From 065b97048312a35ad71369b7e2a3d1bf0b0d52de Mon Sep 17 00:00:00 2001 From: Daniel Garijo Date: Sun, 31 Dec 2023 12:03:11 +0100 Subject: [PATCH 1/5] fix version for release and added absolute links in readme --- README.md | 12 ++++++------ pom.xml | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 5e3e36d9..7afd039d 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ Just add the dependency and repository to your `pom.xml` file as follows. See th com.github.dgarijo Widoco - v1.4.16 + v1.4.21 @@ -56,7 +56,7 @@ Just add the dependency and repository to your `pom.xml` file as follows. See th WIDOCO helps you to publish and create an enriched and customized documentation of your ontology, by following a series of steps in a wizard. We extend the LODE framework by Silvio Peroni to describe the classes, properties and data properties of the ontology, the OOPS! webservice by María Poveda to print an evaluation and the Licensius service by Victor Rodriguez Doncel to determine the license URI and title being used. In addition, we use WebVowl to visualize the ontology and have extended Bubastis to show a complete changelog between different versions of your ontology. Features of WIDOCO: -* Automatic documentation of the terms in your ontology (based on [LODE](http://www.essepuntato.it/lode/)). Now **you can use Markdown on your class descriptions** (see [example](doc/gallery/index.html)) +* Automatic documentation of the terms in your ontology (based on [LODE](http://www.essepuntato.it/lode/)). Now **you can use Markdown on your class descriptions** (see [example](https://dgarijo.github.io/Widoco/doc/gallery/index.html)) * Massive metadata extraction and support: WIDOCO will enhance your ontology documentation based on your ontology annotations. Now you can add custom logos and images, edit the content of your sections, etc. by just editing metadata. See our [supported metadata](https://github.com/dgarijo/Widoco/blob/master/doc/metadataGuide/guide.md) and [recommendations](https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html) for more information. * Automatic annotation in JSON-LD snippets of the html produced. * Association of a provenance page which includes the history of your vocabulary (W3C PROV-O compliant). @@ -75,7 +75,7 @@ Examples of the features of WIDOCO can be seen on [the gallery](https://dgarijo. A tutorial explaining the main features of the GUI can be found [here](https://dgarijo.github.io/Widoco/doc/tutorial/) ## Metadata usage -To see how WIDOCO recognizes metadata annotations in your ontology to create the documentation files, see [the WIDOCO metadata documentation](doc/metadataGuide/guide.md). To learn which metadata properties we recommend adding to your ontology for producing a nice-looking documentation, have a look at our [best practices guide](https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html). +To see how WIDOCO recognizes metadata annotations in your ontology to create the documentation files, see [the WIDOCO metadata documentation](https://dgarijo.github.io/Widoco/doc/metadataGuide/guide.md). To learn which metadata properties we recommend adding to your ontology for producing a nice-looking documentation, have a look at our [best practices guide](https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html). For example, in order to show your logo in your documentation you just need to use `foaf:logo` as an annotation, as follows: ``` @@ -85,7 +85,7 @@ For example, in order to show your logo in your documentation you just need to u foaf:logo . ``` -and it will show right next to the title. The [WIDOCO metadata documentation](doc/metadataGuide/guide.md) shows all supported metadata fields. +and it will show right next to the title. The [WIDOCO metadata documentation](https://dgarijo.github.io/Widoco/doc/metadataGuide/guide.md) shows all supported metadata fields. ## How to use WIDOCO @@ -138,7 +138,7 @@ docker run -ti --rm \ `-outFolder folderName`: Specifies the name of the folder where to save the documentation. By default is 'myDocumentation' -`-confFile PATH`: Load your own configuration file for the ontology metadata. Incompatible with -getOntologyMetadata. See [the configuration