add navigation links to physicalobject, event and photo deposits as s…

…uggested by @asrivathsan
bio-guoda · Sep 9, 2024 · 75cd696 · 75cd696
1 parent cc33b09
commit 75cd696
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Showing 8 changed files with 156 additions and 122 deletions.
diff --git a/preston-cmd/src/main/java/bio/guoda/preston/cmd/ZenodoMetaUtil.java b/preston-cmd/src/main/java/bio/guoda/preston/cmd/ZenodoMetaUtil.java
@@ -54,6 +54,7 @@ public class ZenodoMetaUtil {
     public static final String UPLOAD_TYPE_EVENT = "event";
     public static final String UPLOAD_TYPE_PHYSICAL_OBJECT = "physicalobject";
     public static final String IMAGE_TYPE_PHOTO = "photo";
+    public static final String RESOURCE_TYPE_PHOTO = "image+inner:image-photo";
     public static final String HAS_VERSION = "hasVersion";
     public static final String IS_COMPILED_BY = "isCompiledBy";
     public static final String RESOURCE_TYPE_SOFTWARE = "software";
@@ -73,6 +74,7 @@ public class ZenodoMetaUtil {
     public static final String FIELD_CUSTOM_GBIF_DWC_RECORDED_BY_ID = "gbif-dwc:recordedByID";
     public static final String FIELD_CUSTOM_DWC_BASIS_OF_RECORD = "dwc:basisOfRecord";
     public static final String FIELD_CUSTOM_DWC_SCIENTIFIC_NAME = "dwc:scientificName";
+    public static final String DOCUMENTS = "documents";
     static final String KEYWORDS = "keywords";
     static final String CUSTOM = "custom";
     public static final Pattern YEAR_PATTERN = Pattern.compile(".*(?<year>[12][0-9]{3}).*");

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
@@ -243,14 +243,15 @@ public static IRI getQueryForExistingDepositions(ZenodoConfig ctx, List<String>
     }
 
     public static IRI getQueryForExistingDepositions(ZenodoConfig ctx, List<String> contentIds, String method, String type) {
-        String query = "q=" + getQueryForIds(contentIds);
+        String prefix = communitiesPrefix(ctx);
+        String query = prefix + "q=" + getQueryForIds(contentIds);
         query = appendTypeClause(type, query);
         return getQuery(ctx.getEndpoint(), query, method);
     }
 
     private static String appendTypeClause(String type, String query) {
         if (StringUtils.isNotBlank(type)) {
-            query = query + "&f=resource_type%3A" + type;
+            query = query + "&f=resource_type%3A" + JavaScriptAndPythonFriendlyURLEncodingUtil.urlEncode(type);
         }
         return query;
     }
@@ -265,13 +266,17 @@ private static void findExistingRecords(ZenodoConfig ctx, List<String> ids, Coll
     }
 
     public static IRI getQueryForExistingRecords(ZenodoConfig ctx, List<String> ids, String type) {
-        String prefix = ctx.getCommunities().size() == 0
-                ? ""
-                : "communities=" + JavaScriptAndPythonFriendlyURLEncodingUtil.urlEncode(StringUtils.join(ctx.getCommunities(), ",")) + "&";
+        String prefix = communitiesPrefix(ctx);
         String queryPath = prefix + "all_versions=false&q=" + getQueryForIds(ids);
         return getQuery(ctx.getEndpoint(), appendTypeClause(type, queryPath), "/api/records");
     }
 
+    private static String communitiesPrefix(ZenodoConfig ctx) {
+        return ctx.getCommunities().size() == 0
+                    ? ""
+                    : "communities=" + JavaScriptAndPythonFriendlyURLEncodingUtil.urlEncode(StringUtils.join(ctx.getCommunities(), ",")) + "&";
+    }
+
     private static String getQueryForIds(List<String> ids) {
         return ids.stream()
                 .map(JavaScriptAndPythonFriendlyURLEncodingUtil::urlEncode)

