| Name: | IRIS_LOCAL_DS |
| Identification: | http://irislocal.irri.org |
| Description: | GCP Data Source for the International Rice Information System(IRIS): Database of Rice Data maintained at IRRI
This data source implements use case 'RetrieveStudies' (version 1.4.2) [Retrieve Studies]:
This use case returns a basic list of Study entities with limited annotation.
A Study is a kind of GCP data Entity analogous to a spreadsheet
(e.g. MS Excel type) or relational database table that documents
experimental data for a single experiment of a specified Project
into a matrix in which columns represent experimental variables
and rows, the distinct observations of those variables.
In addition to an unique identifier plus a human readable name and description,
this use case returns a "studies" attribute of the Study which is strictly
interpreted here to be a parent study that aggregates (i.e. specifies
hierarchical classification of) the given study within a larger study
context (e.g. an ICIS study "folder"). Searches may be made by unique identifier
or by name against, in order to retrieve sub-studies within the classification.
A Study may also have a specified "type", specified by an ontology term
(added in version 1.4 of this use case)
This data source implements use case 'RetrieveGermplasmStudies' (version 1.2.8) [Retrieve Germplasm Studies]:
This use case returns list of GermplasmStudy entities. This use case is a specialization of the core Retrieve Studies use case.
The GermplasmStudy is the derived form of a generic Study and is
associated with observations on a specific GermplasmSet. Such a study
would generally record treatment, growth and environmental conditions
as Treatment and GrowthCondition study factors, for plants grown in
the field, greenhouse or equivalent environment plus the Phenotype
observations of the plant.
This data source implements use case 'RetrieveGenotypeStudies' (version 1.2.3) [Retrieve Genotype Studies]:
This use case returns list of GenotypeStudy entities. This use case
is a specialization of the core Retrieve Germplasm Studies use case.
The GenotypeStudy is the derived form of a generic Study and is
associated with observations on a specific GermplasmSet used in genotyping. Such a study
would generally record the presence or absence of specific alleles for certain markers within the
specific GermplasmSet.
This data source implements use case 'RetrieveGermplasms' (version 1.6.0) [Retrieve Germplasms]:
These use cases refer to the querying of germplasm data. This contains the entrypoint use cases
for client applications/programs. For the International Crop Information System for example,
a typical search will start with getting a list of germplasms with names similar to a
specified germplasm name. Information about a particular germplasm can then be obtained.
Here are some simple Germplasm queries that can be used as entry point queries or as part
of more complex queries. In all the queries below the type of the objects returned from
the find method would be a list of Germplasm.
This data source implements use case 'RetrieveStudyObservationUnits' (version 1.2.6) [Retrieve Study Observation Units]:
This use case returns list of ValueSet entities.
This data source implements use case 'RetrieveStudyEffects' (version 1.2.7) [Retrieve Study Effects]:
This use case returns list of Effect entities.
This data source implements use case 'RetrieveFactorLevels' (version 1.0.0) [Retrieve Factor Levels]:
This use case returns list of Constraint entities.
This data source implements use case 'RetrieveStudyFeatureConstraints' (version 1.0.2) [Retrieve Study Feature Constraints]:
This use case returns list of Constraint entities that is related to a specific study feature.
The Constraint has information of all the possible values of a given study feature.
This data source implements use case 'RetrieveVariateDataRange' (version 1.2.4) [Retrieve Variate DataRange]:
This use case returns list of Constraint entities.
This data source implements use case 'RetrieveGenomicFeatureDetectors' (version 1.1.0) [Retrieve Genomic Feature Detectors]:
This use case returns list of GenomicFeatureDetector entities.
This data source implements use case 'RetrieveDetectedVariants' (version 1.2.5) [Retrieve Detected Variants]:
This use case returns list of DetectedVariant entities.
This data source implements use case 'RetrieveGermplasmSets' (version 1.0.2) [Retrieve Germplasm Sets]:
This use case refers to the retrieval of sets of Germplasm where such
sets are formally managed for example, within the list management
table of the International Crop Information System (ICIS).
This use case only provides some basic search facilities based on list identifier,
name or description. The GermplasmSet returned has Germplasm members that should
be annotated appropropriately with all available information (e.g. the information
found in the ICIS ListData table, for each entry).
This data source implements use case 'RetrieveDocumentedFeatureTypes' (version 1.0.0) [Retrieve Documented Feature Types]:
A simple query by name on a Feature "type" attribute
can be productively used to identify the list of ontology terms
with associated meta-data.
Since the "type" attribute is a SimpleOntologyTerm by definition,
we create an external attribute, "DocumentedType" to
signal the return of such a fully documented Feature type.
The use case supports search filters that return
various subsets of Feature type ontology terms:
* Search by unique identifier of the ontology to which the Feature type ontology term belongs
* Search by name (could be wild card) of the ontology to which the Feature type ontology term belongs
* Search by unique identifier of the Feature type ontology term
* Search by name of the Feature type ontology term
* Search by description (definition) of the Feature type ontology term
* Search by unique identifier of the "parent" ("group") term of the Feature type
* Search by name of the "parent" ("group") term of the Feature type
The return attributes of the "documented type" are left deliberately open ended,
such that the DataSource is free to all available meta-data known about the
type attribute and simply return "null" or "empty" attribute
values for any meta-data field which has no meta-data in the database.
A practical example of this is that the implementation in the ICIS database
of searches against the DMS property table might return "group" (i.e. the parent value),
the property name, the property definition, an acronym (as a "synonym") and
perhaps, even a list of DMS studies annotated with this property.
This data source implements use case 'RetrieveTabularData' (version 1.0.0) [Retrieve Tabular Data]:
The GCP domain model documents a TabularData object
to be of the following Java interface structure:
public interface TabularData extends Value
...
public Object valueAt(int rowIndex, int columnIndex);
public int getColumnCount();
public List(Object) getColumnHeaderList();
public int getRowCount();
public List(Object) getRowHeaderList();
...
This basic use case returns a single tabular data object, where the
columns and the row header objects are assumed to be unique
SimpleFeature objects indexing the values in a table.
The table entries themselves are expected to be to be Value objects
of a given specified data type (specified by the "type" ontology term)
and which have a specified human readable "valueString" value. If the
value is a vector, the human readable label of each member of the vector
should listed in the valueString comma delimited. The "data" attribute
of the value may return a more complex Java representation of the value,
of a sensible Java type that the context of the query might expect.
The "index" attribute of each Value should point to its associated
column and row header SimpleFeature object.
In both cases - for the SimpleFeature row and column headers, as well as,
for the Value entries returned inside the table - the associated
uniqueIdentifiers may be used by applications in other use cases
that retrieve more complex representations of the underlying objects
concerned. The uniqueIdentifiers, following the adopted LSID
formatting protocol specified in the Identification domain model
documentation for the GCP domain model, may be parsed to identify
the kind of row, column and entry data types in the table.
The searchable attributes on this use case are somewhat very generic.
It is suggested, therefore, that this use case be judiciously extended by
other more context specific use cases that need to return TabularData,
in order to enrich it with additional searchable attributes for specific
usage contexts (e.g. returning specific kinds of TabularData,
like GenotypeStudy tables, etc.)
No particular searchable attribute is specified as "mandatory" but
clearly, at least one searchable attribute needs to be specified
so that the query makes sense (datatype has "requiredSearch" set).
The default returned attributes are null, implying that the use case should
just to return a sensibly complete implementation of a TabularData object.
Note that the TabularData itself extends Value which extends SimpleFeature
which extends SimpleIdentifier. Hence, the full attributes available
in the top level object should include those of the superclass interfaces:
uniqueIdentifier: should generally identify the source data set/study
name: should be a human readable title sensibly labeling the table
type: the "type" attribute of the object should generally be
taken from a controlled vocabulary that specifies information (for developers
and/or users, and embodied in the code of applications accessing the object)
about the format of the complete "data" format returned.
valueString: at the level of the full tabular data, it is suggested that
the object return a comma delimited (CSV-style) listing of the data table
that facilitates text serialization of the table to the end user.
data: What the "data" attribute of the implementation returns is
context-specific (not defined fully by this use case). This should
ideally be a Java computable data structure suitable for the intended
purpose and code-level manipulations of the data (if not directly wrapped
by a direct extension/implementation of the TabularData interface itself)
index: this use case doesn't provide any specific semantics for index. Can be null.
constraints: if the TabularData returned is less than the full underlying
data set from which the tabular data is constructed, then constraint
objects may be (optionally) returned which indicates discrete enumeration
or numeric range limits of the returned data table. That said, this use
case gives no prescription on what these specific constraints should
look like (it is suggested that use case extensions provide such information).
Implementation of this class should likely be carefully designed to provide
proxy "lazy loading" for TabularData attributes, since data sets potentially
wrapped by TabularData may effectively be quite large.
This data source implements use case 'RetrieveTabularDataWithGenericConstraints' (version 1.0.0) [Retrieve Tabular Data With Generic Constraints]:
Extends the Retrieve Tabular Data use case by providing a genetic way to
constrain the row and columns by column id or name, and/or row id or name
The searchable attributes on this use case are somewhat very generic.
It is suggested, therefore, that this use case be judiciously extended by
other more context specific use cases that need to return TabularData,
in order to enrich it with additional searchable attributes for specific
usage contexts (e.g. returning specific kinds of TabularData,
like GenotypeStudy tables, etc.)
No particular searchable attribute is specified as "mandatory" but
clearly, at least one searchable attribute needs to be specified
so that the query makes sense (datatype has "requiredSearch" set).
The default returned attributes are null, implying that the use case should
just to return a sensibly complete implementation of a TabularData object.
This data source implements use case 'RetrieveReference' (version 1.0.1) [Retrieve Reference]:
This use case provides a base use case for all Reference use cases
by providing details of the returned attributes, but not searchable attributes.
This use case MUST not be implemented directly. A sub use case defining one or more
searchable attributes must be used.
The GCP domain model documents a Reference object
to be of the following Java interface structure:
public interface Reference extends Value
...
public Date getCreationDate();
public Date getExpirationDate();
public URL getURL();
public String getMimeType();
public Long getFileSize();
public String getUserFriendlyFilename();
...
