diff --git a/README.md b/README.md index 75662f78..b08f18b7 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,43 @@ # SM2KG Software Metadata 2 Knowledge Graphs: A tool for automatically extracting relevant information from readme files + +Installation Instructions - + +`pip3 install -r requirements.txt` + +Create a config.json file using the sample file in the repository. + +Command Line Interface - + +createJSON.py generates a JSON object after extracting useful information from the github repository. It classifies the readme file into one of four categories - description, invocation, installation, citation depending on highest confidence above a given threshold. + +The createJSON.py file takes as input the following parameters: + +-r / --repo_url: Link to the github repository for extracting information + +-m / --model_path: Path to the pickled models for extraction + +-o / --output: Output file name + +-t / --threshold: Threshold to classify the content of the readme file + +-d / --doc_src: Path of documentation file + + +cli.py generates a JSON object after extracting useful information from the github repository. It classifies the readme file into one of four categories - description, invocation, installation, citation depending on confidence above a given threshold. + +The cli.py file takes as input the following parameters: + +-r / --repo_url: Link to the github repository for extracting information + +-o / --output: Output file name + +-t / --threshold: Threshold to classify the content of the readme file + +-d / --doc_src: Path of documentation file + +Example: + +`python3 createJSON.py -r https://github.com/{owner}/{repository_name} -m ./models/ -o output.json -t 0.5` + +`python3 cli.py -r https://github.com/{owner}/{repository_name} -o output.json -t 0.5` diff --git a/cli.py b/cli.py new file mode 100644 index 00000000..492fc058 --- /dev/null +++ b/cli.py @@ -0,0 +1,228 @@ +# creatJSON.py +# parameters: +## input file: either: url to github repository OR markdown documentation file path +## output file: json with each excerpt marked with all four classification scores + +import argparse +import json +import base64 +from urllib.parse import urlparse +import sys +import os +from os import path +import requests +from markdown import Markdown +from bs4 import BeautifulSoup +from io import StringIO +import pickle +import pprint +import pandas as pd +import numpy as np +import re + +## Markdown to plain text conversion: begin ## +# code snippet from https://stackoverflow.com/a/54923798 +def unmark_element(element, stream=None): + if stream is None: + stream = StringIO() + if element.text: + stream.write(element.text) + for sub in element: + unmark_element(sub, stream) + if element.tail: + stream.write(element.tail) + return stream.getvalue() + +# patching Markdown +Markdown.output_formats["plain"] = unmark_element +__md = Markdown(output_format="plain") +__md.stripTopLevelTags = False + +def unmark(text): + return __md.convert(text) +## Markdown to plain text conversion: end ## + +def restricted_float(x): + x = float(x) + if x < 0.0 or x > 1.0: + raise argparse.ArgumentTypeError(f"{x} not in range [0.0, 1.0]") + return x + +categories = ['description','citation','installation','invocation'] +keep_keys = ('description', 'name', 'owner', 'license', 'languages_url', 'forks_url') + + +## Function uses the repository_url provided to load required information from github. +## Information kept from the repository is written in keep_keys. +## Returns the readme text and required metadata +def load_repository_metadata(repository_url): + print("Loading Repository Information....") + ## load general response of the repository + url = urlparse(repository_url) + if url.netloc != 'github.com': + sys.exit("Error: repository must come from github") + _, owner, repo_name = url.path.split('/') + general_resp = requests.get(f"https://api.github.com/repos/{owner}/{repo_name}", headers=header).json() + + if 'message' in general_resp.keys() and general_resp['message']=="Not Found": + sys.exit("Error: repository name is incorrect") + + ## Remove extraneous data + filtered_resp = {k: general_resp[k] for k in keep_keys} + + ## Condense owner information + if filtered_resp['owner'] and 'login' in filtered_resp['owner'].keys(): + filtered_resp['owner'] = filtered_resp['owner']['login'] + + ## condense license information + license_info = {} + for k in ('name', 'url'): + if filtered_resp['license'] and k in filtered_resp['license'].keys(): + license_info[k] = filtered_resp['license'][k] + filtered_resp['license'] = license_info + + # get keywords / topics + topics_headers = {} + topics_headers.update(header) + topics_headers = {'accept': 'application/vnd.github.mercy-preview+json'} + topics_resp = requests.get('https://api.github.com/repos/' + owner + "/" + repo_name + '/topics', headers=topics_headers).json() + if topics_resp and 'names' in topics_resp.keys(): + filtered_resp['topics'] = topics_resp['names'] + + ## get languages + filtered_resp['languages'] = list(requests.get(filtered_resp['languages_url']).json().keys()) + del filtered_resp['languages_url'] + + ## get default README + readme_info = requests.get('https://api.github.com/repos/' + owner + "/" + repo_name + '/readme', headers=topics_headers).json() + readme = base64.b64decode(readme_info['content']).decode("utf-8") + text = unmark(readme) + filtered_resp['readme_url'] = readme_info['html_url'] + + ## get releases + releases_list = requests.get('https://api.github.com/repos/' + owner + "/" + repo_name + '/releases', headers=header).json() + releases_list = map(lambda release : {'tag_name': release['tag_name'], 'name': release['name'], 'author_name': release['author']['login'], 'body': release['body'], 'tarball_url': release['tarball_url'], 'zipball_url': release['zipball_url'], 'html_url':release['html_url'], 'url':release['url']}, releases_list) + filtered_resp['releases'] = list(releases_list) + + print("Repository Information Successfully Loaded.") + return text, filtered_resp + +## Function takes readme text as input and divides it into excerpts +## Returns the extracted excerpts +def create_excerpts(text): + divisions = text.splitlines() + divisions = [i for i in divisions if i] + return divisions + +## Function takes readme text as input and runs the provided classifiers on it +## Returns the dictionary containing scores for each excerpt. +def run_classifiers(text): + score_dict={} + for category in categories: + excerpts = create_excerpts(text) + file_name = file_paths[category] + if file_name=="": + print('I am here') + continue + if not path.exists(file_name): + sys.exit("Error: File/Directory does not exist") + print("Classifying excerpts for the catgory",category) + classifier = pickle.load(open(file_name, 'rb')) + scores = classifier.predict_proba(excerpts) + score_dict[category]={'excerpt': excerpts, 'confidence': scores[:,1]} + print("Excerpt Classification Successful for the Category",category) + return score_dict + +## Function takes scores dictionary and a threshold as input +## Returns predictions containing excerpts with a confidence above the given threshold. +def classify(scores, threshold): + print("Checking Thresholds for Excerpt Classification.") + predictions = {} + for ele in scores.keys(): + print("Running for",ele) + flag = False + predictions[ele] = [] + excerpt="" + confid=[] + for i in range(len(scores[ele]['confidence'])): + if scores[ele]['confidence'][i]>=threshold: + if flag==False: + excerpt=excerpt+scores[ele]['excerpt'][i]+' \n' + confid.append(scores[ele]['confidence'][i]) + flag=True + else: + excerpt=excerpt+scores[ele]['excerpt'][i]+' \n' + confid.append(scores[ele]['confidence'][i]) + else : + if flag==True: + element = {'excerpt':excerpt,'confidence':confid} + predictions[ele].append(element) + excerpt="" + confid=[] + flag=False + print("Run completed.") + print("All Excerpts below the given Threshold Removed.") + return predictions + +## Function takes readme text as input and runs a regex parser on it +## Returns a list of bibtex citations +def extract_bibtex(readme_text): + print("Extracting bibtex citation from readme") + regex = r'\@[a-zA-z]+\{[.\n\S\s]+?[author|title][.\n\S\s]+?[author|title][.\n\S\s]+?\n\}' + excerpts = readme_text + citations = re.findall(regex,excerpts) + print("Extracting bibtex citation from readme completed.") + print(citations) + print(len(citations)) + return citations + +## Function takes metadata, readme text predictions, bibtex citations and path to the output file +## Performs some combinations and saves the final json Object in the file +def save_json(git_data, repo_data, citations, outfile): + + for i in git_data.keys(): + if i == 'description': + if 'description' not in repo_data.keys(): + repo_data['description'] = [] + repo_data['description'].append(git_data[i]) + else: + repo_data[i] = git_data[i] + + for i in range(len(citations)): + if 'citation' not in repo_data.keys(): + repo_data['citation'] = [] + repo_data['citation'].append({'excerpt': citations[i]}) + + print("Saving json data to",outfile) + with open(outfile, 'w') as output: + json.dump(repo_data, output) + +header = {} +with open('config.json') as fh: + file_paths = json.load(fh) +header['Authorization'] = file_paths['Authorization'] +header['accept'] = 'application/vnd.github.v3+json' + +argparser = argparse.ArgumentParser(description="Fetch Github README, split paragraphs, run classifiers and output json containing repository information, classified excerpts and confidence.") +src = argparser.add_mutually_exclusive_group(required=True) +src.add_argument('-r', '--repo_url', help="URL of the Github repository") +src.add_argument('-d', '--doc_src', help='path to documentation file') +argparser.add_argument('-o', '--output', help="path for output json", required=True) +argparser.add_argument('-t','--threshold', help="threshold score", type=restricted_float, default=0.5) +argv = argparser.parse_args() + +github_data = {} +if (argv.repo_url): + text, github_data = load_repository_metadata(argv.repo_url) +elif (argv.doc_src): + # Documentation from already downloaded Markdown file. + with open(argv.doc_src, 'r') as doc_fh: + text = unmark(doc_fh.read()) + +score_dict = run_classifiers(text) + +predictions = classify(score_dict, argv.threshold) + +citations = extract_bibtex(text) + +save_json(github_data, predictions, citations, argv.output) diff --git a/config.json b/config.json new file mode 100644 index 00000000..357c285a --- /dev/null +++ b/config.json @@ -0,0 +1,7 @@ +{ + "Authorization" : "token PersonalAccessToken", + "description" : "./models/description.sk", + "citation" : "./models/citation.sk", + "installation" : "./models/installation.sk", + "invocation" : "./models/invocation.sk" +} \ No newline at end of file diff --git a/createJSON.py b/createJSON.py new file mode 100644 index 00000000..73d0a832 --- /dev/null +++ b/createJSON.py @@ -0,0 +1,183 @@ +# creatJSON.py +# parameters: +## input file: either: url to github repository OR markdown documentation file path +## output file: json with each paragraph marked with