diff --git a/preston-taxodros/src/main/java/bio/guoda/preston/cmd/DarkTaxonUtil.java b/preston-taxodros/src/main/java/bio/guoda/preston/cmd/DarkTaxonUtil.java
diff --git a/preston-taxodros/src/test/resources/bio/guoda/preston/cmd/darktaxon/event-zenodo.json b/preston-taxodros/src/test/resources/bio/guoda/preston/cmd/darktaxon/event-zenodo.json
@@ -8,25 +8,23 @@
       "dwc:verbatimEventDate" : [ "2024-05-04/2024-05-08" ],
       "dwc:locality" : [ "Berlin, Swiss Embassy" ],
       "dwc:recordedBy" : [ "Donat Agosti" ],
-      "dwc:recordedByID" : [ "https://orcid.org/0000-0001-9286-1200" ],
-      "gbif-dwc:recordedByID" : [ "https://orcid.org/0000-0001-9286-1200" ]
+      "dwc:recordedByID" : [ "https://orcid.org/0000-0001-9286-1200" ]
     },
     "filename" : "event.json",
     "related_identifiers" : [ {
-      "relation" : "isAlternateIdentifier",
-      "identifier" : "urn:lsid:MfN:Ento:SchweiBo1"
-    }, {
-      "relation" : "isVersionOf",
-      "identifier" : "https://sandbox.zenodo.org/search?q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ASchweiBo1%22&f=resource_type%3Aevent"
-    }, {
-      "relation" : "isVersionOf",
-      "identifier" : "https://sandbox.zenodo.org/api/records?communities=mfn-test&all_versions=false&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ASchweiBo1%22&f=resource_type%3Aevent"
-    }, {
       "relation" : "isAlternateIdentifier",
       "identifier" : "hash://md5/672a403a43a9f8575ad5feeffc21bdc2"
     }, {
       "relation" : "hasVersion",
       "identifier" : "hash://md5/672a403a43a9f8575ad5feeffc21bdc2"
+    }, {
+      "relation" : "isAlternateIdentifier",
+      "identifier" : "urn:lsid:MfN:Ento:SchweiBo1",
+      "resource_type" : "event"
+    }, {
+      "relation" : "isVersionOf",
+      "identifier" : "https://sandbox.zenodo.org/search?communities=mfn-test&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ASchweiBo1%22&f=resource_type%3Aevent",
+      "resource_type" : "event"
     } ],
     "upload_type" : "event",
     "creators" : [ {

diff --git a/preston-taxodros/src/test/resources/bio/guoda/preston/cmd/darktaxon/multimedia-zenodo.json b/preston-taxodros/src/test/resources/bio/guoda/preston/cmd/darktaxon/multimedia-zenodo.json
@@ -5,6 +5,7 @@
       "dwc:catalogNumber" : [ "BMT0009388" ],
       "dwc:materialSampleID" : [ "urn:lsid:MfN:Ento:BMT0009388" ],
       "ac:associatedSpecimenReference" : [ "urn:lsid:MfN:Ento:BMT0009388" ],
+      "dwc:institutionCode" : [ "MfN" ],
       "ac:subjectPart" : [ "whole specimen" ],
       "ac:captureDevice" : [ "CAMERA MAKE AND MODEL" ],
       "ac:resourceCreationTechnique" : [ "Focal Stacking" ]
@@ -20,25 +21,20 @@
       "identifier" : "hash://md5/f052cbac398bf340a620c421bfefa16d"
     }, {
       "relation" : "isAlternateIdentifier",
-      "identifier" : "urn:lsid:MfN:Ento:BMT0009388:BMT121_BMT0009388_stacked_01.tiff"
+      "identifier" : "urn:lsid:MfN:Ento:BMT0009388:BMT121_BMT0009388_stacked_01.tiff",
+      "resource_type" : "image+inner:image-photo"
     }, {
-      "relation" : "isDerivedFrom",
-      "identifier" : "urn:lsid:MfN:Ento:BMT0009388"
+      "relation" : "documents",
+      "identifier" : "urn:lsid:MfN:Ento:BMT0009388",
+      "resource_type" : "physicalobject"
     }, {
       "relation" : "isVersionOf",
-      "identifier" : "https://sandbox.zenodo.org/search?q=alternate.identifier:%22hash%3A%2F%2Fmd5%2Ff052cbac398bf340a620c421bfefa16d%22&f=resource_type%3Aimage%2Binner%3Aimage-photo"
+      "identifier" : "https://sandbox.zenodo.org/search?communities=mfn-test&q=alternate.identifier:%22hash%3A%2F%2Fmd5%2Ff052cbac398bf340a620c421bfefa16d%22&f=resource_type%3Aimage%2Binner%3Aimage-photo",
+      "resource_type" : "image+inner:image-photo"
     }, {
-      "relation" : "isVersionOf",
-      "identifier" : "https://sandbox.zenodo.org/api/records?communities=mfn-test&all_versions=false&q=alternate.identifier:%22hash%3A%2F%2Fmd5%2Ff052cbac398bf340a620c421bfefa16d%22&f=resource_type%3Aimage%2Binner%3Aimage-photo"
-    }, {
-      "relation" : "isDerivedFrom",
-      "identifier" : "https://sandbox.zenodo.org/search?q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0009388%22&f=resource_type%3Aphysicalobject"
-    }, {
-      "relation" : "isDerivedFrom",
-      "identifier" : "https://sandbox.zenodo.org/api/records?communities=mfn-test&all_versions=false&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0009388%22&f=resource_type%3Aphysicalobject"
-    }, {
-      "relation" : "isDocumentedBy",
-      "identifier" : "https://zenodo.org/search?q=_files.checksum%3A%22md5%3Af052cbac398bf340a620c421bfefa16d%22&f=allversions%3Atrue"
+      "relation" : "documents",
+      "identifier" : "https://sandbox.zenodo.org/search?communities=mfn-test&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0009388%22&f=resource_type%3Aphysicalobject",
+      "resource_type" : "physicalobject"
     } ],
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : "image/tiff",
     "upload_type" : "image",