This basic use case returns a single reference object with attributes namely:
url: should be a URL object containing the real file path/address of the reference searched
mimetype: returns the type of information a file contains
creation date: the expiration date of the file from the given url
expiration date: the expiration date of the file from the given url
filesize: the size of the file from the given url
userfriendlyfilename: the suggested file name that is easily read or understood by users
Note that the TabularData itself extends Value which extends SimpleFeature
which extends SimpleIdentifier. Hence, the full attributes available
in the top level object should include those of the superclass interfaces:
uniqueIdentifier: should generally identify the source data set/study
name: should be a human readable title sensibly labeling the reference
type: the "type" attribute of the object should generally be
taken from a controlled vocabulary that specifies information (for developers
and/or users, and embodied in the code of applications accessing the object)
about the format of the complete "data" format returned.
valueString: this use case doesn't provide any specific semantics for index. Can be null.
data: this use case doesn't provide any specific semantics for index. Can be null.
index: this use case doesn't provide any specific semantics for index. Can be null.
constraints: this use case doesn't provide any specific semantics for index. Can be null.
Implementation of this class should likely be carefully designed to provide
proxy "lazy loading" for Reference attributes, since data sets potentially
wrapped by Reference may effectively be quite large.
When invoking this use case using a find method from a DataSource
...
public List(Object) find(String dataTypeIdentifier,
SearchFilter[] searchFilters,
String[] includedAttributes,
Map options)
...
This data source implements use case 'RetrieveTableReference' (version 1.0.1) [Retrieve Table Reference]:
This use case provides a base use case for all Table Reference use cases
by providing details of the returned attributes, but not searchable attributes.
This use case MUST not be implemented directly. A sub use case defining one or more
searchable attributes must be used.
The GCP domain model documents a Reference object
to be of the following Java interface structure:
public interface Table Reference extends Value
...
public int getColumnCount();
public List(Object) getColumnHeaderList();
public int getRowCount();
public List(Object) getRowHeaderList();
...
This basic use case returns a single table reference object consisting
of a url which points to a file that can be associated as a table or matrix.
The file may OPTIONALLY have headers, which can be one of the following:
1) SimpleFeature identifier objects
2) Primitive values of type String or Number.
For row and column headers of type SimpleFeature and elements of
type Value the associated uniqueIdentifiers may be used by
applications in other use cases that retrieve more complex
representations of the underlying objects concerned.
The uniqueIdentifiers, following the adopted LSID
formatting protocol specified in the Identification domain model
documentation for the GCP domain model, may be parsed to identify
the kind of row, column and entry data types in the table.
Note that the TableReference itself extends Reference which extends Value which extends SimpleFeature
which extends SimpleIdentifier. Hence, the full attributes available
in the top level object should include those of the superclass interfaces:
url: should be a URL object containing the real file path/address of the reference searched
mimetype: returns the type of information a file contains
creation date: the creation date of the file from the given url
expiration date: the expiration date of the file from the given url
filesize: the size of the file from the given url
userfriendlyfilename: the suggested file name that is easily read or understood by users
uniqueIdentifier: should generally identify the source data set/study
name: should be a human readable title sensibly labeling the reference
type: the "type" attribute of the object should generally be
taken from a controlled vocabulary that specifies information (for developers
and/or users, and embodied in the code of applications accessing the object)
about the format of the complete "data" format returned.
valueString: this use case doesn't provide any specific semantics for index. Can be null.
data: this use case doesn't provide any specific semantics for index. Can be null.
index: this use case doesn't provide any specific semantics for index. Can be null.
constraints: this use case doesn't provide any specific semantics for index. Can be null.
Implementation of this class should likely be carefully designed to provide
proxy "lazy loading" for Reference attributes, since data sets potentially
wrapped by Reference may effectively be quite large.
When invoking this use case using a find method from a DataSource
...
public List(Object) find(String dataTypeIdentifier,
SearchFilter[] searchFilters,
String[] includedAttributes,
Map options)
...
This data source implements use case 'RetrieveTableReferenceWithGenericConstraints' (version 1.0.1) [Retrieve Table Reference With Generic Constraints]:
Extends the Retrieve Table Reference use case by providing a generic way to
constrain the row and columns by column id or name, and/or row id or name of a file.
The searchable attributes on this use case are somewhat very generic.
It is suggested, therefore, that this use case be judiciously extended by
other more context specific use cases that need to return Table Reference,
in order to enrich it with additional searchable attributes for specific
usage contexts (e.g. returning specific kinds of Table Reference,
like Passport Table References, etc.)
No particular searchable attribute is specified as "mandatory" but
clearly, at least one searchable attribute needs to be specified
so that the query makes sense (datatype has "requiredSearch" set).
The default returned attributes are null, implying that the use case should
just to return a sensibly complete implementation of a Table Reference object.
|
| METADATA | NAME | VALUE |
| DataType|org.generationcp.model.data.genotype.GenotypeStudyD ataTypeAttribute|java.lang.String|org.generationcp.model.dat a.genotype.GenotypeStudy#name |
GCP_WARDA | |
| use-case | 'RetrieveStudies' (version 1.4.2) [classification: /Study] [Retrieve Studies]
This use case returns a basic list of Study entities with limited annotation.
A Study is a kind of GCP data Entity analogous to a spreadsheet
(e.g. MS Excel type) or relational database table that documents
experimental data for a single experiment of a specified Project
into a matrix in which columns represent experimental variables
and rows, the distinct observations of those variables.
In addition to an unique identifier plus a human readable name and description,
this use case returns a "studies" attribute of the Study which is strictly
interpreted here to be a parent study that aggregates (i.e. specifies
hierarchical classification of) the given study within a larger study
context (e.g. an ICIS study "folder"). Searches may be made by unique identifier
or by name against, in order to retrieve sub-studies within the classification.
A Study may also have a specified "type", specified by an ontology term
(added in version 1.4 of this use case)
,'RetrieveGermplasmStudies' (version 1.2.8) [classification: /Study/GermplasmStudy] extends: RetrieveStudies [Retrieve Germplasm Studies]
This use case returns list of GermplasmStudy entities. This use case is a specialization of the core Retrieve Studies use case.
The GermplasmStudy is the derived form of a generic Study and is
associated with observations on a specific GermplasmSet. Such a study
would generally record treatment, growth and environmental conditions
as Treatment and GrowthCondition study factors, for plants grown in
the field, greenhouse or equivalent environment plus the Phenotype
observations of the plant.
,'RetrieveGenotypeStudies' (version 1.2.3) [classification: /Study/GermplasmStudy/LaboratoryGermplasmStudy/GenotypeStudy] extends: RetrieveGermplasmStudies [Retrieve Genotype Studies]
This use case returns list of GenotypeStudy entities. This use case
is a specialization of the core Retrieve Germplasm Studies use case.
The GenotypeStudy is the derived form of a generic Study and is
associated with observations on a specific GermplasmSet used in genotyping. Such a study
would generally record the presence or absence of specific alleles for certain markers within the
specific GermplasmSet.
,'RetrieveGermplasms' (version 1.6.0) [classification: /Germplasm] [Retrieve Germplasms]
These use cases refer to the querying of germplasm data. This contains the entrypoint use cases
for client applications/programs. For the International Crop Information System for example,
a typical search will start with getting a list of germplasms with names similar to a
specified germplasm name. Information about a particular germplasm can then be obtained.
Here are some simple Germplasm queries that can be used as entry point queries or as part
of more complex queries. In all the queries below the type of the objects returned from
the find method would be a list of Germplasm.
,'RetrieveStudyObservationUnits' (version 1.2.6) [classification: /Study/ObservationUnit] [Retrieve Study Observation Units]
This use case returns list of ValueSet entities.
,'RetrieveStudyEffects' (version 1.2.7) [classification: /Study/Effect] [Retrieve Study Effects]
This use case returns list of Effect entities.
,'RetrieveFactorLevels' (version 1.0.0) [classification: /Study/Factor/Levels] [Retrieve Factor Levels]
This use case returns list of Constraint entities.
,'RetrieveStudyFeatureConstraints' (version 1.0.2) [classification: /Study/Feature] [Retrieve Study Feature Constraints]
This use case returns list of Constraint entities that is related to a specific study feature.
The Constraint has information of all the possible values of a given study feature.
,'RetrieveVariateDataRange' (version 1.2.4) [classification: /Study/Variate/DataRange] [Retrieve Variate DataRange]
This use case returns list of Constraint entities.
,'RetrieveGenomicFeatureDetectors' (version 1.1.0) [classification: /Genotype/GenomicFeatureDetector] [Retrieve Genomic Feature Detectors]
This use case returns list of GenomicFeatureDetector entities.
,'RetrieveDetectedVariants' (version 1.2.5) [classification: /Genotype/DetectedVariant] [Retrieve Detected Variants]
This use case returns list of DetectedVariant entities.
,'RetrieveGermplasmSets' (version 1.0.2) [classification: /Germplasm] [Retrieve Germplasm Sets]
This use case refers to the retrieval of sets of Germplasm where such
sets are formally managed for example, within the list management
table of the International Crop Information System (ICIS).
This use case only provides some basic search facilities based on list identifier,
name or description. The GermplasmSet returned has Germplasm members that should
be annotated appropropriately with all available information (e.g. the information
found in the ICIS ListData table, for each entry).
,'RetrieveDocumentedFeatureTypes' (version 1.0.0) [classification: /Feature] [Retrieve Documented Feature Types]
A simple query by name on a Feature "type" attribute
can be productively used to identify the list of ontology terms
with associated meta-data.
Since the "type" attribute is a SimpleOntologyTerm by definition,
we create an external attribute, "DocumentedType" to
signal the return of such a fully documented Feature type.
The use case supports search filters that return
various subsets of Feature type ontology terms:
* Search by unique identifier of the ontology to which the Feature type ontology term belongs
* Search by name (could be wild card) of the ontology to which the Feature type ontology term belongs
* Search by unique identifier of the Feature type ontology term
* Search by name of the Feature type ontology term
* Search by description (definition) of the Feature type ontology term
* Search by unique identifier of the "parent" ("group") term of the Feature type
* Search by name of the "parent" ("group") term of the Feature type
The return attributes of the "documented type" are left deliberately open ended,
such that the DataSource is free to all available meta-data known about the
type attribute and simply return "null" or "empty" attribute
values for any meta-data field which has no meta-data in the database.
