Add --input-format option
#1269
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -317,12 +317,27 @@ public OWLOntology loadOntology(String ontologyPath) throws IOException { | |
| * @throws IOException on any problem | ||
| */ | ||
| public OWLOntology loadOntology(String ontologyPath, boolean useCatalog) throws IOException { | ||
| return loadOntology(ontologyPath, useCatalog, null); | ||
| } | ||
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| /** | ||
| * Load an ontology from a String path, optionally using a catalog file if available and with an | ||
| * explicit input format. | ||
| * | ||
| * @param ontologyPath the path to the ontology file | ||
| * @param useCatalog if true, a catalog file will be used if one is found | ||
| * @param inputFormat the expected format of the ontology or null | ||
| * @return a new ontology object, with a new OWLManager | ||
| * @throws IOException on any problem | ||
| */ | ||
| public OWLOntology loadOntology(String ontologyPath, boolean useCatalog, String inputFormat) | ||
| throws IOException { | ||
| File ontologyFile = new File(ontologyPath); | ||
| File catalogFile = null; | ||
| if (useCatalog) { | ||
| catalogFile = guessCatalogFile(ontologyFile); | ||
| } | ||
| return loadOntology(ontologyFile, catalogFile, inputFormat); | ||
| } | ||
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| /** | ||
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@@ -339,6 +354,22 @@ public OWLOntology loadOntology(String ontologyPath, String catalogPath) throws | |
| return loadOntology(ontologyFile, catalogFile); | ||
| } | ||
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| /** | ||
| * Load an ontology from a String path, with optional catalog file and explicit document format. | ||
| * | ||
| * @param ontologyPath the path to the ontology file | ||
| * @param catalogPath the path to the catalog file or null | ||
| * @param inputFormat the expected input format of the ontology or null | ||
| * @return a new ontology object, with a new OWLManager | ||
| * @throws IOException on any problem | ||
| */ | ||
| public OWLOntology loadOntology(String ontologyPath, String catalogPath, String inputFormat) | ||
| throws IOException { | ||
| File ontologyFile = new File(ontologyPath); | ||
| File catalogFile = catalogPath != null ? new File(catalogPath) : null; | ||
| return loadOntology(ontologyFile, catalogFile, inputFormat); | ||
| } | ||
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|
||
| /** | ||
| * Load an ontology from a File, using a catalog file if available. | ||
| * | ||
|
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@@ -364,11 +395,26 @@ public OWLOntology loadOntology(File ontologyFile) throws IOException { | |
| * @throws IOException on any problem | ||
| */ | ||
| public OWLOntology loadOntology(File ontologyFile, boolean useCatalog) throws IOException { | ||
| return loadOntology(ontologyFile, useCatalog, null); | ||
| } | ||
|
|
||
| /** | ||
| * Load an ontology from a File, with option to use a catalog file and to expect an explicit | ||
| * format. | ||
| * | ||
| * @param ontologyFile the ontology file to load | ||
| * @param useCatalog when true, a catalog file will be used if one is found | ||
| * @param inputFormat the expected format of the ontology or null | ||
| * @return a new ontology object, with a new OWLManager | ||
| * @throws IOException on any problem | ||
| */ | ||
| public OWLOntology loadOntology(File ontologyFile, boolean useCatalog, String inputFormat) | ||
| throws IOException { | ||
| File catalogFile = null; | ||
| if (useCatalog) { | ||
| catalogFile = guessCatalogFile(ontologyFile); | ||
| } | ||
| return loadOntology(ontologyFile, catalogFile, inputFormat); | ||
| } | ||
|
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||
| /** | ||
|
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@@ -380,6 +426,20 @@ public OWLOntology loadOntology(File ontologyFile, boolean useCatalog) throws IO | |
| * @throws IOException on any problem | ||
| */ | ||
| public OWLOntology loadOntology(File ontologyFile, File catalogFile) throws IOException { | ||
