#8765 - make pids coming from apis as hypelinks in export

dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java

@@ -1192,7 +1192,7 @@ public class DataManagementPlanManager {
     }
 
     public FileEnvelope getWordDocument(String id, Principal principal, ConfigLoader configLoader, Boolean versioned) throws IOException {
-        WordBuilder wordBuilder = new WordBuilder(this.environment);
+        WordBuilder wordBuilder = new WordBuilder(this.environment, configLoader);
         VisibilityRuleService visibilityRuleService = new VisibilityRuleServiceImpl();
         DatasetWizardModel dataset = new DatasetWizardModel();
         XWPFDocument document = configLoader.getDocument();

dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetManager.java

@@ -397,7 +397,7 @@ public class DatasetManager {
     }
 
     private XWPFDocument getWordDocument(ConfigLoader configLoader, eu.eudat.data.entities.Dataset datasetEntity, VisibilityRuleService visibilityRuleService, Principal principal) throws IOException {
-        WordBuilder wordBuilder = new WordBuilder(this.environment);
+        WordBuilder wordBuilder = new WordBuilder(this.environment, configLoader);
         DatasetWizardModel dataset = new DatasetWizardModel();
         XWPFDocument document = configLoader.getDatasetDocument();
 
@@ -509,7 +509,7 @@ public class DatasetManager {
     }
 
     private XWPFDocument getLightWordDocument(ConfigLoader configLoader, DatasetWizardModel dataset, VisibilityRuleService visibilityRuleService) throws IOException {
-        WordBuilder wordBuilder = new WordBuilder(this.environment);
+        WordBuilder wordBuilder = new WordBuilder(this.environment, configLoader);
         XWPFDocument document = configLoader.getDocument();
 
         // Space below Dataset title.

dmp-backend/web/src/main/java/eu/eudat/logic/proxy/config/configloaders/ConfigLoader.java

@@ -3,6 +3,7 @@ package eu.eudat.logic.proxy.config.configloaders;
 import eu.eudat.logic.proxy.config.ExternalUrls;
 import eu.eudat.logic.proxy.config.Semantic;
 import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.ConfigurableProviders;
+import eu.eudat.models.data.pid.PidLinks;
 import org.apache.poi.xwpf.usermodel.XWPFDocument;
 
 import java.util.List;
@@ -14,5 +15,6 @@ public interface ConfigLoader {
     XWPFDocument getDocument();
     XWPFDocument getDatasetDocument();
     ConfigurableProviders getConfigurableProviders();
+    PidLinks getPidLinks();
     Map<String, String> getKeyToSourceMap();
 }

dmp-backend/web/src/main/java/eu/eudat/logic/proxy/config/configloaders/DefaultConfigLoader.java

@@ -6,6 +6,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.logic.proxy.config.ExternalUrls;
 import eu.eudat.logic.proxy.config.Semantic;
 import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.ConfigurableProviders;
+import eu.eudat.models.data.pid.PidLinks;
 import org.apache.poi.xwpf.usermodel.XWPFDocument;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -41,6 +42,7 @@ public class DefaultConfigLoader implements ConfigLoader {
     private XWPFDocument document;
     private XWPFDocument datasetDocument;
     private ConfigurableProviders configurableProviders;
+    private PidLinks pidLinks;
     private Map<String, String> keyToSourceMap;
 
     @Autowired
@@ -134,6 +136,25 @@ public class DefaultConfigLoader implements ConfigLoader {
         }
     }
 
+    private void setPidLinks() {
+        String filePath = environment.getProperty("configuration.pid_links");
+        logger.info("Loaded also config file: " + filePath);
+        InputStream is = null;
+        try {
+            is = getStreamFromPath(filePath);
+            ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+            this.pidLinks = mapper.readValue(is, PidLinks.class);
+        } catch (IOException | NullPointerException e) {
+            logger.error(e.getMessage(), e);
+        } finally {
+            try {
+                if (is != null) is.close();
+            } catch (IOException e) {
+                logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
+            }
+        }
+    }
+
     private void setKeyToSourceMap() {
         String filePath = this.environment.getProperty("configuration.externalUrls");
         logger.info("Loaded also config file: " + filePath);
@@ -192,6 +213,14 @@ public class DefaultConfigLoader implements ConfigLoader {
         return configurableProviders;
     }
 