A practical example of this is that the implementation in the ICIS database
of searches against the DMS property table might return "group" (i.e. the parent value),
the property name, the property definition, an acronym (as a "synonym") and
perhaps, even a list of DMS studies annotated with this property.
,'RetrieveTabularData' (version 1.0.0) [classification: /Value/TabularData] [Retrieve Tabular Data]
The GCP domain model documents a TabularData object
to be of the following Java interface structure:
public interface TabularData extends Value
...
public Object valueAt(int rowIndex, int columnIndex);
public int getColumnCount();
public List(Object) getColumnHeaderList();
public int getRowCount();
public List(Object) getRowHeaderList();
...
This basic use case returns a single tabular data object, where the
columns and the row header objects are assumed to be unique
SimpleFeature objects indexing the values in a table.
The table entries themselves are expected to be to be Value objects
of a given specified data type (specified by the "type" ontology term)
and which have a specified human readable "valueString" value. If the
value is a vector, the human readable label of each member of the vector
should listed in the valueString comma delimited. The "data" attribute
of the value may return a more complex Java representation of the value,
of a sensible Java type that the context of the query might expect.
The "index" attribute of each Value should point to its associated
column and row header SimpleFeature object.
In both cases - for the SimpleFeature row and column headers, as well as,
for the Value entries returned inside the table - the associated
uniqueIdentifiers may be used by applications in other use cases
that retrieve more complex representations of the underlying objects
concerned. The uniqueIdentifiers, following the adopted LSID
formatting protocol specified in the Identification domain model
documentation for the GCP domain model, may be parsed to identify
the kind of row, column and entry data types in the table.
The searchable attributes on this use case are somewhat very generic.
It is suggested, therefore, that this use case be judiciously extended by
other more context specific use cases that need to return TabularData,
in order to enrich it with additional searchable attributes for specific
usage contexts (e.g. returning specific kinds of TabularData,
like GenotypeStudy tables, etc.)
No particular searchable attribute is specified as "mandatory" but
clearly, at least one searchable attribute needs to be specified
so that the query makes sense (datatype has "requiredSearch" set).
The default returned attributes are null, implying that the use case should
just to return a sensibly complete implementation of a TabularData object.
Note that the TabularData itself extends Value which extends SimpleFeature
which extends SimpleIdentifier. Hence, the full attributes available
in the top level object should include those of the superclass interfaces:
uniqueIdentifier: should generally identify the source data set/study
name: should be a human readable title sensibly labeling the table
type: the "type" attribute of the object should generally be
taken from a controlled vocabulary that specifies information (for developers
and/or users, and embodied in the code of applications accessing the object)
about the format of the complete "data" format returned.
valueString: at the level of the full tabular data, it is suggested that
the object return a comma delimited (CSV-style) listing of the data table
that facilitates text serialization of the table to the end user.
data: What the "data" attribute of the implementation returns is
context-specific (not defined fully by this use case). This should
ideally be a Java computable data structure suitable for the intended
purpose and code-level manipulations of the data (if not directly wrapped
by a direct extension/implementation of the TabularData interface itself)
index: this use case doesn't provide any specific semantics for index. Can be null.
constraints: if the TabularData returned is less than the full underlying
data set from which the tabular data is constructed, then constraint
objects may be (optionally) returned which indicates discrete enumeration
or numeric range limits of the returned data table. That said, this use
case gives no prescription on what these specific constraints should
look like (it is suggested that use case extensions provide such information).
Implementation of this class should likely be carefully designed to provide
proxy "lazy loading" for TabularData attributes, since data sets potentially
wrapped by TabularData may effectively be quite large.
,'RetrieveTabularDataWithGenericConstraints' (version 1.0.0) [classification: /Value/TabularData] extends: RetrieveTabularData [Retrieve Tabular Data With Generic Constraints]
Extends the Retrieve Tabular Data use case by providing a genetic way to
constrain the row and columns by column id or name, and/or row id or name
The searchable attributes on this use case are somewhat very generic.
It is suggested, therefore, that this use case be judiciously extended by
other more context specific use cases that need to return TabularData,
in order to enrich it with additional searchable attributes for specific
usage contexts (e.g. returning specific kinds of TabularData,
like GenotypeStudy tables, etc.)
No particular searchable attribute is specified as "mandatory" but
clearly, at least one searchable attribute needs to be specified
so that the query makes sense (datatype has "requiredSearch" set).
The default returned attributes are null, implying that the use case should
just to return a sensibly complete implementation of a TabularData object.
,'RetrieveReference' (version 1.0.1) [classification: /Value/Reference] [Retrieve Reference]
This use case provides a base use case for all Reference use cases
by providing details of the returned attributes, but not searchable attributes.
This use case MUST not be implemented directly. A sub use case defining one or more
searchable attributes must be used.
The GCP domain model documents a Reference object
to be of the following Java interface structure:
public interface Reference extends Value
...
public Date getCreationDate();
public Date getExpirationDate();
public URL getURL();
public String getMimeType();
public Long getFileSize();
public String getUserFriendlyFilename();
...
This basic use case returns a single reference object with attributes namely:
url: should be a URL object containing the real file path/address of the reference searched
mimetype: returns the type of information a file contains
creation date: the expiration date of the file from the given url
expiration date: the expiration date of the file from the given url
filesize: the size of the file from the given url
userfriendlyfilename: the suggested file name that is easily read or understood by users
Note that the TabularData itself extends Value which extends SimpleFeature
which extends SimpleIdentifier. Hence, the full attributes available
in the top level object should include those of the superclass interfaces:
uniqueIdentifier: should generally identify the source data set/study
name: should be a human readable title sensibly labeling the reference
type: the "type" attribute of the object should generally be
taken from a controlled vocabulary that specifies information (for developers
and/or users, and embodied in the code of applications accessing the object)
about the format of the complete "data" format returned.
valueString: this use case doesn't provide any specific semantics for index. Can be null.
data: this use case doesn't provide any specific semantics for index. Can be null.
index: this use case doesn't provide any specific semantics for index. Can be null.
constraints: this use case doesn't provide any specific semantics for index. Can be null.
Implementation of this class should likely be carefully designed to provide
proxy "lazy loading" for Reference attributes, since data sets potentially
wrapped by Reference may effectively be quite large.
When invoking this use case using a find method from a DataSource
...
public List(Object) find(String dataTypeIdentifier,
SearchFilter[] searchFilters,
String[] includedAttributes,
Map options)
...
,'RetrieveTableReference' (version 1.0.1) [classification: /Value/Reference/TableReference] extends: RetrieveReference [Retrieve Table Reference]
This use case provides a base use case for all Table Reference use cases
by providing details of the returned attributes, but not searchable attributes.
This use case MUST not be implemented directly. A sub use case defining one or more
searchable attributes must be used.
The GCP domain model documents a Reference object
to be of the following Java interface structure:
public interface Table Reference extends Value
...
public int getColumnCount();
public List(Object) getColumnHeaderList();
public int getRowCount();
public List(Object) getRowHeaderList();
...
This basic use case returns a single table reference object consisting
of a url which points to a file that can be associated as a table or matrix.
The file may OPTIONALLY have headers, which can be one of the following:
1) SimpleFeature identifier objects
2) Primitive values of type String or Number.
For row and column headers of type SimpleFeature and elements of
type Value the associated uniqueIdentifiers may be used by
applications in other use cases that retrieve more complex
representations of the underlying objects concerned.
The uniqueIdentifiers, following the adopted LSID
formatting protocol specified in the Identification domain model
documentation for the GCP domain model, may be parsed to identify
the kind of row, column and entry data types in the table.
Note that the TableReference itself extends Reference which extends Value which extends SimpleFeature
which extends SimpleIdentifier. Hence, the full attributes available
in the top level object should include those of the superclass interfaces:
url: should be a URL object containing the real file path/address of the reference searched
mimetype: returns the type of information a file contains
creation date: the creation date of the file from the given url
expiration date: the expiration date of the file from the given url
filesize: the size of the file from the given url
userfriendlyfilename: the suggested file name that is easily read or understood by users
uniqueIdentifier: should generally identify the source data set/study
name: should be a human readable title sensibly labeling the reference
type: the "type" attribute of the object should generally be
taken from a controlled vocabulary that specifies information (for developers
and/or users, and embodied in the code of applications accessing the object)
about the format of the complete "data" format returned.
valueString: this use case doesn't provide any specific semantics for index. Can be null.
data: this use case doesn't provide any specific semantics for index. Can be null.
index: this use case doesn't provide any specific semantics for index. Can be null.
constraints: this use case doesn't provide any specific semantics for index. Can be null.
Implementation of this class should likely be carefully designed to provide
proxy "lazy loading" for Reference attributes, since data sets potentially
wrapped by Reference may effectively be quite large.
When invoking this use case using a find method from a DataSource
...
public List(Object) find(String dataTypeIdentifier,
SearchFilter[] searchFilters,
String[] includedAttributes,
Map options)
...
,'RetrieveTableReferenceWithGenericConstraints' (version 1.0.1) [classification: /Value/Reference/TableReference] extends: RetrieveTableReference [Retrieve Table Reference With Generic Constraints]
Extends the Retrieve Table Reference use case by providing a generic way to
constrain the row and columns by column id or name, and/or row id or name of a file.
The searchable attributes on this use case are somewhat very generic.
It is suggested, therefore, that this use case be judiciously extended by
other more context specific use cases that need to return Table Reference,
in order to enrich it with additional searchable attributes for specific
usage contexts (e.g. returning specific kinds of Table Reference,
like Passport Table References, etc.)
No particular searchable attribute is specified as "mandatory" but
clearly, at least one searchable attribute needs to be specified
so that the query makes sense (datatype has "requiredSearch" set).
