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pkiraly wants to merge 2 commits into from
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5336 code formatting issues #5337

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5508277
Merge pull request #2 from IQSS/develop
pkiraly Nov 21, 2018
6fd71cf
issue #5336: fixing the issues reported by checkstyle.
pkiraly Nov 21, 2018
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9 changes: 4 additions & 5 deletions src/main/java/edu/harvard/iq/dataverse/ConfigureFragmentBean.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@

@ViewScoped
@Named
public class ConfigureFragmentBean implements java.io.Serializable{
public class ConfigureFragmentBean implements java.io.Serializable {

private static final Logger logger = Logger.getLogger(ConfigureFragmentBean.class.getName());

Expand Down Expand Up @@ -63,11 +63,11 @@ public ExternalTool getConfigurePopupTool() {
}

public ExternalToolHandler getConfigurePopupToolHandler() {
if(fileId == null) {
if (fileId == null) {
//on first UI load, method is called before fileId is set. There may be a better way to handle this
return null;
}
if(toolHandler != null) {
if (toolHandler != null) {
return toolHandler;
}

Expand All @@ -84,8 +84,7 @@ public ExternalToolHandler getConfigurePopupToolHandler() {
return toolHandler;
}

public void setConfigureFileId(Long setFileId)
{
public void setConfigureFileId(Long setFileId) {
fileId = setFileId;
}
}
23 changes: 13 additions & 10 deletions src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValue.java
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Expand Up @@ -64,9 +64,9 @@ public void setId(Long id) {
public String getStrValue() {
return strValue;
}

public void setStrValue(String strValue) {
this.strValue = strValue;

}

private String identifier;
Expand All @@ -78,20 +78,24 @@ public String getIdentifier() {
public void setIdentifier(String identifier) {
this.identifier = identifier;
}




private int displayOrder;
public int getDisplayOrder() { return this.displayOrder;}
public void setDisplayOrder(int displayOrder) {this.displayOrder = displayOrder;}



public int getDisplayOrder() {
return this.displayOrder;
}

public void setDisplayOrder(int displayOrder) {
this.displayOrder = displayOrder;
}

@ManyToOne
// @JoinColumn( nullable = false ) TODO this breaks for the N/A value. need to create an N/A type for that value.
private DatasetFieldType datasetFieldType;
public DatasetFieldType getDatasetFieldType() {
return datasetFieldType;
}

public void setDatasetFieldType(DatasetFieldType datasetFieldType) {
this.datasetFieldType = datasetFieldType;
}
Expand All @@ -107,7 +111,6 @@ public void setControlledVocabAlternates(Collection<ControlledVocabAlternate> co
this.controlledVocabAlternates = controlledVocabAlternates;
}


@Override
public int hashCode() {
int hash = 0;
Expand All @@ -128,5 +131,5 @@ public boolean equals(Object object) {
public String toString() {
return "edu.harvard.iq.dataverse.ControlledVocabularyValue[ id=" + id + " ]";
}

}
12 changes: 5 additions & 7 deletions src/main/java/edu/harvard/iq/dataverse/DataCitation.java
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Expand Up @@ -69,7 +69,6 @@ public DataCitation(DatasetVersion dsv) {
this(dsv, false);
}


public DataCitation(DatasetVersion dsv, boolean direct) {
this.direct = direct;
getCommonValuesFrom(dsv);
Expand Down Expand Up @@ -196,7 +195,7 @@ public String toString(boolean html) {
}

if (persistentId != null) {
// always show url format
// always show url format
citationList.add(formatURL(persistentId.toURL().toString(), persistentId.toURL().toString(), html));
}
citationList.add(formatString(publisher, html));
Expand Down Expand Up @@ -596,13 +595,13 @@ private void createEndNoteXML(XMLStreamWriter xmlw) throws XMLStreamException {

}

public Map<String, String> getDataCiteMetadata() {
public Map<String, String> getDataCiteMetadata() {
Map<String, String> metadata = new HashMap<>();
String authorString = getAuthorsString();

if (authorString.isEmpty()) {
authorString = ":unav";
}
}
String producerString = getPublisher();

if (producerString.isEmpty()) {
Expand All @@ -614,10 +613,9 @@ public Map<String, String> getDataCiteMetadata() {
metadata.put("datacite.publisher", producerString);
metadata.put("datacite.publicationyear", getYear());
return metadata;
}
}


