depositions queries do not appears to support type queries; related to …

…https://github.com/darktaxon/mfn-malaisetrap/issues/7; zenodo/zenodo#2545
bio-guoda · Sep 10, 2024 · 78dc7d7 · 78dc7d7
1 parent a398289
commit 78dc7d7
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Showing 5 changed files with 11 additions and 89 deletions.
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
@@ -231,21 +231,12 @@ public static ZenodoContext upload(ZenodoContext ctx, String filename, HttpEntit
         }
     }
 
-    public static Collection<Pair<Long, String>> findByAlternateIds(ZenodoConfig ctx, List<String> ids, String type, Dereferencer<InputStream> dereferencer) throws IOException {
+    public static Collection<Pair<Long, String>> findRecordsByAlternateIds(ZenodoConfig ctx, List<String> ids, String type, Dereferencer<InputStream> dereferencer) throws IOException {
         Collection<Pair<Long, String>> foundIds = new TreeSet<>();
         findExistingRecords(ctx, ids, foundIds, type, dereferencer);
-        findExistingDepositions(ctx, ids, foundIds, type, dereferencer);
         return foundIds;
     }
 
-    private static void findExistingDepositions(ZenodoConfig ctx, List<String> ids, Collection<Pair<Long, String>> foundIds, String type, Dereferencer<InputStream> dereferencer) throws IOException {
-        IRI query1 = getQueryForExistingDepositions(ctx, ids, type);
-        executeQueryAndCollectIds(foundIds, query1, dereferencer);
-    }
-
-    public static IRI getQueryForExistingDepositions(ZenodoConfig ctx, List<String> contentIds, String type) {
-        return getQueryForExistingDepositions(ctx, contentIds, "/api/deposit/depositions", type);
-    }
 
     public static IRI getQueryForExistingDepositions(ZenodoConfig ctx, List<String> contentIds, String method, String type) {
         String prefix = communitiesPrefix(ctx);
@@ -271,7 +262,10 @@ private static String appendTypeClause(String type, String query, String method)
     }
 
     public static IRI getSearchPageForExistingRecords(ZenodoConfig ctx, List<String> contentIds, String type) {
-        return getQueryForExistingDepositions(ctx, contentIds, "/search", type);
+        String prefix = communitiesPrefix(ctx);
+        String query = prefix + "q=" + getQueryForIds(contentIds);
+        query = appendTypeClause(type, query, "/search");
+        return getQuery(ctx.getEndpoint(), query, "/search");
     }
 
     private static void findExistingRecords(ZenodoConfig ctx, List<String> ids, Collection<Pair<Long, String>> foundIds, String type, Dereferencer<InputStream> dereferencer) throws IOException {

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
@@ -103,13 +103,12 @@ private void attemptToHandleJSON(String line, IRI coordinate) throws IOException
             }
 
             Dereferencer<InputStream> adHocQueryDereferencer = ResourcesHTTP::asInputStream;
-            Collection<Pair<Long, String>> foundDeposits = ZenodoUtils.findByAlternateIds(
+            Collection<Pair<Long, String>> foundDeposits = ZenodoUtils.findRecordsByAlternateIds(
                     ctx,
                     recordIds,
                     resourceType,
                     adHocQueryDereferencer
             );
-            deleteDraftsIfPresent(foundDeposits, recordIds);
             createNewVersion(coordinate, zenodoMetadata, recordIds, contentIds, origins, foundDeposits);
 
         }
@@ -146,29 +145,6 @@ private void collectIds(JsonNode zenodoMetadata, List<String> recordIds, List<St
         }
     }
 