diff --git a/.../src/test/resources/bio/guoda/preston/cmd/darktaxon/occurrence-with-key-image-zenodo.json b/.../src/test/resources/bio/guoda/preston/cmd/darktaxon/occurrence-with-key-image-zenodo.json
@@ -1,7 +1,5 @@
 {
   "metadata" : {
-    "title" : "Physical object urn:lsid:MfN:Ento:BMT0009388 sampled through event urn:lsid:MfN:Ento:SchweiBo1 on 2019-07-04",
-    "description" : "Physical object urn:lsid:MfN:Ento:BMT0009388 sampled through event urn:lsid:MfN:Ento:SchweiBo1 on 2019-07-04",
     "custom" : {
       "dwc:institutionCode" : [ "MfN" ],
       "dwc:eventDate" : [ "2019-07-04" ],
@@ -15,29 +13,33 @@
     "filename" : "BMT121_BMT0009388_stacked_01.tiff",
     "related_identifiers" : [ {
       "relation" : "isAlternateIdentifier",
-      "identifier" : "urn:lsid:MfN:Ento:BMT0009388"
+      "identifier" : "hash://md5/f052cbac398bf340a620c421bfefa16d"
     }, {
-      "relation" : "isVersionOf",
-      "identifier" : "https://sandbox.zenodo.org/search?q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0009388%22&f=resource_type%3Aphysicalobject"
+      "relation" : "hasVersion",
+      "identifier" : "hash://md5/f052cbac398bf340a620c421bfefa16d"
     }, {
-      "relation" : "isVersionOf",
-      "identifier" : "https://sandbox.zenodo.org/api/records?communities=mfn-test&all_versions=false&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0009388%22&f=resource_type%3Aphysicalobject"
+      "relation" : "isAlternateIdentifier",
+      "identifier" : "urn:lsid:MfN:Ento:BMT0009388",
+      "resource_type" : "physicalobject"
     }, {
-      "relation" : "isDerivedFrom",
-      "identifier" : "urn:lsid:MfN:Ento:SchweiBo1"
+      "relation" : "isVersionOf",
+      "identifier" : "https://sandbox.zenodo.org/search?communities=mfn-test&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0009388%22&f=resource_type%3Aphysicalobject",
+      "resource_type" : "physicalobject"
     }, {
       "relation" : "isDerivedFrom",
-      "identifier" : "https://sandbox.zenodo.org/search?q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ASchweiBo1%22&f=resource_type%3Aevent"
+      "identifier" : "urn:lsid:MfN:Ento:SchweiBo1",
+      "resource_type" : "event"
     }, {
       "relation" : "isDerivedFrom",
-      "identifier" : "https://sandbox.zenodo.org/api/records?communities=mfn-test&all_versions=false&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ASchweiBo1%22&f=resource_type%3Aevent"
-    }, {
-      "relation" : "isAlternateIdentifier",
-      "identifier" : "hash://md5/f052cbac398bf340a620c421bfefa16d"
+      "identifier" : "https://sandbox.zenodo.org/search?communities=mfn-test&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ASchweiBo1%22&f=resource_type%3Aevent",
+      "resource_type" : "event"
     }, {
-      "relation" : "hasVersion",
-      "identifier" : "hash://md5/f052cbac398bf340a620c421bfefa16d"
+      "relation" : "isDocumentedBy",
+      "identifier" : "https://sandbox.zenodo.org/search?communities=mfn-test&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0009388%22&f=resource_type%3Aimage%2Binner%3Aimage-photo",
+      "resource_type" : "image+inner:image-photo"
     } ],
+    "title" : "Physical object urn:lsid:MfN:Ento:BMT0009388 sampled through event urn:lsid:MfN:Ento:SchweiBo1 on 2019-07-04",
+    "description" : "Physical object urn:lsid:MfN:Ento:BMT0009388 sampled through event urn:lsid:MfN:Ento:SchweiBo1 on 2019-07-04",
     "upload_type" : "physicalobject",
     "creators" : [ {
       "name" : "Museum für Naturkunde Berlin"