all four classification scores + +import argparse +import json +import base64 +from urllib.parse import urlparse +import sys +import os +from os import path +import requests +from markdown import Markdown +from bs4 import BeautifulSoup +from io import StringIO +import pickle +import pprint +import pandas as pd +import numpy as np + +with open('config.json') as fh: + header = json.load(fh) +header['accept'] = 'application/vnd.github.v3+json' + +## Markdown to plain text conversion: begin ## +# code snippet from https://stackoverflow.com/a/54923798 +def unmark_element(element, stream=None): + if stream is None: + stream = StringIO() + if element.text: + stream.write(element.text) + for sub in element: + unmark_element(sub, stream) + if element.tail: + stream.write(element.tail) + return stream.getvalue() + +# patching Markdown +Markdown.output_formats["plain"] = unmark_element +__md = Markdown(output_format="plain") +__md.stripTopLevelTags = False + +def unmark(text): + return __md.convert(text) +## Markdown to plain text conversion: end ## + +def restricted_float(x): + x = float(x) + if x < 0.0 or x > 1.0: + raise argparse.ArgumentTypeError(f"{x} not in range [0.0, 1.0]") + return x + +def load_repository_information(repository_url): + ## load general response of the repository + url = urlparse(repository_url) + if url.netloc != 'github.com': + sys.exit("Error: repository must come from github") + _, owner, repo_name = url.path.split('/') + general_resp = requests.get(f"https://api.github.com/repos/{owner}/{repo_name}", headers=header).json() + + if 'message' in general_resp.keys() and general_resp['message']=="Not Found": + sys.exit("Error: repository name is incorrect") + + ## Remove extraneous data + keep_keys = ('description', 'name', 'owner', 'license', 'languages_url', 'forks_url') + filtered_resp = {k: general_resp[k] for k in keep_keys} + + ## Condense owner information + if filtered_resp['owner'] and 'login' in filtered_resp['owner'].keys(): + filtered_resp['owner'] = filtered_resp['owner']['login'] + + + ## condense license information + license_info = {} + for k in ('name', 'url'): + if filtered_resp['license'] and k in filtered_resp['license'].keys(): + license_info[k] = filtered_resp['license'][k] + filtered_resp['license'] = license_info + + # get keywords / topics + topics_headers = {} + topics_headers.update(header) + topics_headers = {'accept': 'application/vnd.github.mercy-preview+json'} + topics_resp = requests.get('https://api.github.com/repos/' + owner + "/" + repo_name + '/topics', headers=topics_headers).json() + if topics_resp and 'names' in topics_resp.keys(): + filtered_resp['topics'] = topics_resp['names'] + + ## get languages + filtered_resp['languages'] = list(requests.get(filtered_resp['languages_url']).json().keys()) + del filtered_resp['languages_url'] + + ## get default README + readme_info = requests.get('https://api.github.com/repos/' + owner + "/" + repo_name + '/readme', headers=topics_headers).json() + readme = base64.b64decode(readme_info['content']).decode("utf-8") + text = unmark(readme) + filtered_resp['readme_url'] = readme_info['html_url'] + + ## get releases + releases_list = requests.get('https://api.github.com/repos/' + owner + "/" + repo_name + '/releases', headers=header).json() + releases_list = map(lambda release : {'tag_name': release['tag_name'], 'name': release['name'], 'author_name': release['author']['login'], 'body': release['body'], 'tarball_url': release['tarball_url'], 'zipball_url': release['zipball_url'], 'html_url':release['html_url'], 'url':release['url']}, releases_list) + filtered_resp['releases'] = list(releases_list) + + return text, filtered_resp + +def run_classifiers(path_to_models, text): + score_dict={} + if(not path.exists(path_to_models)): + sys.exit("Error: File/Directory does not exist") + if(path.isfile(path_to_models)): + classifier = pickle.load(open(path_to_models, 'rb')) + classifier_name = os.path.basename(path_to_models) + excerpts = text.splitlines() + excerpts = [i for i in excerpts if i] + scores = classifier.predict_proba(excerpts) + score_dict={'excerpt': excerpts, classifier_name: scores[:,1]} + else : + for file in os.listdir(path_to_models): + classifier = pickle.load(open(path_to_models+'/'+file, 'rb')) + classifier_name = os.path.basename(file) + excerpts = text.splitlines() + excerpts = [i for i in excerpts if i] + scores = classifier.predict_proba(excerpts) + if 'excerpt' not in score_dict.keys(): + score_dict={'excerpt': excerpts, classifier_name: scores[:,1]} + else : + score_dict[classifier_name]=scores[:,1] + return score_dict + +def classify_into_one(scores, threshold): + results = pd.DataFrame(scores) + col = results[results.columns[1:]].idxmax(axis=1) + maxval = results[results.columns[1:]].max(axis=1) + pred = np.column_stack((results['excerpt'],col,maxval)) + pred = pred[pred[:,2] >= threshold] + predictions = {'description.sk':[],'invocation.sk':[],'installation.sk':[],'citation.sk':[]} + curr="" + excerpt="" + for ele in range(len(pred)): + if curr=="": + excerpt=excerpt+pred[ele][0]+' \n' + curr = pred[ele][1] + elif curr==pred[ele][1]: + excerpt=excerpt+pred[ele][0]+' \n' + else : + predictions[pred[ele][1]].append(excerpt) + excerpt = pred[ele][0]+' \n' + curr = pred[ele][1] + return predictions + +def synthRepoData(git_data, repo_data, outfile): + + for i in git_data.keys(): + if(i == 'description'): + repo_data['description.sk'].append(git_data[i]) + else: + repo_data[i] = git_data[i] + + with open(outfile, 'w') as output: + json.dump(repo_data, output) + + +argparser = argparse.ArgumentParser(description="Fetch Github README, split paragraphs, run classifiers and output json containing repository information, classified excerpts and confidence.") +src = argparser.add_mutually_exclusive_group(required=True) +src.add_argument('-r', '--repo_url', help="URL of the Github repository") +src.add_argument('-d', '--doc_src', help='path to documentation file') +argparser.add_argument('-m', '--model_path', help='path to pickled model', required=True) +argparser.add_argument('-o', '--output', help="path for output json", required=True) +argparser.add_argument('-t','--threshold', help="threshold score", type=restricted_float, default=0.5) +argv = argparser.parse_args() + +if (argv.repo_url): + text, github_data = load_repository_information(argv.repo_url) +elif (argv.doc_src): + # Documentation from already downloaded Markdown file. + with open(argv.doc_src, 'r') as doc_fh: + text = unmark(doc_fh.read()) + +score_dict = run_classifiers(argv.model_path, text) + +predictions = classify_into_one(score_dict, argv.threshold) + +synthRepoData(github_data, predictions, argv.output) diff --git a/experiment.json b/experiment.json new file mode 100644 index 00000000..5d41fd1f --- /dev/null +++ b/experiment.json @@ -0,0 +1,297 @@ +{ + "description.sk": [ + "Description \n", + "* Integration with diagram creators (WebVOWL). \n", + "Examples \n", + "Tutorial \n", + "java -jar widoco-VERSION-jar-with-dependencies.jar [-ontFile file] or [-ontURI uri] [-outFolder folderName] [-confFile propertiesFile] or [-getOntologyMetadata] [-oops] [-rewriteAll] [-crossRef] [-saveConfig configOutFile] [-useCustomStyle] [-lang lang1-lang2] [-includeImportedOntologies] [-htaccess] [-webVowl] [-licensius] [-ignoreIndividuals] [-analytics analyticsCode] [-doNotDisplaySerializations][-displayDirectImportsOnly] [-rewriteBase rewriteBasePath] [-excludeIntroduction] [-uniteSections] \n", + "The -outFolder option specifies where you want to place the output. \n", + "The -oops flag creates an html page with the evaluation from the OOPS service (http://oops.linkeddata.es/) \nThe -rewriteAll option will tell WIDOCO to rewrite files if the new generate files are replacing existing files. Otherwise the tool will promt a window asking the user. \n", + "The -includeAnnotationProperties flag will include annotation properties defined in your ontology (by default they are not included) \n", + "The -rewriteBase flag allows changing the default rewrite base path (until the documentation folder). By default it is \"/\". \n", + "How can I make WIDOCO automatically recognize my vocabulary annotations? \n", + "(WIN) chrome.exe --allow-file-access-from-files, \n(OSX) open /Applications/Google\\ Chrome.app/ --args --allow-file-access-from-files \n(UNX) /usr/bin/google-chrome --allow-file-access-from-files \nCurrent improvements \n", + "* Means to add examples to your ontology terms. \n", + "Otherwise, you will probably experience an \"Unsupported major.minor version 52.0\" exception when executing the JAR file. \nContribution guidelines \n", + "Wizard for documenting ontologies. WIDOCO is a step by step generator of HTML templates with the documentation of your ontology. It uses the LODE environment to create part of the template." + ], + "invocation.sk": [ + "Author: Daniel Garijo Verdejo (@dgarijo) \nContributors: María Poveda, Idafen Santana, Almudena Ruiz, Miguel Angel García, Oscar Corcho, Daniel Vila, Sergio Barrio, Martin Scharm, Maxime Lefrancois, Alfredo Serafini, @kartgk. \nCiting WIDOCO: Please cite the latest version of WIDOCO in Zenodo: https://zenodo.org/badge/latestdoi/11427075. \nISWC 2017 paper: https://iswc2017.semanticweb.org/paper-138 \n@inproceedings{garijo2017widoco, \n title={WIDOCO: a wizard for documenting ontologies}, \n author={Garijo, Daniel}, \n booktitle={International Semantic Web Conference}, \n pages={94--102}, \n year={2017}, \n organization={Springer, Cham}, \n doi = {10.1007/978-3-319-68204-4_9}, \n", + "To download WIDOCO, you need to download a JAR executable file. Check the latest release for more details: (https://github.com/dgarijo/WIDOCO/releases/latest). \n", + "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. \nFeatures of WIDOCO: \n* Automatic documentation of the terms in your ontology (based on LODE) \n* Automatic annotation in JSON-LD snippets of the html produced. \n* Association of a provenance page which includes the history of your vocabulary (W3C PROV-O compliant). \n* Metadata extraction from the ontology plus the means to complete it on the fly when generating your ontology. Check the best practice document to know more about the terms recognized by WIDOCO. \n* Guidelines on the main sections that your document should have and how to complete them. \n", + "* Automatic changelog of differences between the actual and the previous version of the ontology (based on Bubastis). \n* Separation of the sections of your html page so you can write them independently and replace only those needed. \n* Content negotiation and serialization of your ontology according to W3C best practices \n", + "Examples of the features of WIDOCO can be seen on the gallery \n", + "A tutorial explaining the main features of the GUI can be found here \nHow to use WIDOCO \n", + "The ontFile and ontURI options allow you to choose the ontology file or ontology URI of your ontology. \n", + "The -confFile allows you to choose your own configuration file for the ontology metadata. However you can tell WIDOCO to try to extract some of the metadata from