RDF

class omexmeta::RDF : public omexmeta::IRDF

Public Functions

explicit RDF(const std::string &storage_type = ~~"memory"~~, const std::string &storage_name = ~~"OmexMetaStore"~~, const char *storage_options = nullptr, const char *model_options = nullptr)

constructor for RDF class

Parameters

storage_type. – Defaults to memory. Other options include: “hashes”, “file”, “mysql”, “postgresql”, “sqlite”, “uri”,
storage_name – name used for storage. When storage is not internally held in memory, this becomes the name of the file or database.
storage_options – options that get passed on to storage. Please study http://librdf.org/docs/api/redland-storage-modules.html for more information. @model_options options that get passed to the model. Please see http://librdf.org/docs/api/index.html for more details.

~RDF() = default: destructor for RDF

RDF(const RDF &rdf) = delete

copy constructor for RDF class

RDF instances are not copyable due to restrictions within the redland libraries. You must instead move RDF objects.

RDF(RDF &&rdf) noexcept: move constructor for RDF class

RDF &operator=(const RDF &rdf) = delete

copy assignment constructor for RDF ojects

Copy assignment functionality is prohibited for RDF objects. Use move semantics insead.

RDF &operator=(RDF &&rdf) noexcept: move assignment operator for RDF

virtual int size() const override: returns the number of triples currently present in the RDF graph.

virtual bool empty() const override

indicator for whether the RDF graph is empty

Returns: true if RDF graph has no triples, false otherwise.

virtual void addFromString(const std::string &str, const std::string &syntax = ~~"guess"~~) override: non-static variant of RDF::fromString(). Reads rdf into an RDF instance. See RDF::fromString() for argument requirements.

virtual void addFromUri(const std::string &uri_string, const std::string &syntax = ~~"guess"~~) override

non-static counterpart of RDF::fromUri. Downloads and parses rdf from a URI.

See RDF::fromUri for details.

virtual void addFromFile(const std::string &filename, const std::string &syntax) override

non-static counter part of RDF::fromFile. Reads rdf from annotations in a file

Uses LibrdfParser::fromFile under the hood

Parameters

filename – the filename to read as string
syntax – the syntax of the RDF in filename

Returns

an instantiated RDF object

virtual std::string toString(const std::string &syntax = ~~"turtle"~~, const char *mime_type = nullptr, const char *type_uri = nullptr) override

serialize RDF graph to string

Parameters: syntax – the expected output syntax. Options include: “ntriples”, “turtle”, “rdfxml-xmp”, “rdfxml-abbrev”, “rdfxml”, “dot”, “json-triples”, “json”, “nquads”, “html”.

virtual void toFile(const std::string &filename, const std::string &syntax = ~~"turtle"~~, const char *mime_type = nullptr, const char *type_uri = nullptr) override

Write annotations to file.

Parameters

syntax – the expected output syntax. Options include: “ntriples”, “turtle”, “rdfxml-xmp”, “rdfxml-abbrev”, “rdfxml”, “dot”, “json-triples”, “json”, “nquads”, “html”.
filename – full path of file to write
mime_type – optional valid mime
type_uri – optional type uri

virtual Editor toEditor(const std::string &xml, bool generate_new_metaids = false, bool sbml_semantic_extraction = true) override

instantiate an Editor object.

Parameters

xml – the xml you want to open for editing. This can be any type of xml document, but SBML and CellML are most common.
generate_new_metaids – When true, will add metaids onto a copy of the xml source code for annotation. Default = false.
OmexMetaXmlType – an indicator enum specifying whether the xml is sbml, cellml or unknown. Default is “OMEXMETA_TYPE_NOTSET”

virtual Editor *toEditorPtr(const std::string &xml, bool generate_new_metaids = false, bool sbml_semantic_extraction = true) override

instantiate an Editor object and return a new pointer to it. Memory returned is owned by the caller and needs deleting.

Parameters

xml – the xml you want to open for editing. This can be any type of xml document, but SBML and CellML are most common.
generate_new_metaids – When true, will add metaids onto a copy of the xml source code for annotation. Default = false.
OmexMetaXmlType – an indicator enum specifying whether the xml is sbml, cellml or unknown. Default is “OMEXMETA_TYPE_NOTSET”

virtual LibrdfModel getModel() const override

virtual LibrdfStorage getStorage() const override

virtual int commitTransaction() const override

virtual int startTransaction() const override

virtual void *getTransactionHandle() const override

virtual int startTransactionWithHandle(void *handle) const override

virtual int getTransactionRollback() const override

virtual std::string queryResultsAsString(const std::string &query_str, const std::string &results_syntax) override

virtual ResultsMap queryResultsAsMap(const std::string &query_str) override

virtual std::unordered_map<std::string, std::string> propagateNamespacesFromParser(const std::vector<std::string> &seen_namespaces) override

compared namespaces seen with namespaces known and ensures models that use a known namespace use that namespace.

