feat: added additional formats used with the Physiome Model Repository

biosimulators · Jan 1, 2022 · f6797fd · f6797fd
1 parent 424b789
commit f6797fd
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Showing 2 changed files with 42 additions and 8 deletions.
diff --git a/biosimulators_utils/_version.py b/biosimulators_utils/_version.py
@@ -1 +1 @@
-__version__ = '0.1.153'
+__version__ = '0.1.154'
diff --git a/biosimulators_utils/combine/data_model.py b/biosimulators_utils/combine/data_model.py
@@ -119,30 +119,39 @@ def is_equal(self, other):
 
 class CombineArchiveContentFormat(str, enum.Enum):
     """ Format for the content of COMBINE/OMEX archives """
+    ACTIONSCRIPT = 'http://purl.org/NET/mediatypes/text/x-actionscript'
+    ADOBE_FLASH = 'http://purl.org/NET/mediatypes/application/x-shockwave-flash'
     AI = 'http://purl.org/NET/mediatypes/application/pdf'
+    BioPAX = 'http://identifiers.org/combine.specifications/biopax'
     BMP = 'http://purl.org/NET/mediatypes/image/bmp'
     BNGL = 'http://purl.org/NET/mediatypes/text/bngl+plain'
-    BioPAX = 'http://identifiers.org/combine.specifications/biopax'
+    BOURNE_SHELL = 'http://purl.org/NET/mediatypes/text/x-sh'
     C = 'http://purl.org/NET/mediatypes/text/x-c'
     CellML = 'http://identifiers.org/combine.specifications/cellml'
     CopasiML = 'http://purl.org/NET/mediatypes/application/x-copasi'
     CPP_HEADER = 'http://purl.org/NET/mediatypes/text/x-c++hdr'
     CPP_SOURCE = 'http://purl.org/NET/mediatypes/text/x-c++src'
+    CSS = 'http://purl.org/NET/mediatypes/text/css'
+    CSV = 'http://purl.org/NET/mediatypes/text/csv'
     DLL = 'http://purl.org/NET/mediatypes/application/vnd.microsoft.portable-executable'
     DOC = 'http://purl.org/NET/mediatypes/application/msword'
     DOCX = 'http://purl.org/NET/mediatypes/application/vnd.openxmlformats-officedocument.wordprocessingml.document'
-    CSV = 'http://purl.org/NET/mediatypes/text/csv'
     EPS = 'http://purl.org/NET/mediatypes/application/postscript'
     Escher = 'http://purl.org/NET/mediatypes/application/escher+json'
     GIF = 'http://purl.org/NET/mediatypes/image/gif'
     GINML = 'http://purl.org/NET/mediatypes/application/ginml+xml'
     GMSH_MESH = 'http://purl.org/NET/mediatypes/model/mesh'
+    GRAPHML = 'http://purl.org/NET/mediatypes/application/graphml+xml'
     HDF5 = 'http://purl.org/NET/mediatypes/application/x-hdf'
     HOC = 'http://purl.org/NET/mediatypes/text/x-hoc'
     HTML = 'http://purl.org/NET/mediatypes/text/html'
+    ICO = 'http://purl.org/NET/mediatypes/image/x-icon'   
     INI = 'http://purl.org/NET/mediatypes/text/x-ini'
     IPython_Notebook = 'http://purl.org/NET/mediatypes/application/x-ipynb+json'
-    JavaScript = 'http://purl.org/NET/mediatypes/text/javascript'
+    JAVA_ARCHIVE = 'http://purl.org/NET/mediatypes/application/java-archive'
+    JAVA_CLASS = 'http://purl.org/NET/mediatypes/application/java-vm'
+    JAVA_SOURCE = 'http://purl.org/NET/mediatypes/text/x-java'
+    JAVASCRIPT = 'http://purl.org/NET/mediatypes/text/javascript'
     JPEG = 'http://purl.org/NET/mediatypes/image/jpeg'
     JSON = 'http://purl.org/NET/mediatypes/application/json'
     Kappa = 'http://purl.org/NET/mediatypes/text/x-kappa'
@@ -153,16 +162,21 @@ class CombineArchiveContentFormat(str, enum.Enum):
     MorpheusML = 'http://purl.org/NET/mediatypes/application/morpheusml+xml'
     NeuroML = 'http://identifiers.org/combine.specifications/neuroml'