the ontology with getOntologyMetadata. \n", + "The -crossRef option will ONLY generate the overview and cross reference sections. The index document will NOT be generated. The htaccess, provenance page, etc., will not be generated unless requested by other flags. This flag in intended to be used only after a first version of the documentation exists. \nThe -saveConfig option allows you to save a configuration file on the \"configOutFile\" route with the properties of a given ontology. \nThe -useCustomStyle option allows exporting the documentation using alternate css files (thanks to Daniel Vila). \nThe -lang option allows showing the languages in which the documentation will be published (separated by \"-\"). Note that if the language is not supported, the system will load the labels in english. For example: en-pt-es \nThe -includeImportedOntologies flag indicates whether the terms of the imported ontologies of the current ontology should be documented as well or not. \nThe -htaccess flag creates a bundle for publication ready to be deployed on your apache server. \nThe -webVowl flag provides a link to a visualization based on WebVowl (http://vowl.visualdataweb.org/webvowl/index.html#). \nThe -licensius flag uses the Licensius web services (http://licensius.com/apidoc/index.html) to retrieve license metadata. Only works if the -getOntologyMetadata flag is enabled. \nThe -ignoreIndividuals flag allows you to ignore the named individuals in the ontology. \n", + "The -analytics flag will add a code snippet for Google analytics to track your page. You need to add your code next to it. For example: UA-1234 \nThe -doNotDisplaySerializations flag allows not displaying available serializations of the ontology. \nThe -displayDirectImportsOnly flag allows displaying only those imported ontologies that are directly imported in the ontology being documented. \n", + "There are two ways for making WIDOCO get your vocabulary metadata annotations and use them automatically to document the ontology. \nAdd them in your OWL file. For guidelines on which ones to include, follow our Best Practices document, which indicates which ones we recommend. \nEdit 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). \nBrowser issues (Why can't I see the generated documentation / visualization?) \nThe result of executing WIDOCO is an HTML file. We have successfully tested it in Mozilla, IE, Safari and Chrome. When the page is stored in a server, WIDOCO's HTML works correctly in all browsers. If you view the file on your local browser, we recommend you to use Mozilla Firefox, Safari or Internet Explorer. Google Chrome will not show the contents correctly, as it doesn't allow XMLHttpRequest without HTTP. If you want to view the page locally with Google Chrome you have two possibilities: \na) Place the file in a server and access it via its URL (for example, put it in dropbox and access through its public url, or on a Github page). \nb) Execute Chrome with the following commands (Thanks to Alejandro Fernandez Carrera): \n", + "We are working on the following features: \n", + "Requirements \nYou will need Java 1.8 or higher (SDK 1.8 or JRE 8) for WIDOCO to work \n" + ], + "installation.sk": [ + " funding = {USNSF ICER-1541029, NIH 1R01GM117097-01}, \n url={http://dgarijo.com/papers/widoco-iswc2017.pdf} \n} \nDownloading the executable \n=================== \n", + "Download all the files of the \"JAR\" folder into the same folder. Then just double click the .jar file. \nNow you can execute WIDOCO through the console. Usage: \n", + "The -excludeIntroduction flag skips adding an introduction section. \nThe -uniteSections includes all sections in the same HTML document. \n", + "* Previsualization of the terms that will be generated. \nFor a complete list, check the project open issues. \n" + ], + "citation.sk": [ + "WIzard for DOCumenting Ontologies (WIDOCO) \n" + ], + "name": "Widoco", + "owner": "dgarijo", + "license": { + "name": "Other", + "url": null + }, + "forks_url": "https://api.github.com/repos/dgarijo/Widoco/forks", + "topics": [ + "ontology", + "wizard", + "metadata", + "documentation", + "ontology-diagram", + "ontology-evaluation" + ], + "languages": [ + "Java", + "XSLT", + "CSS", + "JavaScript", + "HTML" + ], + "readme_url": "https://github.com/dgarijo/Widoco/blob/master/README.md", + "releases": [ + { + "tag_name": "v1.4.13", + "name": "WIDOCO 1.4.13: Linking evaluation in documentation", + "author_name": "dgarijo", + "body": "This version of WIDOCO removes a few of unused dependencies and, if desired, shows a link to the OOPS! evaluation generated in the documentation. Before, this link had to be added manually. \r\n\r\nThanks to @HaydarAk for the suggestions on how to show it in the main page.\r\n\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.13", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.13", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.13", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/22775882" + }, + { + "tag_name": "v1.4.12", + "name": "WIDOCO 1.4.12: Big fixes and new configurations", + "author_name": "dgarijo", + "body": "This version of WIDOCO addresses the following issues (thanks to @pmcb55 for his contributions!!)\r\n * #354: The page would display centered in the visualization instead of the element loaded.\r\n * #362: Upgraded to latest version of OWL API\r\n * #361: Allowed adding a \"-uniteAllSections\" flag that will print all sections on the same document. Hence, dynamic loading will be removed.\r\n * Tidying up PROV rendering.\r\n * Small typo fixes in the default html ", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.12", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.12", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.12", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/21002818" + }, + { + "tag_name": "v1.4.11", + "name": "WIDOCO 1.4.11: Better logging and bug fixes", + "author_name": "dgarijo", + "body": "This version of WIDOCO integrates the pull requests from @seralf to improve logging and simplify dependencies.\r\nIn addition, it addresses the following issues:\r\n * #344: Now double \"#\" errors have been removed from changelog.\r\n * #350: Fixed an issue in which the references would overwrite the main section ", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.11", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.11", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.11", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/17596778" + }, + { + "tag_name": "v1.4.10", + "name": "WIDOCO 1.4.10: Pull requests, updates and bug fixes", + "author_name": "dgarijo", + "body": "This version of WIDOCO incorporates pull requests from @seralf and @jgeluk (updating to the latest version of WebVowl) and fixes the following issues:\r\n* #333 Now if there is an error in one of the imports the application will continue running instead of failing.\r\n* #217 Now the changelog can be expanded and collapsed, which makes it easier to navigate\r\n* #313 A link will be added in the index page if provided in the config file (using contextURI=\"YOUR URL\")\r\n* #339 Now WIDOCO will generate the folders four your htaccess file as well.\r\n\r\nIn addition, now the base encoding is UTF-8.", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.10", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.10", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.10", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/17029600" + }, + { + "tag_name": "v1.4.9", + "name": "WIDOCO 1.4.9: Supporting schema.org", + "author_name": "dgarijo", + "body": "This version of WIDOCO addresses the following:\r\n* #274: Now WIDOCO will include the domain and range if you use schema:domainIncludes and schema:rangeIncludes to declare it in your object properties or data properties with . Note that WIDOCO still does not support plain rdf:Property.\r\n* Reduced the level of logging", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.9", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.9", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.9", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/15737608" + }, + { + "tag_name": "v1.4.8", + "name": "WIDOCO 1.4.8: Logging and automated citation", + "author_name": "dgarijo", + "body": "This release of WIDOCO includes:\r\n* Fixes from @jgeluk to do proper logging.\r\n* Fix #264: now an automated citation will be produced for your ontology by default (if the appropriate metadata is there: creators, revision, and URL (this version)\r\n* JenaCatalogIRIMapper now supports Jena's ont-policy.rdf file to resolve imports with local files\r\n* Fixed #321, now WIDOCO uses a more recent version of OWL API \r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.8", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.8", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.8", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/15474861" + }, + { + "tag_name": "v1.4.7", + "name": "WIDOCO 1.4.7: Dependency and bug fixes", + "author_name": "dgarijo", + "body": "This release of WIDOCO fixes the following issues:\r\n* #305: Now when you launch WIDOCO without parameters, the console will also show a description of the tool and will explain how to run it. \r\n* #309 Removed the absolute layout dependency that prevented WIDOCO JAR from being run.\r\n* #311 Now the publisher will show on the GUI correctly (before it would only if it had a URL)\r\n* #314: Added an html tag around the external sections so the browser won't complain\r\n* #316 Fixed the generation of the table of contents so \"back to TOC\" wouldn't appear\r\n* #317 Fixed the GUI so the \"Imported ontologies\" label appears as imported and not \"extended\"\r\nIt also removes the restlet dependency, which had a vulnerability and was not used anymore.", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.7", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.7", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.7", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/13944540" + }, + { + "tag_name": "v1.4.6", + "name": "WIDOCO 1.4.6: Tutorial and bug fixes", + "author_name": "dgarijo", + "body": "This version of WIDOCO includes the following updates:\r\n* Updated the OWL2Vowl library to the latest version (old library was producing errors in some ontologies)\r\n* Included a tutorial (http://dgarijo.github.io/Widoco/doc/tutorial/) describing the GUI step by step and all its functionality\r\n* Added support for selecting ontologies in JSON\r\n* Added contributing guidelines into readme.md\r\n* Fixed namespaces when selecting documentation in several languages\r\n* Now it's possible to edit the rewrite base path in the .htaccess file.\r\n* Fixed a typo in the .htaccess for serving json\r\n* Fixed an encoding problem when showing french labels.\r\n* @kartgk fixed an error with the import closure of ontologies (in case not all imports of imported ontologies wanted to be displayed)\r\n* Added the correct version numbers to pom file.