org.molgenis.omx.ngs
Class Project

java.lang.Object
  org.molgenis.util.AbstractEntity
      org.molgenis.omx.ngs.Project

All Implemented Interfaces:

Serializable, Autoid, Entity

@Entity
public class Project
extends AbstractEntity
implements Autoid

Project: A Project bundles information about one project..

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

static String	DECLARATIONNR
static String	GCCANALYSIS
static String	GCCINSTRUCTIONS
static String	ID
static String	LANEAMOUNT
static String	PREPKIT
static String	PREPKIT_PREPKITNAME
static String	PROJECTANALIST
static String	PROJECTANALIST_USERNAME
static String	PROJECTCOMMENT
static String	PROJECTCUSTOMER
static String	PROJECTCUSTOMER_USERNAME
static String	PROJECTNAME
static String	PROJECTPLANNEDFINISHDATE
static String	RESULTFILESDIR
static String	RESULTSHIPPEDDATE
static String	RESULTSHIPPEDTO
static String	RESULTSHIPPEDTO_USERNAME
static String	RESULTSHIPPEDUSER
static String	RESULTSHIPPEDUSER_USERNAME
static String	SAMPLEAMOUNT
static String	SAMPLETYPE
static String	SEQTYPE

Constructor Summary

Project()

Project(Project copyMe)
copy constructor

Method Summary

Project	create(Tuple tuple)
boolean	equals(Object obj)
static List<? extends Project>	find(Database db, QueryRule... rules) Shorthand for db.find(Project.class, org.molgenis.framework.db.QueryRule ...
static Project	findById(Database db, Integer id)
static Project	findByProjectName(Database db, String projectName)
Object	get(String name) Generic getter.
String	getDeclarationNr() Get the The Declaration Nr of a project..
String	getDeclarationNr(Database db) Deprecated.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Project.
String	getFields(String sep) Deprecated.
Boolean	getGccAnalysis() Get the Indication if variant calling has to be performed on the experiment..
Boolean	getGccAnalysis(Database db) Deprecated.
String	getGccInstructions() Get the Specific instructions for GCC members for the analysis..
String	getGccInstructions(Database db) Deprecated.
Integer	getId() Get the automatically generated internal id, only for internal use..
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
Integer	getLaneAmount() Get the Number of lanes planned in this project.
Integer	getLaneAmount(Database db) Deprecated.
Integer	getPrepKit_Id()
String	getPrepKit_PrepKitName() Get a pretty label PrepKitName for cross reference PrepKit to PrepKit.Id.
PrepKit	getPrepKit() Get the Preparation kit used on the sample for this experiment.
PrepKit	getPrepKit(Database db) Deprecated.
List<Integer>	getProjectAnalist_Id()
List<String>	getProjectAnalist_UserName() Get a pretty label for cross reference ProjectAnalist to NgsUser.Id.
List<NgsUser>	getProjectAnalist() Get the The user which will be responsible for performing the wet-lab activities..
List<NgsUser>	getProjectAnalist(Database db) Deprecated.
String	getProjectComment() Get the The comment of a project..
String	getProjectComment(Database db) Deprecated.
Integer	getProjectCustomer_Id()
String	getProjectCustomer_UserName() Get a pretty label UserName for cross reference ProjectCustomer to NgsUser.Id.
NgsUser	getProjectCustomer() Get the The user who ordered the project..
NgsUser	getProjectCustomer(Database db) Deprecated.
String	getProjectName() Get the The name of a project.
String	getProjectName(Database db) Deprecated.
Date	getProjectPlannedFinishDate() Get the The date a project is expected to be finished.
Date	getProjectPlannedFinishDate(Database db) Deprecated.
String	getResultFilesDir() Get the File location of the resulting files after analysis occurred (for file download purpose).
String	getResultFilesDir(Database db) Deprecated.
Date	getResultShippedDate() Get the The date the result of the experiment is shipped to the custumor..
Date	getResultShippedDate(Database db) Deprecated.
Integer	getResultShippedTo_Id()
String	getResultShippedTo_UserName() Get a pretty label UserName for cross reference ResultShippedTo to NgsUser.Id.
NgsUser	getResultShippedTo() Get the Name of the person to which the data has been shipped..
NgsUser	getResultShippedTo(Database db) Deprecated.
Integer	getResultShippedUser_Id()
String	getResultShippedUser_UserName() Get a pretty label UserName for cross reference ResultShippedUser to NgsUser.Id.