The default returned attributes are null, implying that the use case should
just to return a sensibly complete implementation of a Table Reference object.
| |
| DataType|org.generationcp.model.data.genotype.DetectedVarian tDataTypeAttribute|org.generationcp.model.data.genotype.Geno micFeatureDetector|org.generationcp.model.data.genotype.Dete ctedVariant#detector&DataTypeAttribute|java.lang.String|org. generationcp.model.data.genotype.GenomicFeatureDetector#uniq ueIdentifier |
29 | |
| DataType|org.generationcp.model.core.ontology.OntologyTerm|o rg.generationcp.model.core.feature.Feature#documentedTypeDat aType|org.generationcp.model.core.ontology.OntologyTerm|org. generationcp.model.core.feature.Feature#documentedType&DataT ypeAttribute|java.lang.String|org.generationcp.model.core.on tology.OntologyTerm#uniqueIdentifier |
1003 | |
| DataType|org.generationcp.model.core.ontology.OntologyTerm|o rg.generationcp.model.core.feature.Feature#documentedTypeDat aType|org.generationcp.model.core.ontology.OntologyTerm|org. generationcp.model.core.feature.Feature#documentedType&DataT ypeAttribute|java.lang.String|org.generationcp.model.core.on tology.OntologyTerm#name |
GRAIN YIELD | |
| DataType|org.generationcp.model.core.value.ValueSet|org.gene rationcp.model.core.study.Study#observationUnitsDataTypeAttr ibute|org.generationcp.model.core.value.ValueSet|org.generat ioncp.model.core.study.Study#observationUnits&DataTypeAttrib ute|org.generationcp.model.core.value.Value|org.generationcp .model.core.value.ValueSet#values&DataTypeAttribute|java.lan g.String|org.generationcp.model.core.value.Value#valueString |
225503 | |
| DataType|org.generationcp.model.data.germplasm.GermplasmStud yDataTypeAttribute|java.lang.String|org.generationcp.model.d ata.germplasm.GermplasmStudy#uniqueIdentifier |
641 | |
| DataType|org.generationcp.model.data.genotype.DetectedVarian tDataTypeAttribute|org.generationcp.model.core.study.Study|o rg.generationcp.model.data.genotype.DetectedVariant#studies& DataTypeAttribute|java.lang.String|org.generationcp.model.da ta.genotype.GenotypeStudy#name |
GCP_WARDA | |
| DataType|org.generationcp.model.data.germplasm.GermplasmData TypeAttribute|org.generationcp.model.core.identification.Ide ntifierSet|org.generationcp.model.data.germplasm.Germplasm#s ynonyms&DataTypeAttribute|org.generationcp.model.core.identi fication.SimpleIdentifier|org.generationcp.model.core.identi fication.IdentifierSet#identifiers&DataTypeAttribute|java.la ng.String|org.generationcp.model.core.identification.SimpleI dentifier#name |
IR 64 | |
| DataType|org.generationcp.model.data.genotype.DetectedVarian tDataTypeAttribute|org.generationcp.model.core.study.Study|o rg.generationcp.model.data.genotype.DetectedVariant#studies& DataTypeAttribute|org.generationcp.model.data.germplasm.Germ plasmSet|org.generationcp.model.data.genotype.GenotypeStudy# germplasm&DataTypeAttribute|java.lang.String|org.generationc p.model.data.germplasm.Germplasm#uniqueIdentifier |
-4620 | |
| DataType|org.generationcp.model.data.germplasm.GermplasmSetD ataTypeAttribute|java.lang.String|org.generationcp.model.dat a.germplasm.GermplasmSet#name |
2002-018 | |
| DataType|org.generationcp.model.data.genotype.DetectedVarian tDataTypeAttribute|org.generationcp.model.core.study.Study|o rg.generationcp.model.data.genotype.DetectedVariant#studies& DataTypeAttribute|java.lang.String|org.generationcp.model.da ta.genotype.GenotypeStudy#uniqueIdentifier |
638 | |
| DataType|org.generationcp.model.core.value.constraint.Constr aint|org.generationcp.model.core.study.Factor#levelsDataType Attribute|java.lang.String|org.generationcp.model.core.study .Factor#uniqueIdentifier |
200 | |
| DataType|org.generationcp.model.data.genotype.DetectedVarian tDataTypeAttribute|org.generationcp.model.data.genotype.Geno micFeatureDetector|org.generationcp.model.data.genotype.Dete ctedVariant#detector&DataTypeAttribute|java.lang.String|org. generationcp.model.data.genotype.GenomicFeatureDetector#name |
RM338 | |
| DataType|org.generationcp.model.data.germplasm.GermplasmStud yDataTypeAttribute|org.generationcp.model.data.germplasm.Ger mplasmSet|org.generationcp.model.data.germplasm.GermplasmStu dy#germplasm&DataTypeAttribute|java.lang.String|org.generati oncp.model.data.germplasm.Germplasm#uniqueIdentifier |
242 | |
| DataType|org.generationcp.model.data.genotype.DetectedVarian tDataTypeAttribute|java.lang.String|org.generationcp.model.d ata.genotype.DetectedVariant#uniqueIdentifier |
10 | |
| DataType|org.generationcp.model.data.germplasm.GermplasmData TypeAttribute|java.lang.String|org.generationcp.model.data.g ermplasm.Germplasm#uniqueIdentifier |
urn:lsid:irri.org:IRIS.Germplasm:1:1 | |
| DataType|org.generationcp.model.data.genotype.GenomicFeature DetectorDataTypeAttribute|java.lang.String|org.generationcp. model.data.genotype.GenomicFeatureDetector#name |
RM431 | |
| DataType|org.generationcp.model.core.ontology.OntologyTerm|o rg.generationcp.model.core.feature.Feature#documentedTypeDat aType|org.generationcp.model.core.ontology.OntologyTerm|org. generationcp.model.core.feature.Feature#documentedType&DataT ypeAttribute|org.generationcp.model.core.ontology.Ontology|o rg.generationcp.model.core.ontology.SimpleOntologyTerm#ontol ogy&DataTypeAttribute|java.lang.String|org.generationcp.mode l.core.ontology.Ontology#uniqueIdentifier |
1 | |
| DataType|org.generationcp.model.core.study.StudyDataTypeAttr ibute|java.lang.String|org.generationcp.model.core.study.Stu dy#name |
GCP_IRRI | |
| DataType|org.generationcp.model.core.study.StudyDataTypeAttr ibute|java.lang.String|org.generationcp.model.core.study.Stu dy#uniqueIdentifier |
3 | |
| crop-name | Rice | |
| DataType|org.generationcp.model.core.study.Effect|org.genera tioncp.model.core.study.Study#effectsDataTypeAttribute|java. lang.String|org.generationcp.model.core.study.Study#name |
GCP_IRRI | |
| DataType|org.generationcp.model.data.germplasm.GermplasmSetD ataTypeAttribute|java.lang.String|org.generationcp.model.dat a.germplasm.GermplasmSet#description |
INGER DIRECT NOM IRBN AND IRTN 2004 | |
| DataType|org.generationcp.model.data.genotype.GenomicFeature DetectorDataTypeAttribute|java.lang.String|org.generationcp. model.data.genotype.GenomicFeatureDetector#uniqueIdentifier |
urn:lsid:irri.org:IRIS.GenomicFeatureDetector:1:1 | |
| DataType|org.generationcp.model.data.germplasm.GermplasmStud yDataTypeAttribute|java.lang.String|org.generationcp.model.d ata.germplasm.GermplasmStudy#name |
OYT2001DS | |
| DataType|org.generationcp.model.core.ontology.OntologyTerm|o rg.generationcp.model.core.feature.Feature#documentedTypeDat aType|org.generationcp.model.core.ontology.OntologyTerm|org. generationcp.model.core.feature.Feature#documentedType&DataT ypeAttribute|org.generationcp.model.core.ontology.SimpleOnto logyTerm|org.generationcp.model.core.ontology.SimpleOntology Term#parentTerm&DataTypeAttribute|java.lang.String|org.gener ationcp.model.core.ontology.SimpleOntologyTerm#uniqueIdentif ier |
1 | |
| use-case-source | jar:file:/C:/Documents%20and%20Settings/manacleto/.m2/reposi | |
| DataType|org.generationcp.model.data.genotype.GenotypeStudyD ataTypeAttribute|java.lang.String|org.generationcp.model.dat a.genotype.GenotypeStudy#uniqueIdentifier |
640 | |
| DataType|org.generationcp.model.data.genotype.DetectedVarian tDataTypeAttribute|org.generationcp.model.core.study.Study|o rg.generationcp.model.data.genotype.DetectedVariant#studies& DataTypeAttribute|org.generationcp.model.data.germplasm.Germ plasmSet|org.generationcp.model.data.genotype.GenotypeStudy# germplasm&DataTypeAttribute|java.lang.String|org.generationc p.model.data.germplasm.Germplasm#name |
ZS004 | |
| DataType|org.generationcp.model.data.genotype.GenomicFeature DetectorDataTypeAttribute|org.generationcp.model.core.study. Study|org.generationcp.model.data.genotype.GenomicFeatureDet ector#studies&DataTypeAttribute|java.lang.String|org.generat ioncp.model.data.genotype.GenotypeStudy#uniqueIdentifier |
640 | |
| DataType|org.generationcp.model.data.genotype.DetectedVarian tDataTypeAttribute|java.lang.String|org.generationcp.model.d ata.genotype.DetectedVariant#name |
181 | |
| DataType|org.generationcp.model.core.ontology.OntologyTerm|o rg.generationcp.model.core.feature.Feature#documentedTypeDat aType|org.generationcp.model.core.ontology.OntologyTerm|org. generationcp.model.core.feature.Feature#documentedType&DataT ypeAttribute|java.lang.String|org.generationcp.model.core.on tology.OntologyTerm#description |
Weight of harvested grain expressed as tons/ha with a moisture content of 14%. | |
| DataType|org.generationcp.model.core.value.ValueSet|org.gene rationcp.model.core.study.Study#observationUnitsDataTypeAttr ibute|org.generationcp.model.core.study.Effect|org.generatio ncp.model.core.study.Study#effects&DataTypeAttribute|java.la ng.String|org.generationcp.model.core.study.Effect#uniqueIde ntifier |
1532 | |
| DataType|org.generationcp.model.data.germplasm.GermplasmSetD ataTypeAttribute|java.lang.String|org.generationcp.model.dat a.germplasm.GermplasmSet#uniqueIdentifier |
1 | |
| DataType|org.generationcp.model.data.genotype.GenotypeStudyD ataTypeAttribute|org.generationcp.model.data.germplasm.Germp lasmSet|org.generationcp.model.data.germplasm.GermplasmStudy #germplasm&DataTypeAttribute|java.lang.String|org.generation cp.model.data.germplasm.Germplasm#uniqueIdentifier |
402913 | |
| DataType|org.generationcp.model.data.germplasm.GermplasmData TypeAttribute|org.generationcp.model.data.germplasm.Germplas mLocation|org.generationcp.model.data.germplasm.Germplasm#lo cations&DataTypeAttribute|java.lang.String|org.generationcp. model.data.germplasm.GermplasmLocation#name |
PHILIPPINES | |
| DataType|org.generationcp.model.core.study.Effect|org.genera tioncp.model.core.study.Study#effectsDataTypeAttribute|java. lang.String|org.generationcp.model.core.study.Study#uniqueId entifier |
586 | |
| DataType|org.generationcp.model.core.ontology.OntologyTerm|o rg.generationcp.model.core.feature.Feature#documentedTypeDat aType|org.generationcp.model.core.ontology.OntologyTerm|org. generationcp.model.core.feature.Feature#documentedType&DataT ypeAttribute|org.generationcp.model.core.ontology.SimpleOnto logyTerm|org.generationcp.model.core.ontology.SimpleOntology Term#parentTerm&DataTypeAttribute|java.lang.String|org.gener ationcp.model.core.ontology.SimpleOntologyTerm#name |
AGRONOMIC | |
| DataType|org.generationcp.model.core.value.constraint.Constr aint|org.generationcp.model.core.study.Variate#dataRangeData TypeAttribute|java.lang.String|org.generationcp.model.core.s tudy.Variate#uniqueIdentifier |
2 | |
| DataType|org.generationcp.model.data.genotype.GenomicFeature DetectorDataTypeAttribute|org.generationcp.model.core.study. Study|org.generationcp.model.data.genotype.GenomicFeatureDet ector#studies&DataTypeAttribute|java.lang.String|org.generat ioncp.model.data.genotype.GenotypeStudy#name |
GCP_IRRI | |
| DataType|org.generationcp.model.core.value.TabularDataDataTy peAttribute|java.lang.String|org.generationcp.model.core.val ue.TabularData#uniqueIdentifier |