     NuML = 'http://purl.org/NET/mediatypes/application/numl+xml'
+    ODT = 'http://purl.org/NET/mediatypes/application/vnd.oasis.opendocument.text'
     OMEX = 'http://identifiers.org/combine.specifications/omex'
     OMEX_MANIFEST = 'http://identifiers.org/combine.specifications/omex-manifest'
     OMEX_METADATA = 'http://identifiers.org/combine.specifications/omex-metadata'
     OWL = 'http://purl.org/NET/mediatypes/application/rdf+xml'
     PDF = 'http://purl.org/NET/mediatypes/application/PDF'
+    PERL = 'http://purl.org/NET/mediatypes/text/x-perl'
     pharmML = 'http://purl.org/NET/mediatypes/application/pharmml+xml'
+    PHP = 'http://purl.org/NET/mediatypes/application/x-httpd-php'
     PNG = 'http://purl.org/NET/mediatypes/image/png'
     PPT = 'http://purl.org/NET/mediatypes/application/vnd.ms-powerpoint'
     PPTX = 'http://purl.org/NET/mediatypes/application/vnd.openxmlformats-officedocument.presentationml.presentation'
+    PSD = 'http://purl.org/NET/mediatypes/image/vnd.adobe.photoshop'
     Python = 'http://purl.org/NET/mediatypes/application/x-python-code'
+    QUICKTIME = 'http://purl.org/NET/mediatypes/video/quicktime'
     R = 'http://purl.org/NET/mediatypes/text/x-r'
     R_Project = 'http://purl.org/NET/mediatypes/application/x-r-project'
     RBA = 'http://purl.org/NET/mediatypes/application/rba+zip'
@@ -175,11 +189,13 @@ class CombineArchiveContentFormat(str, enum.Enum):
     SBOL_VISUAL = 'http://identifiers.org/combine.specifications/sbol-visual'
     Scilab = 'http://purl.org/NET/mediatypes/application/x-scilab'
     SED_ML = 'http://identifiers.org/combine.specifications/sed-ml'
+    SHOCKWAVE_FLASH = 'http://purl.org/NET/mediatypes/application/x-shockwave-flash'
     SimBiology_Project = 'http://purl.org/NET/mediatypes/application/x-sbproj'
     Smoldyn = 'http://purl.org/NET/mediatypes/text/smoldyn+plain'
     SO = 'http://purl.org/NET/mediatypes/application/x-sharedlib'
+    SQL = 'http://purl.org/NET/mediatypes/application/sql'
     SVG = 'http://purl.org/NET/mediatypes/image/svg+xml'
-    SVGZ = 'http://purl.org/NET/mediatypes/image/svg+xml'
+    SVGZ = 'http://purl.org/NET/mediatypes/image/svg+xml-compressed'
     TEXT = 'http://purl.org/NET/mediatypes/text/plain'
     TIFF = 'http://purl.org/NET/mediatypes/image/tiff'
     TSV = 'http://purl.org/NET/mediatypes/text/tab-separated-values'
@@ -191,6 +207,7 @@ class CombineArchiveContentFormat(str, enum.Enum):
     XPP = 'http://purl.org/NET/mediatypes/text/x-xpp'
     XLS = 'http://purl.org/NET/mediatypes/application/vnd.ms-excel'
     XLSX = 'http://purl.org/NET/mediatypes/application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'
+    XSL = 'http://purl.org/NET/mediatypes/application/xslfo+xml'
     XUL = 'http://purl.org/NET/mediatypes/text/xul'
     XYZ = 'http://purl.org/NET/mediatypes/chemical/x-xyz'
     YAML = 'http://purl.org/NET/mediatypes/application/x-yaml'
@@ -201,15 +218,19 @@ class CombineArchiveContentFormat(str, enum.Enum):
 
 class CombineArchiveContentFormatPattern(str, enum.Enum):
     """ Format for the content of COMBINE/OMEX archives """
+    ACTIONSCRIPT = r'^https?://purl\.org/NET/mediatypes/text/x-actionscript$'
+    ADOBE_FLASH = r'^https?://purl\.org/NET/mediatypes/(application/x-shockwave-flash|application/vnd\.adobe\.flash-movie)$'
     AI = r'^https?://purl\.org/NET/mediatypes/(application/pdf|application/postscript)$'
+    BioPAX = r'^https?://identifiers\.org/combine\.specifications/biopax($|\.)'
