do not allow zenodo pubs without publication date by default; provide…

… an override; associated with #303

preston-zenodo/src/main/java/bio/guoda/preston/zenodo/CmdZenodo.java

@@ -47,7 +47,7 @@ public class CmdZenodo extends LoggingPersisting implements Runnable {
     private List<String> communities = Collections.emptyList();
 
     @CommandLine.Option(
-            names = {"--restricted-only"},
+            names = {"--restricted-access-only"},
             description = "always set [access_right] to [restricted]"
     )
     private boolean publishRestrictedOnly = false;
@@ -58,6 +58,12 @@ public class CmdZenodo extends LoggingPersisting implements Runnable {
     )
     private boolean updateMetadataOnly;
 
+    @CommandLine.Option(
+            names = {"--allow-empty-publication-date"},
+            description = "Zenodo accepts deposits with empty publication dates. On accepting a deposit without publication date, Zenodo sets the publication date to current date/time by default."
+    )
+    private boolean allowEmptyPublicationDate;
+
 
     @Override
     public void run() {
@@ -82,6 +88,7 @@ public void run(BlobStoreReadOnly blobStoreReadOnly) {
         zenodoContext.setCreateNewVersionForExisting(createNewVersionForExisting);
         zenodoContext.setPublishRestrictedOnly(publishRestrictedOnly);
         zenodoContext.setUpdateMetadataOnly(updateMetadataOnly);
+        zenodoContext.setAllowEmptyPublicationDate(allowEmptyPublicationDate);
         StatementsListener textMatcher = new ZenodoMetadataFileExtractor(
                 this,
                 blobStoreReadOnly,

preston-zenodo/src/main/java/bio/guoda/preston/zenodo/ZenodoConfig.java

@@ -22,4 +22,8 @@ public interface ZenodoConfig {
     void setUpdateMetadataOnly(boolean updateMetadataOnly);
 
     boolean shouldUpdateMetadataOnly();
+
+    void setAllowEmptyPublicationDate(boolean allowEmptyPublicationDate);
+
+    boolean shouldAllowEmptyPublicationDate();
 }

preston-zenodo/src/main/java/bio/guoda/preston/zenodo/ZenodoContext.java

@@ -18,8 +18,9 @@ public class ZenodoContext implements ZenodoConfig {
 
 
     private boolean createNewVersionForExisting = false;
-    private boolean restrictedOnly;
-    private boolean updateMetadataOnly;
+    private boolean restrictedOnly = false;
+    private boolean updateMetadataOnly = false;
+    private boolean allowEmptyPublicationDate = false;
 
     public ZenodoContext(String accessToken) {
         this(accessToken, "https://sandbox.zenodo.org");
@@ -111,4 +112,14 @@ public void setUpdateMetadataOnly(boolean updateMetadataOnly) {
     public boolean shouldUpdateMetadataOnly() {
         return updateMetadataOnly;
     }
+
+    @Override
+    public void setAllowEmptyPublicationDate(boolean allowEmptyPublicationDate) {
+        this.allowEmptyPublicationDate = allowEmptyPublicationDate;
+    }
+
+    @Override
+    public boolean shouldAllowEmptyPublicationDate() {
+        return allowEmptyPublicationDate;
+    }
 }

preston-zenodo/src/main/java/bio/guoda/preston/zenodo/ZenodoMetadataFileStreamHandler.java

@@ -155,6 +155,10 @@ private void createNewVersion(IRI coordinate, JsonNode zenodoMetadata, List<Stri
 
         ZenodoContext ctxLocal = new ZenodoContext(this.ctx);
 
+        if (hasAllowedPublicationDate(zenodoMetadata, ctx)) {
+            throw new IOException("missing publication date for [" + zenodoMetadata.toPrettyString() + "]");
+        }
+
         if (ctx.shouldPublishRestrictedOnly()) {
             JsonNode at = zenodoMetadata.at("/metadata");
             if (at.isObject()) {
@@ -193,6 +197,11 @@ private void createNewVersion(IRI coordinate, JsonNode zenodoMetadata, List<Stri
         }
     }
 
+    public static boolean hasAllowedPublicationDate(JsonNode zenodoMetadata, ZenodoConfig ctx) {
+        return !zenodoMetadata.at("/metadata/publication_date").isMissingNode()
+                || ctx.shouldAllowEmptyPublicationDate();
+    }
+
     private void emitRefreshed(ZenodoContext ctxLocal) {
         emitter.emit(
                 RefNodeFactory.toStatement(

preston-zenodo/src/test/java/bio/guoda/preston/zenodo/ZenodoMetadataFileStreamHandlerTest.java