\r\n* Fixed an issue in lang cs that made the table of namespaces not to show correctly", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.6", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.6", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.6", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/13019723" + }, + { + "tag_name": "v1.4.5", + "name": "WIDOCO 1.4.5: Updated WebVowl and support for Czech", + "author_name": "dgarijo", + "body": "This version of WIDOCO includes the following updates:\r\n* Updated webVowl to version 1.1.2 (latest)\r\n* Allowed disabling showing ontology serializations (-doNotDisplaySerializations flag). Both in the console and GUI\r\n* Added support for Czech localization (also in GUI)\r\n\r\nThanks to Petr Kremen for contributing with the Czech localization", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.5", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.5", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.5", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/12049594" + }, + { + "tag_name": "v1.4.4", + "name": "WIDOCO 1.4.4: Added support for Google Analytics", + "author_name": "dgarijo", + "body": "This version of WIDOCO allows to add a Google Analytics code to track the traffic received in one of the pages. WIDOCO assumes you have a UA code. You can use it on the GUI, through a config file or in the command line by adding `-analytics yourcode`\r\n\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.4", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.4", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.4", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/11300894" + }, + { + "tag_name": "v1.4.3", + "name": "WIDOCO 1.4.3: Bug Fixes and support for french", + "author_name": "dgarijo", + "body": "This release fixes the following issues:\r\n* Added support for french (thanks to Maxime Lefrancois)\r\n* When imported ontologies had characters like \"<\" they were not showing.\r\n* Added JSON-LD serialization for ontologies automatically\r\n* When annotation properties have blank nodes, they will now be ignored instead of failing\r\n* Updated contributor list\r\n* Blank nodes are now absent from the provenance page.\r\n* Fixed default language when restarting WIDOCO.\r\n* Fixed the language form (now french can be selected, and it has the proper icons)\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.3", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.3", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.3", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/10556972" + }, + { + "tag_name": "v1.4.2", + "name": "WIDOCO 1.4.2: Small fixes and merged contributions", + "author_name": "dgarijo", + "body": "This release includes the latest contributions to the project:\r\n* Fixes in HTML\r\n* Fixes in how OOPS! is called\r\nAlso, now the license name is the URI if no name is provided (and URI is) instead of \"license name goes here\", and the java encoding has been included in the pom file to prevent UTF-8 errors in compilation.", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.2", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.2", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.2", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/9846306" + }, + { + "tag_name": "v1.4.1", + "name": "WIDOCO 1.4.1: Metadata support and major bug fixes", + "author_name": "dgarijo", + "body": "WIDOCO now will comply with most of the terms listed in https://w3id.org/widoco/bestPractices. A few of them are still unsopported (e.g., rdfs:seeAlso) and will be added in next releases.\r\n\r\nIn this version, I have added support for all the deprecation terms in LODE, as well as support for skos:prefLabel and better recognition of some of the terms when the range can be a String or a resource.\r\n\r\nChanges:\r\n* Now the examples have a \"pre\" label, so if they include rdf text or json text they show properly.\r\n* A pointer to the guidelines has been added in the interface\r\n* When invoking the program using command line, the default behavior is to load the properties from the ontology. Only if a config file is provided, the properties won't be loaded. There is still a flag, which I have preferred to leave for possible legacy issues.\r\n* Markup is now recognized in all sections\r\n* The diagram is now optional (by default it was always produced in older versions)\r\n* This release also includes a doc folder with guidelines on the metadata properties to use, a benchmark of ontologies used for testing, a gallery with what WIDOCO can accomplish and a summary of projects that have adopted WIDOCO.\r\n\r\nBug fixes: \r\n* Changed the pom file with another plugin for creating the JAR, because some of the RIO parsers were not creating the appropriate serializations of the ontology.\r\n* Added robustness when the changelog was created. If a wrong URI is provided, then the changelog will not be created.\r\n* Changed how the ontology is chosen so there won't be errors in MAC systems.\r\n* Fixed some of the language tags.\r\n* Polished some errors related to the interface.", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.1", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.1", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.1", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/6527938" + }, + { + "tag_name": "v1.4.0", + "name": "WIDOCO 1.4.0: Inline visualization diagrams", + "author_name": "dgarijo", + "body": "This release removes the external dependency to WebVowl, and creates a visualization that can be seen in the ontology document itself (overview section). In addition, the following changes have been made:\r\n * Migrated the framework to use a recent version of OWL API (hence the size of the JAR)\r\n * Bug fixes in meta data (more to come in future releases)\r\n * Made WIDOCO more robust to errors\r\n * Published a benchmark of ontologies used to test WIDOCO. If you want us to try a new one, just open an issue!\r\n * Published a draft of the best practices for ontology annotation (currently under work). These are meant\r\n * Published a showcase gallery with examples of WIDOCO's features\r\n * Published a report on the known usages by WIDOCO. \r\n\r\n![webvowl](https://cloud.githubusercontent.com/assets/1520666/26068984/54eff946-3954-11e7-81b8-c72db0bd93bb.png)\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.0", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.0", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.0", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/6390471" + }, + { + "tag_name": "v1.3.1", + "name": "Widoco 1.3.1: Bug fixes and metadata enrichment", + "author_name": "dgarijo", + "body": "This release fixes several issues and extends LODE to accept more metadata options for defining terms and adding examples.\r\n* Fixed an issue with the changelog that produced an empty bullet when the domain or range of a property was an union or intersection.\r\n* Added tests with different ontologies that help inspecting whether a new change leads to errors or not.\r\n* Extended LODE to accept: prov:definition, vann:example, obo:definition (with the appropriate class name), obo:usageExample, vaem:rationale, skos:definition and terms:source.\r\n* Extended Widoco to accept terms:bibliographicCitation, bibo:status, bibo:doi and owl:backwardsCompatibleWith\r\n* If an error is produced while generating the changelog or the evaluation reports, the section is not generated. Before, an empty section would remain.\r\n* Fixed table of contents not being translated.\r\n* When generating the documentation of an ontology, if it imports another ontology that cannot be imported for any reason, Widoco will ignore the import instead of failing.\r\n* Added the possibility to ignore namedIndividuals when generating the documentation through console.\r\n\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.3.1", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.3.1", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.3.1", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/5951267" + }, + { + "tag_name": "v1.3.0", + "name": "Widoco 1.3.0: Automated changelog section", + "author_name": "dgarijo", + "body": "This version of Widoco creates an automated changelog section of your ontology. For all classes, properties and data properties, Widoco will calculate the new changes, additions and deletions and present them in a human-readable manner. In order to benefit from this feature, you just have to annotate your ontology with the URI of the previous version. You can use owl:priorVersion, dc:replaces or prov:wasRevisionOf to annotate your ontology (Widoco will only consider one file to compare against).\r\n\r\nAdditional improvements:\r\n* RDF-a annotations are replaced with JSON-LD snippets. The page is just annotated with schema.org. The rdf-a annotations made it difficult to maintain, and the structured extraction tool provided by Google did not work. With the JSON-LD snippet everything is clearer. The provenance of the page itself is published separately.\r\n* Now it is possible to generate ONLY the cross reference section of an ontology.\r\n* Bug fix that led to errors when opening some ontologies like OBI\r\n\r\nOverview sample of the changelog:\r\n![overview](https://cloud.githubusercontent.com/assets/1520666/23640611/ac4407f6-02a3-11e7-8a88-b597ba740721.png)\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.3.0", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.3.0", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.3.0", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/5659212" + }, + { + "tag_name": "v1.2.3", + "name": "Widoco 1.2.3: [Bug fix] Licensius is optional", + "author_name": "dgarijo", + "body": "The Licensius web service has been unstable lately. This led to long waits from the server, even with a timer on the request. Therefore retrieving the license using this service is now optional and loading metadata properties from the ontology is faster.\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.2.3", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.2.3", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.2.3", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/4659138" + }, + { + "tag_name": "v1.2.2", + "name": "Widoco 1.2.2: Major bug fixes and improvements", + "author_name": "dgarijo", + "body": "This version fixes the following issues/improvements:\n- 188: lang separator doesn't work on unix systems. Changed \";\" to \"-\" as separator\n- 189: return a non-zero value if there are problems generating the doc\n- 151: text area in the table should be bigger \n- 177: Ability to provide authors institution URI in the config \n- 155: allow possibility of adding Zenodo URI (DOI) \n- 132: could improve placeholder text\n- 174: Dynamic sections \n- 170: Check why isDefinedBy is not recognized sometimes\n- 171: Separate configuration from vocabulary metadata \n\nIn addition, I have fixed the custom style CSS, saving the publisher in the config file, producing an alt in images to avoid broken images when no connection is available and issues with the consistency in sections and back to toc titles.