documentation](doc/configuration/configuration_doc.md) for more information about the accepted fields. +`-confFile PATH`: Load your own configuration file for the ontology metadata. Incompatible with -getOntologyMetadata. See [the configuration documentation](https://dgarijo.github.io/Widoco/doc/configuration/configuration_doc.md) for more information about the accepted fields. `-getOntologyMetadata`: Extract ontology metadata from the given ontology @@ -191,7 +191,7 @@ There are two alternative ways for making WIDOCO get your vocabulary metadata an * The recommended way: add them in your OWL file. For guidelines on which ones to include, follow our [best practices document](https://w3id.org/widoco/bestPractices), which indicates which ones we recommend. * Alternatively, edit the project properties of /config/config.properties. This is a key-value pair file with metadata properties. Some people consider it easier than adding the property annotations to the OWL file, although I recommend doing the former option. Note that the character ";" is used for lists (for instance first author; second author; third author). -For more information, see the [Widoco metadata guide](doc/metadataGuide/guide.md) +For more information, see the [Widoco metadata guide](https://dgarijo.github.io/Widoco/doc/metadataGuide/guide.md) ## Browser issues (Why can't I see the generated documentation / visualization?) WIDOCO separates the contents of different sections in HTML files, which are then loaded in the `index.html` file. WIDOCO was designed this way because it's easier to edit your introduction or description sections independently without being all aggregated together in a huge HTML document. **When all the contents generated by WIDOCO are stored in a server, you will be able to see the documentation of your ontology using any browser**. However, if you open the `index.html` file **on your local browser**, you may see a document missing most of the sections in your documentation. This happens because browsers don't allow loading separate content when opening a file locally for security reasons. If you want to explore how your ontology would look locally, you have two options: diff --git a/pom.xml b/pom.xml index da0c4b7f..fcbd88b7 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ es.oeg widoco jar - 1.4.20 + 1.4.21 Widoco From 2e55e276d1ac85276111f3fb41df36c463436755 Mon Sep 17 00:00:00 2001 From: Daniel Garijo Date: Sun, 31 Dec 2023 12:05:23 +0100 Subject: [PATCH 2/5] fixing links again --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 7afd039d..ceb698e8 100644 --- a/README.md +++ b/README.md @@ -85,7 +85,7 @@ For example, in order to show your logo in your documentation you just need to u foaf:logo . ``` -and it will show right next to the title. The [WIDOCO metadata documentation](https://dgarijo.github.io/Widoco/doc/metadataGuide/guide.md) shows all supported metadata fields. +and it will show right next to the title. The [WIDOCO metadata documentation](doc/metadataGuide/guide.md) shows all supported metadata fields. ## How to use WIDOCO @@ -138,7 +138,7 @@ docker run -ti --rm \ `-outFolder folderName`: Specifies the name of the folder where to save the documentation. By default is 'myDocumentation' -`-confFile PATH`: Load your own configuration file for the ontology metadata. Incompatible with -getOntologyMetadata. See [the configuration documentation](https://dgarijo.github.io/Widoco/doc/configuration/configuration_doc.md) for more information about the accepted fields. +`-confFile PATH`: Load your own configuration file for the ontology metadata. Incompatible with -getOntologyMetadata. See [the configuration documentation](doc/configuration/configuration_doc.md) for more information about the accepted fields. `-getOntologyMetadata`: Extract ontology metadata from the given ontology @@ -191,7 +191,7 @@ There are two alternative ways for making WIDOCO get your vocabulary metadata an * The recommended way: add them in your OWL file. For guidelines on which ones to include, follow our [best practices document](https://w3id.org/widoco/bestPractices), which indicates which ones we recommend. * Alternatively, edit the project properties of /config/config.properties. This