METADATA
- public class FileBasedMolecularModelManager<METADATA> extends CoreMolecularModelManager<METADATA>
CoreMolecularModelManager
Constructor and Description |
---|
FileBasedMolecularModelManager(OWLGraphWrapper graph) |
Modifier and Type | Method and Description |
---|---|
String |
exportModel(String modelId,
ModelContainer model)
Export the ABox for the given modelId in the default
OWLOntologyFormat . |
String |
exportModel(String modelId,
ModelContainer model,
String format)
Export the ABox for the given modelId in the given ontology format.
Warning: The mapping from String to OWLOntologyFormat does not map every format! |
String |
generateBlankModel(String db,
METADATA metadata)
Generates a new model taking as input a database D.
|
String |
generateBlankModelWithTaxon(String taxonId,
METADATA metadata)
Generates a new blank model, add protein label for the given as import.
|
String |
generateDerivedModel(String sourceModelId,
METADATA metadata) |
String |
generateModel(org.semanticweb.owlapi.model.OWLClass processCls,
String db,
METADATA metadata)
Generates a new model taking as input a biological process P and a database D.
|
Set<String> |
getAvailableModelIds()
Retrieve a collection of all available model ids.
Note: Models may not be loaded at this point. |
Set<String> |
getCurrentModelIds()
Retrieve a collection of all model ids currently in memory.
|
GafDocument |
getGaf(String db) |
String |
getPathToGafs() |
String |
getPathToOWLFiles()
Note this may move to an implementation-specific subclass in future
|
Set<String> |
getStoredModelIds()
Retrieve a collection of all file/stored model ids found in the repo.
Note: Models may not be loaded at this point. |
GafDocument |
loadGaf(String db)
loads/register a Gaf document
|
GafDocument |
loadGaf(String db,
File gafFile)
Loads and caches a GAF document from a specified location
|
protected void |
loadModel(String modelId,
boolean isOverride) |
protected org.semanticweb.owlapi.model.OWLOntology |
loadModelABox(String modelId) |
void |
saveAllModels(Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations,
METADATA metadata)
Save all models to disk.
|
void |
saveModel(String modelId,
ModelContainer m,
Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations,
METADATA metadata)
Save a model to disk.
|
void |
setPathToGafs(String pathToGafs)
Can either be an HTTP prefix, or an absolute file path
|
void |
setPathToOWLFiles(String pathToOWLFiles) |
addAnnotations, addAnnotations, addFact, addFact, addImports, addObsoleteImportIRIs, addObsoleteImports, addToHistory, addType, addType, createFact, createIndividual, createIndividual, createType, deleteIndividual, dispose, exportModel, exportModelLegacy, getGraph, getImports, getIndividuals, getIndividualsByQuery, getModel, getModelAbox, getModelIds, getOntology, getOWLDataFactory, getOWLOntologyManager, getTboxIRI, importModel, init, isConsistent, loadOntologyIRI, removeAnnotations, removeFact, removeType, removeType, unlinkModel, updateImports
public FileBasedMolecularModelManager(OWLGraphWrapper graph) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
graph
- org.semanticweb.owlapi.model.OWLOntologyCreationException
public String getPathToGafs()
public void setPathToGafs(String pathToGafs)
pathToGafs
- public String getPathToOWLFiles()
public void setPathToOWLFiles(String pathToOWLFiles)
pathToOWLFiles
- public GafDocument loadGaf(String db) throws IOException, URISyntaxException
db
- IOException
URISyntaxException
public GafDocument loadGaf(String db, File gafFile) throws IOException, URISyntaxException
db
- gafFile
- IOException
URISyntaxException
public GafDocument getGaf(String db) throws IOException, URISyntaxException
db
- IOException
URISyntaxException
public String generateModel(org.semanticweb.owlapi.model.OWLClass processCls, String db, METADATA metadata) throws org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException, URISyntaxException
LegoModelGenerator.buildNetwork(OWLClass, java.util.Collection)
And also https://docs.google.com/document/d/1TV8Eb9sSvFY-weVZaIfzCxF1qbnmkUaiUhTm9Bs3gRE/edit
Note the resulting model is uniquely identified by the modeId, which is currently constructed
as a concatenation of the db and the P id. This means that if there is an existing model by
this ID it will be overwrittenprocessCls
- db
- metadata
- org.semanticweb.owlapi.model.OWLOntologyCreationException
URISyntaxException
IOException
public String generateBlankModel(String db, METADATA metadata) throws org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException, URISyntaxException
db
- metadata
- org.semanticweb.owlapi.model.OWLOntologyCreationException
URISyntaxException
IOException
public String generateBlankModelWithTaxon(String taxonId, METADATA metadata) throws org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException, URISyntaxException
taxonId
- metadata
- org.semanticweb.owlapi.model.OWLOntologyCreationException
URISyntaxException
IOException
public String generateDerivedModel(String sourceModelId, METADATA metadata) throws org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException, URISyntaxException
org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException
URISyntaxException
public void saveAllModels(Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations, METADATA metadata) throws org.semanticweb.owlapi.model.OWLOntologyStorageException, org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException
annotations
- metadata
- org.semanticweb.owlapi.model.OWLOntologyStorageException
org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException
public void saveModel(String modelId, ModelContainer m, Collection<org.apache.commons.lang3.tuple.Pair<String,String>> annotations, METADATA metadata) throws org.semanticweb.owlapi.model.OWLOntologyStorageException, org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException
modelId
- m
- annotations
- metadata
- org.semanticweb.owlapi.model.OWLOntologyStorageException
org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException
public String exportModel(String modelId, ModelContainer model) throws org.semanticweb.owlapi.model.OWLOntologyStorageException
OWLOntologyFormat
.modelId
- model
- org.semanticweb.owlapi.model.OWLOntologyStorageException
public String exportModel(String modelId, ModelContainer model, String format) throws org.semanticweb.owlapi.model.OWLOntologyStorageException
OWLOntologyFormat
does not map every format!modelId
- model
- format
- org.semanticweb.owlapi.model.OWLOntologyStorageException
public Set<String> getStoredModelIds() throws IOException
IOException
public Set<String> getCurrentModelIds() throws IOException
getCurrentModelIds
in class CoreMolecularModelManager<METADATA>
IOException
public Set<String> getAvailableModelIds() throws IOException
IOException
protected void loadModel(String modelId, boolean isOverride) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
loadModel
in class CoreMolecularModelManager<METADATA>
org.semanticweb.owlapi.model.OWLOntologyCreationException
protected org.semanticweb.owlapi.model.OWLOntology loadModelABox(String modelId) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
loadModelABox
in class CoreMolecularModelManager<METADATA>
org.semanticweb.owlapi.model.OWLOntologyCreationException
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