-    private void deleteDraftsIfPresent(Collection<Pair<Long, String>> foundDeposits, List<String> recordIds) throws IOException {
-        List<Long> draftIds = foundDeposits
-                .stream()
-                .filter(x -> StringUtils.equals(x.getValue(), "unsubmitted"))
-                .map(Pair::getKey)
-                .distinct()
-                .collect(Collectors.toList());
-
-        ZenodoContext ctxLocal = new ZenodoContext(this.ctx);
-        for (Long draftId : draftIds) {
-            ctxLocal.setDepositId(draftId);
-            try {
-                String msg = "deleting draft deposit [" + ctxLocal.getDepositId() + "] associated with [{" + StringUtils.join(recordIds, "\"}, {\"") + "}]";
-                LOG.info(msg + " ...");
-                ZenodoUtils.delete(ctxLocal);
-                LOG.info(msg + " done.");
-            } catch (IOException ex) {
-                throw new IOException("failed to delete draft/unsubmitted deposit id [" + draftId + "]");
-            }
-
-        }
-    }
-
     private void createNewVersion(IRI coordinate, JsonNode zenodoMetadata, List<String> recordIds, List<String> contentIds, List<String> origins, Collection<Pair<Long, String>> foundDeposits) throws IOException {
         List<Long> existingIds = foundDeposits
                 .stream()

diff --git a/preston-zenodo/src/test/java/bio/guoda/preston/zenodo/ZenodoUtilsTaxoDrosIT.java b/preston-zenodo/src/test/java/bio/guoda/preston/zenodo/ZenodoUtilsTaxoDrosIT.java
@@ -74,7 +74,7 @@ public void delete() throws IOException {
     }
 
     private void cleanupPreExisting() throws IOException {
-        Collection<Pair<Long, String>> byAlternateIds = ZenodoUtils.findByAlternateIds(ctx, Arrays.asList(getContentId(), getLsid()), "", uri -> ResourcesHTTP.asInputStream(uri));
+        Collection<Pair<Long, String>> byAlternateIds = ZenodoUtils.findRecordsByAlternateIds(ctx, Arrays.asList(getContentId(), getLsid()), "", uri -> ResourcesHTTP.asInputStream(uri));
         byAlternateIds
                 .stream()
                 .filter(d -> StringUtils.equals(d.getValue(), "unsubmitted"))
@@ -116,7 +116,7 @@ public void findDepositByBothContentIdAndTaxoDrosId() throws IOException {
 
     private void assertOneRecordWithMatchingId(List<String> contentId) throws IOException {
 
-        Collection<Pair<Long, String>> ids = ZenodoUtils.findByAlternateIds(ctx, contentId, "", uri -> ResourcesHTTP.asInputStream(uri));
+        Collection<Pair<Long, String>> ids = ZenodoUtils.findRecordsByAlternateIds(ctx, contentId, "", uri -> ResourcesHTTP.asInputStream(uri));
         assertThat(ids, not(nullValue()));
         List<Long> filteredIds = ids
                 .stream()
@@ -253,7 +253,7 @@ public void findDepositByBothContentIdAndTaxoDrosIdPickMostRecentVersion() throw
         List<String> contentIds = Arrays.asList(
                 "hash://md5/8ec637e349f8bbce57cd0054d20d9d8f",
                 "urn:lsid:taxodros.uzh.ch:id:aboul-nasr,%201954b");
-        Collection<Pair<Long, String>> ids = ZenodoUtils.findByAlternateIds(ctx, contentIds, "", uri -> ResourcesHTTP.asInputStream(uri));
+        Collection<Pair<Long, String>> ids = ZenodoUtils.findRecordsByAlternateIds(ctx, contentIds, "", uri -> ResourcesHTTP.asInputStream(uri));
         assertThat(ids, not(nullValue()));
         List<Long> filteredIds = ids
                 .stream()