NgsUser	getResultShippedUser() Get the The user who shipped the date..
NgsUser	getResultShippedUser(Database db) Deprecated.
Integer	getSampleAmount() Get the Number of samples planned in this project.
Integer	getSampleAmount(Database db) Deprecated.
String	getSampleType() Get the Type of sample.
String	getSampleType(Database db) Deprecated.
String	getSampleTypeLabel() Get tha label for enum SampleType.
List<ValueLabel>	getSampleTypeOptions() SampleType is enum.
String	getSeqType() Get the The type of sequencing..
String	getSeqType(Database db) Deprecated.
String	getSeqTypeLabel() Get tha label for enum SeqType.
List<ValueLabel>	getSeqTypeOptions() SeqType is enum.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Project>	query(Database db) Shorthand for db.query(Project.class).
void	set(Tuple tuple, boolean strict)
void	setDeclarationNr(String declarationNr) Set the The Declaration Nr of a project..
void	setGccAnalysis(Boolean gccAnalysis) Set the Indication if variant calling has to be performed on the experiment..
void	setGccInstructions(String gccInstructions) Set the Specific instructions for GCC members for the analysis..
void	setId(Integer id) Set the automatically generated internal id, only for internal use..
void	setLaneAmount(Integer laneAmount) Set the Number of lanes planned in this project.
void	setPrepKit_Id(Integer prepKit_id) Set foreign key for field prepKit.
void	setPrepKit_PrepKitName(String prepKit_PrepKitName) Set a pretty label for cross reference PrepKit to PrepKit.Id.
void	setPrepKit(Integer prepKit_id)
void	setPrepKit(PrepKit prepKit) Set the Preparation kit used on the sample for this experiment.
void	setProjectAnalist_Id(Integer... projectAnalist)
void	setProjectAnalist_Id(List<Integer> projectAnalist_id) Set foreign key for field projectAnalist.
void	setProjectAnalist_UserName(List<String> projectAnalist_UserName) Update the foreign key ProjectAnalist This sets projectAnalist to null until next database transaction.
void	setProjectAnalist(List<NgsUser> projectAnalist) Set the The user which will be responsible for performing the wet-lab activities..
void	setProjectAnalist(NgsUser... projectAnalist)
void	setProjectComment(String projectComment) Set the The comment of a project..
void	setProjectCustomer_Id(Integer projectCustomer_id) Set foreign key for field projectCustomer.
void	setProjectCustomer_UserName(String projectCustomer_UserName) Set a pretty label for cross reference ProjectCustomer to NgsUser.Id.
void	setProjectCustomer(Integer projectCustomer_id)
void	setProjectCustomer(NgsUser projectCustomer) Set the The user who ordered the project..
void	setProjectName(String projectName) Set the The name of a project.
void	setProjectPlannedFinishDate(Date projectPlannedFinishDate) Set the The date a project is expected to be finished.
void	setResultFilesDir(String resultFilesDir) Set the File location of the resulting files after analysis occurred (for file download purpose).
void	setResultShippedDate(Date resultShippedDate) Set the The date the result of the experiment is shipped to the custumor..
void	setResultShippedDate(String datestring) Set the The date the result of the experiment is shipped to the custumor..
void	setResultShippedTo_Id(Integer resultShippedTo_id) Set foreign key for field resultShippedTo.
void	setResultShippedTo_UserName(String resultShippedTo_UserName) Set a pretty label for cross reference ResultShippedTo to NgsUser.Id.
void	setResultShippedTo(Integer resultShippedTo_id)
void	setResultShippedTo(NgsUser resultShippedTo) Set the Name of the person to which the data has been shipped..
void	setResultShippedUser_Id(Integer resultShippedUser_id) Set foreign key for field resultShippedUser.
void	setResultShippedUser_UserName(String resultShippedUser_UserName) Set a pretty label for cross reference ResultShippedUser to NgsUser.Id.
void	setResultShippedUser(Integer resultShippedUser_id)
void	setResultShippedUser(NgsUser resultShippedUser) Set the The user who shipped the date..
void	setSampleAmount(Integer sampleAmount) Set the Number of samples planned in this project.
void	setSampleType(String sampleType) Set the Type of sample.
void	setSeqType(String seqType) Set the The type of sequencing..
String	toString()
String	toString(boolean verbose)
void	validate()