urn:lsid:irri.org:IRIS.Representation:2:1 |
| sort-asc | true,true |
distinct | false |
sorted-by | DataTypeAttribute|java.lang.Object|org.generationcp.model.co |
| Tabular Data | Name: | Tabular Data |
| Identification: | DataType|org.generationcp.model.core.value.TabularData | |
| Description: | Simple Tabular Data with SimpleFeature Row and Column Headers indexing Value Entries | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Tabular Data Unique Identifier | |
| DESCRIPTION | Unique identifier of the tabular data set, usually of a Study Effect from which the data was retrieved Filter search by data set unique identifier (e.g. a Study Effects unique identifier) | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Tabular Data Name | |
| DESCRIPTION | Name of the tabular data set, usually of a Study Effect from which the data was retrieved Filter search by data set name (e.g. a Study Effects name) | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|org.generationcp.model.core.ontology.Simpl | |
| NAME | Tabular Data Type Unique Identifier | |
| DESCRIPTION | Unique Identifier of the Ontology Term for Tabular Data Type Search against the "type" of the TabularData, where the type value is an "SimpleOntologyTerm" drawn from an ontology that identifies the DataSource-specified complex semantics of the table of data returned, e.g. "GenotypeMatrix". This ontology may express the scope of data of the elements in the table. For example the data may be all string values, primitive values (int, double, string etc), Value objects. If the type of value is a domain model object, the scope of the object may be defined. That is which attributes would filled, such as simple identifier, name etc. | |
| OPERATOR | org.generationcp.demeter:operators:equal | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Column Header Type Ontology Term UniqueIdentifier | |
| DESCRIPTION | Unique Identifier of the Ontology Term of the Type of TabularData Column Header Specify the type of feature to be set as the column headers. | |
| OPERATOR | org.generationcp.demeter:operators:equal_in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Row Header Type Ontology Term UniqueIdentifier | |
| DESCRIPTION | Unique Identifier of the Ontology Term of the Type of TabularData Row Header Specify the type of features to be set as the row headers. More than one such type may be provided for matrix tables whose rows will be indexed by values of more than one row type. | |
| OPERATOR | org.generationcp.demeter:operators:equal_in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Column Header Name | |
| DESCRIPTION | Name of Tabular Data Column Header Filter table returned, by column identifier name | |
| OPERATOR | org.generationcp.demeter:operators:equal_in org.generationcp.demeter:operators:like_in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Row Header Name | |
| DESCRIPTION | Name of Tabular Data Row Header Filter table rows returned, by row identifier name | |
| OPERATOR | org.generationcp.demeter:operators:equal_in org.generationcp.demeter:operators:like_in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Entry ValueString | |
| DESCRIPTION | Tabular Data Entry Value Type Unique Identifier Retrieves only rows and columns which contain Value objects of a particular type, (e.g. Study Variates of a particular kind...) specified by an ontology term unique identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Entry ValueString | |
| DESCRIPTION | Tabular Data Entry Value ValueString Retrieves only rows and columns which contain a specified table entry, with hits modeled as matches against the valueString of the Value | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Entry Constraints | |
| DESCRIPTION | Tabular Data Entry Value Constraints
Retrieves only rows and columns which contain a specified table entry
satisfying specified Constraints on the Value.
This searchable attribute is potentially a very powerful filter on the
data Value objects to be returned. This use case does not document all
all possible constraints but it is suggested here that as a minimum,
the specification of row and column range constraints be supported, as follows:
1) Constraint of the range of column indices to be returned, expressed as an
IdentifierEnumeration object type. The "constraintDefinition" attribute
string should say "Column Identifier Constraint" to identify this kind of constraint
to the DataSource.
2) Constraint of the range of row indices returned, expressed as an
IdentifierEnumeration object type. The "constraintDefinition" attribute
string should say "Row Identifier Constraint" to identify this kind of
constraint to the DataSource.
3) If only two "identifiers" are provided in aforementioned IdentifierEnumeration object,
and the "constraintDefinition" attribute string reads "Column Identifier Range
Constraint" (for columns) or "Row Identifier Range Constraint" (for rows),
it can be assumed that they specify a range bounded by the two identifiers
specified, based on the collation order of that column or row identifier/entity type.
These kind of constraints may, in implementations of this use case, wish to avail
of some sort of "Constraint.type" ontology, to provide more precise semantics.
| |
| OPERATOR | org.generationcp.demeter:operators:constraint | |
| ID | DataTypeAttribute|org.generationcp.model.core.ontology.Simpl | |
| NAME | Tabular Data Type Unique Identifier | |
| DESCRIPTION | Unique Identifier of the Ontology Term for Tabular Data Type Search against the "type" of the TabularData, where the type value is an "SimpleOntologyTerm" drawn from an ontology that identifies the DataSource-specified complex semantics of the table of data returned, e.g. "GenotypeMatrix". This ontology may express the scope of data of the elements in the table. For example the data may be all string values, primitive values (int, double, string etc), Value objects. If the type of value is a domain model object, the scope of the object may be defined. That is which attributes would filled, such as simple identifier, name etc. | |
| OPERATOR | org.generationcp.demeter:operators:equal | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Column Header Type Ontology Term UniqueIdentifier | |
| DESCRIPTION | Unique Identifier of the Ontology Term of the Type of TabularData Column Header Specify the type of feature to be set as the column headers. | |
| OPERATOR | org.generationcp.demeter:operators:equal_in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Row Header Type Ontology Term UniqueIdentifier | |
| DESCRIPTION | Unique Identifier of the Ontology Term of the Type of TabularData Row Header Specify the type of features to be set as the row headers. More than one such type may be provided for matrix tables whose rows will be indexed by values of more than one row type. | |
| OPERATOR | org.generationcp.demeter:operators:equal_in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Column Header Unique Identifier | |
| DESCRIPTION | Unique Identifier of Tabular Data Column Header Filter table returned, by column identifier unique identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Column Header Name | |
| DESCRIPTION | Name of Tabular Data Column Header Filter table returned, by column identifier name | |
| OPERATOR | org.generationcp.demeter:operators:equal_in org.generationcp.demeter:operators:like_in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Row Header Unique Identifier | |
| DESCRIPTION | Unique Identifier of Tabular Data Row Header Filter table rows returned, by row identifier unique identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Row Header Name | |
| DESCRIPTION | Name of Tabular Data Row Header Filter table rows returned, by row identifier name | |
| OPERATOR | org.generationcp.demeter:operators:equal_in org.generationcp.demeter:operators:like_in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Entry ValueString | |
| DESCRIPTION | Tabular Data Entry Value Type Unique Identifier Retrieves only rows and columns which contain Value objects of a particular type, (e.g. Study Variates of a particular kind...) specified by an ontology term unique identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Tabular Data Entry ValueString | |
| DESCRIPTION | Tabular Data Entry Value ValueString Retrieves only rows and columns which contain a specified table entry, with hits modeled as matches against the valueString of the Value | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|org.generationcp.model.core.value.constrai | |
| NAME | Tabular Data Entry Constraints | |
| DESCRIPTION | Specifies the constraints that have been applied to this Tabular Data. See main description for valid values Retrieves only specified rows and/or columns or row and/or columns that contain a specified table elements satisfying specified Constraints on the Value. This attribute must be used in conjunction with one or Constraint objects. These Constraint objects must be included in the Constraints attribute of returned TabularData object. This searchable attribute is potentially a very powerful filter on which elements are to be returned. The following Constraints are possible 1) Specified Columns: Constrain the range and order of the columns to be returned. For data with column headers, the an enumeration object should be used containing the headers themselves. Possible constraint types are: a) IdentifierEnumeration should be used for column headers of type SimpleIdentifier b) TermEnumeration should be used for column headers of type SimpleOntologyTerm c) StringEnumeration should be used for column headers of type String d) ValueEnumeration should be used for column headers of all other types and in the cases where column headers are not available and a simple zero-based index is used e) NumericalRange can be used to define zero-based index range for the required columns. In this case the column order would be the natural of the data The "constraintDefinition" attribute string should say "Column Identifier Constraint" to identify this kind of constraint to the DataSource. 2) TabularDataConstraint of the range of row indices returned, having a constraint object of type IdentiferEnumeration which was retrieved from the getConstraint method of the given TabularDataConstraint object. The "constraintDefinition" attribute string should say "Row Identifier Constraint" to identify this kind of constraint to the DataSource. 2) Specified Rows: Constrain the range and order of the rows to be returned. For data with row headers, the an enumeration object should be used containing the headers themselves. Possible constraint types are: a) IdentifierEnumeration should be used for column headers of type SimpleIdentifier b) TermEnumeration should be used for row headers of type SimpleOntologyTerm c) StringEnumeration should be used for row headers of type String d) ValueEnumeration should be used for row headers of all other types and in the cases where row headers are not available and a simple zero-based index is used e) NumericalRange can be used to define zero-based index range for the required rows. In this case the row order would be the natural of the data The "constraintDefinition" attribute string should say "Row Identifier Constraint" to identify this kind of constraint to the DataSource. 3) Constraint on values in columns or rows. Constrain the columns or rows returned based on values in these rows or columns The only possible constraint type is TabularDataConstraint. The 'header' property of this TabularDataConstaint determines the column or row to which the 'constraint' of this TabularDataConstaint is applied. The value of 'constraint' can be any Constraint sub-type, its validity will depend on the type of the elements in the TabularData By default in the case of 1) and 2) if Constraint is not TabularDataConstraint "constraintDefinition" attribute does not specify if the Constraint is to be placed on columns or row, then it should be assumed that the Constraint is on columns. | |
