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Use more generics, less trailing whitespace in the dataverse package (#775) #2422

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Use more generics, less trailing whitespace in the dataverse package (#775) #2422

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244 changes: 124 additions & 120 deletions src/main/java/edu/harvard/iq/dataverse/DataFile.java
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20 changes: 14 additions & 6 deletions src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java
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Expand Up @@ -21,6 +21,7 @@
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.Query;
import javax.persistence.TypedQuery;

/**
*
Expand Down Expand Up @@ -118,7 +119,7 @@ public class DataFileServiceBean implements java.io.Serializable {
private static final String MIME_TYPE_UNDETERMINED_BINARY = "application/binary";

public DataFile find(Object pk) {
return (DataFile) em.find(DataFile.class, pk);
return em.find(DataFile.class, pk);
}

/*public DataFile findByMD5(String md5Value){
Expand All @@ -136,14 +137,14 @@ public List<DataFile> findByDatasetId(Long studyId) {
Sure, we don't have *studies* any more, in 4.0; it's a tribute
to the past. -- L.A.
*/
Query query = em.createQuery("select o from DataFile o where o.owner.id = :studyId order by o.id");
TypedQuery<DataFile> query = em.createQuery("select o from DataFile o where o.owner.id = :studyId order by o.id", DataFile.class);
query.setParameter("studyId", studyId);
return query.getResultList();
}

public List<DataFile> findIngestsInProgress() {
if ( em.isOpen() ) {
Query query = em.createQuery("select object(o) from DataFile as o where o.ingestStatus =:scheduledStatusCode or o.ingestStatus =:progressStatusCode order by o.id");
TypedQuery<DataFile> query = em.createQuery("select object(o) from DataFile as o where o.ingestStatus =:scheduledStatusCode or o.ingestStatus =:progressStatusCode order by o.id", DataFile.class);
query.setParameter("scheduledStatusCode", DataFile.INGEST_STATUS_SCHEDULED);
query.setParameter("progressStatusCode", DataFile.INGEST_STATUS_INPROGRESS);
return query.getResultList();
Expand All @@ -160,7 +161,7 @@ public DataTable findDataTableByFileId(Long fileId) {
}

public List<DataFile> findAll() {
return em.createQuery("select object(o) from DataFile as o order by o.id").getResultList();
return em.createQuery("select object(o) from DataFile as o order by o.id", DataFile.class).getResultList();
}

public DataFile save(DataFile dataFile) {
Expand All @@ -170,9 +171,9 @@ public DataFile save(DataFile dataFile) {
}

public Boolean isPreviouslyPublished(Long fileId){
Query query = em.createQuery("select object(o) from FileMetadata as o where o.dataFile.id =:fileId");
TypedQuery<FileMetadata> query = em.createQuery("select object(o) from FileMetadata as o where o.dataFile.id =:fileId", FileMetadata.class);
query.setParameter("fileId", fileId);
List retList = query.getResultList();
List<FileMetadata> retList = query.getResultList();
return (retList.size() > 1);
}

Expand Down Expand Up @@ -331,6 +332,9 @@ public boolean ingestableAsTabular(DataFile dataFile) {
* main code base, so we can just go through a hard-coded list of mime
* types. -- L.A.
*/
if (dataFile == null) {
return false;
}

String mimeType = dataFile.getContentType();

Expand Down Expand Up @@ -372,6 +376,10 @@ public String getFileClassById (Long fileId) {
}

public String getFileClass (DataFile file) {
if (file == null) {
return null;
}

if (isFileClassImage(file)) {
return FILE_CLASS_IMAGE;
}
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/edu/harvard/iq/dataverse/DataFileTag.java
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Expand Up @@ -81,7 +81,7 @@ public enum TagType {Survey, TimeSeries, Panel, Event, Genomics, Network, Geospa
}

public static List<String> listTags() {
List<String> retlist = new ArrayList();
List<String> retlist = new ArrayList<>();

for(TagType t : TagType.values()) {
retlist.add(TagTypeToLabels.get(t));
Expand Down
100 changes: 50 additions & 50 deletions src/main/java/edu/harvard/iq/dataverse/DataTable.java
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Expand Up @@ -31,78 +31,78 @@
/**
*
* @author Leonid Andreev
*
*
* Largely based on the the DataTable entity from the DVN v2-3;
* original author: Ellen Kraffmiller (2006).
*
*
*/

@Entity
@Table(indexes = {@Index(columnList="datafile_id")})
public class DataTable implements Serializable {

/** Creates a new instance of DataTable */
public DataTable() {
}

private static final long serialVersionUID = 1L;
@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
private Long id;

/**
* unf: the Universal Numeric Signature of the
* unf: the Universal Numeric Signature of the
* data table.
*/
@Column( nullable = false )
private String unf;
/*