Methods inherited from class org.molgenis.util.AbstractEntity

get__Type, get__TypeLabel, get__TypeOptions, getLabelValue, getValues, isObjectRepresentation, isReadonly, set__Type, set, set, setReadonly, setValuesFromString, string2date

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.molgenis.util.Entity

getLabelValue, getValues, isReadonly, set, set, setReadonly

Field Detail

ID

public static final String ID

See Also:

Constant Field Values

PROJECTNAME

public static final String PROJECTNAME

See Also:

Constant Field Values

PROJECTCOMMENT

public static final String PROJECTCOMMENT

See Also:

Constant Field Values

PROJECTCUSTOMER

public static final String PROJECTCUSTOMER

See Also:

Constant Field Values

PROJECTCUSTOMER_USERNAME

public static final String PROJECTCUSTOMER_USERNAME

See Also:

Constant Field Values

PROJECTANALIST

public static final String PROJECTANALIST

See Also:

Constant Field Values

PROJECTANALIST_USERNAME

public static final String PROJECTANALIST_USERNAME

See Also:

Constant Field Values

PROJECTPLANNEDFINISHDATE

public static final String PROJECTPLANNEDFINISHDATE

See Also:

Constant Field Values

LANEAMOUNT

public static final String LANEAMOUNT

See Also:

Constant Field Values

SAMPLEAMOUNT

public static final String SAMPLEAMOUNT

See Also:

Constant Field Values

SAMPLETYPE

public static final String SAMPLETYPE

See Also:

Constant Field Values

SEQTYPE

public static final String SEQTYPE

See Also:

Constant Field Values

PREPKIT

public static final String PREPKIT

See Also:

Constant Field Values

PREPKIT_PREPKITNAME

public static final String PREPKIT_PREPKITNAME

See Also:

Constant Field Values

DECLARATIONNR

public static final String DECLARATIONNR

See Also:

Constant Field Values

GCCANALYSIS

public static final String GCCANALYSIS

See Also:

Constant Field Values

GCCINSTRUCTIONS

public static final String GCCINSTRUCTIONS

See Also:

Constant Field Values

RESULTFILESDIR

public static final String RESULTFILESDIR

See Also:

Constant Field Values

RESULTSHIPPEDUSER

public static final String RESULTSHIPPEDUSER

See Also:

Constant Field Values

RESULTSHIPPEDUSER_USERNAME

public static final String RESULTSHIPPEDUSER_USERNAME

See Also:

Constant Field Values

RESULTSHIPPEDTO

public static final String RESULTSHIPPEDTO

See Also:

Constant Field Values

RESULTSHIPPEDTO_USERNAME

public static final String RESULTSHIPPEDTO_USERNAME

See Also:

Constant Field Values

RESULTSHIPPEDDATE

public static final String RESULTSHIPPEDDATE

See Also:

Constant Field Values

Constructor Detail

Project

public Project()

Project

public Project(Project copyMe)
        throws Exception

copy constructor

Throws:

Exception

Method Detail

query

public static Query<? extends Project> query(Database db)

Shorthand for db.query(Project.class).

find

public static List<? extends Project> find(Database db,
                                           QueryRule... rules)
                                    throws DatabaseException

Shorthand for db.find(Project.class, org.molgenis.framework.db.QueryRule ... rules).

Throws:

DatabaseException

findById

public static Project findById(Database db,
                               Integer id)
                        throws DatabaseException

Throws:

DatabaseException

findByProjectName

public static Project findByProjectName(Database db,
                                        String projectName)
                                 throws DatabaseException

Throws:

DatabaseException

getId

public Integer getId()

Get the automatically generated internal id, only for internal use..