// helper methods
// helper methods
private String formatString(String value, boolean escapeHtml) {
return formatString(value, escapeHtml, "");
}
Expand Down
35 changes: 17 additions & 18 deletions src/main/java/edu/harvard/iq/dataverse/DataCiteRESTfullClient.java
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Expand Up @@ -222,25 +222,24 @@ public String inactiveDataset(String doi) {
public static void main(String[] args) throws Exception {
String doi = "10.5072/DVN/274533";
DataCiteRESTfullClient client = new DataCiteRESTfullClient("https://mds.test.datacite.org", "DATACITE.HARVARD", "DVNapitest");
// System.out.println(client.getUrl(doi));
// System.out.println(client.getMetadata(doi));
// System.out.println(client.postMetadata(readAndClose("C:/Users/luopc/Desktop/datacite.xml", "utf-8")));
// System.out.println(client.postUrl("10.5072/000000001", "http://opendata.pku.edu.cn/dvn/dv/DAIM/faces/study/StudyPage.xhtml?globalId=hdl:TEST/10027&studyListingIndex=1_1acc4e9f23fa10b3cc0500d9eb5e"));
// client.close();
// String doi2 = "10.1/1.0003";
// SimpleRESTfullClient client2 = new SimpleRESTfullClient("https://162.105.140.119:8443/mds", "PKULIB.IR", "luopengcheng","localhost.keystore");
// System.out.println(client2.getUrl("10.1/1.0002"));
// System.out.println(client2.getUrl("10.1/1.0002"));
// System.out.println(client2.getMetadata(doi2));
// client2.postUrl("10.1/1.0003", "http://ir.pku.edu.cn");
// System.out.println(client2.postUrl("10.1/1.0008", "http://ir.pku.edu.cn"));
// System.out.println(client2.postMetadata(FileUtil.loadAsString(new File("C:/Users/luopc/Desktop/test/datacite-example-ResourceTypeGeneral_Collection-v3.0.xml"), "utf-8")));
// System.out.println(client2.getMetadata("10.1/1.0007"));
// System.out.println(client2.inactiveDataSet("10.1/1.0007"));
// client2.close();
}
// System.out.println(client.getUrl(doi));
// System.out.println(client.getMetadata(doi));
// System.out.println(client.postMetadata(readAndClose("C:/Users/luopc/Desktop/datacite.xml", "utf-8")));
// System.out.println(client.postUrl("10.5072/000000001", "http://opendata.pku.edu.cn/dvn/dv/DAIM/faces/study/StudyPage.xhtml?globalId=hdl:TEST/10027&studyListingIndex=1_1acc4e9f23fa10b3cc0500d9eb5e"));
// client.close();
// String doi2 = "10.1/1.0003";
// SimpleRESTfullClient client2 = new SimpleRESTfullClient("https://162.105.140.119:8443/mds", "PKULIB.IR", "luopengcheng","localhost.keystore");
// System.out.println(client2.getUrl("10.1/1.0002"));
// System.out.println(client2.getUrl("10.1/1.0002"));
// System.out.println(client2.getMetadata(doi2));
// client2.postUrl("10.1/1.0003", "http://ir.pku.edu.cn");
// System.out.println(client2.postUrl("10.1/1.0008", "http://ir.pku.edu.cn"));
// System.out.println(client2.postMetadata(FileUtil.loadAsString(new File("C:/Users/luopc/Desktop/test/datacite-example-ResourceTypeGeneral_Collection-v3.0.xml"), "utf-8")));
// System.out.println(client2.getMetadata("10.1/1.0007"));
// System.out.println(client2.inactiveDataSet("10.1/1.0007"));
// client2.close();
}