/**
* caseQuantity: Number of observations
*/
private Long caseQuantity;
/*
*/
private Long caseQuantity;


/**
* varQuantity: Number of variables
*/
private Long varQuantity;

/*
/**
* recordsPerCase: this property is specific to fixed-field data files
* in which rows of observations may represented by *multiple* lines.
* The only known use case (so far): the fixed-width data files from
* ICPSR.
* The only known use case (so far): the fixed-width data files from
* ICPSR.
*/
private Long recordsPerCase;

/**
* DataFile that stores the data for this DataTable
*/
private Long recordsPerCase;

/*
* DataFile that stores the data for this DataTable
*/
@ManyToOne
@JoinColumn(nullable=false)
private DataFile dataFile;

/*
* DataVariables in this DataTable:
@ManyToOne
@JoinColumn(nullable=false)
private DataFile dataFile;

/**
* DataVariables in this DataTable:
*/
@OneToMany (mappedBy="dataTable", cascade={ CascadeType.REMOVE, CascadeType.MERGE,CascadeType.PERSIST})
@OrderBy ("fileOrder")
private List<DataVariable> dataVariables;
/*

/**
* originalFileType: the format of the file from which this data table was
* extracted (STATA, SPSS, R, etc.)
* Note: this was previously stored in the StudyFile.
* Note: this was previously stored in the StudyFile.
*/
private String originalFileFormat;
/*

/**
* originalFormatVersion: the version/release number of the original file
* format; for example, STATA 9, SPSS 12, etc.
* format; for example, STATA 9, SPSS 12, etc.
*/
private String originalFormatVersion;

/*
* Getter and Setter methods:
*/
Expand All @@ -124,46 +124,46 @@ public void setUnf(String unf) {

public Long getCaseQuantity() {
return this.caseQuantity;
}
}

public void setCaseQuantity(Long caseQuantity) {
this.caseQuantity = caseQuantity;
}

public Long getVarQuantity() {
return this.varQuantity;
}

public void setVarQuantity(Long varQuantity) {
this.varQuantity = varQuantity;
}
}

public Long getRecordsPerCase() {
return recordsPerCase;
}

public void setRecordsPerCase(Long recordsPerCase) {
this.recordsPerCase = recordsPerCase;
}

public DataFile getDataFile() {
return this.dataFile;
}

public void setDataFile(DataFile dataFile) {
this.dataFile = dataFile;
}


public List<DataVariable> getDataVariables() {
return this.dataVariables;
}


public void setDataVariables(List<DataVariable> dataVariables) {
this.dataVariables = dataVariables;
}
}

public String getOriginalFileFormat() {
return originalFileFormat;
}
Expand All @@ -172,19 +172,19 @@ public void setOriginalFileFormat(String originalFileType) {
this.originalFileFormat = originalFileType;
}


public String getOriginalFormatVersion() {
return originalFormatVersion;
}

public void setOriginalFormatVersion(String originalFormatVersion) {
this.originalFormatVersion = originalFormatVersion;
}
/*

/*
* Custom overrides for hashCode(), equals() and toString() methods:
*/

@Override
public int hashCode() {
int hash = 0;
Expand All @@ -205,5 +205,5 @@ public boolean equals(Object object) {
public String toString() {
return "edu.harvard.iq.dataverse.DataTable[ id=" + id + " ]";
}

}
14 changes: 7 additions & 7 deletions src/main/java/edu/harvard/iq/dataverse/Dataset.java
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Expand Up @@ -42,7 +42,7 @@ public class Dataset extends DvObjectContainer {
private static final long serialVersionUID = 1L;

@OneToMany(mappedBy = "owner", cascade = CascadeType.MERGE)
private List<DataFile> files = new ArrayList();
private List<DataFile> files = new ArrayList<>();

private String protocol;
private String authority;
Expand All @@ -56,7 +56,7 @@ public class Dataset extends DvObjectContainer {
private String identifier;
@OneToMany(mappedBy = "dataset", orphanRemoval = true, cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
@OrderBy("versionNumber DESC, minorVersionNumber DESC")
private List<DatasetVersion> versions = new ArrayList();
private List<DatasetVersion> versions = new ArrayList<>();
@OneToOne(mappedBy = "dataset", cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
private DatasetLock datasetLock;
@OneToOne(cascade = {CascadeType.MERGE, CascadeType.PERSIST})
Expand Down Expand Up @@ -87,7 +87,7 @@ public Dataset() {
DatasetVersion datasetVersion = new DatasetVersion();
datasetVersion.setDataset(this);
datasetVersion.setVersionState(DatasetVersion.VersionState.DRAFT);
datasetVersion.setFileMetadatas(new ArrayList());
datasetVersion.setFileMetadatas(new ArrayList<FileMetadata>());
datasetVersion.setVersionNumber(new Long(1));
datasetVersion.setMinorVersionNumber(new Long(0));
versions.add(datasetVersion);
Expand Down Expand Up @@ -218,7 +218,7 @@ public void setVersions(List<DatasetVersion> versions) {
private DatasetVersion createNewDatasetVersion(Template template) {
DatasetVersion dsv = new DatasetVersion();
dsv.setVersionState(DatasetVersion.VersionState.DRAFT);
dsv.setFileMetadatas(new ArrayList());
dsv.setFileMetadatas(new ArrayList<FileMetadata>());
DatasetVersion latestVersion = null;