Specified by:

getId in interface Autoid

Returns:

id.

setId

public void setId(Integer id)

Set the automatically generated internal id, only for internal use..

Specified by:

setId in interface Autoid

Parameters:

id -

getProjectName

public String getProjectName()

Get the The name of a project.

Returns:

projectName.

getProjectName

@Deprecated
public String getProjectName(Database db)

Deprecated.

setProjectName

public void setProjectName(String projectName)

Set the The name of a project.

Parameters:

projectName -

getProjectComment

public String getProjectComment()

Get the The comment of a project..

Returns:

projectComment.

getProjectComment

@Deprecated
public String getProjectComment(Database db)

Deprecated.

setProjectComment

public void setProjectComment(String projectComment)

Set the The comment of a project..

Parameters:

projectComment -

getProjectCustomer

public NgsUser getProjectCustomer()

Get the The user who ordered the project..

Returns:

projectCustomer.

getProjectCustomer

@Deprecated
public NgsUser getProjectCustomer(Database db)

Deprecated.

setProjectCustomer

public void setProjectCustomer(NgsUser projectCustomer)

Set the The user who ordered the project..

Parameters:

projectCustomer -

setProjectCustomer_Id

public void setProjectCustomer_Id(Integer projectCustomer_id)

Set foreign key for field projectCustomer. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

setProjectCustomer

public void setProjectCustomer(Integer projectCustomer_id)

getProjectCustomer_Id

public Integer getProjectCustomer_Id()

getProjectCustomer_UserName

public String getProjectCustomer_UserName()

Get a pretty label UserName for cross reference ProjectCustomer to NgsUser.Id.

setProjectCustomer_UserName

public void setProjectCustomer_UserName(String projectCustomer_UserName)

Set a pretty label for cross reference ProjectCustomer to NgsUser.Id. Implies setProjectCustomer(null) until save

getProjectAnalist

public List<NgsUser> getProjectAnalist()

Get the The user which will be responsible for performing the wet-lab activities..

Returns:

projectAnalist.

getProjectAnalist

@Deprecated
public List<NgsUser> getProjectAnalist(Database db)

Deprecated.

setProjectAnalist

public void setProjectAnalist(List<NgsUser> projectAnalist)

Set the The user which will be responsible for performing the wet-lab activities..

Parameters:

projectAnalist -

setProjectAnalist_Id

public void setProjectAnalist_Id(Integer... projectAnalist)

setProjectAnalist

public void setProjectAnalist(NgsUser... projectAnalist)

setProjectAnalist_Id

public void setProjectAnalist_Id(List<Integer> projectAnalist_id)

Set foreign key for field projectAnalist. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

getProjectAnalist_Id

public List<Integer> getProjectAnalist_Id()

getProjectAnalist_UserName

public List<String> getProjectAnalist_UserName()

Get a pretty label for cross reference ProjectAnalist to NgsUser.Id.

setProjectAnalist_UserName

public void setProjectAnalist_UserName(List<String> projectAnalist_UserName)

Update the foreign key ProjectAnalist This sets projectAnalist to null until next database transaction.

getProjectPlannedFinishDate

public Date getProjectPlannedFinishDate()

Get the The date a project is expected to be finished.

Returns:

projectPlannedFinishDate.

getProjectPlannedFinishDate

@Deprecated
public Date getProjectPlannedFinishDate(Database db)

Deprecated.

setProjectPlannedFinishDate

public void setProjectPlannedFinishDate(Date projectPlannedFinishDate)

Set the The date a project is expected to be finished.

Parameters:

projectPlannedFinishDate -

getLaneAmount

public Integer getLaneAmount()

Get the Number of lanes planned in this project.

Returns:

laneAmount.

getLaneAmount

@Deprecated
public Integer getLaneAmount(Database db)

Deprecated.

setLaneAmount

public void setLaneAmount(Integer laneAmount)

Set the Number of lanes planned in this project.

Parameters:

laneAmount -

getSampleAmount

public Integer getSampleAmount()

Get the Number of samples planned in this project.