| return loadOntology(ontologyFile, catalogFile, null); | ||
| } | ||
|
|
||
| /** | ||
| * Load an ontology from a File, with optional catalog File and input format. | ||
| * | ||
| * @param ontologyFile the ontology file to load | ||
| * @param catalogFile the catalog file to use | ||
| * @param inputFormat the expected format of the ontology or null | ||
| * @return a new ontology object, with a new OWLManager | ||
| * @throws IOException on any problem | ||
| */ | ||
| public OWLOntology loadOntology(File ontologyFile, File catalogFile, String inputFormat) | ||
| throws IOException { | ||
| logger.debug("Loading ontology {} with catalog file {}", ontologyFile, catalogFile); | ||
| Object jsonObject = null; | ||
| OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); | ||
|
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@@ -417,14 +477,15 @@ public OWLOntology loadOntology(File ontologyFile, File catalogFile) throws IOEx | |
| // Maybe unzip | ||
| if (ontologyFile.getPath().endsWith(".gz")) { | ||
| if (catalogFile == null) { | ||
| return loadCompressedOntology(ontologyFile, null, inputFormat); | ||
| } else { | ||
| return loadCompressedOntology(ontologyFile, catalogFile.getAbsolutePath(), inputFormat); | ||
| } | ||
| } | ||
|
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| // Otherwise load from file using default method | ||
| OWLDocumentFormat fmt = inputFormat != null ? getFormat(inputFormat) : null; | ||
| return loadOntology(manager, new FileDocumentSource(ontologyFile, fmt)); | ||
|
Contributor
There was a problem hiding this comment. Note to next reviewer: I expect that FileDocumentSource(,) handles the case where fmt is
Contributor
Author
There was a problem hiding this comment. Yes. Calling the |
||
| } catch (JsonLdError | OWLOntologyCreationException e) { | ||
| throw new IOException(String.format(invalidOntologyFileError, ontologyFile.getName()), e); | ||
| } | ||
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@@ -442,7 +503,7 @@ public OWLOntology loadOntology(InputStream ontologyStream) throws IOException { | |
| } | ||
|
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| /** | ||
| * Load an ontology from an InputStream with an optional catalog file. | ||
| * | ||
| * @param ontologyStream the ontology stream to load | ||
| * @param catalogPath the catalog file to use or null | ||
|
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@@ -451,6 +512,20 @@ public OWLOntology loadOntology(InputStream ontologyStream) throws IOException { | |
| */ | ||
| public OWLOntology loadOntology(InputStream ontologyStream, String catalogPath) | ||
| throws IOException { | ||
| return loadOntology(ontologyStream, catalogPath, null); | ||
| } | ||
|
|
||
| /** | ||
| * Load an ontology from an InputStream with an optional catalog file and input format. | ||
| * | ||
| * @param ontologyStream the ontology stream to load | ||
| * @param catalogPath the catalog file to use or null | ||
| * @param inputFormat the expected format of the ontology or null | ||
| * @return a new ontology object, with a new OWLManager | ||
| * @throws IOException on any problem | ||
| */ | ||
| public OWLOntology loadOntology( | ||
| InputStream ontologyStream, String catalogPath, String inputFormat) throws IOException { | ||
| OWLOntology ontology; | ||
| // Maybe load a catalog file | ||
| File catalogFile = null; | ||
|
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@@ -465,7 +540,18 @@ public OWLOntology loadOntology(InputStream ontologyStream, String catalogPath) | |
| if (catalogFile != null) { | ||
| manager.setIRIMappers(Sets.newHashSet(new CatalogXmlIRIMapper(catalogFile))); | ||
| } | ||
| OWLOntologyDocumentSource source = null; | ||
| if (inputFormat != null) { | ||
| source = | ||
| new StreamDocumentSource( | ||
| ontologyStream, | ||
| StreamDocumentSource.getNextDocumentIRI("inputstream:ontology"), | ||
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|
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| getFormat(inputFormat), | ||
| null); | ||
| } else { | ||
| source = new StreamDocumentSource(ontologyStream); | ||
| } | ||