| OPERATOR | org.generationcp.demeter:operators:constraint | |
| AVAILABLE ATTRIBUTES (ALL) | ||
| SUPPORTED OPTIONS | FILEPATH | Put here the path to where the files will be saved before download. |
| Reference | Name: | Reference |
| Identification: | DataType|org.generationcp.model.core.value.Reference | |
| Description: | Simple Reference that has url information of a file. | |
| SEARCHABLE ATTRIBUTES (NONE) | ||
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Reference Unique Identifier | |
| DESCRIPTION | Unique identifier of the reference, usually of a Study Effect from which the data was retrieved Unique identifier of the Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Reference Name | |
| DESCRIPTION | Name of the reference, usually of a Study Effect from which the data was retrieved Name of the Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Reference Creation Date | |
| DESCRIPTION | Date to when the file was created Creation Date of the Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Reference Expiration Date | |
| DESCRIPTION | Date to when the file will expire Expiration Date of the Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Reference URL | |
| DESCRIPTION | The URL of the file which the user usually needs for download URL of the Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Reference Mimetype | |
| DESCRIPTION | This has information of the type of file the user is expecting Mimetype of the Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Reference File Size | |
| DESCRIPTION | The size of a file. Usually used so that the user may know how large the file they want to download. File Size of the Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Reference User Friendly Filename | |
| DESCRIPTION | The suggested file name when saving/downloading the file. User Friendly Filename of the Reference | |
| SUPPORTED OPTIONS | ||
| Germplasm Study | Name: | Germplasm Study |
| Identification: | DataType|org.generationcp.model.data.germplasm.GermplasmStud | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Germplasm Study Unique Identifier | |
| DESCRIPTION | Search By Germplasm Study Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Germplasm Study Name | |
| DESCRIPTION | Search By Germplasm Study Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|org.generationcp.model.data.germplasm.Germ | |
| NAME | Germplasm Unique Identifier | |
| DESCRIPTION | Search By Germplasm Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Germplasm Study Unique Identifier | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Germplasm Study Name | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Germplasm Study Description | |
| SUPPORTED OPTIONS (NONE) | ||
| GenomicFeatureDetector | Name: | GenomicFeatureDetector |
| Identification: | DataType|org.generationcp.model.data.genotype.GenomicFeature | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | GenomicFeatureDetector Unique Identifier | |
| DESCRIPTION | Search by Genomic Feature Detector Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Genomic Feature Detector Name | |
| DESCRIPTION | Search by Genomic Feature Detector Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Genotype Study Unique Identifier | |
| DESCRIPTION | Search by Genotype Study Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Genotype Study Name | |
| DESCRIPTION | Search by Genotype Study Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | GenomicFeatureDetector Unique Identifier | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Genomic Feature Detector Name | |
| SUPPORTED OPTIONS (NONE) | ||
| Detected Variant | Name: | Detected Variant |
| Identification: | DataType|org.generationcp.model.data.genotype.DetectedVarian | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Detected Variant Unique Identifier | |
| DESCRIPTION | Search by Detected Variant Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Detected Variant Name | |
| DESCRIPTION | Search by Detected Variant Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|org.generationcp.model.data.genotype.Genom | |
| NAME | Genomic Feature Unique Identifier | |
| DESCRIPTION | Search by Genomic Feature Detector Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|org.generationcp.model.data.genotype.Genom | |
| NAME | Genomic Feature Name | |
| DESCRIPTION | Search by Genomic Feature Detector Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Germplasm Unique Identifier | |
| DESCRIPTION | Search by Germplasm Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Germplasm Name | |
| DESCRIPTION | Search by Germplasm Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Genotype Study Unique Identifier | |
| DESCRIPTION | Search by Genotype Study Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Genotype Study Name | |
| DESCRIPTION | Search by Genotype Study Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Detected Variant Unique Identifier | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Detected Variant Name | |
| ID | Detector | |
| NAME | Detector | |
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Genotype Study Description | |
| ID | DataTypeAttribute|org.generationcp.model.data.genotype.Genom | |
| NAME | Genomic Feature Unique Identifier | |
| ID | DataTypeAttribute|org.generationcp.model.data.genotype.Genom | |
| NAME | Genomic Feature Name | |
| SUPPORTED OPTIONS (NONE) | ||
| Germplasm | Name: | Germplasm |
| Identification: | DataType|org.generationcp.model.data.germplasm.Germplasm | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Germplasm Unique Identifier | |
| DESCRIPTION | Search by Germplasm Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Germplasm Name | |
| DESCRIPTION | Search by Germplasm Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|org.generationcp.model.data.germplasm.Germ | |
| NAME | Germplasm Country of Origin Name | |
| DESCRIPTION | search by country of origin | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Germplasm Unique Identifier | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Germplasm Name | |
| ID | DataTypeAttribute|org.generationcp.model.data.germplasm.Biol | |
| NAME | Germplasm BiologicalStatus | |
| ID | DataTypeAttribute|org.generationcp.model.core.organization.p | |
| NAME | Germplasm IntellectualProperty | |
| ID | DataTypeAttribute|org.generationcp.model.core.value.TimeValu | |
| NAME | Germplasm AcquisitionDate | |
| ID | DataTypeAttribute|org.generationcp.model.core.identification | |
| NAME | Germplasm Annotations | |
| DESCRIPTION | List of Feature objects that contain verious Germplasm details or attributes | |
| ID | DataTypeAttribute|org.generationcp.model.core.EntityRelation | |
| NAME | Germplasm Relationships | |
| DESCRIPTION |
List of EntityRelationship objects, one of this contains a List of Germplasm
objects which are the parents of this Germplasm
| |
| ID | DataTypeAttribute|org.generationcp.model.core.identification | |
| NAME | Germplasm CropName | |
| ID | DataTypeAttribute|org.generationcp.model.data.germplasm.Germ | |
| NAME | Germplasm Locations | |
| DESCRIPTION |
List of GermplasmLocation objects, one for country of origin, and one for location of collecting site
| |
| ID | DataTypeAttribute|org.generationcp.model.core.identification | |
| NAME | Germplasm Synonyms | |
| DESCRIPTION |
IdentifierSet object containg List of Identifier objects, for germplasm alternate names
| |
| ID | DataTypeAttribute|org.generationcp.model.core.publication.Bi | |
| NAME | Germplasm PrimaryCitation | |
| DESCRIPTION |
BiblioReference object containg info on publication about the germplasm
| |
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Germplasm Studies | |
| DESCRIPTION |
Studies involving this Germplasm
| |
| SUPPORTED OPTIONS (NONE) | ||
| Study Effects | Name: | Study Effects |
| Identification: | DataType|org.generationcp.model.core.study.Effect|org.genera | |
| Description: | Study Effects | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Study Unique Identifier | |
| DESCRIPTION | Search by Study Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Study Name | |
| DESCRIPTION | Search by Study Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|org.generationcp.model.core.study.Effect|o | |
| NAME | Effect Unique Identifier | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Study Unique Identifier | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Study Name | |
| SUPPORTED OPTIONS (NONE) | ||
| GermplasmSet | Name: | GermplasmSet |
| Identification: | DataType|org.generationcp.model.data.germplasm.GermplasmSet | |
| Description: | A list of Germplasm is represented in the GCP domain model by the GermplasmSet model, which inherits attributes from the Entity model some of which are returned by this use case as available attributes. | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | GermplasmSet Unique Identifier | |
| DESCRIPTION | Search by GermplasmSet Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | GermplasmSet Name | |
| DESCRIPTION | Search by GermplasmSet Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | GermplasmSet Description | |
| DESCRIPTION | Title or description of the GermplasmSet Search by GermplasmSet Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | GermplasmSet Unique Identifier | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | GermplasmSet Name | |
| ID | DataTypeAttribute|org.generationcp.model.core.ontology.Simpl | |
| NAME | GermplasmSet Type | |
| ID | DataTypeAttribute|org.generationcp.model.core.identification | |
| NAME | GermplasmSet Annotations | |
| DESCRIPTION | List of Feature objects that contain various ad hoc GermplasmSet meta-data such as list status (expressed as a SimpleOntologyTerm) | |
| ID | DataTypeAttribute|org.generationcp.model.core.EntityRelation | |
| NAME | GermplasmSet Relationships | |
| DESCRIPTION |
List of EntityRelationship objects pointing to enclosing GermplasmSet objects which represent aggregations
(folders) of this and other related GermplasmSets (i.e. dereferenced by the LIST_HIERARCHY attribute
of the ICIS LISTNAMES table).