\n\nFinally, the toc will be now dynamic, so it will get updated if new headers with class \"list\" are added to the document.\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.2.2", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.2.2", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.2.2", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/3832172" + }, + { + "tag_name": "v1.2.1", + "name": "Widoco 1.2.1: Interface bug fixes", + "author_name": "dgarijo", + "body": "In this release a couple of bugs have been fixed.\nFirst, a bug that froze the program after hitting the \"back\" button, once the ontology properties had been loaded.\nAnother bug fix is that now \"publisher\" will not appear if it's not filled in the .properties file.\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.2.1", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.2.1", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.2.1", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/3701886" + }, + { + "tag_name": "v1.2.0", + "name": "Widoco 1.2.0: Extended metadata enrichment", + "author_name": "dgarijo", + "body": "This version automatically extracts the properties \"publisher\" and \"versionIRI\" from the ontology. In addition, it adds a link to webVowl and fixes some minor issues.\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.2.0", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.2.0", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.2.0", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/3683077" + }, + { + "tag_name": "v1.1.1", + "name": "Widoco1.1.1: Integration with Licensius is back online", + "author_name": "dgarijo", + "body": "This release contains the time outs for using Licensius (for retrieveing license names from the ontology) and OOPS! (for evaluation)\nIn addition, it also fixes some small issued with content negotiation when loading Protégé. By default, the .htaccess file will serve rdf/xml when asking for \\* / \\* and turtle when asking for text/*\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.1.1", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.1.1", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.1.1", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/3673322" + }, + { + "tag_name": "v1.1.0", + "name": "Content negotiation bundle", + "author_name": "dgarijo", + "body": "Now Widoco can create a content negotiation bundle that helps you deploy your vocabulary on your server. In addition, now different serializations of a vocabulary are saved locally, in order to facilitate users pointing to them.\n\nNote: due to time outs in Licensius, it is disabled in this version\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.1.0", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.1.0", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.1.0", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/3599226" + }, + { + "tag_name": "v1.0.0", + "name": "First stable release of Widoco", + "author_name": "dgarijo", + "body": "This release fixes multiple bugs from the earlier release, and allows customizing a label on the side with the current status of the document.\n\nThis version also improves how an ontology is loaded, applying content negotiation when necessary.\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.0.0", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.0.0", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.0.0", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/3263232" + } + ] +} \ No newline at end of file diff --git a/output.json b/output.json new file mode 100644 index 00000000..bbdf1b40 --- /dev/null +++ b/output.json @@ -0,0 +1,658 @@ +{ + "description": [ + { + "excerpt": "WIzard for DOCumenting Ontologies (WIDOCO) \n", + "confidence": [ + 0.8073788059002611 + ] + }, + { + "excerpt": "Citing WIDOCO: Please cite the latest version of WIDOCO in Zenodo: https://zenodo.org/badge/latestdoi/11427075. \n", + "confidence": [ + 0.5380148763720959 + ] + }, + { + "excerpt": "Downloading the executable \n", + "confidence": [ + 0.589941174902783 + ] + }, + { + "excerpt": "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. \nFeatures of WIDOCO: \n* Automatic documentation of the terms in your ontology (based on LODE) \n* Automatic annotation in JSON-LD snippets of the html produced. \n* Association of a provenance page which includes the history of your vocabulary (W3C PROV-O compliant). \n* Metadata extraction from the ontology plus the means to complete it on the fly when generating your ontology. Check the best practice document to know more about the terms recognized by WIDOCO. \n* Guidelines on the main sections that your document should have and how to complete them. \n* Integration with diagram creators (WebVOWL). \n* Automatic changelog of differences between the actual and the previous version of the ontology (based on Bubastis). \n* Separation of the sections of your html page so you can write them independently and replace only those needed. \n* Content negotiation and serialization of your ontology according to W3C best practices \n", + "confidence": [ + 0.8676245545215737, + 0.8434615223618694, + 0.7057329842826681, + 0.7052120748336989, + 0.6741134181133629, + 0.7431826624380229, + 0.6229285628530826, + 0.5609615660579162, + 0.7892729155918689, + 0.6631520283901499, + 0.6329823134823336 + ] + }, + { + "excerpt": "Examples of the features of WIDOCO can be seen on the gallery \n", + "confidence": [ + 0.8444800568394065 + ] + }, + { + "excerpt": "A tutorial explaining the main features of the GUI can be found here \nHow to use WIDOCO \nDownload all the files of the \"JAR\" folder into the same folder. Then just double click the .jar file. \nNow you can execute WIDOCO through the console. Usage: \njava -jar widoco-VERSION-jar-with-dependencies.jar [-ontFile file] or [-ontURI uri] [-outFolder folderName] [-confFile propertiesFile] or [-getOntologyMetadata] [-oops] [-rewriteAll] [-crossRef] [-saveConfig configOutFile] [-useCustomStyle] [-lang lang1-lang2] [-includeImportedOntologies] [-htaccess] [-webVowl] [-licensius] [-ignoreIndividuals] [-analytics analyticsCode] [-doNotDisplaySerializations][-displayDirectImportsOnly] [-rewriteBase rewriteBasePath] [-excludeIntroduction] [-uniteSections] \nThe ontFile and ontURI options allow you to choose the ontology file or ontology URI of your ontology. \nThe -outFolder option specifies where you want to place the output. \nThe -confFile allows you to choose your own configuration file for the ontology metadata. However you can tell WIDOCO to try to extract some of the metadata from the ontology with getOntologyMetadata. \nThe -oops flag creates an html page with the evaluation from the OOPS service (http://oops.linkeddata.es/) \nThe -rewriteAll option will tell WIDOCO to rewrite files if the new generate files are replacing existing files. Otherwise the tool will promt a window asking the user. \nThe -crossRef option will ONLY generate the overview and cross reference sections. The index document will NOT be generated. The htaccess, provenance page, etc., will not be generated unless requested by other flags. This flag in intended to be used only after a first version of the documentation exists. \nThe -saveConfig option allows you to save a configuration file on the \"configOutFile\" route with the properties of a given ontology. \nThe -useCustomStyle option allows exporting the documentation using alternate css files (thanks to Daniel Vila). \nThe -lang option allows showing the languages in which the documentation will be published (separated by \"-\"). Note that if the language is not supported, the system will load the labels in english. For example: en-pt-es \nThe -includeImportedOntologies flag indicates whether the terms of the imported ontologies of the current ontology should be documented as well or not. \nThe -htaccess flag creates a bundle for publication ready to be deployed on your apache server. \nThe -webVowl flag provides a link to a visualization based on WebVowl (http://vowl.visualdataweb.org/webvowl/index.html#). \nThe -licensius flag uses the Licensius web services (http://licensius.com/apidoc/index.html) to retrieve license metadata. Only works if the -getOntologyMetadata flag is enabled. \nThe -ignoreIndividuals flag allows you to ignore the named individuals in the ontology. \nThe -includeAnnotationProperties flag will include annotation properties defined in your ontology (by default they are not included) \nThe -analytics flag will add a code snippet for Google analytics to track your page. You need to add your code next to it. For example: UA-1234 \nThe -doNotDisplaySerializations flag allows not displaying available serializations of the ontology. \nThe -displayDirectImportsOnly flag allows displaying only those imported ontologies that are directly imported in the ontology being documented. \nThe -rewriteBase flag allows changing the default rewrite base path (until the documentation folder). By default it is \"/\". \nThe -excludeIntroduction flag skips adding an introduction section. \nThe -uniteSections includes all sections in the same HTML document. \n", + "confidence": [ + 0.7294725932852963, + 0.6155919564359572, + 0.6485630403731563, + 0.5304013435407224, + 0.5754212010962264, + 0.7616719999833607, + 0.6274931085112424, + 0.8013879032297736, + 0.6178676501744003, + 0.626753885937295, + 0.7308486989429855, + 0.803562806149038, + 0.6751147828065674, + 0.7737332938407381, + 0.7983539921907916, + 0.6544399630427565, + 0.6427070658598666, + 0.6365698833245319, + 0.72897006792718, + 0.5142843813438018, + 0.6705677838304225, + 0.7037564638758089, + 0.679633539055841, + 0.6151733764179571, + 0.7215795818826714, + 0.6659200031789076 + ] + }, + { + "excerpt": "There are two ways for making WIDOCO get your vocabulary metadata annotations and use them automatically to document the ontology. \nAdd them in your OWL file. For guidelines on which ones to include, follow our Best Practices document, which indicates which ones we recommend. \nEdit 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). \nBrowser issues (Why can't I see the generated documentation / visualization?) \nThe result of executing WIDOCO is an HTML file. We have successfully tested it in Mozilla, IE, Safari and Chrome. When the page is stored in a server, WIDOCO's HTML works correctly in all browsers. If you view the file on your local browser, we recommend you to use Mozilla Firefox, Safari or Internet Explorer. Google Chrome will not show the contents correctly, as it doesn't allow XMLHttpRequest without HTTP. If you want to view the page locally with Google Chrome you have two possibilities: \na) Place the file in a server and access it via its URL (for example, put it in dropbox and access through its public url, or on a Github page). \nb) Execute Chrome with the following commands (Thanks to Alejandro Fernandez Carrera): \n", + "confidence": [ + 0.6609924055003863, + 0.6230039023159415, + 0.7069710203337009, + 0.5941160863084669, + 0.7406356639640443, + 