style: apply pre-commit hooks

.github/dependabot.yml

@@ -1,14 +1,14 @@
 version: 2
 updates:
-  - package-ecosystem: github-actions
-    directory: /
-    schedule:
-      interval: monthly
-  - package-ecosystem: pip
-    directory: /
-    schedule:
-      interval: monthly
-  - package-ecosystem: docker
-    directory: /
-    schedule:
-      interval: monthly
+- package-ecosystem: github-actions
+  directory: /
+  schedule:
+    interval: monthly
+- package-ecosystem: pip
+  directory: /
+  schedule:
+    interval: monthly
+- package-ecosystem: docker
+  directory: /
+  schedule:
+    interval: monthly

fuji_server/data/ResourceTypes.txt

@@ -1,46 +1,37 @@
-Audiovisual
-Collection
-DataPaper
-Dataset
-Event
-Image
-InteractiveResource
-Model
-PhysicalObject
-Service
-Software
-Sound
-Text
-Workflow
-MovingImage
-Service
-Software
-StillImage
-CreativeWork
 AmpStory
 ArchiveComponent
 Article
 Atlas
+Audiovisual
+BioChemEntity
+BioSample
 Blog
 Book
 Chapter
+ChemicalSubstance
 Claim
 Clip
+Collection
 ComicStory
 Comment
 Conversation
 Course
+CreativeWork
 CreativeWorkSeason
 CreativeWorkSeries
 DataCatalog
+DataPaper
+Dataset
 DefinedTermSet
 Diet
 DigitalDocument
 Drawing
 EducationalOccupationalCredential
 Episode
+Event
 ExercisePlan
 Game
+Gene
 Guide
 HowTo
 HowToDirection
@@ -49,6 +40,8 @@ HowToStep
 HowToTip
 HyperToc
 HyperTocEntry
+Image
+InteractiveResource
 LearningResource
 Legislation
 Manuscript
@@ -58,36 +51,43 @@ MediaObject
 Menu
 MenuSection
 Message
+Model
+MolecularEntity
 Movie
+MovingImage
 MusicComposition
 MusicPlaylist
 MusicRecording
 Painting
 Photograph
+PhysicalObject
 Play
 Poster
+Protein
 PublicationIssue
 PublicationVolume
 Quotation
 Review
 Sculpture
+Service
+Service
 SheetMusic
 ShortStory
+Software
+Software
 SoftwareApplication
 SoftwareSourceCode
+Sound
 SpecialAnnouncement
+StillImage
 TVSeason
 TVSeries
+Taxon
+Text
 Thesis
 VisualArtwork
 WebContent
 WebPage
 WebPageElement
 WebSite
-BioChemEntity
-BioSample
-ChemicalSubstance
-Gene
-MolecularEntity
-Protein
-Taxon
+Workflow

fuji_server/data/bioschemastypes.txt

@@ -33,4 +33,4 @@ SequenceRange
 Study
 Taxon
 TaxonName
-TrainingMaterial
+TrainingMaterial