Parameters: seen_namespaces – a vector of strings of namespaces the parser has seen before.

virtual OmexMetaXmlType getXmlType() const override

getter for xmlType attribue.

when the rdf graph is sbml, it will return OMEXMETA_TYPE_SBML. When cellML it will return OMEXMETA_TYPE_CELLML. Otherwise it is OMEXMETA_TYPE_UNKNOWN.

bool operator==(const RDF &rhs) const

bool operator!=(const RDF &rhs) const

virtual void setXmlType(OmexMetaXmlType xmlType) override

set the xml type for the current graph.

If you have been reading from an SBML you cannot then read from another syntax (such as cellml).

virtual const std::string &getRepositoryUri() const override: getter for repository uri which defaults to “http://omex-library.org/”

virtual void setRepositoryUri(const std::string &repositoryName) override

setter for the repository uri which defaults to “http://omex-library.org/”.

Parameters: repositoryName – the repository uri.

virtual const std::string &getArchiveUri() const override

getter for archiveUri attribute.

default to http://omex-library.org/NewOmex.omex/

virtual void setArchiveUri(const std::string &archiveName) override

setter for archiveUri attribute.

default to http://omex-library.org/NewOmex.omex/

Parameters: archiveName – the new name for archive uri attribute

virtual const std::string &getModelUri() const override

getter for model uri.

defaults to http://omex-library.org/NewOmex.omex/NewModel.xml

virtual void setModelUri(std::string modelName) override

setter for model uri.

defaults to http://omex-library.org/NewOmex.omex/NewModel.xml

Parameters: modelName – string for new model uri.

virtual const std::string &getModelMetaid() override: gets the uri fragment used for model level annotations. This must be a valid metaid in your model and should be attached to a “model” element

virtual void setModelMetaid(const std::string &modelMetaid) override: sets the uri fragment used for model level annotations. This must be a valid metaid in your model and should be attached to a “model” element

virtual std::string getModelLevelAnnotationUri() override

get the full uri for model level annotations.

the modelUri concatonated with the model metaid fragment

virtual const std::string &getLocalUri() const override

getter for local uri attribute.

defaults to http://omex-library.org/NewOmex.omex/NewModel.rdf#

virtual void addTriple(const Triple &triple) override: add a Triple to the current model

virtual void addTriples(Triples &triples) override: add a set of Triples to the current model

virtual UriHandler &getUriHandler() override

void purgeRDFBag(): remove rdf:Bag constructs from the current rdf graph

void translateVcard(): Translate VCARD into foaf

Public Members

NamespaceMap namespaces_: Storage for namespaces and prefixes

std::vector<std::string> seen_namespaces_

Part of the mechanism that propogates namespaces through to serializer.

todo observer pattern might make for more elegant design.

const std::string OMEXlib_ = ~~"http://OMEXlibrary.org/"~~: Default repository uri

Public Static Functions

static RDF fromString(const std::string &str, const std::string &syntax = ~~"guess"~~)

instantiate an RDF instance and read annotations from a string. This is a static method.

Parameters

str – a reference to the string containing annotations
syntax – which syntax str is in. Default=”guess” : try to guess.

static RDF fromUri(const std::string &uri_string, const std::string &syntax = ~~"guess"~~)

parse RDF directly from a uri

downloads uri from the internet and creates an RDF graph. See Librdf::parseUri() for more details.

Parameters

uri_string – the uri to download containing RDF
syntax – the syntax that the RDF is in

Returns

RDF an instantiated RDF object.

static RDF fromFile(const std::string &filename, const std::string &syntax)

read rdf from annotations in a file

Uses LibrdfParser::fromFile under the hood

Parameters

filename – the filename to read as string
syntax – the syntax of the RDF in filename

Returns

an instantiated RDF object

static std::ostringstream listOptions()

static bool equals(RDF *actual, const std::string &expected, const std::string &syntax = ~~"turtle"~~, bool verbose = false)

test for equality between

Parameters

actual – and
expected –

static bool equals(const Triple &actual, const std::string &expected, const std::string &syntax = ~~"turtle"~~, bool verbose = false)

test for equality between

Parameters

actual – and
expected –

static bool equals(Triples &actual, const std::string &expected, const std::string &syntax = ~~"turtle"~~, bool verbose = false)

test for equality between

Parameters

actual – and
expected –

static bool equals(RDF *actual, RDF *expected, const std::string &syntax = ~~"turtle"~~, bool verbose = false)

test for equality between

Parameters

actual – and
expected –

static bool equals(const std::string &first, const std::string &second, const std::string &first_syntax = ~~"turtle"~~, const std::string &second_syntax = ~~"turtle"~~, bool verbose = false)

test for equality between

Parameters

first – and
second –

Private Functions

void classifyXmlType(const std::string &xml, const std::string &input_syntax): autoset the xmlType variable based on xml content.

void classifyXmlTypeFromFile(const std::string &xml_file, const std::string &input_syntax): reads xml from file before calling classifyXmlType

void extractSemanticInformationFromSBML(const std::string &sbml): pull semantic information out of the sbml int the RDF graph

void freeRDF()

release memory consumed by RDF.

Memory consumed by RDF is destructed using RAII so users normally do not need this function.

void setLogHandlers(): set custom handler functions for librdf, raptor and rasqal

Private Members

LibrdfStorage storage_

LibrdfModel model_

OmexMetaXmlType xmlType = OMEXMETA_TYPE_NOTSET

UriHandler uriHandler_