is a key-value pair file with metadata properties. Some people consider it easier than adding the property annotations to the OWL file, although I recommend doing the former option. Note that the character ";" is used for lists (for instance first author; second author; third author). -For more information, see the [Widoco metadata guide](https://dgarijo.github.io/Widoco/doc/metadataGuide/guide.md) +For more information, see the [Widoco metadata guide](doc/metadataGuide/guide.md) ## Browser issues (Why can't I see the generated documentation / visualization?) WIDOCO separates the contents of different sections in HTML files, which are then loaded in the `index.html` file. WIDOCO was designed this way because it's easier to edit your introduction or description sections independently without being all aggregated together in a huge HTML document. **When all the contents generated by WIDOCO are stored in a server, you will be able to see the documentation of your ontology using any browser**. However, if you open the `index.html` file **on your local browser**, you may see a document missing most of the sections in your documentation. This happens because browsers don't allow loading separate content when opening a file locally for security reasons. If you want to explore how your ontology would look locally, you have two options: From 4cb6b64c75008383a659d741cbc760ce36b9946a Mon Sep 17 00:00:00 2001 From: Daniel Garijo Date: Sun, 31 Dec 2023 18:33:47 +0100 Subject: [PATCH 3/5] Fix #642 --- doc/configuration/config.properties | 1 - doc/configuration/configuration_doc.md | 3 +-- doc/metadataGuide/guide.md | 14 +++++++------- 3 files changed, 8 insertions(+), 10 deletions(-) diff --git a/doc/configuration/config.properties b/doc/configuration/config.properties index a152abc9..5a7e4103 100644 --- a/doc/configuration/config.properties +++ b/doc/configuration/config.properties @@ -26,7 +26,6 @@ licenseIconURL=https://i.creativecommons.org/l/by/2.0/88x31.png logo="https://example.org/logo.svg" ontologyName=Example ontologyPrefix=exo -modified="15 April, 2023" ontologyNamespaceURI=https://w3id.org/example previousVersionURI=https://w3id.org/example/1.0.0 publisher=Ontology Engineering Group diff --git a/doc/configuration/configuration_doc.md b/doc/configuration/configuration_doc.md index 86fb03da..9935407f 100644 --- a/doc/configuration/configuration_doc.md +++ b/doc/configuration/configuration_doc.md @@ -9,6 +9,7 @@ abstract=An example ontology backwardCompatibleWith=https://w3id.org/example/1.0.0 citeAs="add some citattion text here." dateCreated="13 Nov, 2022" +dateIssued= dateModified="15 Nov, 2022" authors=First Author;Second Author authorsURI=http://example.org/author1;http://example.org/author2 @@ -24,7 +25,6 @@ DOI= funder= fundingGrant= incompatibleWith= -issued= images=image1.png;image2.png licenseURI=http://creativecommons.org/licenses/by/2.0/ licenseName=CC-BY @@ -32,7 +32,6 @@ licenseIconURL=https://i.creativecommons.org/l/by/2.0/88x31.png logo="https://example.org/logo.svg" ontologyName=Example ontologyPrefix=exo -modified="15 April, 2023" ontologyNamespaceURI=https://w3id.org/example previousVersionURI=https://w3id.org/example/1.0.0 publisher=Ontology Engineering Group diff --git a/doc/metadataGuide/guide.md b/doc/metadataGuide/guide.md index 2a044364..94817556 100644 --- a/doc/metadataGuide/guide.md +++ b/doc/metadataGuide/guide.md @@ -45,7 +45,7 @@ The table below shows which ontology metadata annotations are recognized in WIDO |Abstract |[dc:abstract], [dcterms:abstract]|abstract |[Sec 3.2.4] **[OPTIONAL]**|[Text]|[ontology](#onto), [config]| |Backwards compatible|[owl:backwardCompatibleWith] |backwardCompatibleWith|[Sec 3.3.3] **[OPTIONAL]**|[URI] |[ontology](#onto), [config]| |Bibliographic citation|[dcterms:bibliographicCitation], [schema:citation]|citeAs|[Sec 3.6.2] **[OPTIONAL]**|[Text]|[ontology](#onto), [config]| -|Creation date|[dcterms:created], [schema:dateCreated], [prov:generatedAtTime], [pav:createdOn], [doap:created]|creationDate|[Sec 3.4.2] **[OPTIONAL]**|[Text]|[ontology](#onto), [config]| +|Creation date|[dcterms:created], [schema:dateCreated], [prov:generatedAtTime], [pav:createdOn], [doap:created]|dateCreated|[Sec 