     BMP = r'^https?://purl\.org/NET/mediatypes/image/bmp$'
     BNGL = r'^https?://purl\.org/NET/mediatypes/text/bngl\+plain($|\.)'
-    BioPAX = r'^https?://identifiers\.org/combine\.specifications/biopax($|\.)'
+    BOURNE_SHELL = r'^https?://purl\.org/NET/mediatypes/(text/x-sh|application/x-sh)$'
     C = r'^https?://purl\.org/NET/mediatypes/text/x-c$'
     CellML = r'^https?://identifiers\.org/combine\.specifications/cellml($|\.)'
     CPP_HEADER = r'^https?://purl\.org/NET/mediatypes/text/x-c\+\+hdr$'
     CPP_SOURCE = r'^https?://purl\.org/NET/mediatypes/text/x-c\+\+src$'
     CopasiML = r'^https?://purl\.org/NET/mediatypes/application/x-copasi$'
+    CSS = r'^https?://purl\.org/NET/mediatypes/text/css$'
     CSV = r'^https?://purl\.org/NET/mediatypes/text/csv$'
     DLL = r'^https?://purl\.org/NET/mediatypes/application/vnd\.microsoft\.portable-executable$'
     DOC = r'^https?://purl\.org/NET/mediatypes/application/msword$'
@@ -219,12 +240,17 @@ class CombineArchiveContentFormatPattern(str, enum.Enum):
     GIF = r'^https?://purl\.org/NET/mediatypes/image/gif$'
     GINML = r'^https?://purl\.org/NET/mediatypes/application/ginml\+xml$'
     GMSH_MESH = r'^https?://purl\.org/NET/mediatypes/model/mesh$'
+    GRAPHML = r'^https?://purl\.org/NET/mediatypes/(application/graphml\+xml|application/x-graphml\+xml)$'
     HDF5 = r'^https?://purl\.org/NET/mediatypes/application/x-hdf5?$'
     HOC = r'^https?://purl\.org/NET/mediatypes/text/x-hoc$'
     HTML = r'^https?://purl\.org/NET/mediatypes/(text/html|application/xhtml\+xml)$'
+    ICO = r'^https?://purl\.org/NET/mediatypes/(image/x-icon|image/vnd\.microsoft\.icon)$'
     INI = r'^https?://purl\.org/NET/mediatypes/text/x-ini$'
     IPython_Notebook = r'^https?://purl\.org/NET/mediatypes/application/x-ipynb\+json$'
-    JavaScript = r'^https?://purl\.org/NET/mediatypes/(text/javascript|text/x-javascript|application/javascript|application/x-javascript)$'
+    JAVA_ARCHIVE = r'^https?://purl\.org/NET/mediatypes/(application/java-archive|application/x-java-archive|application/jar|application/x-jar)$'
+    JAVA_CLASS = r'^https?://purl\.org/NET/mediatypes/(application/java-vm|application/x-java-vm|application/java|application/x-java)$'
+    JAVA_SOURCE = r'^https?://purl\.org/NET/mediatypes/(text/x-java|text/x-java-source)$'
+    JAVASCRIPT = r'^https?://purl\.org/NET/mediatypes/(text/javascript|text/x-javascript|application/javascript|application/x-javascript)$'
     JPEG = r'^https?://purl\.org/NET/mediatypes/image/jpeg$'
     JSON = r'^https?://purl\.org/NET/mediatypes/application/json$'
     Kappa = r'^https?://purl\.org/NET/mediatypes/text/x-kappa$'
@@ -235,16 +261,21 @@ class CombineArchiveContentFormatPattern(str, enum.Enum):
     MorpheusML = r'^https?://purl\.org/NET/mediatypes/application/morpheusml\+xml$'
     NeuroML = r'^https?://identifiers\.org/combine\.specifications/neuroml($|\.)'
     NuML = r'^https?://purl\.org/NET/mediatypes/application/numl\+xml$'
+    ODT = r'^https?://purl\.org/NET/mediatypes/application/vnd\.oasis\.opendocument\.text$'
     OMEX = r'^https?://identifiers\.org/combine\.specifications/omex($|\.)'