Returns:

sampleAmount.

getSampleAmount

@Deprecated
public Integer getSampleAmount(Database db)

Deprecated.

setSampleAmount

public void setSampleAmount(Integer sampleAmount)

Set the Number of samples planned in this project.

Parameters:

sampleAmount -

getSampleType

public String getSampleType()

Get the Type of sample.

Returns:

sampleType.

getSampleType

@Deprecated
public String getSampleType(Database db)

Deprecated.

setSampleType

public void setSampleType(String sampleType)

Set the Type of sample.

Parameters:

sampleType -

getSampleTypeLabel

public String getSampleTypeLabel()

Get tha label for enum SampleType.

getSampleTypeOptions

public List<ValueLabel> getSampleTypeOptions()

SampleType is enum. This method returns all available enum options.

getSeqType

public String getSeqType()

Get the The type of sequencing..

Returns:

seqType.

getSeqType

@Deprecated
public String getSeqType(Database db)

Deprecated.

setSeqType

public void setSeqType(String seqType)

Set the The type of sequencing..

Parameters:

seqType -

getSeqTypeLabel

public String getSeqTypeLabel()

Get tha label for enum SeqType.

getSeqTypeOptions

public List<ValueLabel> getSeqTypeOptions()

SeqType is enum. This method returns all available enum options.

getPrepKit

public PrepKit getPrepKit()

Get the Preparation kit used on the sample for this experiment.

Returns:

prepKit.

getPrepKit

@Deprecated
public PrepKit getPrepKit(Database db)

Deprecated.

setPrepKit

public void setPrepKit(PrepKit prepKit)

Set the Preparation kit used on the sample for this experiment.

Parameters:

prepKit -

setPrepKit_Id

public void setPrepKit_Id(Integer prepKit_id)

Set foreign key for field prepKit. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

setPrepKit

public void setPrepKit(Integer prepKit_id)

getPrepKit_Id

public Integer getPrepKit_Id()

getPrepKit_PrepKitName

public String getPrepKit_PrepKitName()

Get a pretty label PrepKitName for cross reference PrepKit to PrepKit.Id.

setPrepKit_PrepKitName

public void setPrepKit_PrepKitName(String prepKit_PrepKitName)

Set a pretty label for cross reference PrepKit to PrepKit.Id. Implies setPrepKit(null) until save

getDeclarationNr

public String getDeclarationNr()

Get the The Declaration Nr of a project..

Returns:

declarationNr.

getDeclarationNr

@Deprecated
public String getDeclarationNr(Database db)

Deprecated.

setDeclarationNr

public void setDeclarationNr(String declarationNr)

Set the The Declaration Nr of a project..

Parameters:

declarationNr -

getGccAnalysis

public Boolean getGccAnalysis()

Get the Indication if variant calling has to be performed on the experiment..

Returns:

gccAnalysis.

getGccAnalysis

@Deprecated
public Boolean getGccAnalysis(Database db)

Deprecated.

setGccAnalysis

public void setGccAnalysis(Boolean gccAnalysis)

Set the Indication if variant calling has to be performed on the experiment..

Parameters:

gccAnalysis -

getGccInstructions

public String getGccInstructions()

Get the Specific instructions for GCC members for the analysis..

Returns:

gccInstructions.

getGccInstructions

@Deprecated
public String getGccInstructions(Database db)

Deprecated.

setGccInstructions

public void setGccInstructions(String gccInstructions)

Set the Specific instructions for GCC members for the analysis..

Parameters:

gccInstructions -

getResultFilesDir

public String getResultFilesDir()

Get the File location of the resulting files after analysis occurred (for file download purpose).

Returns:

resultFilesDir.

getResultFilesDir

@Deprecated
public String getResultFilesDir(Database db)

Deprecated.

setResultFilesDir

public void setResultFilesDir(String resultFilesDir)

Set the File location of the resulting files after analysis occurred (for file download purpose).

Parameters:

resultFilesDir -

getResultShippedUser

public NgsUser getResultShippedUser()

Get the The user who shipped the date..

Returns:

resultShippedUser.

getResultShippedUser

@Deprecated
public NgsUser getResultShippedUser(Database db)

Deprecated.

setResultShippedUser

public void setResultShippedUser(NgsUser resultShippedUser)

Set the The user who shipped the date..