fuji_server/data/creativeworktypes.txt

@@ -1,27 +1,43 @@
+3DModel
+AdvertiserContentArticle
 AmpStory
+Answer
 ArchiveComponent
 Article
 Atlas
+AudioObject
+Audiobook
 Blog
 Book
+BookSeries
 Chapter
 Claim
+ClaimReview
 Clip
 Collection
+ComicCoverArt
 ComicStory
 Comment
 Conversation
+CorrectionComment
+Course
 Course
 CreativeWork
 CreativeWorkSeason
 CreativeWorkSeries
+CriticReview
 DataCatalog
+DataDownload
+DataFeed
 Dataset
 DefinedTermSet
+DefinedTermSet
 Diet
 DigitalDocument
 Drawing
 EducationalOccupationalCredential
+EmailMessage
+EmployerReview
 Episode
 ExercisePlan
 Game
@@ -33,97 +49,81 @@ HowToStep
 HowToTip
 HyperToc
 HyperTocEntry
+ImageObject
 LearningResource
 Legislation
+LegislationObject
+LegislationObject
 Manuscript
 Map
 MathSolver
 MediaObject
+MediaReview
 MediaReviewItem
 Menu
 MenuSection
 Message
 Movie
+MovieClip
+MovieSeries
+MusicAlbum
 MusicComposition
 MusicPlaylist
 MusicRecording
+MusicRelease
+MusicVideoObject
+NewsArticle
+NoteDigitalDocument
 Painting
+Periodical
 Photograph
 Play
+PodcastEpisode
+PodcastSeason
+PodcastSeries
 Poster
+PresentationDigitalDocument
+ProductCollection
 PublicationIssue
 PublicationVolume
+Question
+Quiz
 Quotation
+RadioClip
+RadioEpisode
+RadioSeason
+RadioSeries
+Recipe
+Recommendation
+Report
 Review
+SatiricalArticle
+ScholarlyArticle
 Sculpture
 SheetMusic
 ShortStory
+SocialMediaPosting
 SoftwareApplication
 SoftwareSourceCode
 SpecialAnnouncement
+SpreadsheetDigitalDocument
 Statement
+TVClip
+TVEpisode
+TVSeason
 TVSeason
 TVSeries
+TVSeries
+TechArticle
+TextDigitalDocument
 Thesis
+UserReview
+VideoGame
+VideoGameClip
+VideoGameSeries
+VideoObject
 VisualArtwork
 WebContent
 WebPage
 WebPageElement
 WebSite
-AdvertiserContentArticle
-NewsArticle
-Report
-SatiricalArticle
-ScholarlyArticle
-SocialMediaPosting
-TechArticle
-Audiobook
-MovieClip
-RadioClip
-TVClip
-VideoGameClip
-ProductCollection
-ComicCoverArt
-Answer
-CorrectionComment
-Question
-PodcastSeason
-RadioSeason
-TVSeason
-BookSeries
-MovieSeries
-Periodical
-PodcastSeries
-RadioSeries
-TVSeries
-VideoGameSeries
-DataFeed
-NoteDigitalDocument
-PresentationDigitalDocument
-SpreadsheetDigitalDocument
-TextDigitalDocument
-PodcastEpisode
-RadioEpisode
-TVEpisode
-VideoGame
-Recipe
-Course
-Quiz
-LegislationObject
-3DModel
-AudioObject
-DataDownload
-ImageObject
-LegislationObject
-MusicVideoObject
-VideoObject
-EmailMessage
-MusicAlbum
-MusicRelease
-ClaimReview
-CriticReview
-EmployerReview
-MediaReview
-Recommendation
-UserReview
-DefinedTermSet

fuji_server/data/default_namespaces.txt

@@ -1,25 +1,25 @@
+http://ogp.me/ns#
+http://purl.org/dc/elements/1.1/
+http://purl.org/dc/terms/
+http://schema.org/
 http://www.w3.org/1999/02/22-rdf-syntax-ns#
+http://www.w3.org/1999/XSL/Transform
+http://www.w3.org/1999/xhtml/vocab
 http://www.w3.org/2000/01/rdf-schema#
-http://www.w3.org/ns/rdfa
-http://www.w3.org/2002/07/owl#
+http://www.w3.org/2000/xmlns
 http://www.w3.org/2001/XMLSchema#
+http://www.w3.org/2001/XMLSchema-instance
+http://www.w3.org/2002/07/owl#
 http://www.w3.org/2004/02/skos/core#
-http://www.w3.org/XML/1998/namespace
 http://www.w3.org/2004/07/xpath-functions
-http://www.w3.org/XSL/Transform/1.0
-http://www.w3.org/1999/XSL/Transform
-http://www.w3.org/TR/WD-xsl
-http://www.w3.org/2006/vcard/ns#
-http://www.w3.org/2001/XMLSchema-instance
-http://www.w3.org/2000/xmlns
-http://xmlns.com/foaf/0.1/
-http://purl.org/dc/elements/1.1/
-http://purl.org/dc/terms/
 http://www.w3.org/2005/sparql-results#
-http://www.w3.org/2005/xqt-errors#
 http://www.w3.org/2005/xpath-functions#
-http://schema.org/
-https://schema.org/
-http://ogp.me/ns#
-http://www.w3.org/1999/xhtml/vocab
+http://www.w3.org/2005/xqt-errors#
+http://www.w3.org/2006/vcard/ns#
 http://www.w3.org/2007/05/powder-s#
+http://www.w3.org/TR/WD-xsl
+http://www.w3.org/XML/1998/namespace
+http://www.w3.org/XSL/Transform/1.0
+http://www.w3.org/ns/rdfa
+http://xmlns.com/foaf/0.1/
+https://schema.org/

fuji_server/helper/linked_vocab_helper.py

@@ -144,9 +144,9 @@ def get_linked_vocab_by_iri(self, IRI, isnamespaceIRI=False, firstonly=True):
                                 if reg_res.get("regex"):
                                     comb_regex = reg_res.get("regex").lstrip("^").rstrip("$")
                                 else:
-                                    if '?' in reg_res.get('pattern'):
-                                        reg_res['pattern']=reg_res.get('pattern').replace('?',r'\?')
-                                    comb_regex = reg_res.get('pattern').split('$1')[0].rstrip('/#')
+                                    if "?" in reg_res.get("pattern"):
+                                        reg_res["pattern"] = reg_res.get("pattern").replace("?", r"\?")
+                                    comb_regex = reg_res.get("pattern").split("$1")[0].rstrip("/#")
 
                                 if comb_regex not in tested_patterns:
                                     tested_patterns.append(comb_regex)