0.6808990562343953, + 0.6625867558855812 + ] + }, + { + "excerpt": "We are working on the following features: \n* Means to add examples to your ontology terms. \n* Previsualization of the terms that will be generated. \nFor a complete list, check the project open issues. \n", + "confidence": [ + 0.7232978232209017, + 0.5605769914625431, + 0.7083330550894784, + 0.6227145093770529 + ] + }, + { + "excerpt": "You will need Java 1.8 or higher (SDK 1.8 or JRE 8) for WIDOCO to work \nOtherwise, you will probably experience an \"Unsupported major.minor version 52.0\" exception when executing the JAR file. \n", + "confidence": [ + 0.6367414951932647, + 0.5814799479586049 + ] + }, + "Wizard for documenting ontologies. WIDOCO is a step by step generator of HTML templates with the documentation of your ontology. It uses the LODE environment to create part of the template." + ], + "citation": [ + { + "excerpt": "WIzard for DOCumenting Ontologies (WIDOCO) \nAuthor: Daniel Garijo Verdejo (@dgarijo) \nContributors: María Poveda, Idafen Santana, Almudena Ruiz, Miguel Angel García, Oscar Corcho, Daniel Vila, Sergio Barrio, Martin Scharm, Maxime Lefrancois, Alfredo Serafini, @kartgk. \nCiting WIDOCO: Please cite the latest version of WIDOCO in Zenodo: https://zenodo.org/badge/latestdoi/11427075. \nISWC 2017 paper: https://iswc2017.semanticweb.org/paper-138 \n@inproceedings{garijo2017widoco, \n title={WIDOCO: a wizard for documenting ontologies}, \n author={Garijo, Daniel}, \n booktitle={International Semantic Web Conference}, \n pages={94--102}, \n year={2017}, \n organization={Springer, Cham}, \n doi = {10.1007/978-3-319-68204-4_9}, \n funding = {USNSF ICER-1541029, NIH 1R01GM117097-01}, \n url={http://dgarijo.com/papers/widoco-iswc2017.pdf} \n} \n", + "confidence": [ + 0.5842602046714032, + 0.8273918360294598, + 0.5453876700347428, + 0.615000258845131, + 0.6356788571097686, + 0.9132063211932561, + 0.8493415301144451, + 0.8273918360294598, + 0.7110098892025157, + 0.6557563570707792, + 0.8595081760750233, + 0.6448348221890952, + 0.6781271475254176, + 0.5453876700347428, + 0.5105712459954294, + 0.5453876700347428 + ] + }, + { + "excerpt": "=================== \n", + "confidence": [ + 0.5453876700347428 + ] + }, + { + "excerpt": "Description \n", + "confidence": [ + 0.5453876700347428 + ] + }, + { + "excerpt": "* Content negotiation and serialization of your ontology according to W3C best practices \n", + "confidence": [ + 0.5246513683661227 + ] + }, + { + "excerpt": "Tutorial \n", + "confidence": [ + 0.5453876700347428 + ] + }, + { + "excerpt": "Add them in your OWL file. For guidelines on which ones to include, follow our Best Practices document, which indicates which ones we recommend. \n", + "confidence": [ + 0.5064504818593589 + ] + }, + { + "excerpt": "Current improvements \n", + "confidence": [ + 0.5183765422789443 + ] + }, + { + "excerpt": "Contribution guidelines \n", + "confidence": [ + 0.5453876700347428 + ] + }, + { + "excerpt": "@inproceedings{garijo2017widoco,\n title={WIDOCO: a wizard for documenting ontologies},\n author={Garijo, Daniel},\n booktitle={International Semantic Web Conference},\n pages={94--102},\n year={2017},\n organization={Springer, Cham},\n doi = {10.1007/978-3-319-68204-4_9},\n funding = {USNSF ICER-1541029, NIH 1R01GM117097-01},\n url={http://dgarijo.com/papers/widoco-iswc2017.pdf}\n}" + } + ], + "installation": [ + { + "excerpt": "To download WIDOCO, you need to download a JAR executable file. Check the latest release for more details: (https://github.com/dgarijo/WIDOCO/releases/latest). \n", + "confidence": [ + 0.6756189927221673 + ] + }, + { + "excerpt": "* Metadata extraction from the ontology plus the means to complete it on the fly when generating your ontology. Check the best practice document to know more about the terms recognized by WIDOCO. \n* Guidelines on the main sections that your document should have and how to complete them. \n", + "confidence": [ + 0.5395263070453569, + 0.5533653194763165 + ] + }, + { + "excerpt": "How to use WIDOCO \n", + "confidence": [ + 0.5241820785602166 + ] + }, + { + "excerpt": "Now you can execute WIDOCO through the console. Usage: \njava -jar widoco-VERSION-jar-with-dependencies.jar [-ontFile file] or [-ontURI uri] [-outFolder folderName] [-confFile propertiesFile] or [-getOntologyMetadata] [-oops] [-rewriteAll] [-crossRef] [-saveConfig configOutFile] [-useCustomStyle] [-lang lang1-lang2] [-includeImportedOntologies] [-htaccess] [-webVowl] [-licensius] [-ignoreIndividuals] [-analytics analyticsCode] [-doNotDisplaySerializations][-displayDirectImportsOnly] [-rewriteBase rewriteBasePath] [-excludeIntroduction] [-uniteSections] \n", + "confidence": [ + 0.6415865886134414, + 0.7758143247142087 + ] + }, + { + "excerpt": "The -outFolder option specifies where you want to place the output. \nThe -confFile allows you to choose your own configuration file for the ontology metadata. However you can tell WIDOCO to try to extract some of the metadata from the ontology with getOntologyMetadata. \n", + "confidence": [ + 0.6223335428972187, + 0.5000957065548255 + ] + }, + { + "excerpt": "The -rewriteAll option will tell WIDOCO to rewrite files if the new generate files are replacing existing files. Otherwise the tool will promt a window asking the user. \n", + "confidence": [ + 0.513109877080257 + ] + }, + { + "excerpt": "The -lang option allows showing the languages in which the documentation will be published (separated by \"-\"). Note that if the language is not supported, the system will load the labels in english. For example: en-pt-es \n", + "confidence": [ + 0.5318708281277784 + ] + }, + { + "excerpt": "The -htaccess flag creates a bundle for publication ready to be deployed on your apache server. \n", + "confidence": [ + 0.5535964708954193 + ] + }, + { + "excerpt": "The -licensius flag uses the Licensius web services (http://licensius.com/apidoc/index.html) to retrieve license metadata. Only works if the -getOntologyMetadata flag is enabled. \n", + "confidence": [ + 0.5116943456269532 + ] + }, + { + "excerpt": "The -includeAnnotationProperties flag will include annotation properties defined in your ontology (by default they are not included) \nThe -analytics flag will add a code snippet for Google analytics to track your page. You need to add your code next to it. For example: UA-1234 \n", + "confidence": [ + 0.562328708902558, + 0.5514401017594123 + ] + }, + { + "excerpt": "The -rewriteBase flag allows changing the default rewrite base path (until the documentation folder). By default it is \"/\". \n", + "confidence": [ + 0.5312102681235781 + ] + }, + { + "excerpt": "How can I make WIDOCO automatically recognize my vocabulary annotations? \n", + "confidence": [ + 0.6283619549395677 + ] + }, + { + "excerpt": "Browser issues (Why can't I see the generated documentation / visualization?) \n", + "confidence": [ + 0.510885854799806 + ] + }, + { + "excerpt": "b) Execute Chrome with the following commands (Thanks to Alejandro Fernandez Carrera): \n", + "confidence": [ + 0.586383757545377 + ] + }, + { + "excerpt": "Current improvements \nWe are working on the following features: \n", + "confidence": [ + 0.5262260210976475, + 0.5561204415522281 + ] + }, + { + "excerpt": "For a complete list, check the project open issues. \nRequirements \nYou will need Java 1.8 or higher (SDK 1.8 or JRE 8) for WIDOCO to work \nOtherwise, you will probably experience an \"Unsupported major.minor version 52.0\" exception when executing the JAR file. \n", + "confidence": [ + 0.5176480646572161, + 0.83412016338525, + 0.6859831708805074, + 0.6033446058999854 + ] + } + ], + "invocation": [ + { + "excerpt": " pages={94--102}, \n", + "confidence": [ + 0.5375440594212295 + ] + }, + { + "excerpt": " organization={Springer, Cham}, \n doi = {10.1007/978-3-319-68204-4_9}, \n funding = {USNSF ICER-1541029, NIH 1R01GM117097-01}, \n url={http://dgarijo.com/papers/widoco-iswc2017.pdf} \n} \nDownloading the executable \n=================== \n", + "confidence": [ + 0.5024643905702276, + 0.5700115988593752, + 0.7981991290765549, + 0.5426742466654296, + 0.6253537343153588, + 0.5987305525192003, + 0.6253537343153588 + ] + }, + { + "excerpt": "Description \n", + "confidence": [ + 0.6051300517248024 + ] + }, + { + "excerpt": "* Automatic annotation in JSON-LD snippets of the html produced. \n", + "confidence": [ + 0.5891033823183361 + ] + }, + { + "excerpt": "* Metadata extraction from the ontology plus the means to complete it on the fly when generating your ontology. Check the best practice document to know more about the terms recognized by WIDOCO. \n", + "confidence": [ + 0.51305763358465 + ] + }, + { + "excerpt": "* Integration with diagram creators (WebVOWL). \n", + "confidence": [ + 0.6358796811144762 + ] + }, + { + "excerpt": "Examples \n", + "confidence": [ + 0.8698197885997628 + ] + }, + { + "excerpt": "Tutorial \nA tutorial explaining the main features of the GUI can be found here \nHow to use WIDOCO \nDownload all the files of the \"JAR\" folder into the same folder. Then just double click the .jar file. \nNow you can execute WIDOCO through the console. Usage: \njava -jar widoco-VERSION-jar-with-dependencies.jar [-ontFile file] or [-ontURI uri] [-outFolder folderName] [-confFile propertiesFile] or [-getOntologyMetadata] [-oops] [-rewriteAll] [-crossRef] [-saveConfig configOutFile] [-useCustomStyle] [-lang lang1-lang2] [-includeImportedOntologies] [-htaccess] [-webVowl] [-licensius] [-ignoreIndividuals] [-analytics analyticsCode] [-doNotDisplaySerializations][-displayDirectImportsOnly] [-rewriteBase rewriteBasePath] [-excludeIntroduction] [-uniteSections] \nThe ontFile and ontURI options allow you to choose the ontology file or ontology URI of your ontology. \nThe -outFolder option specifies where you want to place the output. \n", + "confidence": [ + 0.7095445405479481, + 0.5204985919200906, + 0.5066097116442825, + 0.8347651310791816, + 0.7233411254715865, + 0.5931315477794302, + 0.5040051341203743, + 0.6652328240670206 + ] + }, + { + "excerpt": "The -oops flag creates an html page with the evaluation from the OOPS service (http://oops.linkeddata.es/) \nThe -rewriteAll option will tell WIDOCO to rewrite files if the new generate files are replacing existing files. Otherwise the tool will promt a window asking the user. \nThe -crossRef option will ONLY generate the overview and cross reference sections. The index document will NOT be generated. The htaccess, provenance page, etc., will not be generated unless requested by other flags. This flag in intended to be used only after a first version of the documentation exists. \nThe -saveConfig option allows you to save a configuration file on the \"configOutFile\" route with the properties of a given ontology. \nThe -useCustomStyle option allows exporting the documentation using alternate css files (thanks to Daniel Vila). \nThe -lang option allows showing the languages in which the documentation will be published (separated by \"-\"). Note that if the language is not supported, the system will load the labels in english. For example: en-pt-es \nThe -includeImportedOntologies flag indicates whether the terms of the imported ontologies of the current ontology should be documented as well or not. \n", + "confidence": [ + 0.627937647954913, + 0.7243088524717736, + 0.548249447486742, + 0.5089681400685672, + 0.5585411194181614, + 0.5943391409345902, + 0.5597852471570235 + ] + }, + { + "excerpt": "The -includeAnnotationProperties flag will include annotation properties defined in your ontology (by default they are not included) \n", + "confidence": [ + 0.6450522141828473 + ] + }, + { + "excerpt": "The -displayDirectImportsOnly flag allows displaying only those imported ontologies that are directly imported in the ontology being documented. \nThe -rewriteBase flag allows changing the default rewrite base path (until the documentation folder). By default it is \"/\". \nThe -excludeIntroduction flag skips adding an introduction section. \nThe -uniteSections includes all sections in the same HTML document. \nHow can I make WIDOCO automatically recognize my vocabulary annotations? \n", + "confidence": [ + 0.5799042111333581, + 0.6245580920029208, + 0.5519693603239522, + 0.609759676665765, + 0.6165326934165005 + ] + }, + { + "excerpt": "Add them in your OWL file. For guidelines on which ones to include, follow our Best Practices document, which indicates which ones we recommend. \n", + "confidence": [ + 0.5045646455853418 + ] + }, + { + "excerpt": "Browser issues (Why can't I see the generated documentation / visualization?) \nThe result of executing WIDOCO is an HTML file. We have successfully tested it in Mozilla, IE, Safari and Chrome. When the page is stored in a server, WIDOCO's HTML works correctly in all browsers. If you view the file on your local browser, we recommend you to use Mozilla Firefox, Safari or Internet Explorer. Google Chrome will not show the contents correctly, as it doesn't allow XMLHttpRequest without HTTP. If you want to view the page locally with Google Chrome you have two possibilities: \na) Place the file in a server and access it via its URL (for example, put it in dropbox and access through its public url, or on a Github page). \nb) Execute Chrome with the following commands (Thanks to Alejandro Fernandez Carrera): \n(WIN) chrome.exe --allow-file-access-from-files, \n(OSX) open /Applications/Google\\ Chrome.app/ --args --allow-file-access-from-files \n(UNX) /usr/bin/google-chrome --allow-file-access-from-files \nCurrent improvements \n", + "confidence": [ + 0.5501240204013124, + 0.5412616872202458, + 0.5135747834574199, + 0.5268262712119768, + 0.7610068513627465, + 0.7398041237901458, + 0.7788263263911405, + 0.6571108506699105 + ] + }, + { + "excerpt": "* Means to add examples to your ontology terms. \n* Previsualization of the terms that will be generated. \nFor a complete list, check the project open issues. \n", + "confidence": [ + 0.6373188120752915, + 0.5231879467231124, + 0.5996934650737783 + ] + }, + { + "excerpt": "Otherwise, you will probably experience an \"Unsupported major.minor version 52.0\" exception when executing the JAR file. \nContribution guidelines \n", + "confidence": [ + 0.7442847035663297, + 0.6253537343153588 + ] + } + ], + "name": "Widoco", + "owner": "dgarijo", + "license": { + "name": "Other", + "url": null + }, + "forks_url": "https://api.github.com/repos/dgarijo/Widoco/forks", + "topics": [ + "ontology", + "wizard", + "metadata", + "documentation", + "ontology-diagram", + "ontology-evaluation" + ], + "languages": [ + "Java", + "XSLT", + "CSS", + "JavaScript", + "HTML" + ], + "readme_url": "https://github.com/dgarijo/Widoco/blob/master/README.md", + "releases": [ + { + "tag_name": "v1.4.13", + "name": "WIDOCO 1.4.13: Linking evaluation in documentation", + "author_name": "dgarijo", + "body": "This version of WIDOCO removes a few of unused dependencies and, if desired, shows a link to the OOPS! evaluation generated in the documentation. Before, this link had to be added manually. \r\n\r\nThanks to @HaydarAk for the suggestions on how to show it in the main page.\r\n\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.13", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.13", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.13", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/22775882" + }, + { + "tag_name": "v1.4.12", + "name": "WIDOCO 1.4.12: Big fixes and new configurations", + "author_name": "dgarijo", + "body": "This version of WIDOCO addresses the following issues (thanks to @pmcb55 for his contributions!!)\r\n * #354: The page would display centered in the visualization instead of the element loaded.\r\n * #362: Upgraded to latest version of OWL API\r\n * #361: Allowed adding a \"-uniteAllSections\" flag that will print all sections on the same document. Hence, dynamic loading will be removed.\r\n * Tidying up PROV rendering.\r\n * Small typo fixes in the default html ", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.12", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.12", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.12", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/21002818" + }, + { + "tag_name": "v1.4.11", + "name": "WIDOCO 1.4.11: Better logging and bug fixes", + "author_name": "dgarijo", + "body": "This version of WIDOCO integrates the pull requests from @seralf to improve logging and simplify dependencies.\r\nIn addition, it addresses the following issues:\r\n * #344: Now double \"#\" errors have been removed from changelog.\r\n * #350: Fixed an issue in which the references would overwrite the main section ", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.11", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.11", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.11", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/17596778" + }, + { + "tag_name": "v1.4.10", + "name": "WIDOCO 1.4.10: Pull requests, updates and bug fixes", + "author_name": "dgarijo", + "body": "This version of WIDOCO incorporates pull requests from @seralf and @jgeluk (updating to the latest version of WebVowl) and fixes the following issues:\r\n* #333 Now if there is an error in one of the imports the application will continue running instead of failing.\r\n* #217 Now the changelog can be expanded and collapsed, which makes it easier to navigate\r\n* #313 A link will be added in the index page if provided in the config file (using contextURI=\"YOUR URL\")\r\n* #339 Now WIDOCO will generate the folders four your htaccess file as well.\r\n\r\nIn addition, now the base encoding is UTF-8.", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.10", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.10", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.10", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/17029600" + }, + { + "tag_name": "v1.4.9", + "name": "WIDOCO 1.4.9: Supporting schema.org", + "author_name": "dgarijo", + "body": "This version of WIDOCO addresses the following:\r\n* #274: Now WIDOCO will include the domain and range if you use schema:domainIncludes and schema:rangeIncludes to declare it in your object properties or data properties with . Note that WIDOCO still does not support plain rdf:Property.\r\n* Reduced the level of logging", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.9", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.9", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.9", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/15737608" + }, + { + "tag_name": "v1.4.8", + "name": "WIDOCO 1.4.8: Logging and automated citation", + "author_name": "dgarijo", + "body": "This release of WIDOCO includes:\r\n* Fixes from @jgeluk to do proper logging.\r\n* Fix #264: now an automated citation will be produced for your ontology by default (if the appropriate metadata is there: creators, revision, and URL (this version)\r\n* JenaCatalogIRIMapper now supports Jena's ont-policy.rdf file to resolve imports with local files\r\n* Fixed #321, now WIDOCO uses a more recent version of OWL API \r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.8", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.8", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.8", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/15474861" + }, + { + "tag_name": "v1.4.7", + "name": "WIDOCO 1.4.7: Dependency and bug fixes", + "author_name": "dgarijo", + "body": "This release of WIDOCO fixes the following issues:\r\n* #305: Now when you launch WIDOCO without parameters, the console will also show a description of the tool and will explain how to run it. \r\n* #309 Removed the absolute layout dependency that prevented WIDOCO JAR from being run.\r\n* #311 Now the publisher will show on the GUI correctly (before it would only if it had a URL)\r\n* #314: Added an html tag around the external sections so the browser won't complain\r\n* #316 Fixed the generation of the table of contents so \"back to TOC\" wouldn't appear\r\n* #317 Fixed the GUI so the \"Imported ontologies\" label appears as imported and not \"extended\"\r\nIt also removes the restlet dependency, which had a vulnerability and was not used anymore.", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.7", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.7", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.7", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/13944540" + }, + { + "tag_name": "v1.4.6", + "name": "WIDOCO 1.4.6: Tutorial and bug fixes", + "author_name": "dgarijo", + "body": "This version of WIDOCO includes the following updates:\r\n* Updated the OWL2Vowl library to the latest version (old library was producing errors in some ontologies)\r\n* Included a tutorial (http://dgarijo.github.io/Widoco/doc/tutorial/) describing the GUI step by step and all its functionality\r\n* Added support for selecting ontologies in JSON\r\n* Added contributing guidelines into readme.md\r\n* Fixed namespaces when selecting documentation in several languages\r\n* Now it's possible to edit the rewrite base path in the .htaccess file.\r\n* Fixed a typo in the .htaccess for serving json\r\n* Fixed an encoding problem when showing french labels.\r\n* @kartgk fixed an error with the import closure of ontologies (in case not all imports of imported ontologies wanted to be displayed)\r\n* Added the correct version numbers to pom file.