| |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | GermplasmSet Description | |
| DESCRIPTION | Title or description of the GermplasmSet | |
| ID | DataTypeAttribute|org.generationcp.model.core.organization.L | |
| NAME | GermplasmSet Owner | |
| DESCRIPTION | Owner of the GermplasmSet | |
| ID | DataTypeAttribute|org.generationcp.model.core.value.TimeValu | |
| NAME | GermplasmSet Creation Date | |
| DESCRIPTION | Creation date of the GermplasmSet | |
| ID | DataTypeAttribute|org.generationcp.model.data.germplasm.Germ | |
| NAME | GermplasmSet Members | |
| DESCRIPTION | Germplasm objects that are Members of the GermplasmSet (i.e. as documented in the ICIS ListData table) | |
| SUPPORTED OPTIONS (NONE) | ||
| Feature Type as Ontology Term | Name: | Feature Type as Ontology Term |
| Identification: | DataType|org.generationcp.model.core.ontology.OntologyTerm|o | |
| Description: |
This subsidiary use case defines general retrievals of a fully documented OntologyTerm object
corresponding to the "type" attribute of a Feature, treated as a DataType.
| |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataType|org.generationcp.model.core.ontology.OntologyTerm|o | |
| NAME | Feature Type Ontology Unique Identifier | |
| DESCRIPTION | Unique Identifier of the Ontology to which the Feature Type Ontology Term belongs Search by unique identifier of the ontology to which the Feature "type" ontology term belongs | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataType|org.generationcp.model.core.ontology.OntologyTerm|o | |
| NAME | Feature Type Ontology Name | |
| DESCRIPTION | Name of the Ontology to which the Feature Type Ontology Term belongs Search by name of the ontology to which the Feature "type" ontology term belongs | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataType|org.generationcp.model.core.ontology.OntologyTerm|o | |
| NAME | Feature Type Unique identifier | |
| DESCRIPTION | Unique Identifier of the Feature Type Ontology Term Search by Feature "type" ontology term unique identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataType|org.generationcp.model.core.ontology.OntologyTerm|o | |
| NAME | Feature Type Name | |
| DESCRIPTION | Name of the Feature Type Ontology Term Search by Feature "type" ontology term name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataType|org.generationcp.model.core.ontology.OntologyTerm|o | |
| NAME | Feature Type Description | |
| DESCRIPTION | Description ("definition") of the Feature Type Ontology Term
Search by Feature "type" ontology term description | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataType|org.generationcp.model.core.ontology.OntologyTerm|o | |
| NAME | Feature Type Parent Term Unique Identifier | |
| DESCRIPTION | Unique Identifier of Feature type "Parent" term ("group") | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataType|org.generationcp.model.core.ontology.OntologyTerm|o | |
| NAME | Feature Type Parent Term Name | |
| DESCRIPTION | Name of the Feature type "Parent" term ("group") | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| AVAILABLE ATTRIBUTES (ALL) | ||
| SUPPORTED OPTIONS (NONE) | ||
| Study | Name: | Study |
| Identification: | DataType|org.generationcp.model.core.study.Study | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Study Unique Identifier | |
| DESCRIPTION | The Study unique identifier is the global, computer readable, study identifier (i.e. LSID) Search by Study Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Study Name | |
| DESCRIPTION | The Study name is usually a human readable short identifier of the study. Search by Study Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|org.generationcp.model.core.ontology.Simpl | |
| NAME | Study Type Unique Identifier | |
| DESCRIPTION | Search by Unique Identifier of the Study Type Ontology Term | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|org.generationcp.model.core.ontology.Simpl | |
| NAME | Study Type Name | |
| DESCRIPTION | Search by Name of the Study Type Ontology Term | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Study (Super) Study Unique Identifier | |
| DESCRIPTION | The unique identifier of a Study super classification (see also Study.studies attribute) which may be searched. Search by the Unique Identifier of an enclosing Study classification (i.e. ICIS Study folder identifier) | |
| OPERATOR | org.generationcp.demeter:operators:equal_in | |
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Study (Super) Study Name | |
| DESCRIPTION | The name of a Study super classification (see also Study.studies attribute) which may be searched. Search by the Name of an enclosing Study classification (i.e. ICIS Study folder identifier) | |
| OPERATOR | org.generationcp.demeter:operators:equal_in org.generationcp.demeter:operators:like_in | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Study Unique Identifier | |
| DESCRIPTION | The Study unique identifier is the global, computer readable, study identifier (i.e. LSID) | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Study Name | |
| DESCRIPTION | The Study name is usually a human readable short identifier of the study. | |
| ID | DataTypeAttribute|org.generationcp.model.core.ontology.Simpl | |
| NAME | Study Type | |
| DESCRIPTION | The Study type is an ontology term classifying the type of the study. | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Study Description | |
| DESCRIPTION | The Study Description is usually the full title of the Study. | |
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Study (Super) Studies | |
| DESCRIPTION | The Study "studies" attribute is generally a list of (usually one) hierarchical classification under which the current Study is classified (i.e. an ICIS Study folder). May be null if no such super study exists. | |
| SUPPORTED OPTIONS (NONE) | ||
| Simple Feature | Name: | Simple Feature |
| Identification: | DataType|java.lang.String|org.generationcp.model.core.featur | |
| Description: |
This use case returns list of Constraint entities.
These constraint has information of all the possible values of a given Study Feature.
It is required for this use case to specify the Simple Feature to be used as filter/limiting factor.
Note that the Constraint itself extends SimpleIdentifier.
Hence, the full attributes available in the top level object should include those of
the superclass interfaces:
uniqueIdentifier: should generally identify the constraint given.
name: not specified to be returned so can be null or may have the uniqueidentifier value as well.
There are more attributes that this object can fill but currently,
these are the attributes currently populated at the moment.
Take note as well that a Constraint has subinterfaces that is used for identification of the type of
Constraint it is in terms of the format, datatype or object structure of it in general.
The types are:
NumericRange - numeric data that are sually used for data which is continuous or dynamic in nature.
ValueEnumeration - can be character or numeric that usually gives a fixed range of values, usually done with labelling.
StringEnumeration - character that is usually an enumeration as well.
etc.
| |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Study Feature Name | |
| DESCRIPTION |
This dataTypeAttribute is used as a limiting filter for retrieving a list of Study Features.
This is also returned as a result by this use case.
Search by Study Simple Feature Name | |
| OPERATOR | org.generationcp.demeter:operators:equal | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|org.generationcp.model.core.study.Study|or | |
| NAME | Constraint Unique Identifier | |
| DESCRIPTION |
This is the dataTypeAttribute returned by this use case.
This is a list of GCP Constraint Objects.
| |
| SUPPORTED OPTIONS (NONE) | ||
| Study Observation Units | Name: | Study Observation Units |
| Identification: | DataType|org.generationcp.model.core.value.ValueSet|org.gene | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|org.generationcp.model.core.study.Effect|o | |
| NAME | Effect Unique Identifier | |
| DESCRIPTION |
This dataTypeAttribute is used as a limiting filter for retrieving a list of GCP ValueSet Objects.
This searchfilter is always required/mandatory.
Search by Effect Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:in org.generationcp.demeter:operators:equal | |
| ID | DataTypeAttribute|org.generationcp.model.core.value.ValueSet | |
| NAME | Value Value String | |
| DESCRIPTION |
This dataTypeAttribute is used as a limiting filter for retrieving a list of GCP ValueSet Objects.
Search by Level No | |
| OPERATOR | org.generationcp.demeter:operators:in org.generationcp.demeter:operators:equal | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|org.generationcp.model.core.value.ValueSet | |
| NAME | Study Observation Units | |
| DESCRIPTION |
This is a dataTypeAttribute returned by this use case.
Returns the list of GCP ValueSet Objects.
| |
| SUPPORTED OPTIONS (NONE) | ||
| Variate Data Range | Name: | Variate Data Range |
| Identification: | DataType|org.generationcp.model.core.value.constraint.Constr | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Variate Unique Identifier | |
| DESCRIPTION |
This dataTypeAttribute is used as a limiting filter for retrieving a list of GCP ValueSet Objects.
This searchfilter is always required/mandatory.
Search by Variate ID | |
| OPERATOR | org.generationcp.demeter:operators:equal | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|org.generationcp.model.core.value.Value|or | |
| NAME | Constraint Unique Identifier | |
| DESCRIPTION |
This is the dataTypeAttribute returned by this use case.
This is a list of GCP Constraint Objects. A Constraint object maybe be of different types (NumericRange or ValueEnumeration)
A GCP NumericRange Object is a GCP Constraint Object showing the lower bounds and upper bounds value of a specified variate.
A GCP ValueEnumeration Object is a GCP constraint Object that dispalys the fixed possible values of a given variate.
A variate value with a constraint of type NumericRange may have the following values seen below.
Example:
Variate Name: GRNELON
Constraint ID: urn:lsid:irri.org:IRIS.NumericRange:18829:1 Constraint Name: GRNELON Constraint Definition: Numeric Range
Range: 1.51...2.31
Lower Bound: 1.51
Upper Bound: 2.31
On the other hand, a variate value with a constraint of type ValueEnumeration may have the following values seen below.