| ontology = loadOntology(manager, source); | ||
| } catch (OWLOntologyCreationException e) { | ||
| throw new IOException(invalidOntologyStreamError, e); | ||
| } | ||
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@@ -492,6 +578,20 @@ public OWLOntology loadOntology(IRI ontologyIRI) throws IOException { | |
| * @throws IOException on any problem | ||
| */ | ||
| public OWLOntology loadOntology(IRI ontologyIRI, String catalogPath) throws IOException { | ||
| return loadOntology(ontologyIRI, catalogPath, null); | ||
| } | ||
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| /** | ||
| * Load an ontology from an IRI with an optional catalog file and input format. | ||
| * | ||
| * @param ontologyIRI the ontology IRI to load | ||
| * @param catalogPath the catalog file to use or null | ||
| * @param inputFormat the expected format of the ontology or null | ||
| * @return a new ontology object, with a new OWLManager | ||
| * @throws IOException on any problem | ||
| */ | ||
| public OWLOntology loadOntology(IRI ontologyIRI, String catalogPath, String inputFormat) | ||
| throws IOException { | ||
| OWLOntology ontology; | ||
| // Maybe load a catalog file | ||
| File catalogFile = null; | ||
|
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@@ -509,11 +609,18 @@ public OWLOntology loadOntology(IRI ontologyIRI, String catalogPath) throws IOEx | |
| } | ||
| // Maybe load a zipped ontology | ||
| if (ontologyIRI.toString().endsWith(".gz")) { | ||
| ontology = | ||
| loadCompressedOntology(new URL(ontologyIRI.toString()), catalogPath, inputFormat); | ||
| } else { | ||
| // Otherwise load ontology as normal | ||
| IRI documentIRI = getDocumentIRIFromMappers(manager, ontologyIRI); | ||
| OWLOntologyDocumentSource source = null; | ||
| if (inputFormat != null) { | ||
| source = new IRIDocumentSource(documentIRI, getFormat(inputFormat), null); | ||
| } else { | ||
| source = new IRIDocumentSource(documentIRI); | ||
| } | ||
| ontology = loadOntology(manager, source); | ||
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|
||
| } | ||
| } catch (OWLOntologyCreationException e) { | ||
| throw new IOException(e); | ||
|
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@@ -1724,13 +1831,15 @@ private static Set<IRI> getUndeclaredPredicates( | |
| * | ||
| * @param gzipFile compressed File to load ontology from | ||
| * @param catalogPath the path to the catalog file or null | ||
| * @param inputFormat the expected format of the ontology or null | ||
| * @return a new ontology object with a new OWLManager | ||
| * @throws IOException on any problem | ||
| */ | ||
| private OWLOntology loadCompressedOntology(File gzipFile, String catalogPath, String inputFormat) | ||
| throws IOException { | ||
| FileInputStream fis = new FileInputStream(gzipFile); | ||
| GZIPInputStream gis = new GZIPInputStream(fis); | ||
| return loadOntology(gis, catalogPath, inputFormat); | ||
| } | ||
|
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| /** | ||
|
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@@ -1739,10 +1848,12 @@ private OWLOntology loadCompressedOntology(File gzipFile, String catalogPath) th | |
| * | ||
| * @param url URL to load from | ||
| * @param catalogPath the path to the catalog file or null | ||
| * @param inputFormat the expected format of the ontology or null | ||
| * @return a new ontology object with a new OWLManager | ||
| * @throws IOException on any problem | ||
| */ | ||
| private OWLOntology loadCompressedOntology(URL url, String catalogPath, String inputFormat) | ||
| throws IOException { | ||
| // Check for redirects | ||
| url = followRedirects(url); | ||
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@@ -1754,7 +1865,7 @@ private OWLOntology loadCompressedOntology(URL url, String catalogPath) throws I | |
| throw new IOException(String.format(invalidOntologyIRIError, url)); | ||
| } | ||
| GZIPInputStream gis = new GZIPInputStream(is); | ||
| return loadOntology(gis, catalogPath, inputFormat); | ||
| } | ||
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| /** | ||
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