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handlers.py
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handlers.py
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import abc
import dataclasses
import functools
import re
from typing import Any, Dict, List, Optional, Pattern, Set, Tuple
from manubot.util import import_function
from .citekey import CiteKey
"""
Non-citation prefixes used by the pandoc-xnos suite of Pandoc filters,
including pandoc-fignos, pandoc-tablenos, pandoc-eqnos, and pandoc-secnos.
"""
_pandoc_xnos_prefixes: Set[str] = {"fig", "tbl", "eq", "sec"}
_local_handlers: List[str] = [
"manubot.cite.arxiv.Handler_arXiv",
"manubot.cite.doi.Handler_DOI",
"manubot.cite.isbn.Handler_ISBN",
"manubot.cite.pubmed.Handler_PMC",
"manubot.cite.pubmed.Handler_PubMed",
"manubot.cite.url.Handler_URL",
"manubot.cite.wikidata.Handler_Wikidata",
]
_infer_prefix_patterns: List[Tuple[str, str]] = [
("doi", "accession_pattern"),
("doi", "shortdoi_pattern"),
("pmc", "accession_pattern"),
("pubmed", "accession_pattern"),
("wikidata", "accession_pattern"),
("arxiv", "accession_pattern"),
]
"""
Each list element is a tuple of (handler, pattern attribute).
Handler is the handler prefix (lowercase).
Pattern attribute refers to the Handler attribute containing a regex pattern.
A citekey prefix is inferred from the first matching pattern in this list.
"""
def infer_prefix(dealiased_id: str) -> Optional[str]:
"""
Infer the prefix for citekey by matching it against a sequence of regexes.
If a match is found, return the coressponding standard prefix.
Otherwise, return None.
"""
for prefix, pattern_attrib in _infer_prefix_patterns:
handler = get_handler(prefix)
pattern = handler._get_pattern(attribute=pattern_attrib)
if pattern.fullmatch(dealiased_id):
return handler.standard_prefix
return None
@functools.lru_cache(maxsize=10_000)
def get_handler(prefix_lower: str) -> "Handler":
if not isinstance(prefix_lower, str):
raise TypeError(
f"prefix_lower should be a str, instead received {prefix_lower.__class__.__name__}"
)
assert prefix_lower == prefix_lower.lower()
handler = prefix_to_handler[prefix_lower]
handler = import_function(handler)(prefix_lower)
return handler
def _generate_prefix_to_handler() -> Dict[str, str]:
"""
Generate complete dictionary for prefix_to_handler.
"""
import inspect
from .curie import get_curie_handlers
curie_handlers = get_curie_handlers()
pth = {}
for handler in curie_handlers + _local_handlers:
if isinstance(handler, str):
handler = import_function(handler)("dummy_prefix_lower")
for prefix in handler.prefixes:
pth[
prefix
] = f"{inspect.getmodule(handler).__name__}.{handler.__class__.__name__}"
pth = dict(sorted(pth.items())) # sort for clean diffs of serialized dict
return pth
@dataclasses.dataclass
class Handler:
"""
A Handler is a class that provides support for a certain type of citekey.
For example, a Handler subclass could provide support for DOI citekeys.
Subclasses enable custom logic for different citekey prefixes,
including how to standardize the citekey and how to retrieve CSL Item metadata.
"""
prefix_lower: str
prefixes = []
def _get_pattern(self, attribute: str = "accession_pattern") -> Optional[Pattern]:
"""
Return a compiled regex pattern stored by `attribute`.
By default, return `self.accession_pattern`, which Handler subclasses
can set to provide the expected pattern for `self.accession`.
"""
# todo: consider caching compilation
pattern = getattr(self, attribute, None)
if not pattern:
return None
if not isinstance(pattern, Pattern):
pattern = re.compile(pattern)
return pattern
def inspect(self, citekey: CiteKey) -> Optional[str]:
"""
Check citekeys adhere to expected formats. If an issue is detected a
string describing the issue is returned. Otherwise returns None.
"""
pattern = self._get_pattern("accession_pattern")
if not pattern:
return None
if not pattern.fullmatch(citekey.accession):
return f"{citekey.accession} does not match regex {pattern.pattern}"
def standardize_prefix_accession(self, accession: str) -> Tuple[str, str]:
"""
Return (prefix, accession) in standardized form.
This method defaults to returning `self.standard_prefix`
(or `self.prefix_lower` if standard_prefix is not defined).
Subclasses can override this method with more specific standardization logic.
"""
standard_prefix = getattr(self, "standard_prefix", self.prefix_lower)
standard_accession = accession
return standard_prefix, standard_accession
@abc.abstractmethod
def get_csl_item(self, citekey: CiteKey) -> Dict[str, Any]:
"""
Return a CSL_Item with bibliographic details for citekey.
"""
raise NotImplementedError(
f"Manubot does not know how to generate a csl_item for {citekey.standard_id!r}"
)
"""
Mapping from lowercase prefix to Handler class function location as string.
This output is automatically generated using `_generate_prefix_to_handler`.
Hardcoding this mapping reduces startup time and helps keep imports to a minimum,
allowing installations without the full dependencies to function.