@@ -0,0 +1,56 @@
+package bio.guoda.preston.zenodo;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.junit.Test;
+
+import java.io.IOException;
+
+import static org.junit.Assert.*;
+
+public class ZenodoMetadataFileStreamHandlerTest {
+
+    @Test
+    public void allowedDefinedPubDate() throws IOException {
+        JsonNode jsonNode = new ObjectMapper().readTree(getClass().getResourceAsStream("batlit-data/example-batlit.json"));
+
+        ZenodoContext contextDefault = new ZenodoContext("bla");
+        assertTrue(ZenodoMetadataFileStreamHandler.hasAllowedPublicationDate(jsonNode, contextDefault));
+    }
+
+    @Test
+    public void allowedEmptyPubDate() throws IOException {
+        JsonNode jsonNode = new ObjectMapper().readTree(getClass().getResourceAsStream("batlit-data/example-batlit-no-pubdate.json"));
+
+        ZenodoContext contextDefault = new ZenodoContext("bla");
+        contextDefault.setAllowEmptyPublicationDate(true);
+        assertTrue(ZenodoMetadataFileStreamHandler.hasAllowedPublicationDate(jsonNode, contextDefault));
+    }
+
+    @Test
+    public void nonEmptyPubDateAllowed() throws IOException {
+        JsonNode jsonNode = new ObjectMapper().readTree(getClass().getResourceAsStream("batlit-data/example-batlit.json"));
+
+        ZenodoContext contextDefault = new ZenodoContext("bla");
+        contextDefault.setAllowEmptyPublicationDate(false);
+        assertTrue(ZenodoMetadataFileStreamHandler.hasAllowedPublicationDate(jsonNode, contextDefault));
+    }
+
+    @Test
+    public void emptyPubDateNotAllowed() throws IOException {
+        JsonNode jsonNode = new ObjectMapper().readTree(getClass().getResourceAsStream("batlit-data/example-batlit-no-pubdate.json"));
+
+        ZenodoContext contextDefault = new ZenodoContext("bla");
+        assertFalse(ZenodoMetadataFileStreamHandler.hasAllowedPublicationDate(jsonNode, contextDefault));
+    }
+
+    @Test
+    public void emptyPubDateNotAllowed2() throws IOException {
+        JsonNode jsonNode = new ObjectMapper().readTree(getClass().getResourceAsStream("batlit-data/example-batlit-no-pubdate.json"));
+
+        ZenodoContext contextDefault = new ZenodoContext("bla");
+        contextDefault.setAllowEmptyPublicationDate(false);
+        assertFalse(ZenodoMetadataFileStreamHandler.hasAllowedPublicationDate(jsonNode, contextDefault));
+    }
+
+}

preston-zenodo/src/test/resources/bio/guoda/preston/zenodo/batlit-data/example-batlit-no-pubdate.json

@@ -0,0 +1 @@
+{"metadata":{"filename":"Thomas - 1912 - XXII.— A new Vespertilionine bat from Angolai.pdf","related_identifiers":[{"relation":"isAlternateIdentifier","identifier":"hash://md5/4c64e5b3477ea92404d0c915eaf06da3"},{"relation":"isAlternateIdentifier","identifier":"urn:lsid:zotero.org:groups:5435545:items:BF9WCVE5"},{"relation":"hasVersion","identifier":"hash://md5/4c64e5b3477ea92404d0c915eaf06da3"},{"relation":"hasVersion","identifier":"hash://sha256/691316c043fb8e6d686b034dd604cfd5e78e60205d4b2c0f404ce0cb81af9764"},{"relation":"isDerivedFrom","identifier":"zotero://select/groups/5435545/items/BF9WCVE5"},{"relation":"isDerivedFrom","identifier":"https://zotero.org/groups/5435545/items/BF9WCVE5"},{"relation":"isDerivedFrom","identifier":"https://linker.bio/cut:hash://md5/bd79ea31e23eae8897a9291bf4d7f24a!/b164740-167173"},{"relation":"isPartOf","identifier":"hash://md5/26f7ce5dd404e33c6570edd4ba250d20"},{"relation":"isAlternateIdentifier","identifier":"10.1080/00222931208693218"},{"relation":"isCompiledBy","identifier":"10.5281/zenodo.1410543","resource_type":"software"}],"communities":[{"identifier":"batlit"},{"identifier":"biosyslit"}],"http://www.w3.org/ns/prov#wasDerivedFrom":"https://linker.bio/cut:hash://md5/bd79ea31e23eae8897a9291bf4d7f24a!/b164740-167173","upload_type":"publication","http://www.w3.org/1999/02/22-rdf-syntax-ns#type":"application/json","referenceId":"https://api.zotero.org/groups/5435545/items/BF9WCVE5","creators":[{"name":"Thomas, Oldfield"}],"publication_type":"article","title":"A new Vespertilionine bat from Angola","journal_title":"Annals and Magazine of Natural History","journal_volume":"10","journal_issue":"56","journal_pages":"204-206","keywords":["Biodiversity","Mammalia","Chiroptera","Chordata","Animalia","bats","bat"],"custom":{"dwc:kingdom":["Animalia"],"dwc:phylum":["Chordata"],"dwc:class":["Mammalia"],"dwc:order":["Chiroptera"]},"description":"(Uploaded by Plazi for the Bat Literature Project) No abstract provided."}}