3.4.2] **[OPTIONAL]**|[Text]|[ontology](#onto), [config]| |Creators|[dcterms:creator], [dc:creator], [schema:creator], [pav:createdBy], [pav:authoredBy], [prov:wasAttributedTo], [doap:developer], [foaf:maker]|authors, authorsURI, authorsInstitution, authorsInstitutionURI|[Sec 3.5.1] **[RECOMMENDED]**|[Text] or [Person] or [BNode]|[ontology](#onto), [config]| |Contributors|[dcterms:contributor], [dc:contributor], [schema:contributor], [pav:contributedBy], [doap:documenter], [doap:maintainer], [doap:helper], [doap:translator]|contributors, contributorsURI, contributorsInstitution, contributorsInstitutionURI|[Sec 3.5.2] **[RECOMMENDED]**|[Text] or [Person] or [BNode]|[ontology](#onto), [config]| |Description|[dc:description], [dcterms:description], [schema:description], [rdfs:comment], [skos:note], [doap:description], [doap:shortdesc]|description|[Sec 3.2.3] **[OPTIONAL]**|[Text]|[ontology](#onto), [config]| @@ -56,13 +56,13 @@ The table below shows which ontology metadata annotations are recognized in WIDO |Funding grants |[schema:funding] |fundingGrant|[Sec 3.5.5] **[OPTIONAL]**|[Text] or [URI]|[ontology](#onto), [config]| |Incompatible with |[owl:incompatibleWith] |incompatibleWith|[Sec 3.3.4] **[OPTIONAL]** |[URI] |[ontology](#onto), [config]| |Imported ontologies |[owl:imports] |importedOntologyNames, importedOntologyURIs|N/A **[RECOMMENDED]** (good practice in ontology engineering) | [URI] | [ontology](#onto), [config]| -|Issued date |[dcterms:issued], [schema:dateIssued] |issued |[Sec 3.4.4] **[OPTIONAL]** |[Text] |[ontology](#onto), [config]| +|Issued date |[dcterms:issued], [schema:dateIssued] |dateIssued |[Sec 3.4.4] **[OPTIONAL]** |[Text] |[ontology](#onto), [config]| |License|[dc:rights], [dcterms:license], [schema:license], [cc:license], [doap:license]|licenseName, licenseURI, licenseIconURL|[Sec 3.7] **[OPTIONAL]**|[Text] or [URI]|[ontology](#onto), [config]| |Logo |[foaf:logo], [schema:logo] |logo |[Sec 3.8.1] **[OPTIONAL]** |[URI] |[ontology](#onto), [config]| |Name|[rdfs:label], [mod:acronym], [schema:alternateName], [skos:prefLabel]|ontologyName|[Sec 3.2.1] **[RECOMMENDED]**|[Text]|[ontology](#onto), [config]| |Namespace prefix |[vann:preferredNamespacePrefix]|ontologyPrefix |[Sec 3.1.2] **[RECOMMENDED]**|[Text] |[ontology](#onto), [config]| |Namespace URI |[vann:preferredNamespaceUri] |ontologyNamespaceURI|[Sec 3.1.1] **[RECOMMENDED]**|[URI] |[ontology](#onto), [config]| -|Modification date|[dcterms:modified], [schema:dateModified] [pav:lastUpdatedOn]|modified|[Sec 3.4.3] **[OPTIONAL]**|[Text] |[ontology](#onto), [config]| +|Modification date|[dcterms:modified], [schema:dateModified] [pav:lastUpdatedOn]|dateModified|[Sec 3.4.3] **[OPTIONAL]**|[Text] |[ontology](#onto), [config]| |Previous version |[dc:replaces], [dcterms:replaces], [prov:wasRevisionOf], [pav:previousVersion], [owl:priorVersion]|previousVersionURI|[Sec 3.4.1] **[RECOMMENDED]**|[URI]|[ontology](#onto), [config]| |Publisher|[dcterms:publisher], [dc:publisher], [schema:publisher]|publisher, publisherURI, publisherInstitution, publisherInstitutionURI|[Sec 3.5.3] **[OPTIONAL]**|[Text] or [Organization] or [BNode]|[ontology](#onto), [config]| |Similar resources|[rdfs:seeAlso] | |[Sec 3.9] **[OPTIONAL]** |[Text] |[ontology](#onto), [config]| @@ -141,7 +141,7 @@ The following `Turtle` code block shows sample annotations for each of the metad foaf:fundedBy ; schema:funding ; widoco:introduction "A paragraph with the introduction section of the documentation about your resource"@en ; - widoco:rdfxmlSerialization "https://example.org/serialization/ontology.xml"^^xsd:anyURI ; + widoco:rdfxmlSerialization "https://example.org/serialization/ontology.xml"^^xsd:anyURI ; owl:versionInfo "1.0.1" . #If content negotiation is enabled, the widoco:rdfxmlSerialization annotation may not be needed. ``` @@ -214,7 +214,6 @@ Create a `config.properties` file and use the `-confFile` option to invoke Widoc abstract=An example ontology backwardCompatibleWith=https://w3id.org/example/1.0.0 citeAs="add some citattion text here." -creationDate="13 Nov, 2022" authors=First Author;Second Author authorsURI=http://example.org/author1;http://example.org/author2 authorsInstitution=First author institution;Second