Example:
Variate Name: BLAST
Constraint ID: urn:lsid:irri.org:IRIS.ValueEnumeration:18841:1 Constraint Name: BLAST Constraint Definition: Value Enumeration
ValueSet ID: urn:lsid:irri.org:IRIS.ValueSet:18841.21:1
ValueSet Name: 1884121
Value[1]'s ID: urn:lsid:irri.org:IRIS.EnumValue:4:1
Value[1]'s Name: 4
Value[1]'s Data: Typical susceptible blast lesions 3 mm or longer, infecting less than 4% of the leaf area
Value[2]'s ID: urn:lsid:irri.org:IRIS.EnumValue:8:1
Value[2]'s Name: 8
Value[2]'s Data: Typical blast lesions infecting 51-75% of the leaf area and many leaves dead
Value[3]'s ID: urn:lsid:irri.org:IRIS.EnumValue:5:1
Value[3]'s Name: 5
Value[3]'s Data: Typical blast lesions infecting 4-10% of the leaf area
Value[4]'s ID: urn:lsid:irri.org:IRIS.EnumValue:7:1
Value[4]'s Name: 7
Value[4]'s Data: Typical blast lesions infecting 26-50%% of the leaf area
Value[5]'s ID: urn:lsid:irri.org:IRIS.EnumValue:6:1
Value[5]'s Name: 6
Value[5]'s Data: Typical blast lesions infecting 11-25% of the leaf area
Value[6]'s ID: urn:lsid:irri.org:IRIS.EnumValue:2:1
Value[6]'s Name: 2
Value[6]'s Data: Small roundish to slightly elongated, necrotic gray spots, about 1-2mm in diam., with a distinct brown margin, mostly found on the lower leaves
Value[7]'s ID: urn:lsid:irri.org:IRIS.EnumValue:1:1
Value[7]'s Name: 1
Value[7]'s Data: Small brown specks of pin-point size or larger brown specks without sporulating center
Value[8]'s ID: urn:lsid:irri.org:IRIS.EnumValue:9:1
Value[8]'s Name: 9
Value[8]'s Data: More than 75% leaf area affected
alue[9]'s ID: urn:lsid:irri.org:IRIS.EnumValue:3:1
Value[9]'s Name: 3
Value[9]'s Data: Lesion type is the same as in scale 2, but a significant number of lesions are on the upper leaves
| |
| SUPPORTED OPTIONS (NONE) | ||
| Factor Levels | Name: | Factor Levels |
| Identification: | DataType|org.generationcp.model.core.value.constraint.Constr | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Factor Unique Identifier | |
| DESCRIPTION |
This dataTypeAttribute is used as a limiting filter for retrieving a list of GCP ValueSet Objects.
This searchfilter is always required/mandatory.
Search by Label ID | |
| OPERATOR | org.generationcp.demeter:operators:equal | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|org.generationcp.model.core.value.Value|or | |
| NAME | Constraint Unique Identifier | |
| DESCRIPTION |
This is the dataTypeAttribute returned by this use case.
This is a list of GCP Constraint Objects. A Constraint object maybe be of different types (ValueEnumeration, etc.)
A GCP ValueEnumeration Object is a GCP constraint Object that displays the fixed possible values of a given factor.
A factor value with a constraint of type ValueEnumeration may have the following values seen below.
Example:
Constraint ID: urn:lsid:irri.org:IRIS.ValueEnumeration:200:1 Constraint Name: GID Constraint Definition: Value Enumeration
ValueSet ID: urn:lsid:irri.org:IRIS.ValueSet:200.197:1
ValueSet Name: 200197
Value[1]'s ID: urn:lsid:irri.org:IRIS.FactorEnumValue:242.0:1
Value[1]'s Data: 242.0
Value[2]'s ID: urn:lsid:irri.org:IRIS.FactorEnumValue:715.0:1
Value[2]'s Data: 715.0
Value[3]'s ID: urn:lsid:irri.org:IRIS.FactorEnumValue:902.0:1
Value[3]'s Data: 902.0
Value[4]'s ID: urn:lsid:irri.org:IRIS.FactorEnumValue:1171.0:1
Value[4]'s Data: 1171.0
Value[5]'s ID: urn:lsid:irri.org:IRIS.FactorEnumValue:1709.0:1
Value[5]'s Data: 1709.0
Value[6]'s ID: urn:lsid:irri.org:IRIS.FactorEnumValue:2298.0:1
Value[6]'s Data: 2298.0
Value[7]'s ID: urn:lsid:irri.org:IRIS.FactorEnumValue:2444.0:1
Value[7]'s Data: 2444.0
Value[8]'s ID: urn:lsid:irri.org:IRIS.FactorEnumValue:2722.0:1
Value[8]'s Data: 2722.0
Value[9]'s ID: urn:lsid:irri.org:IRIS.FactorEnumValue:7845.0:1
Value[9]'s Data: 7845.0
Value[10]'s ID: urn:lsid:irri.org:IRIS.FactorEnumValue:9756.0:1
Value[10]'s Data: 9756.0
Value[11]'s ID: urn:lsid:irri.org:IRIS.FactorEnumValue:10565.0:1
Value[11]'s Data: 10565.0
.....
| |
| SUPPORTED OPTIONS (NONE) | FILEPATH | Put here the path to where the files will be saved before download. |
sort-asc | true,true,true,true |
distinct | false |
sorted-by | DataTypeAttribute|java.lang.Object|org.generationcp.model.co |
| TableReference | Name: | TableReference |
| Identification: | DataType|org.generationcp.model.core.value.TableReference | |
| Description: | Simple Reference that has url infornmation of a file which follows the basic format of a Table/Matrix. Usually the files are of type csv, tsv or xls or any other files with simple row or column structures. | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Table Reference Unique Identifier | |
| DESCRIPTION | Unique identifier of the table reference, usually of a Study Effect from which the data was retrieved Search by Table Reference Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Table Reference Column Header Unique Identifier | |
| DESCRIPTION | Unique Identifier of Table Reference Column Header Filter table returned, by column identifier unique identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Table Reference Column Header Name | |
| DESCRIPTION | Name of Table Reference Column Header Filter table returned, by column identifier name | |
| OPERATOR | org.generationcp.demeter:operators:equal_in org.generationcp.demeter:operators:like_in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Table Reference Row Header Unique Identifier | |
| DESCRIPTION | Unique Identifier of Table Reference Row Header Filter reference rows returned, by row identifier unique identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.Object|org.generationcp.model.co | |
| NAME | Table Reference Row Header Name | |
| DESCRIPTION | Name of Table Reference Row Header Filter reference rows returned, by row identifier name | |
| OPERATOR | org.generationcp.demeter:operators:equal_in org.generationcp.demeter:operators:like_in | |
| ID | DataTypeAttribute|org.generationcp.model.core.value.constrai | |
| NAME | Table Reference Entry Constraints | |
| DESCRIPTION | Specifies the constraints that have been applied to this Reference. See main description for valid values Retrieves only specified rows and/or columns or row and/or columns that contain a specified table elements of a file satisfying specified Constraints on the Value. This attribute must be used in conjunction with one or Constraint objects. These Constraint objects must be included in the Constraints attribute of returned TableReference object. This searchable attribute is potentially a very powerful filter on which elements are to be returned. The following Constraints are possible 1) Specified Columns: Constrain the range and order of the columns to be returned. For data with column headers, the an enumeration object should be used containing the headers themselves. Possible constraint types are: a) IdentifierEnumeration should be used for column headers of type SimpleIdentifier b) TermEnumeration should be used for column headers of type SimpleOntologyTerm c) StringEnumeration should be used for column headers of type String d) ValueEnumeration should be used for column headers of all other types and in the cases where column headers are not available and a simple zero-based index is used e) NumericalRange can be used to define zero-based index range for the required columns. In this case the column order would be the natural of the data The "constraintDefinition" attribute string should say "Column Identifier Constraint" to identify this kind of constraint to the DataSource. 2) TableReferenceConstraint of the range of row indices returned, having a constraint object of type IdentiferEnumeration which was retrieved from the getConstraint method of the given TableReferenceConstraint object. The "constraintDefinition" attribute string should say "Row Identifier Constraint" to identify this kind of constraint to the DataSource. 2) Specified Rows: Constrain the range and order of the rows of the file to be returned. For data with row headers, the an enumeration object should be used containing the headers themselves. Possible constraint types are: a) IdentifierEnumeration should be used for column headers of type SimpleIdentifier b) TermEnumeration should be used for row headers of type SimpleOntologyTerm c) StringEnumeration should be used for row headers of type String d) ValueEnumeration should be used for row headers of all other types and in the cases where row headers are not available and a simple zero-based index is used e) NumericalRange can be used to define zero-based index range for the required rows. In this case the row order would be the natural of the data The "constraintDefinition" attribute string should say "Row Identifier Constraint" to identify this kind of constraint to the DataSource. 3) Constraint on values in columns or rows. Constrain the columns or rows of the file returned based on values in these rows or columns The only possible constraint type is TableReferenceConstraint. The 'header' property of this TableReferenceConstaint determines the column or row to which the 'constraint' of this TableReferenceConstaint is applied. The value of 'constraint' can be any Constraint sub-type, its validity will depend on the type of the elements in the TableReference By default in the case of 1) and 2) if Constraint is not TableReferenceConstraint "constraintDefinition" attribute does not specify if the Constraint is to be placed on columns or row, then it should be assumed that the Constraint is on columns. | |
| OPERATOR | org.generationcp.demeter:operators:constraint | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Table Reference Unique Identifier | |
| DESCRIPTION | Unique identifier of the table reference, usually of a Study Effect from which the data was retrieved Unique identifier of the Table Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Table Reference Name | |
| DESCRIPTION | Name of the table reference, usually of a Study Effect from which the data was retrieved Name of the Table Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Table Reference Creation Date | |
| DESCRIPTION | Date to when the file was created Creation Date of the Table Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Table Reference Expiration Date | |
| DESCRIPTION | Date to when the file will expire Expiration Date of the Table Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Table Reference URL | |
| DESCRIPTION | The URL of the file which the user usually needs for download URL of the Table Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Table Reference Mimetype | |
| DESCRIPTION | This has information of the type of file the user is expecting Mimetype of the Table Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Table Reference File Size | |
| DESCRIPTION | The size of a file. Usually used so that the user may know how large the file they want to download. File Size of the Table Reference | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.co | |
| NAME | Table Reference User Friendly Filename | |
| DESCRIPTION | The suggested file name when saving/downloading the file. User Friendly Filename of the Table Reference | |
| SUPPORTED OPTIONS | ||
| Genotype Study | Name: | Genotype Study |
| Identification: | DataType|org.generationcp.model.data.genotype.GenotypeStudy | |
| SEARCHABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Genotype Study Unique Identifier | |
| DESCRIPTION | Search By Genotype Study Unique Identifier | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:in | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Genotype Study Name | |
| DESCRIPTION | Search By Genotype Study Name | |
| OPERATOR | org.generationcp.demeter:operators:equal org.generationcp.demeter:operators:like | |
| AVAILABLE ATTRIBUTES | ||
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Genotype Study Unique Identifier | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Genotype Study Name | |
| ID | DataTypeAttribute|java.lang.String|org.generationcp.model.da | |
| NAME | Genotype Study Description | |
| SUPPORTED OPTIONS (NONE) | ||