Parameters:

resultShippedUser -

setResultShippedUser_Id

public void setResultShippedUser_Id(Integer resultShippedUser_id)

Set foreign key for field resultShippedUser. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

setResultShippedUser

public void setResultShippedUser(Integer resultShippedUser_id)

getResultShippedUser_Id

public Integer getResultShippedUser_Id()

getResultShippedUser_UserName

public String getResultShippedUser_UserName()

Get a pretty label UserName for cross reference ResultShippedUser to NgsUser.Id.

setResultShippedUser_UserName

public void setResultShippedUser_UserName(String resultShippedUser_UserName)

Set a pretty label for cross reference ResultShippedUser to NgsUser.Id. Implies setResultShippedUser(null) until save

getResultShippedTo

public NgsUser getResultShippedTo()

Get the Name of the person to which the data has been shipped..

Returns:

resultShippedTo.

getResultShippedTo

@Deprecated
public NgsUser getResultShippedTo(Database db)

Deprecated.

setResultShippedTo

public void setResultShippedTo(NgsUser resultShippedTo)

Set the Name of the person to which the data has been shipped..

Parameters:

resultShippedTo -

setResultShippedTo_Id

public void setResultShippedTo_Id(Integer resultShippedTo_id)

Set foreign key for field resultShippedTo. This will erase any foreign key objects currently set. FIXME: can we autoload the new object?

setResultShippedTo

public void setResultShippedTo(Integer resultShippedTo_id)

getResultShippedTo_Id

public Integer getResultShippedTo_Id()

getResultShippedTo_UserName

public String getResultShippedTo_UserName()

Get a pretty label UserName for cross reference ResultShippedTo to NgsUser.Id.

setResultShippedTo_UserName

public void setResultShippedTo_UserName(String resultShippedTo_UserName)

Set a pretty label for cross reference ResultShippedTo to NgsUser.Id. Implies setResultShippedTo(null) until save

getResultShippedDate

public Date getResultShippedDate()

Get the The date the result of the experiment is shipped to the custumor..

Returns:

resultShippedDate.

getResultShippedDate

@Deprecated
public Date getResultShippedDate(Database db)

Deprecated.

setResultShippedDate

public void setResultShippedDate(Date resultShippedDate)

Set the The date the result of the experiment is shipped to the custumor..

Parameters:

resultShippedDate -

setResultShippedDate

public void setResultShippedDate(String datestring)
                          throws ParseException

Set the The date the result of the experiment is shipped to the custumor.. Automatically converts string into date;

Parameters:

resultShippedDate -

Throws:

ParseException

get

public Object get(String name)

Generic getter. Get the property by using the name.

Specified by:

get in interface Entity

validate

public void validate()
              throws DatabaseException

Specified by:

validate in interface Entity

Throws:

DatabaseException

set

public void set(Tuple tuple,
                boolean strict)
         throws Exception

Specified by:

set in interface Entity

Throws:

Exception

toString

public String toString()

Overrides:

toString in class Object

toString

public String toString(boolean verbose)

getFields

public Vector<String> getFields(boolean skipAutoIds)

Get the names of all public properties of Project.

Specified by:

getFields in interface Entity

getFields

public Vector<String> getFields()

Specified by:

getFields in interface Entity

getIdField

public String getIdField()

Specified by:

getIdField in interface Entity

getLabelFields

public List<String> getLabelFields()

Specified by:

getLabelFields in interface Entity

getFields

@Deprecated
public String getFields(String sep)

Deprecated.

Specified by:

getFields in interface Entity

getIdValue

public Object getIdValue()

Specified by:

getIdValue in interface Entity

getXrefIdFieldName

public String getXrefIdFieldName(String fieldName)

Specified by:

getXrefIdFieldName in interface Entity

getValues

@Deprecated
public String getValues(String sep)

Deprecated.

Specified by:

getValues in interface Entity

Overrides:

getValues in class AbstractEntity

create

public Project create(Tuple tuple)
               throws Exception

Specified by:

create in interface Entity

Throws:

Exception

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object