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
@@ -17,39 +17,6 @@
 
 public class ZenodoUtilsTest {
 
-    @Test
-    public void queryForSpecificDeposition() {
-        ZenodoContext ctx = new ZenodoContext("secret");
-        IRI queryForExistingDepositions = ZenodoUtils.getQueryForExistingDepositions(ctx, Arrays.asList("urn:lsid:biodiversitylibrary.org:part:79807"), "");
-
-        assertThat(
-                queryForExistingDepositions.getIRIString(),
-                is("https://sandbox.zenodo.org/api/deposit/depositions?q=alternate.identifier:%22urn%3Alsid%3Abiodiversitylibrary.org%3Apart%3A79807%22")
-        );
-    }
-
-    @Test
-    public void htmlSearchResultPageForSpecificDeposition() {
-        ZenodoContext ctx = new ZenodoContext("secret");
-        IRI queryForExistingDepositions = ZenodoUtils.getSearchPageForExistingRecords(ctx, Arrays.asList("urn:lsid:biodiversitylibrary.org:part:79807"), "");
-
-        assertThat(
-                queryForExistingDepositions.getIRIString(),
-                is("https://sandbox.zenodo.org/search?q=alternate.identifier:%22urn%3Alsid%3Abiodiversitylibrary.org%3Apart%3A79807%22")
-        );
-    }
-
-    @Test
-    public void queryForExistingDepositions() {
-        ZenodoContext ctx = new ZenodoContext("secret");
-        IRI queryForExistingDepositions = ZenodoUtils.getQueryForExistingDepositions(ctx, Arrays.asList("foo:bar", "foo:bar"), "");
-
-        assertThat(
-                queryForExistingDepositions.getIRIString(),
-                is("https://sandbox.zenodo.org/api/deposit/depositions?q=alternate.identifier:%22foo%3Abar%22%20AND%20alternate.identifier:%22foo%3Abar%22")
-        );
-    }
-
 
     @Test
     public void queryForExistingRecords() {
@@ -116,21 +83,6 @@ public void queryForExistingRecordsPhysicalObject() {
         );
     }
 
-    @Test
-    public void queryForExistingDepositionsPhysicalObject() {
-        IRI queryForExistingRecords = ZenodoUtils.getQueryForExistingDepositions(
-                new ZenodoContext("secret", "https://sandbox.zenodo.org"),
-                Arrays.asList("urn:lsid:MfN:Ento:BMT0004596"),
-                "physicalobject"
-        );
-
-        assertThat(queryForExistingRecords.getIRIString(), Is.is(
-                "https://sandbox.zenodo.org/api/deposit/depositions" +
-                        "?q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0004596%22" +
-                        "&type=physicalobject")
-        );
-    }
-
     @Test
     public void searchPageForExistingRecordsPhysicalObject() {
         IRI queryForExistingRecords = ZenodoUtils.getSearchPageForExistingRecords(

diff --git a/preston-zenodo/src/test/java/bio/guoda/preston/zenodo/ZenodoUtilsZoteroIT.java b/preston-zenodo/src/test/java/bio/guoda/preston/zenodo/ZenodoUtilsZoteroIT.java
@@ -74,7 +74,7 @@ public void delete() throws IOException {
     }
 
     private void cleanupPreExisting() throws IOException {
-        Collection<Pair<Long, String>> byAlternateIds = ZenodoUtils.findByAlternateIds(ctx, Arrays.asList(getContentId(), getLsid()), "", uri -> ResourcesHTTP.asInputStream(uri));
+        Collection<Pair<Long, String>> byAlternateIds = ZenodoUtils.findRecordsByAlternateIds(ctx, Arrays.asList(getContentId(), getLsid()), "", uri -> ResourcesHTTP.asInputStream(uri));
         byAlternateIds
                 .stream()
                 .filter(d -> StringUtils.equals(d.getValue(), "unsubmitted"))
@@ -117,7 +117,7 @@ public void findDepositByBothContentIdAndTaxoDrosId() throws IOException {
 
 
     private void assertOneRecordWithMatchingId(List<String> contentId) throws IOException {
-        Collection<Pair<Long, String>> ids = ZenodoUtils.findByAlternateIds(ctx, contentId, "", uri -> ResourcesHTTP.asInputStream(uri));
+        Collection<Pair<Long, String>> ids = ZenodoUtils.findRecordsByAlternateIds(ctx, contentId, "", uri -> ResourcesHTTP.asInputStream(uri));
         assertThat(ids, not(nullValue()));
         List<Long> filteredIds = ids
                 .stream()