
+
+        assertStateOfDepositedFiles(outputStream, fileChecksumOld);
+
+        outputStream = new ByteArrayOutputStream();
+        String resourceNew = "darktaxon-delete/97/4c/974c37be498a377c3795bcbdb6e20581";
+        String fileChecksumNew = "md5:c157a79031e1c40f85931829bc5fc552";
+        publishNewVersionOfResource(outputStream, resourceNew);
+
+        assertStateOfDepositedFiles(outputStream, fileChecksumNew);
+
+
+
+    }
+
+    private void assertStateOfDepositedFiles(ByteArrayOutputStream outputStream, String fileChecksumOld) throws IOException {
+        String log = new String(outputStream.toByteArray(), StandardCharsets.UTF_8);
+        String[] split = StringUtils.split(log, '\n');
+        assertThat(split.length, greaterThan(0));
+
+        assertThat(log, containsString("https://sandbox.zenodo.org/records/"));
+
+        Pattern compile = Pattern.compile(".*https://sandbox.zenodo.org/records/(?<depositId>[0-9]+).*");
+        Matcher matcher = compile.matcher(StringUtils.replace(log, "\n", " "));
+        assertThat(matcher.matches(), Is.is(true));
+
+
+        String depositId = matcher.group("depositId");
+        JsonNode depositMetadata = requestDepositMetadata(depositId);
+        ZenodoContext ctx = new ZenodoContext("secret", "https://sandbox.zenodo.org");
+        ctx.setMetadata(depositMetadata);
+        ctx.setDepositId(Long.parseLong(depositId));
+        List<IRI> fileEndpoints = ZenodoUtils.getFileEndpoints(ctx);
+
+        assertThat(fileEndpoints.size(), is(1));
+
+        System.out.println(depositMetadata.toPrettyString());
+
+        JsonNode at = depositMetadata.at("/files/0/checksum");
+        assertThat(at.isMissingNode(), is(false));
+        assertThat(at.asText(), is(fileChecksumOld));
+    }
+
+    private void publishNewVersionOfResource(ByteArrayOutputStream outputStream, String resourceOld) throws IOException {
+        CmdZenodo cmdZenodo1 = new CmdZenodo();
+
+        URL resource = getClass().getResource(resourceOld);
+        URI remote = new File(resource.getFile()).getParentFile().getParentFile().getParentFile().toURI();
+
+
+        File dataDir = folder.newFolder();
+        cmdZenodo1.setLocalDataDir(dataDir.getAbsolutePath());
+        cmdZenodo1.setRemotes(Arrays.asList(remote));
+        cmdZenodo1.setHashType(HashType.md5);
+        cmdZenodo1.setApiEndpoint("https://sandbox.zenodo.org");
+        cmdZenodo1.setCreateNewVersionForExisting(true);
+
+        System.setProperty("ZENODO_TOKEN", ZenodoTestUtil.getAccessToken());
+
+        cmdZenodo1.setInputStream(getClass().getResourceAsStream(resourceOld));
+        cmdZenodo1.setOutputStream(outputStream);
+        cmdZenodo1.setCacheEnabled(false);
+
+        // first make sure a deposit exists
+        cmdZenodo1.run();
+    }
+
+
     private CmdZenodo createCmd(ByteArrayOutputStream outputStream) throws IOException {
         CmdZenodo cmdZenodo = new CmdZenodo();
         String resourceURI = "batlit-data/31/31/3131a4dd8ed099a31e2f2032c0248ba7";

diff --git a/preston-zenodo/src/test/java/bio/guoda/preston/zenodo/ZenodoUtilsTest.java b/preston-zenodo/src/test/java/bio/guoda/preston/zenodo/ZenodoUtilsTest.java
@@ -1,9 +1,15 @@
 package bio.guoda.preston.zenodo;
 
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.apache.commons.rdf.api.IRI;
+import org.hamcrest.core.Is;
 import org.junit.Test;
 
+import java.io.IOException;
+import java.io.InputStream;
 import java.util.Arrays;
+import java.util.List;
 
 import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.MatcherAssert.assertThat;
@@ -58,4 +64,39 @@ public void queryForExistingRecords() {
         );
     }
 
