parse "metadata" for publications

src/main/java/es/bsc/inb/elixir/biotools/git/populous/BiotoolsConverter.java

@@ -58,12 +58,17 @@ import es.bsc.inb.elixir.openebench.model.Tool;
 import es.bsc.inb.elixir.openebench.model.ToolLinkType;
 import es.bsc.inb.elixir.openebench.model.ToolType;
 import es.bsc.inb.elixir.openebench.model.Topic;
+import java.time.ZonedDateTime;
+import java.time.format.DateTimeParseException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import javax.json.JsonArray;
+import javax.json.JsonNumber;
 import javax.json.JsonObject;
+import javax.json.JsonValue;
+import javax.json.JsonValue.ValueType;
 
 /**
  * @author Dmitry Repchevsky
@@ -383,10 +388,55 @@ public class BiotoolsConverter {
                 publication.setVersion(jpublication.getString("version", null));
 
                 final String type = jpublication.getString("type", null);
-                try {
-                    publication.setType(PublicationType.fromValue(type));
-                } catch(IllegalArgumentException ex) {
-                    Logger.getLogger(BiotoolsConverter.class.getName()).log(Level.INFO, "unrecognized publication type: {0}", type);
+                if (type != null) {
+                    try {
+                        publication.setType(PublicationType.fromValue(type));
+                    } catch(IllegalArgumentException ex) {
+                        Logger.getLogger(BiotoolsConverter.class.getName()).log(Level.INFO, "unrecognized publication type: {0}", type);
+                    }
+                }
+                
+                final JsonValue jmetadata_value = jpublication.get("metadata");
+                if (jmetadata_value != null && jmetadata_value.getValueType() == ValueType.OBJECT) {
+                    final JsonObject jmetadata = jmetadata_value.asJsonObject();
+
+                    final String title = jmetadata.getString("title", null);
+                    final String abridge = jmetadata.getString("abstract", null);
+                    final String journal = jmetadata.getString("journal", null);
+                    
+                    publication.setTitle(title);
+                    publication.setAbstract(abridge);
+                    publication.setJournal(journal);
+                    
+                    final String date = jmetadata.getString("date", null);
+                    if (date != null) {
+                        try {
+                            final ZonedDateTime date_time = ZonedDateTime.parse(date);
+                            publication.setYear(date_time.toLocalDate().toString());
+                        } catch (DateTimeParseException ex) {
+                            Logger.getLogger(BiotoolsConverter.class.getName()).log(Level.INFO, "invalid date format: {0}", date);
+                        }
+                    }
+                    
+                    final JsonNumber cit_count = jmetadata.getJsonNumber("citationCount");
+                    if (cit_count != null) {
+                        publication.setCitationsCount(cit_count.intValue());
+                    }
+                    
+                    final JsonArray jauthors = jmetadata.getJsonArray("authors");
+                    if (jauthors != null && jauthors.size() > 0) {
+                        final List<String> authors = new ArrayList(jauthors.size());
+                        publication.setAuthors(authors);
+                        for (int j = 0, m = jauthors.size(); j < m; j++) {
+                            final JsonObject jauthor = jauthors.getJsonObject(j);
+                            if (jauthor != null) {
+                                final String author = jauthor.getString("name", null);
+                                if (author != null) {
+                                    authors.add(author);
+                                }
+                            }
+                        }
+                    }
                 }
             }
         }