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testing to add ccs verions
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lzehl committed Jul 16, 2023
1 parent bcfd5c5 commit 45f45f4
Showing 1 changed file with 32 additions and 18 deletions.
50 changes: 32 additions & 18 deletions pipeline/instance.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,6 +119,11 @@ def _extract_datatypes(self, datatypes:List) -> str:
linklist.append(f"`{name} <{link}>`_")
return ", ".join(linklist)

def _extract_species(self, species:Dict) -> str:
name = self.instances_libraries["terminologies"]["species"][species["@id"].split("/")[-1]]["name"]
link = os.path.join(self.readthedocs_url, self.version, "libraries", "terminologies", f"species.html#{name.replace(' ', '-')}")
return f"`{name} <{link}>`_"

def _build_terminology(self, target_file:str, name:str, data_to_display:Dict):
with open(f"{target_file}.rst", "w") as output_file:
doc = RstCloth(output_file, line_width=100000)
Expand Down Expand Up @@ -228,16 +233,12 @@ def _build_brain_atlas(self, target_file:str, name:str, data_to_display:Dict):
doc.newline()
field_list_indent = 3
doc.field(name="semantic name", value=atlas["@id"], indent=field_list_indent)
space_shortName = atlas["shortName"] if "shortName" in atlas and atlas["shortName"] else "\-"
doc.field(name="short name", value=space_shortName, indent=field_list_indent)
space_fullName = atlas["fullName"] if "fullName" in atlas and atlas["fullName"] else "\-"
doc.field(name="full name", value=space_fullName, indent=field_list_indent)
space_abbr = atlas["abbreviation"] if "abbreviation" in atlas and atlas["abbreviation"] else "\-"
doc.field(name="abbreviation", value=space_abbr, indent=field_list_indent)
if "usedSpecies" in atlas and atlas["usedSpecies"]:
species_name = self.instances_libraries["terminologies"]["species"][atlas["usedSpecies"]["@id"].split("/")[-1]]["name"]
species_link = os.path.join(self.readthedocs_url, self.version, "libraries", "terminologies", f"species.html#{species_name.replace(' ', '-')}")
else:
species_link = "\-"
doc.field(name="used species", value=species_link, indent=field_list_indent)
usedSpecies = self._extract_species(atlas["usedSpecies"]) if "usedSpecies" in atlas and atlas["usedSpecies"] else "\-"
doc.field(name="used species", value=usedSpecies, indent=field_list_indent)
space_digitalID = atlas["digitalIdentifier"] if "digitalIdentifier" in atlas and atlas["digitalIdentifier"] else "\-"
doc.field(name="digital ID", value=space_digitalID, indent=field_list_indent)
space_ontologyID = atlas["ontologyIdentifier"] if "ontologyIdentifier" in atlas and atlas["ontologyIdentifier"] else "\-"
Expand All @@ -247,6 +248,8 @@ def _build_brain_atlas(self, target_file:str, name:str, data_to_display:Dict):
space_citation = atlas["howToCite"] if "howToCite" in atlas and atlas["howToCite"] else "\-"
doc.field(name="howToCite", value=space_citation, indent=field_list_indent)

def _extract_research_product_versions(self):

def _build_common_coordinate_space(self, target_file:str, name:str, data_to_display:Dict):
with open(f"{target_file}.rst", "w") as output_file:
space = data_to_display["space"]
Expand All @@ -257,16 +260,12 @@ def _build_common_coordinate_space(self, target_file:str, name:str, data_to_disp
doc.newline()
field_list_indent = 3
doc.field(name="semantic name", value=space["@id"], indent=field_list_indent)
space_shortName = space["shortName"] if "shortName" in space and space["shortName"] else "\-"
doc.field(name="short name", value=space_shortName, indent=field_list_indent)
space_fullName = space["fullName"] if "fullName" in space and space["fullName"] else "\-"
doc.field(name="full name", value=space_fullName, indent=field_list_indent)
space_abbr = space["abbreviation"] if "abbreviation" in space and space["abbreviation"] else "\-"
doc.field(name="abbreviation", value=space_abbr, indent=field_list_indent)
if "usedSpecies" in space and space["usedSpecies"]:
species_name = self.instances_libraries["terminologies"]["species"][space["usedSpecies"]["@id"].split("/")[-1]]["name"]
species_link = os.path.join(self.readthedocs_url, self.version, "libraries", "terminologies", f"species.html#{species_name.replace(' ', '-')}")
else:
species_link = "\-"
doc.field(name="used species", value=species_link, indent=field_list_indent)
usedSpecies = self._extract_species(space["usedSpecies"]) if "usedSpecies" in space and space["usedSpecies"] else "\-"
doc.field(name="used species", value=usedSpecies, indent=field_list_indent)
space_digitalID = space["digitalIdentifier"] if "digitalIdentifier" in space and space["digitalIdentifier"] else "\-"
doc.field(name="digital ID", value=space_digitalID, indent=field_list_indent)
space_ontologyID = space["ontologyIdentifier"] if "ontologyIdentifier" in space and space["ontologyIdentifier"] else "\-"
Expand All @@ -275,6 +274,21 @@ def _build_common_coordinate_space(self, target_file:str, name:str, data_to_disp
doc.field(name="homepage", value=space_homepage, indent=field_list_indent)
space_citation = space["howToCite"] if "howToCite" in space and space["howToCite"] else "\-"
doc.field(name="howToCite", value=space_citation, indent=field_list_indent)
# hasVersions = self._extract_research_product_versions(space["hasVersion"]) if "hasVersion" in space and space["hasVersion"] else "\-"
# doc.field(name="has versions", value=hasVersions, indent=field_list_indent)
doc.newline()
doc.content("------------")
doc.newline()
doc.content("------------")
doc.newline()
if "hasVersion" in space and space["hasVersion"]:
spaceV_title_list = []
for spaceV_name, spaceV_data in space["hasVersion"]:
spaceV_title = f"{spaceV_data['shortName']} \({spaceV_data['shortName']}\)"
spaceV_title_list.append(spaceV_title)
doc.heading(f"{spaceV_title}", char="#")
doc.newline()
#https://openminds-documentation.readthedocs.io/en/latest/libraries/licenses.html#ebrains-dua-4-hdg

def build(self):
# build RST docu for each terminology
Expand All @@ -295,14 +309,14 @@ def build(self):

# build RST docu for each brain atlas
for ba_name, ba_data in self.instances_libraries["brainAtlases"].items():
ba_title = ba_data["atlas"]["fullName"].replace("(", "\(").replace(")", "\)")
ba_title = ba_data["atlas"]["shortName"]
target_file = self._target_file_without_extension("/".join(["brainAtlases", ba_title]))
os.makedirs(os.path.dirname(target_file), exist_ok=True)
self._build_brain_atlas(target_file, ba_title, ba_data)

# build RST docu for each common coordinate space
for ccs_name, ccs_data in self.instances_libraries["commonCoordinateSpaces"].items():
ccs_title = ccs_data["space"]["fullName"].replace("(", "\(").replace(")", "\)")
ccs_title = ccs_data["space"]["shortName"]
target_file = self._target_file_without_extension("/".join(["commonCoordinateSpaces", ccs_title]))
os.makedirs(os.path.dirname(target_file), exist_ok=True)
self._build_common_coordinate_space(target_file, ccs_title, ccs_data)

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