+    @Test
+    public void extractFileIds() throws IOException {
+        ZenodoContext ctx = getContext();
+
+        InputStream is = getClass().getResourceAsStream("darktaxon-delete/to-be-deleted.json");
+
+
+        JsonNode jsonNode = new ObjectMapper().readTree(is);
+
+        ctx.setMetadata(jsonNode);
+        List<IRI> fileEndpoints = ZenodoUtils.getFileEndpoints(ctx);
+
+        assertThat(fileEndpoints.size(), Is.is(1));
+        assertThat(fileEndpoints.get(0).getIRIString(), Is.is("https://sandbox.example.org/api/deposit/depositions/123/files/ba1a0c80-d8a0-4afc-997b-4059b1c03ae5"));
+    }
+
+    private ZenodoContext getContext() {
+        ZenodoContext ctx = new ZenodoContext("bla", "https://sandbox.example.org");
+        ctx.setDepositId(123L);
+        return ctx;
+    }
+
+    @Test
+    public void extractFileIdsNoMatching() throws IOException {
+        InputStream is = getClass().getResourceAsStream("darktaxon-delete/to-be-deleted-no-files.json");
+
+        JsonNode jsonNode = new ObjectMapper().readTree(is);
+        ZenodoContext context = getContext();
+        context.setMetadata(jsonNode);
+        List<IRI> fileEndpoints = ZenodoUtils.getFileEndpoints(context);
+
+        assertThat(fileEndpoints.size(), Is.is(0));
+
+    }
+
 }
diff --git a/...esources/bio/guoda/preston/zenodo/darktaxon-delete/12/4c/124cf285b566fbf4f3c1342c541ac1b2 b/...esources/bio/guoda/preston/zenodo/darktaxon-delete/12/4c/124cf285b566fbf4f3c1342c541ac1b2
@@ -0,0 +1,20 @@
+<https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#SoftwareAgent> <urn:uuid:694e11f8-fbb5-449e-bedf-d9f40688d1c8> .
+<https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> <urn:uuid:694e11f8-fbb5-449e-bedf-d9f40688d1c8> .
+<https://preston.guoda.bio> <http://purl.org/dc/terms/description> "Preston is a software program that finds, archives and provides access to biodiversity datasets."@en <urn:uuid:694e11f8-fbb5-449e-bedf-d9f40688d1c8> .
+<urn:uuid:694e11f8-fbb5-449e-bedf-d9f40688d1c8> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> <urn:uuid:694e11f8-fbb5-449e-bedf-d9f40688d1c8> .
+<urn:uuid:694e11f8-fbb5-449e-bedf-d9f40688d1c8> <http://purl.org/dc/terms/description> "A crawl event that discovers biodiversity archives."@en <urn:uuid:694e11f8-fbb5-449e-bedf-d9f40688d1c8> .
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+<https://doi.org/10.5281/zenodo.1410543> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/dc/dcmitype/Software> <urn:uuid:694e11f8-fbb5-449e-bedf-d9f40688d1c8> .
+<https://doi.org/10.5281/zenodo.1410543> <http://purl.org/dc/terms/bibliographicCitation> "Jorrit Poelen, Icaro Alzuru, & Michael Elliott. 2018-2024. Preston: a biodiversity dataset tracker (Version 0.9.7-SNAPSHOT) [Software]. Zenodo. https://doi.org/10.5281/zenodo.1410543"@en <urn:uuid:694e11f8-fbb5-449e-bedf-d9f40688d1c8> .
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+<urn:uuid:81682088-29a9-4d81-9704-0080b4ddf0a8> <http://www.w3.org/ns/prov#wasInformedBy> <urn:uuid:694e11f8-fbb5-449e-bedf-d9f40688d1c8> <urn:uuid:81682088-29a9-4d81-9704-0080b4ddf0a8> .
+<urn:uuid:81682088-29a9-4d81-9704-0080b4ddf0a8> <http://www.w3.org/ns/prov#used> <urn:uuid:89d01646-f2c1-4cf7-aa0e-c3b154de6b74> <urn:uuid:81682088-29a9-4d81-9704-0080b4ddf0a8> .
+<urn:uuid:89d01646-f2c1-4cf7-aa0e-c3b154de6b74> <http://purl.org/pav/hasVersion> <hash://md5/c157a79031e1c40f85931829bc5fc552> <urn:uuid:81682088-29a9-4d81-9704-0080b4ddf0a8> .
diff --git a/...esources/bio/guoda/preston/zenodo/darktaxon-delete/27/f5/27f552c25bc733d05a5cc67e9ba63850 b/...esources/bio/guoda/preston/zenodo/darktaxon-delete/27/f5/27f552c25bc733d05a5cc67e9ba63850
@@ -0,0 +1 @@
+hash://md5/c8e5dd65f2bb814f6d5b3eab58281b55
diff --git a/...esources/bio/guoda/preston/zenodo/darktaxon-delete/29/cc/29ccb90cb281069a23b4e07ec10583c8 b/...esources/bio/guoda/preston/zenodo/darktaxon-delete/29/cc/29ccb90cb281069a23b4e07ec10583c8
@@ -0,0 +1,20 @@
+<https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#SoftwareAgent> <urn:uuid:e125f1df-603c-4ed5-aa13-2acd0044903c> .
+<https://preston.guoda.bio> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Agent> <urn:uuid:e125f1df-603c-4ed5-aa13-2acd0044903c> .
+<https://preston.guoda.bio> <http://purl.org/dc/terms/description> "Preston is a software program that finds, archives and provides access to biodiversity datasets."@en <urn:uuid:e125f1df-603c-4ed5-aa13-2acd0044903c> .
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+<https://doi.org/10.5281/zenodo.1410543> <http://purl.org/dc/terms/bibliographicCitation> "Jorrit Poelen, Icaro Alzuru, & Michael Elliott. 2018-2024. Preston: a biodiversity dataset tracker (Version 0.9.7-SNAPSHOT) [Software]. Zenodo. https://doi.org/10.5281/zenodo.1410543"@en <urn:uuid:e125f1df-603c-4ed5-aa13-2acd0044903c> .
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diff --git a/...esources/bio/guoda/preston/zenodo/darktaxon-delete/50/38/5038c9fe5167b58b7f81d17aca139a71 b/...esources/bio/guoda/preston/zenodo/darktaxon-delete/50/38/5038c9fe5167b58b7f81d17aca139a71
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