author institution @@ -224,6 +223,9 @@ contributorsURI=http://example.org/contributor1;http://example.org/contributor2 contributorsInstitution=First contributor institution;Second contributor institution contributorsInstitutionURI=https://isi.edu/;https://isi.edu/ description=A description of what the ontology does goes here +dateCreated="13 Nov, 2022" +dateIssued="14 Nov, 2022" +dateModified="15 April, 2023" diagram="https://example.org/diagram.svg" extendedOntologyNames=test1; test2 extendedOntologyURIs=http://example.org/test1; http://example.org/test2 @@ -234,14 +236,12 @@ incompatibleWith=https://w3id.org/example/0.0.1 importedOntologyNames=Imported Ontology 1; Imported Ontology 2 importedOntologyURIs=http://example.org/test11; http://example.org/test22 introduction=A brief text for the introduction section may be written here. -issued= licenseURI=http://creativecommons.org/licenses/by/2.0/ licenseName=CC-BY licenseIconURL=https://i.creativecommons.org/l/by/2.0/88x31.png logo="https://example.org/logo.svg" ontologyName=The Cohort Ontology ontologyPrefix=exo -modified="15 April, 2023" ontologyNamespaceURI=https://w3id.org/example previousVersionURI=https://w3id.org/example/1.0.0 publisher= From e2049e80da73f11c28ec49227b386cf504c3e43d Mon Sep 17 00:00:00 2001 From: Daniel Garijo Date: Sun, 31 Dec 2023 19:05:06 +0100 Subject: [PATCH 4/5] Fix #572 --- src/main/java/widoco/Configuration.java | 5 +++-- src/main/java/widoco/Constants.java | 11 ++++++----- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/src/main/java/widoco/Configuration.java b/src/main/java/widoco/Configuration.java index 86a0529d..e8e0c0f5 100644 --- a/src/main/java/widoco/Configuration.java +++ b/src/main/java/widoco/Configuration.java @@ -240,8 +240,9 @@ private void loadPropertyFile(String path) throws IOException { abstractSection = propertyFile.getProperty(Constants.PF_ABSTRACT_SECTION_CONTENT); contextURI = propertyFile.getProperty(Constants.PF_CONTEXT_URI, ""); mainOntologyMetadata.setTitle(propertyFile.getProperty(Constants.PF_ONT_TITLE, "Title goes here")); - mainOntologyMetadata.setCreationDate(propertyFile.getProperty(Constants.PF_DATE_CREATED, "Creation date")); - mainOntologyMetadata.setModifiedDate(propertyFile.getProperty(Constants.PF_DATE_MODIFIED, "Modified date")); + mainOntologyMetadata.setCreationDate(propertyFile.getProperty(Constants.PF_DATE_CREATED, "Date created")); + mainOntologyMetadata.setModifiedDate(propertyFile.getProperty(Constants.PF_DATE_MODIFIED, "Date modified")); + mainOntologyMetadata.setIssuedDate(propertyFile.getProperty(Constants.PF_DATE_ISSUED, "Date issued")); mainOntologyMetadata.setPreviousVersion(propertyFile.getProperty(Constants.PF_PREVIOUS_VERSION)); mainOntologyMetadata.setThisVersion(propertyFile.getProperty(Constants.PF_THIS_VERSION_URI)); mainOntologyMetadata.setLatestVersion(propertyFile.getProperty(Constants.PF_LATEST_VERSION_URI)); diff --git a/src/main/java/widoco/Constants.java b/src/main/java/widoco/Constants.java index 046a5baf..10fcd0c7 100644 --- a/src/main/java/widoco/Constants.java +++ b/src/main/java/widoco/Constants.java @@ -237,6 +237,7 @@ public class Constants { public static final String PF_CONTRIBUTORS_INSTITUTION = "contributorsInstitution"; public static final String PF_CONTRIBUTORS_INSTITUTION_URI = "contributorsInstitutionURI"; public static final String PF_DATE_CREATED = "dateCreated"; + public static final String PF_DATE_ISSUED = "dateIssued"; public static final String PF_DATE_MODIFIED = "dateModified"; public static final String PF_DESCRIPTION = "description"; public static final String PF_DOI = "DOI"; @@ -498,15 +499,15 @@ private static String getAgents(ArrayList auth) { } if (currAuth.getInstitutionName() != null && !"".equals(currAuth.getInstitutionName())) { if (currAuth.getInstitutionURL() != null && !"".equals(currAuth.getInstitutionURL())) { - agents += ", (" + currAuth.getInstitutionName() - + ")"; + agents += ", " + currAuth.getInstitutionName() + + ""; } else { agents += ", " + currAuth.getInstitutionName(); } } else { if (currAuth.getInstitutionURL() != null && !"".equals(currAuth.getInstitutionURL())) { - agents += ", (" + currAuth.getInstitutionURL() - + ")"; + agents += ", " + currAuth.getInstitutionURL() + + ""; } } if(currAuth.getEmail()!