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adding more properties to instances docu for atlases and spaces
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lzehl committed Jul 25, 2023
1 parent 049ebfd commit 7542081
Showing 1 changed file with 44 additions and 11 deletions.
55 changes: 44 additions & 11 deletions pipeline/instance.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,16 +39,15 @@ def __init__(self, instances_file_paths:List, version):

def _build_single_term_link(self, termReference:Dict, instanceType:str) -> str:
term_id = termReference["@id"]
term = term_id.split("/")[-1]
name = self.instances_collection[term_id]["name"]
name_mod = name.replace(' ', '-').casefold()
if instanceType == "license":
term = term_id.split("/")[-1].replace(".", "-").casefold()
name = self.instances_collection[term_id]["name"] if "name" in self.instances_collection[term_id] else self.instances_collection[term_id]["shortName"]
if instanceType == "licenses":
linkdir = os.path.join(self.readthedocs_url, self.version, "libraries")
elif instanceType == "contentType":
elif instanceType == "contentTypes":
linkdir = os.path.join(self.readthedocs_url, self.version, "libraries")
else:
linkdir = os.path.join(self.readthedocs_url, self.version, "libraries", "terminologies")
link = os.path.join(linkdir, f"{instanceType}.html#{name_mod}")
link = os.path.join(linkdir, f"{instanceType}.html#{term}")
return f"`{name} <{link}>`_"

def _build_multi_term_links(self, termReferenceList:List, instanceType:str) -> str:
Expand Down Expand Up @@ -164,7 +163,7 @@ def _build_brain_atlas(self, docpath:str, instance_id:str, schemadir:str):
if prop == "digitalIdentifier":
doc.field(name=prop, value=value["@id"], indent=field_list_indent)
if prop == "usedSpecies":
doc.field(name=prop, value=self._build_single_term_link(value, prop), indent=field_list_indent)
doc.field(name=prop, value=self._build_single_term_link(value, "species"), indent=field_list_indent)
if prop == "hasTerminology":
doc.field(name=prop, value="(see below)", indent=field_list_indent)
elif isinstance(value, List):
Expand Down Expand Up @@ -207,14 +206,30 @@ def _build_brain_atlas(self, docpath:str, instance_id:str, schemadir:str):
if isinstance(value, (str, int, float)):
doc.field(name=prop, value=str(value), indent=field_list_indent)
elif isinstance(value, Dict):
if prop == "digitalIdentifier":
if prop in ["digitalIdentifier", "relatedPublication"]:
doc.field(name=prop, value=value["@id"], indent=field_list_indent)
if prop == "coordinateSpace": #TODO
if prop == "accessibility":
doc.field(name=prop, value=self._build_single_term_link(value, "productAccessibility"), indent=field_list_indent)
if prop == "license":
doc.field(name=prop, value=self._build_single_term_link(value, "licenses"), indent=field_list_indent)
if prop == "coordinateSpace":
doc.field(name=prop, value=self._build_single_version_link(value, include_shortName=True), indent=field_list_indent)
if prop == "isNewVersionOf":
doc.field(name=prop, value=self._build_single_version_link(value, include_shortName=True), indent=field_list_indent)
if prop == "type":
doc.field(name=prop, value=self._build_single_term_link(value, "atlasType"), indent=field_list_indent)
elif isinstance(value, List):
if all(isinstance(item, (str, int, float)) for item in value):
sorted_value_list = sorted([str(item) for item in value])
doc.field(name=prop, value=", ".join(sorted_value_list), indent=field_list_indent)
if all(isinstance(item, Dict) for item in value):
if prop == "isAlternativeVersionOf":
multiline_indent = len(prop) + 3 + field_list_indent
version_link_list = self._build_multi_version_links(value, include_shortName=True)
doc.field(name=prop, value=f"| {version_link_list[0]}", indent=field_list_indent)
if len(version_link_list) > 1:
for link in version_link_list[1:]:
doc.content(f"| {link}", indent=multiline_indent)
else:
doc.content(f"TODO")
doc.newline()
Expand Down Expand Up @@ -244,7 +259,7 @@ def _build_common_coordinate_space(self, docpath:str, instance_id:str, schemadir
if prop == "digitalIdentifier":
doc.field(name=prop, value=value["@id"], indent=field_list_indent)
if prop == "usedSpecies":
doc.field(name=prop, value=self._build_single_term_link(value, prop), indent=field_list_indent)
doc.field(name=prop, value=self._build_single_term_link(value, "species"), indent=field_list_indent)
elif isinstance(value, List):
if all(isinstance(item, (str, int, float)) for item in value):
sorted_value_list = sorted([str(item) for item in value])
Expand Down Expand Up @@ -275,12 +290,30 @@ def _build_common_coordinate_space(self, docpath:str, instance_id:str, schemadir
if isinstance(value, (str, int, float)):
doc.field(name=prop, value=str(value), indent=field_list_indent)
elif isinstance(value, Dict):
if prop == "digitalIdentifier":
if prop in ["digitalIdentifier", "relatedPublication"]:
doc.field(name=prop, value=value["@id"], indent=field_list_indent)
if prop == "accessibility":
doc.field(name=prop, value=self._build_single_term_link(value, "productAccessibility"), indent=field_list_indent)
if prop == "license":
doc.field(name=prop, value=self._build_single_term_link(value, "licenses"), indent=field_list_indent)
if prop == "anatomicalAxesOrientation":
doc.field(name=prop, value=self._build_single_term_link(value, prop), indent=field_list_indent)
if prop == "nativeUnit":
doc.field(name=prop, value=self._build_single_term_link(value, "UnitOfMeasurement"), indent=field_list_indent)
if prop == "isNewVersionOf":
doc.field(name=prop, value=self._build_single_version_link(value, include_shortName=True), indent=field_list_indent)
elif isinstance(value, List):
if all(isinstance(item, (str, int, float)) for item in value):
sorted_value_list = sorted([str(item) for item in value])
doc.field(name=prop, value=", ".join(sorted_value_list), indent=field_list_indent)
if all(isinstance(item, Dict) for item in value):
if prop == "isAlternativeVersionOf":
multiline_indent = len(prop) + 3 + field_list_indent
version_link_list = self._build_multi_version_links(value, include_shortName=True)
doc.field(name=prop, value=f"| {version_link_list[0]}", indent=field_list_indent)
if len(version_link_list) > 1:
for link in version_link_list[1:]:
doc.content(f"| {link}", indent=multiline_indent)
else:
doc.content(f"TODO")
doc.newline()
Expand Down

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