//if the latest version has values get them copied over
Expand Down Expand Up @@ -273,7 +273,7 @@ private DatasetVersion createNewDatasetVersion(Template template) {
if (template == null) {
getVersions().add(0, dsv);
} else {
this.setVersions(new ArrayList());
this.setVersions(new ArrayList<DatasetVersion>());
getVersions().add(0, dsv);
}

Expand Down Expand Up @@ -301,9 +301,9 @@ public DatasetVersion getCreateVersion() {
dsv.setVersionState(DatasetVersion.VersionState.DRAFT);
dsv.setDataset(this);
dsv.setDatasetFields(dsv.initDatasetFields());;
dsv.setFileMetadatas(new ArrayList());
dsv.setFileMetadatas(new ArrayList<FileMetadata>());

this.setVersions(new ArrayList());
this.setVersions(new ArrayList<DatasetVersion>());
getVersions().add(0, dsv);

return dsv;
Expand Down
8 changes: 4 additions & 4 deletions src/main/java/edu/harvard/iq/dataverse/DatasetField.java
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Expand Up @@ -170,7 +170,7 @@ public void setParentDatasetFieldCompoundValue(DatasetFieldCompoundValue parentD

@OneToMany(mappedBy = "parentDatasetField", orphanRemoval = true, cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
@OrderBy("displayOrder ASC")
private List<DatasetFieldCompoundValue> datasetFieldCompoundValues = new ArrayList();
private List<DatasetFieldCompoundValue> datasetFieldCompoundValues = new ArrayList<>();

public List<DatasetFieldCompoundValue> getDatasetFieldCompoundValues() {
return datasetFieldCompoundValues;
Expand All @@ -182,7 +182,7 @@ public void setDatasetFieldCompoundValues(List<DatasetFieldCompoundValue> datase

@OneToMany(mappedBy = "datasetField", orphanRemoval = true, cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
@OrderBy("displayOrder ASC")
private List<DatasetFieldValue> datasetFieldValues = new ArrayList();
private List<DatasetFieldValue> datasetFieldValues = new ArrayList<>();

public List<DatasetFieldValue> getDatasetFieldValues() {
return this.datasetFieldValues;
Expand All @@ -194,7 +194,7 @@ public void setDatasetFieldValues(List<DatasetFieldValue> datasetFieldValues) {

@ManyToMany(cascade = {CascadeType.MERGE})
@JoinTable(indexes = {@Index(columnList="datasetfield_id"),@Index(columnList="controlledvocabularyvalues_id")})
private List<ControlledVocabularyValue> controlledVocabularyValues = new ArrayList();
private List<ControlledVocabularyValue> controlledVocabularyValues = new ArrayList<>();

public List<ControlledVocabularyValue> getControlledVocabularyValues() {
return controlledVocabularyValues;
Expand Down Expand Up @@ -271,7 +271,7 @@ public String getCompoundDisplayValue() {
}

public List<String> getValues() {
List returnList = new ArrayList();
List<String> returnList = new ArrayList<>();
if (!datasetFieldValues.isEmpty()) {
for (DatasetFieldValue dsfv : datasetFieldValues) {
returnList.add(dsfv.getValue());
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/edu/harvard/iq/dataverse/DatasetFieldCompoundValue.java
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Expand Up @@ -64,7 +64,7 @@ public static DatasetFieldCompoundValue createNewEmptyDatasetFieldCompoundValue(

@OneToMany(mappedBy = "parentDatasetFieldCompoundValue", orphanRemoval = true, cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
@OrderBy("datasetFieldType ASC")
private List<DatasetField> childDatasetFields = new ArrayList();
private List<DatasetField> childDatasetFields = new ArrayList<>();

public Long getId() {
return id;
Expand Down Expand Up @@ -134,7 +134,7 @@ public DatasetFieldCompoundValue copy(DatasetField parent) {
public Map<DatasetField,String> getDisplayValueMap() {
// todo - this currently only supports child datasetfields with single values
// need to determine how we would want to handle multiple
Map fieldMap = new LinkedHashMap();
Map<DatasetField, String> fieldMap = new LinkedHashMap<>();

for (DatasetField childDatasetField : childDatasetFields) {
// skip the value if it is empty or N/A
Expand Down
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