\r\n* Fixed an issue in lang cs that made the table of namespaces not to show correctly", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.6", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.6", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.6", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/13019723" + }, + { + "tag_name": "v1.4.5", + "name": "WIDOCO 1.4.5: Updated WebVowl and support for Czech", + "author_name": "dgarijo", + "body": "This version of WIDOCO includes the following updates:\r\n* Updated webVowl to version 1.1.2 (latest)\r\n* Allowed disabling showing ontology serializations (-doNotDisplaySerializations flag). Both in the console and GUI\r\n* Added support for Czech localization (also in GUI)\r\n\r\nThanks to Petr Kremen for contributing with the Czech localization", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.5", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.5", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.5", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/12049594" + }, + { + "tag_name": "v1.4.4", + "name": "WIDOCO 1.4.4: Added support for Google Analytics", + "author_name": "dgarijo", + "body": "This version of WIDOCO allows to add a Google Analytics code to track the traffic received in one of the pages. WIDOCO assumes you have a UA code. You can use it on the GUI, through a config file or in the command line by adding `-analytics yourcode`\r\n\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.4", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.4", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.4", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/11300894" + }, + { + "tag_name": "v1.4.3", + "name": "WIDOCO 1.4.3: Bug Fixes and support for french", + "author_name": "dgarijo", + "body": "This release fixes the following issues:\r\n* Added support for french (thanks to Maxime Lefrancois)\r\n* When imported ontologies had characters like \"<\" they were not showing.\r\n* Added JSON-LD serialization for ontologies automatically\r\n* When annotation properties have blank nodes, they will now be ignored instead of failing\r\n* Updated contributor list\r\n* Blank nodes are now absent from the provenance page.\r\n* Fixed default language when restarting WIDOCO.\r\n* Fixed the language form (now french can be selected, and it has the proper icons)\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.3", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.3", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.3", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/10556972" + }, + { + "tag_name": "v1.4.2", + "name": "WIDOCO 1.4.2: Small fixes and merged contributions", + "author_name": "dgarijo", + "body": "This release includes the latest contributions to the project:\r\n* Fixes in HTML\r\n* Fixes in how OOPS! is called\r\nAlso, now the license name is the URI if no name is provided (and URI is) instead of \"license name goes here\", and the java encoding has been included in the pom file to prevent UTF-8 errors in compilation.", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.2", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.2", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.2", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/9846306" + }, + { + "tag_name": "v1.4.1", + "name": "WIDOCO 1.4.1: Metadata support and major bug fixes", + "author_name": "dgarijo", + "body": "WIDOCO now will comply with most of the terms listed in https://w3id.org/widoco/bestPractices. A few of them are still unsopported (e.g., rdfs:seeAlso) and will be added in next releases.\r\n\r\nIn this version, I have added support for all the deprecation terms in LODE, as well as support for skos:prefLabel and better recognition of some of the terms when the range can be a String or a resource.\r\n\r\nChanges:\r\n* Now the examples have a \"pre\" label, so if they include rdf text or json text they show properly.\r\n* A pointer to the guidelines has been added in the interface\r\n* When invoking the program using command line, the default behavior is to load the properties from the ontology. Only if a config file is provided, the properties won't be loaded. There is still a flag, which I have preferred to leave for possible legacy issues.\r\n* Markup is now recognized in all sections\r\n* The diagram is now optional (by default it was always produced in older versions)\r\n* This release also includes a doc folder with guidelines on the metadata properties to use, a benchmark of ontologies used for testing, a gallery with what WIDOCO can accomplish and a summary of projects that have adopted WIDOCO.\r\n\r\nBug fixes: \r\n* Changed the pom file with another plugin for creating the JAR, because some of the RIO parsers were not creating the appropriate serializations of the ontology.\r\n* Added robustness when the changelog was created. If a wrong URI is provided, then the changelog will not be created.\r\n* Changed how the ontology is chosen so there won't be errors in MAC systems.\r\n* Fixed some of the language tags.\r\n* Polished some errors related to the interface.", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.1", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.1", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.1", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/6527938" + }, + { + "tag_name": "v1.4.0", + "name": "WIDOCO 1.4.0: Inline visualization diagrams", + "author_name": "dgarijo", + "body": "This release removes the external dependency to WebVowl, and creates a visualization that can be seen in the ontology document itself (overview section). In addition, the following changes have been made:\r\n * Migrated the framework to use a recent version of OWL API (hence the size of the JAR)\r\n * Bug fixes in meta data (more to come in future releases)\r\n * Made WIDOCO more robust to errors\r\n * Published a benchmark of ontologies used to test WIDOCO. If you want us to try a new one, just open an issue!\r\n * Published a draft of the best practices for ontology annotation (currently under work). These are meant\r\n * Published a showcase gallery with examples of WIDOCO's features\r\n * Published a report on the known usages by WIDOCO. \r\n\r\n![webvowl](https://cloud.githubusercontent.com/assets/1520666/26068984/54eff946-3954-11e7-81b8-c72db0bd93bb.png)\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.4.0", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.4.0", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.4.0", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/6390471" + }, + { + "tag_name": "v1.3.1", + "name": "Widoco 1.3.1: Bug fixes and metadata enrichment", + "author_name": "dgarijo", + "body": "This release fixes several issues and extends LODE to accept more metadata options for defining terms and adding examples.\r\n* Fixed an issue with the changelog that produced an empty bullet when the domain or range of a property was an union or intersection.\r\n* Added tests with different ontologies that help inspecting whether a new change leads to errors or not.\r\n* Extended LODE to accept: prov:definition, vann:example, obo:definition (with the appropriate class name), obo:usageExample, vaem:rationale, skos:definition and terms:source.\r\n* Extended Widoco to accept terms:bibliographicCitation, bibo:status, bibo:doi and owl:backwardsCompatibleWith\r\n* If an error is produced while generating the changelog or the evaluation reports, the section is not generated. Before, an empty section would remain.\r\n* Fixed table of contents not being translated.\r\n* When generating the documentation of an ontology, if it imports another ontology that cannot be imported for any reason, Widoco will ignore the import instead of failing.\r\n* Added the possibility to ignore namedIndividuals when generating the documentation through console.\r\n\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.3.1", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.3.1", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.3.1", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/5951267" + }, + { + "tag_name": "v1.3.0", + "name": "Widoco 1.3.0: Automated changelog section", + "author_name": "dgarijo", + "body": "This version of Widoco creates an automated changelog section of your ontology. For all classes, properties and data properties, Widoco will calculate the new changes, additions and deletions and present them in a human-readable manner. In order to benefit from this feature, you just have to annotate your ontology with the URI of the previous version. You can use owl:priorVersion, dc:replaces or prov:wasRevisionOf to annotate your ontology (Widoco will only consider one file to compare against).\r\n\r\nAdditional improvements:\r\n* RDF-a annotations are replaced with JSON-LD snippets. The page is just annotated with schema.org. The rdf-a annotations made it difficult to maintain, and the structured extraction tool provided by Google did not work. With the JSON-LD snippet everything is clearer. The provenance of the page itself is published separately.\r\n* Now it is possible to generate ONLY the cross reference section of an ontology.\r\n* Bug fix that led to errors when opening some ontologies like OBI\r\n\r\nOverview sample of the changelog:\r\n![overview](https://cloud.githubusercontent.com/assets/1520666/23640611/ac4407f6-02a3-11e7-8a88-b597ba740721.png)\r\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.3.0", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.3.0", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.3.0", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/5659212" + }, + { + "tag_name": "v1.2.3", + "name": "Widoco 1.2.3: [Bug fix] Licensius is optional", + "author_name": "dgarijo", + "body": "The Licensius web service has been unstable lately. This led to long waits from the server, even with a timer on the request. 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By default, the .htaccess file will serve rdf/xml when asking for \\* / \\* and turtle when asking for text/*\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.1.1", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.1.1", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.1.1", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/3673322" + }, + { + "tag_name": "v1.1.0", + "name": "Content negotiation bundle", + "author_name": "dgarijo", + "body": "Now Widoco can create a content negotiation bundle that helps you deploy your vocabulary on your server. In addition, now different serializations of a vocabulary are saved locally, in order to facilitate users pointing to them.\n\nNote: due to time outs in Licensius, it is disabled in this version\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.1.0", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.1.0", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.1.0", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/3599226" + }, + { + "tag_name": "v1.0.0", + "name": "First stable release of Widoco", + "author_name": "dgarijo", + "body": "This release fixes multiple bugs from the earlier release, and allows customizing a label on the side with the current status of the document.\n\nThis version also improves how an ontology is loaded, applying content negotiation when necessary.\n", + "tarball_url": "https://api.github.com/repos/dgarijo/Widoco/tarball/v1.0.0", + "zipball_url": "https://api.github.com/repos/dgarijo/Widoco/zipball/v1.0.0", + "html_url": "https://github.com/dgarijo/Widoco/releases/tag/v1.0.0", + "url": "https://api.github.com/repos/dgarijo/Widoco/releases/3263232" + } + ] +} \ No newline at end of file diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..4baf821a --- /dev/null +++ b/requirements.txt @@ -0,0 +1,9 @@ +numpy +pandas +bs4 +sklearn +nltk +matplotlib +bs4 +requests +markdown \ No newline at end of file