diff --git a/preston-taxodros/src/test/resources/bio/guoda/preston/cmd/darktaxon/occurrence-zenodo.json b/preston-taxodros/src/test/resources/bio/guoda/preston/cmd/darktaxon/occurrence-zenodo.json
@@ -1,7 +1,5 @@
 {
   "metadata" : {
-    "title" : "Physical object urn:lsid:MfN:Ento:BMT0009388 sampled through event urn:lsid:MfN:Ento:SchweiBo1 on 2019-07-04",
-    "description" : "Physical object urn:lsid:MfN:Ento:BMT0009388 sampled through event urn:lsid:MfN:Ento:SchweiBo1 on 2019-07-04",
     "custom" : {
       "dwc:institutionCode" : [ "MfN" ],
       "dwc:eventDate" : [ "2019-07-04" ],
@@ -12,32 +10,36 @@
       "dwc:scientificName" : [ "incertae sedis" ],
       "dwc:materialSampleID" : [ "urn:lsid:MfN:Ento:BMT0009388" ]
     },
-    "filename" : "event.json",
+    "filename" : "occurrence.json",
     "related_identifiers" : [ {
       "relation" : "isAlternateIdentifier",
-      "identifier" : "urn:lsid:MfN:Ento:BMT0009388"
+      "identifier" : "hash://md5/70fa5b4dbb0e09282c907a859b019547"
     }, {
-      "relation" : "isVersionOf",
-      "identifier" : "https://sandbox.zenodo.org/search?q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0009388%22&f=resource_type%3Aphysicalobject"
+      "relation" : "hasVersion",
+      "identifier" : "hash://md5/70fa5b4dbb0e09282c907a859b019547"
     }, {
-      "relation" : "isVersionOf",
-      "identifier" : "https://sandbox.zenodo.org/api/records?communities=mfn-test&all_versions=false&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0009388%22&f=resource_type%3Aphysicalobject"
+      "relation" : "isAlternateIdentifier",
+      "identifier" : "urn:lsid:MfN:Ento:BMT0009388",
+      "resource_type" : "physicalobject"
     }, {
-      "relation" : "isDerivedFrom",
-      "identifier" : "urn:lsid:MfN:Ento:SchweiBo1"
+      "relation" : "isVersionOf",
+      "identifier" : "https://sandbox.zenodo.org/search?communities=mfn-test&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0009388%22&f=resource_type%3Aphysicalobject",
+      "resource_type" : "physicalobject"
     }, {
       "relation" : "isDerivedFrom",
-      "identifier" : "https://sandbox.zenodo.org/search?q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ASchweiBo1%22&f=resource_type%3Aevent"
+      "identifier" : "urn:lsid:MfN:Ento:SchweiBo1",
+      "resource_type" : "event"
     }, {
       "relation" : "isDerivedFrom",
-      "identifier" : "https://sandbox.zenodo.org/api/records?communities=mfn-test&all_versions=false&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ASchweiBo1%22&f=resource_type%3Aevent"
-    }, {
-      "relation" : "isAlternateIdentifier",
-      "identifier" : "hash://md5/70fa5b4dbb0e09282c907a859b019547"
+      "identifier" : "https://sandbox.zenodo.org/search?communities=mfn-test&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ASchweiBo1%22&f=resource_type%3Aevent",
+      "resource_type" : "event"
     }, {
-      "relation" : "hasVersion",
-      "identifier" : "hash://md5/70fa5b4dbb0e09282c907a859b019547"
+      "relation" : "isDocumentedBy",
+      "identifier" : "https://sandbox.zenodo.org/search?communities=mfn-test&q=alternate.identifier:%22urn%3Alsid%3AMfN%3AEnto%3ABMT0009388%22&f=resource_type%3Aimage%2Binner%3Aimage-photo",
+      "resource_type" : "image+inner:image-photo"
     } ],
+    "title" : "Physical object urn:lsid:MfN:Ento:BMT0009388 sampled through event urn:lsid:MfN:Ento:SchweiBo1 on 2019-07-04",
+    "description" : "Physical object urn:lsid:MfN:Ento:BMT0009388 sampled through event urn:lsid:MfN:Ento:SchweiBo1 on 2019-07-04",
     "upload_type" : "physicalobject",
     "creators" : [ {
       "name" : "Museum für Naturkunde Berlin"

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
@@ -11,7 +11,6 @@
 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;