     OMEX_MANIFEST = r'^https?://identifiers\.org/combine\.specifications/omex-manifest($|\.)'
     OMEX_METADATA = r'^https?://identifiers\.org/combine\.specifications/omex-metadata($|\.)'
     OWL = r'^https?://purl\.org/NET/mediatypes/application/rdf\+xml$'
     PDF = r'^https?://purl\.org/NET/mediatypes/application/pdf$'
+    PERL = r'^https?://purl\.org/NET/mediatypes/(text/x-perl|application/x-perl)$'
     pharmML = r'^https?://purl\.org/NET/mediatypes/application/pharmml\+xml$'
+    PHP = r'^https?://purl\.org/NET/mediatypes/(application/x-httpd-php|application/x-httpd-php-source|application/x-php|text/x-php)$'
     PNG = r'^https?://purl\.org/NET/mediatypes/image/png$'
     PPT = r'^https?://purl\.org/NET/mediatypes/application/vnd\.ms-powerpoint$'
     PPTX = r'^https?://purl\.org/NET/mediatypes/application/vnd\.openxmlformats-officedocument\.presentationml\.presentation$'
+    PSD = r'^https?://purl\.org/NET/mediatypes/(image/vnd\.adobe\.photoshop|image/psd|image/x-psd|application/photoshop|application/x-photoshop|application/psd|application/x-psd)$'
     Python = r'^https?://purl\.org/NET/mediatypes/application/x-python-code$'
+    QUICKTIME = r'^https?://purl\.org/NET/mediatypes/(video/quicktime|image/mov)$'
     R = r'^https?://purl\.org/NET/mediatypes/text/x-r$'
     R_Project = r'^https?://purl\.org/NET/mediatypes/application/x-r-project$'
     RBA = r'^https?://purl\.org/NET/mediatypes/application/rba\+zip$'
@@ -257,11 +288,13 @@ class CombineArchiveContentFormatPattern(str, enum.Enum):
     SBOL_VISUAL = r'^https?://identifiers\.org/combine\.specifications/sbol-visual($|\.)'
     Scilab = r'^https?://purl\.org/NET/mediatypes/application/x-scilab$'
     SED_ML = r'^https?://identifiers\.org/combine\.specifications/sed\-?ml($|\.)'
+    SHOCKWAVE_FLASH = r'^https?://purl\.org/NET/mediatypes/(application/x-shockwave-flash|application/vnd\.adobe\.flash-movie)$'
     SimBiology_Project = r'^https?://purl\.org/NET/mediatypes/application/x-sbproj$'
     Smoldyn = r'^https?://purl\.org/NET/mediatypes/text/smoldyn\+plain$'
     SO = r'^https?://purl\.org/NET/mediatypes/application/x-sharedlib$'
+    SQL = r'^https?://purl\.org/NET/mediatypes/application/sql$'
     SVG = r'^https?://purl\.org/NET/mediatypes/image/svg\+xml$'
-    SVGZ = r'^https?://purl\.org/NET/mediatypes/image/svg\+xml$'
+    SVGZ = r'^https?://purl\.org/NET/mediatypes/image/svg\+xml(-compressed)?$'
     TEXT = r'^https?://purl\.org/NET/mediatypes/text/plain$'
     TIFF = r'^https?://purl\.org/NET/mediatypes/image/tiff$'
     TSV = r'^https?://purl\.org/NET/mediatypes/text/tab-separated-values$'
@@ -273,6 +306,7 @@ class CombineArchiveContentFormatPattern(str, enum.Enum):
     XLSX = r'^https?://purl\.org/NET/mediatypes/application/vnd\.openxmlformats-officedocument\.spreadsheetml\.sheet$'
     XML = r'^https?://purl\.org/NET/mediatypes/application/xml$'
     XPP = r'^https?://purl\.org/NET/mediatypes/text/x-xpp$'
+    XSL = r'^https?://purl\.org/NET/mediatypes/(application/xslfo\+xml|text/xsl)$'
     XUL = r'^https?://purl\.org/NET/mediatypes/text/xul$'
     XYZ = r'^https?://purl\.org/NET/mediatypes/chemical/x-xyz$'
     YAML = r'^https?://purl\.org/NET/mediatypes/application/x-yaml$'