+    public PidLinks getPidLinks() {
+        if (pidLinks == null) {
+            pidLinks = new PidLinks();
+            this.setPidLinks();
+        }
+        return pidLinks;
+    }
+
     public Map<String, String> getKeyToSourceMap() {
         if (keyToSourceMap == null) {
             keyToSourceMap = new HashMap<>();

dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/word/WordBuilder.java

@@ -7,11 +7,14 @@ import eu.eudat.data.entities.DMP;
 import eu.eudat.data.entities.Dataset;
 import eu.eudat.data.entities.Organisation;
 import eu.eudat.data.entities.Researcher;
+import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
 import eu.eudat.logic.services.forms.VisibilityRuleService;
 import eu.eudat.logic.utilities.documents.types.ParagraphStyle;
 import eu.eudat.logic.utilities.interfaces.ApplierWithValue;
 import eu.eudat.logic.utilities.json.JavaToJson;
 import eu.eudat.models.data.components.commons.datafield.*;
+import eu.eudat.models.data.pid.PidLink;
+import eu.eudat.models.data.pid.PidLinks;
 import eu.eudat.models.data.user.components.datasetprofile.Field;
 import eu.eudat.models.data.user.components.datasetprofile.FieldSet;
 import eu.eudat.models.data.user.components.datasetprofile.Section;
@@ -71,8 +74,9 @@ public class WordBuilder {
     private Integer indent;
     private final ObjectMapper mapper;
     private Integer imageCount;
+    private ConfigLoader configLoader;
 
-    public WordBuilder(Environment environment) {
+    public WordBuilder(Environment environment, ConfigLoader configLoader) {
         this.cTAbstractNum = CTAbstractNum.Factory.newInstance();
         this.cTAbstractNum.setAbstractNumId(BigInteger.valueOf(1));
         this.indent = 0;
@@ -80,6 +84,7 @@ public class WordBuilder {
         this.mapper = new ObjectMapper();
         this.buildOptions(environment);
         this.buildOptionsInTable(environment);
+        this.configLoader = configLoader;
     }
 
     private void buildOptionsInTable(Environment environment) {
@@ -568,6 +573,37 @@ public class WordBuilder {
         return hasValue;
     }
 