=null && !"".equals(currAuth.getEmail())){ @@ -518,7 +519,7 @@ private static String getAgents(ArrayList auth) { agents += ""; } } catch (Exception e) { - logger.error("Error while writing authors, their urls or their instititions."); + logger.error("Error while writing authors, their urls or their institutions."); } return agents; } From 71ce4fc5f0a34ebcaf34f715356bcf08869cfaec Mon Sep 17 00:00:00 2001 From: Daniel Garijo Date: Sun, 31 Dec 2023 20:27:25 +0100 Subject: [PATCH 5/5] Fix #647 --- src/main/java/lode/LODEGeneration.java | 10 ++-------- src/main/java/widoco/Configuration.java | 3 +++ src/main/java/widoco/LoadOntologyInThread.java | 1 + src/main/java/widoco/gui/GuiController.java | 5 +++-- 4 files changed, 9 insertions(+), 10 deletions(-) diff --git a/src/main/java/lode/LODEGeneration.java b/src/main/java/lode/LODEGeneration.java index 5b4af5af..82ee47cc 100644 --- a/src/main/java/lode/LODEGeneration.java +++ b/src/main/java/lode/LODEGeneration.java @@ -69,17 +69,11 @@ public static String getLODEhtml(Configuration c, File lodeResources) throws Exc c.getMainOntology().getOWLAPIModel()); content = applyXSLTTransformation(content, c.getOntologyURI(), lang, lodeResources); return (content); - } catch (OWLOntologyStorageException e) { - logger.error("Error while applying LODE. Error while applying the XLS file: " + e.getMessage()); - throw e; - } catch (TransformerException e) { - logger.error("Error while applying LODE. Error while applying the XLS file: " + e.getMessage()); - throw e; - } catch (UnsupportedEncodingException e) { + } catch (OWLOntologyStorageException | TransformerException | UnsupportedEncodingException e) { logger.error("Error while applying LODE. Error while applying the XLS file: " + e.getMessage()); throw e; } - } + } /** * Method that uses the loaded ontology and parses it in case there are imports diff --git a/src/main/java/widoco/Configuration.java b/src/main/java/widoco/Configuration.java index e8e0c0f5..48255cff 100644 --- a/src/main/java/widoco/Configuration.java +++ b/src/main/java/widoco/Configuration.java @@ -513,6 +513,9 @@ public void loadPropertiesFromOntology(OWLOntology o) { mainOntologyMetadata.setCiteAs(cite.toString()); } + } + + public void loadNamespaceDeclarations(OWLOntology o){ //load all namespaces in the ontology document. this.namespaceDeclarations = new HashMap<>(); OWLOntologyXMLNamespaceManager nsManager = new OWLOntologyXMLNamespaceManager(o, o.getFormat()); diff --git a/src/main/java/widoco/LoadOntologyInThread.java b/src/main/java/widoco/LoadOntologyInThread.java index de2965a8..a47d1981 100644 --- a/src/main/java/widoco/LoadOntologyInThread.java +++ b/src/main/java/widoco/LoadOntologyInThread.java @@ -45,6 +45,7 @@ public void run() { try { WidocoUtils.loadModelToDocument(c); c.loadPropertiesFromOntology(c.getMainOntology().getOWLAPIModel()); + c.loadNamespaceDeclarations(c.getMainOntology().getOWLAPIModel()); if (showGui) { pointerToMain.switchState("finishedLoading"); } diff --git a/src/main/java/widoco/gui/GuiController.java b/src/main/java/widoco/gui/GuiController.java index 8b9fe298..d29eca74 100644 --- a/src/main/java/widoco/gui/GuiController.java +++ b/src/main/java/widoco/gui/GuiController.java @@ -210,12 +210,12 @@ public GuiController(String[] args) { } i++; } - // this creates the tmp files + // this creates tmp files for the conversion assets config = new Configuration(); try { this.config.reloadPropertyFile(confPath); } catch (Exception e) { - System.out.println("Configuration file could not be loaded: " + e.getMessage()); + logger.error("Configuration file could not be loaded: " + e.getMessage()); return; } @@ -291,6 +291,7 @@ public GuiController(String[] args) { // TO DO: improve this a little so language is passed on to load properties and generate doc. for (String l : config.getLanguagesToGenerateDoc()) { logger.info("Generating documentation for " + ontology + " in lang " + l); + config.loadNamespaceDeclarations(config.getMainOntology().getOWLAPIModel()); if (getOntoMetadata) { logger.info("Load properties from the ontology in lang " + l); config.loadPropertiesFromOntology(config.getMainOntology().getOWLAPIModel());