// private static String readAndClose(String file, String encoding) throws IOException{
// BufferedReader in = new BufferedReader(new InputStreamReader(new FileInputStream(file),encoding));
// StringBuilder str = new StringBuilder();
Expand Down
50 changes: 20 additions & 30 deletions src/main/java/edu/harvard/iq/dataverse/DataFile.java
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Expand Up @@ -54,16 +54,18 @@
* @author gdurand
*/
@NamedQueries({
@NamedQuery( name="DataFile.removeFromDatasetVersion",
query="DELETE FROM FileMetadata f WHERE f.datasetVersion.id=:versionId and f.dataFile.id=:fileId"),
@NamedQuery(name="DataFile.findDataFileByIdProtocolAuth",
query="SELECT s FROM DataFile s WHERE s.identifier=:identifier AND s.protocol=:protocol AND s.authority=:authority")
@NamedQuery(name="DataFile.removeFromDatasetVersion",
query="DELETE FROM FileMetadata f WHERE f.datasetVersion.id=:versionId and f.dataFile.id=:fileId"),
@NamedQuery(name="DataFile.findDataFileByIdProtocolAuth",
query="SELECT s FROM DataFile s WHERE s.identifier=:identifier AND s.protocol=:protocol AND s.authority=:authority")
})
@Entity
@Table(indexes = {@Index(columnList="ingeststatus")
, @Index(columnList="checksumvalue")
, @Index(columnList="contenttype")
, @Index(columnList="restricted")})
@Table(indexes = {
@Index(columnList="ingeststatus"),
@Index(columnList="checksumvalue"),
@Index(columnList="contenttype"),
@Index(columnList="restricted")
})
public class DataFile extends DvObject implements Comparable {
private static final Logger logger = Logger.getLogger(DatasetPage.class.getCanonicalName());
private static final long serialVersionUID = 1L;
Expand All @@ -80,7 +82,6 @@ public class DataFile extends DvObject implements Comparable {
@Column( nullable = false )
@Pattern(regexp = "^.*/.*$", message = "{contenttype.slash}")
private String contentType;


// @Expose
// @SerializedName("storageIdentifier")
Expand Down Expand Up @@ -141,7 +142,6 @@ public String toString() {
@Column(nullable = false)
private String checksumValue;


/* start: FILE REPLACE ATTRIBUTES */

// For the initial version of a file, this will be equivalent to the ID
Expand All @@ -160,9 +160,7 @@ public String toString() {
@Column(nullable=true)
private Long previousDataFileId;
/* endt: FILE REPLACE ATTRIBUTES */




@Expose
@Column(nullable=true)
private Long filesize; // Number of bytes in file. Allows 0 and null, negative numbers not permitted
Expand Down Expand Up @@ -225,8 +223,7 @@ public DataFile(String contentType) {
this.fileMetadatas = new ArrayList<>();
initFileReplaceAttributes();
}



/**
* All constructors should use this method
* to initialize this file replace attributes
Expand Down Expand Up @@ -301,6 +298,7 @@ public JsonArrayBuilder getTagLabelsAsJsonArrayBuilder(){
}
return builder;
}

public void setTags(List<DataFileTag> dataFileTags) {
this.dataFileTags = dataFileTags;
}
Expand Down Expand Up @@ -633,7 +631,6 @@ public String getUnf() {
}
return null;
}


@ManyToMany
@JoinTable(name = "fileaccessrequests",
Expand Down Expand Up @@ -701,12 +698,12 @@ protected String toStringExtras() {
FileMetadata fmd = getLatestFileMetadata();
return "label:" + (fmd!=null? fmd.getLabel() : "[no metadata]");
}
@Override
public <T> T accept( Visitor<T> v ) {
return v.visit(this);
}

@Override
public <T> T accept( Visitor<T> v ) {
return v.visit(this);
}

@Override
public String getDisplayName() {
return getLatestFileMetadata().getLabel();
Expand Down Expand Up @@ -734,7 +731,6 @@ public boolean hasGeospatialTag(){
return false;
}


/**
* Set rootDataFileId
* @param rootDataFileId
Expand Down Expand Up @@ -792,9 +788,7 @@ public String toJSON(){

return serializeAsJSON(false);
}




public JsonObject asGsonObject(boolean prettyPrint){

String overarchingKey = "data";
Expand Down Expand Up @@ -876,7 +870,6 @@ public JsonObject asGsonObject(boolean prettyPrint){
jsonObj.getAsJsonObject().add("checksum", checkSumJSONMap);

return jsonObj.getAsJsonObject();

}

/**
Expand All @@ -890,7 +883,6 @@ private String serializeAsJSON(boolean prettyPrint){

//return fullFileJSON.
return fullFileJSON.toString();

}

public String getPublicationDateFormattedYYYYMMDD() {
Expand All @@ -906,8 +898,6 @@ public String getCreateDateFormattedYYYYMMDD() {
}
return null;
}


} // end of class


Expand Down
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