+    private void createHypeLink(XWPFDocument mainDocumentPart, String format, String pidType, String pid, boolean hasMultiplicityItems, boolean isMultiAutoComplete){
+        PidLink pidLink = this.configLoader.getPidLinks().getPidLinks().stream().filter(pl -> pl.getPid().equals(pidType)).findFirst().orElse(null);
+        if (pidLink != null) {
+            if (!hasMultiplicityItems) {
+                XWPFParagraph paragraph = mainDocumentPart.createParagraph();
+                paragraph.setIndentFromLeft(400 * indent);
+                if (numId != null) {
+                    paragraph.setNumID(numId);
+                }
+            }
+            if (isMultiAutoComplete) {
+                XWPFRun r = mainDocumentPart.getLastParagraph().createRun();
+                r.setText("• ");
+            }
+            XWPFHyperlinkRun run = mainDocumentPart.getLastParagraph().createHyperlinkRun(pidLink.getLink().replace("{pid}", pid));
+            run.setText(format);
+            run.setUnderline(UnderlinePatterns.SINGLE);
+            run.setColor("0000FF");
+            run.setFontSize(11);
+        }
+        else {
+            String newFormat = (isMultiAutoComplete) ? "• " + format : format;
+            if (hasMultiplicityItems) {
+                mainDocumentPart.getLastParagraph().createRun().setText(newFormat);
+            }
+            else {
+                addParagraphContent(newFormat, mainDocumentPart, ParagraphStyle.TEXT, numId, indent);
+            }
+        }
+    }
+
     private Boolean createFields(List<Field> fields, XWPFDocument mainDocumentPart, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService, boolean hasMultiplicityItems) {
         if (createListing) this.addListing(mainDocumentPart, indent, false, false);
         boolean hasValue = false;
@@ -607,6 +643,59 @@ public class WordBuilder {
                             } else if (field.getViewStyle().getRenderStyle().equals("combobox") && field.getData() instanceof AutoCompleteData) {
                                 format = getCommaSeparatedFormatsFromJson(format, "label");
                             }
+                            switch (field.getViewStyle().getRenderStyle()) {
+                                case "organizations":
+                                case "externalDatasets":
+                                case "publications":
+                                    if(format != null && !format.isEmpty()){
+                                        Object hasMultiAutoComplete = mapper.convertValue(field.getData(), Map.class).get("multiAutoComplete");
+                                        boolean isMultiAutoComplete = hasMultiAutoComplete != null && (boolean)hasMultiAutoComplete;
+                                        if(!isMultiAutoComplete){
+                                            Map<String, String> value = mapper.readValue((String)field.getValue(), Map.class);
+                                            if(hasMultiplicityItems){
+                                                createHypeLink(mainDocumentPart, format, value.get("pidTypeField"), value.get("pid"), true, false);
+                                                hasMultiplicityItems = false;
+                                            }
+                                            else{
+                                                createHypeLink(mainDocumentPart, format, value.get("pidTypeField"), value.get("pid"), false, false);
+                                            }
+                                        }
+                                        else{
+                                            mapper.configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
+                                            List<Map<String, Object>> values = new ArrayList<>();
+                                            try {
+                                                values = Arrays.asList(mapper.readValue(field.getValue().toString(), HashMap[].class));
+                                            }
+                                            catch (Exception e) {
+                                                Map <String, Object> map = new HashMap<>();
+                                                map.put("label", field.getValue());
+                                                values.add(map);
+                                            }
+                                            if (values.size() > 1) {
+                                                for (Map<String, Object> value : values) {
+                                                    if(hasMultiplicityItems){
+                                                        createHypeLink(mainDocumentPart, (String) value.get("name"), (String) value.get("pidTypeField"), (String) value.get("pid"), true, true);
+                                                        hasMultiplicityItems = false;
+                                                    }
+                                                    else{
+                                                        createHypeLink(mainDocumentPart, (String) value.get("name"), (String) value.get("pidTypeField"), (String) value.get("pid"), false, true);
+                                                    }
+                                                }
+                                            }
+                                            else if(values.size() == 1){
+                                                if(hasMultiplicityItems){
+                                                    createHypeLink(mainDocumentPart, format, (String) values.get(0).get("pidTypeField"), (String) values.get(0).get("pid"), true, false);
+                                                    hasMultiplicityItems = false;
+                                                }
+                                                else{
+                                                    createHypeLink(mainDocumentPart, format, (String) values.get(0).get("pidTypeField"), (String) values.get(0).get("pid"), false, false);
+                                                }
+                                            }
+                                        }
+                                        hasValue = true;
+                                    }
+                                    break;
+                                default:
                                     boolean isResearcher = field.getViewStyle().getRenderStyle().equals("researchers");
                                     if(format != null && !format.isEmpty()){
                                         Object hasMultiAutoComplete = mapper.convertValue(field.getData(), Map.class).get("multiAutoComplete");
@@ -659,12 +748,13 @@ public class WordBuilder {
                                             }
                                         }
                                     }
-                            if(hasMultiplicityItems && format != null){
+                                    if (format != null) {
+                                        if (hasMultiplicityItems) {
                                             mainDocumentPart.getLastParagraph().createRun().setText(format);
                                             hasMultiplicityItems = false;
                                             hasValue = true;
                                         }
-                            else{
+                                        else {
                                             XWPFParagraph paragraph = addParagraphContent(format, mainDocumentPart, field.getViewStyle().getRenderStyle().equals("richTextarea") ? ParagraphStyle.HTML : ParagraphStyle.TEXT, numId, indent);
                                             if (paragraph != null) {
 //                                                CTDecimalNumber number = paragraph.getCTP().getPPr().getNumPr().addNewIlvl();
@@ -673,6 +763,8 @@ public class WordBuilder {
                                             }
                                         }
                                     }
+                            }
+                        }
                     } catch (IOException e) {
                         logger.error(e.getMessage(), e);
                     }
@@ -881,7 +973,7 @@ public class WordBuilder {
                       //  logger.info("Reverting to custom parsing");
                         identifierData = customParse(field.getValue().toString());
                     }
-                    return "id: " + identifierData.get("identifier") + ", Validation Type: " + identifierData.get("type");
+                    return "id: " + identifierData.get("identifier") + ", Type: " + identifierData.get("type");
                 }
                 return "";
         }

dmp-backend/web/src/main/java/eu/eudat/models/data/pid/PidLink.java

@@ -0,0 +1,21 @@
+package eu.eudat.models.data.pid;
+
+public class PidLink {
+
+    private String pid;
+    private String link;
+
+    public String getPid() {
+        return pid;
+    }
+    public void setPid(String pid) {
+        this.pid = pid;
+    }
+
+    public String getLink() {
+        return link;
+    }
+    public void setLink(String link) {
+        this.link = link;
+    }
+}

dmp-backend/web/src/main/java/eu/eudat/models/data/pid/PidLinks.java

@@ -0,0 +1,16 @@
+package eu.eudat.models.data.pid;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class PidLinks {
+
+    private List<PidLink> pidLinks = new ArrayList<>();
+
+    public List<PidLink> getPidLinks() {
+        return pidLinks;
+    }
+    public void setPidLinks(List<PidLink> pidLinks) {
+        this.pidLinks = pidLinks;
+    }
+}

dmp-backend/web/src/main/resources/config/application-devel.properties

@@ -27,6 +27,7 @@ configuration.semantics=Semantics.json
 configuration.h2020template=documents/h2020.docx
 configuration.h2020datasettemplate=documents/h2020_dataset.docx
 configuration.configurable_login_providers=configurableLoginProviders.json
+configuration.pid_links=pidLinks.json
 
 ####################EMAIL FILE TEMPLATES OVERRIDES CONFIGURATIONS##########
 email.invite=classpath:templates/email/email.html

dmp-backend/web/src/main/resources/config/application-docker.properties

@@ -26,6 +26,7 @@ configuration.externalUrls=externalUrls/ExternalUrls.xml
 configuration.h2020template=documents/h2020.docx
 configuration.h2020datasettemplate=documents/h2020_dataset.docx
 configuration.configurable_login_providers=configurableLoginProviders.json
+configuration.pid_links=pidLinks.json
 
 ####################EMAIL FILE TEMPLATES OVERRIDES CONFIGURATIONS##########
 email.invite=classpath:templates/email/email.html

dmp-backend/web/src/main/resources/config/application-production.properties

@@ -21,6 +21,7 @@ configuration.h2020template=documents/h2020.docx
 configuration.h2020datasettemplate=documents/h2020_dataset.docx
 configuration.configurable_login_providers=ConfigurableLoginProviders.json
 configuration.doi_funder=DOI_Funder.json
+configuration.pid_links=pidLinks.json
 
 ####################SPRING MAIL CONFIGURATIONS#################
 spring.mail.default-encoding=UTF-8

dmp-backend/web/src/main/resources/config/application.properties

@@ -53,6 +53,7 @@ configuration.semantics=Semantics.json
 configuration.h2020template=documents/h2020.docx
 configuration.h2020datasettemplate=documents/h2020_dataset.docx
 configuration.configurable_login_providers=configurableLoginProviders.json
+configuration.pid_links=pidLinks.json
 
 ####################EMAIL FILE TEMPLATES OVERRIDES CONFIGURATIONS##########
 email.invite=file:templates/email/email.html

dmp-backend/web/src/main/resources/pidLinks.json

@@ -0,0 +1,100 @@
+{
+  "pidLinks": [
+    {
+      "pid": "doi",
+      "link": "https://doi.org/{pid}"
+    },
+    {
+      "pid": "uniprot",
+      "link": "https://uniprot.org/uniprotkb/{pid}"
+    },
+    {
+      "pid": "handle",
+      "link": "https://hdl.handle.net/{pid}"
+    },
+    {
+      "pid": "arxiv",
+      "link": "https://arxiv.org/abs/{pid}"
+    },
+    {
+      "pid": "ascl",
+      "link": "https://ascl.net/{pid}"
+    },
+    {
+      "pid": "orcid",
+      "link": "https://orcid.org/{pid}"
+    },
+    {
+      "pid": "pmid",
+      "link": "https://pubmed.ncbi.nlm.nih.gov/{pid}"
+    },
+    {
+      "pid": "ads",
+      "link": "https://ui.adsabs.harvard.edu/#abs/{pid}"
+    },
+    {
+      "pid": "pmcid",
+      "link": "https://ncbi.nlm.nih.gov/pmc/{pid}"
+    },
+    {
+      "pid": "gnd",
+      "link": "https://d-nb.info/gnd/{pid}"
+    },
+    {
+      "pid": "urn",
+      "link": "https://nbn-resolving.org/{pid}"
+    },
+    {
+      "pid": "sra",
+      "link": "https://ebi.ac.uk/ena/data/view/{pid}"
+    },
+    {
+      "pid": "bioproject",
+      "link": "https://ebi.ac.uk/ena/data/view/{pid}"
+    },
+    {
+      "pid": "biosample",
+      "link": "https://ebi.ac.uk/ena/data/view/{pid}"
+    },
+    {
+      "pid": "ensembl",
+      "link": "https://ensembl.org/id/{pid}"
+    },
+    {
+      "pid": "refseq",
+      "link": "https://ncbi.nlm.nih.gov/entrez/viewer.fcgi?val={pid}"
+    },
+    {
+      "pid": "genome",
+      "link": "https://ncbi.nlm.nih.gov/assembly/{pid}"
+    },
+    {
+      "pid": "geo",
+      "link": "https://ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={pid}"
+    },
+    {
+      "pid": "arrayexpress_array",
+      "link": "https://ebi.ac.uk/arrayexpress/arrays/{pid}"
+    },
+    {
+      "pid": "arrayexpress_experiment",
+      "link": "https://ebi.ac.uk/arrayexpress/experiments/{pid}"
+    },
+    {
+      "pid": "hal",
+      "link": "https://hal.archives-ouvertes.fr/{pid}"
+    },
+    {
+      "pid": "swh",
+      "link": "https://archive.softwareheritage.org/{pid}"
+    },
+    {
+      "pid": "ror",
+      "link": "https://ror.org/{pid}"
+    },
+    {
+      "pid": "viaf",
+      "link": "https://viaf.org/viaf/{pid}"
+    }
+  ]
+}