"""
prefix_to_handler: Dict[str, str] = {
"3dmet": "manubot.cite.curie.Handler_CURIE",
"4dn": "manubot.cite.curie.Handler_CURIE",
"4dn.biosource": "manubot.cite.curie.Handler_CURIE",
"4dn.replicate": "manubot.cite.curie.Handler_CURIE",
"aaindex": "manubot.cite.curie.Handler_CURIE",
"aao": "manubot.cite.curie.Handler_CURIE",
"abcd": "manubot.cite.curie.Handler_CURIE",
"abm": "manubot.cite.curie.Handler_CURIE",
"abs": "manubot.cite.curie.Handler_CURIE",
"ac": "manubot.cite.curie.Handler_CURIE",
"aceview.worm": "manubot.cite.curie.Handler_CURIE",
"aclame": "manubot.cite.curie.Handler_CURIE",
"addexbio": "manubot.cite.curie.Handler_CURIE",
"addgene": "manubot.cite.curie.Handler_CURIE",
"ado": "manubot.cite.curie.Handler_CURIE",
"adw": "manubot.cite.curie.Handler_CURIE",
"aeo": "manubot.cite.curie.Handler_CURIE",
"aeo_retired": "manubot.cite.curie.Handler_CURIE",
"aeon": "manubot.cite.curie.Handler_CURIE",
"aero": "manubot.cite.curie.Handler_CURIE",
"affy.probeset": "manubot.cite.curie.Handler_CURIE",
"aftol.taxonomy": "manubot.cite.curie.Handler_CURIE",
"agr": "manubot.cite.curie.Handler_CURIE",
"agricola": "manubot.cite.curie.Handler_CURIE",
"agricola_id": "manubot.cite.curie.Handler_CURIE",
"agrkb": "manubot.cite.curie.Handler_CURIE",
"agro": "manubot.cite.curie.Handler_CURIE",
"agrovoc": "manubot.cite.curie.Handler_CURIE",
"agsd": "manubot.cite.curie.Handler_CURIE",
"aism": "manubot.cite.curie.Handler_CURIE",
"alfred": "manubot.cite.curie.Handler_CURIE",
"allergome": "manubot.cite.curie.Handler_CURIE",
"alzforum.mutation": "manubot.cite.curie.Handler_CURIE",
"alzforum_mut": "manubot.cite.curie.Handler_CURIE",
"alzgene": "manubot.cite.curie.Handler_CURIE",
"ama-cpt": "manubot.cite.curie.Handler_CURIE",
"amoebadb": "manubot.cite.curie.Handler_CURIE",
"amphx": "manubot.cite.curie.Handler_CURIE",
"antibodyregistry": "manubot.cite.curie.Handler_CURIE",
"antweb": "manubot.cite.curie.Handler_CURIE",
"aop": "manubot.cite.curie.Handler_CURIE",
"aop.events": "manubot.cite.curie.Handler_CURIE",
"aop.relationships": "manubot.cite.curie.Handler_CURIE",
"aop.stressor": "manubot.cite.curie.Handler_CURIE",
"apaonto": "manubot.cite.curie.Handler_CURIE",
"apd": "manubot.cite.curie.Handler_CURIE",
"aphidbase.transcript": "manubot.cite.curie.Handler_CURIE",
"apid.interactions": "manubot.cite.curie.Handler_CURIE",
"apidb_plasmodb": "manubot.cite.curie.Handler_CURIE",
"apo": "manubot.cite.curie.Handler_CURIE",
"apollosv": "manubot.cite.curie.Handler_CURIE",
"arachnoserver": "manubot.cite.curie.Handler_CURIE",
"araport": "manubot.cite.curie.Handler_CURIE",
"arba": "manubot.cite.curie.Handler_CURIE",
"archdb": "manubot.cite.curie.Handler_CURIE",
"ardb": "manubot.cite.curie.Handler_CURIE",
"ark": "manubot.cite.curie.Handler_CURIE",
"aro": "manubot.cite.curie.Handler_CURIE",
"arrayexpress": "manubot.cite.curie.Handler_CURIE",
"arrayexpress.platform": "manubot.cite.curie.Handler_CURIE",
"arraymap": "manubot.cite.curie.Handler_CURIE",
"arxiv": "manubot.cite.arxiv.Handler_arXiv",
"asap": "manubot.cite.curie.Handler_CURIE",
"ascl": "manubot.cite.curie.Handler_CURIE",
"asin": "manubot.cite.curie.Handler_CURIE",
"aspgd.locus": "manubot.cite.curie.Handler_CURIE",
"aspgd.protein": "manubot.cite.curie.Handler_CURIE",
"asrp": "manubot.cite.curie.Handler_CURIE",
"astd": "manubot.cite.curie.Handler_CURIE",
"atc": "manubot.cite.curie.Handler_CURIE",
"atc_code": "manubot.cite.curie.Handler_CURIE",
"atcc": "manubot.cite.curie.Handler_CURIE",
"atcvet": "manubot.cite.curie.Handler_CURIE",
"atfdb.family": "manubot.cite.curie.Handler_CURIE",
"ato": "manubot.cite.curie.Handler_CURIE",
"atol": "manubot.cite.curie.Handler_CURIE",
"attc": "manubot.cite.curie.Handler_CURIE",
"autdb": "manubot.cite.curie.Handler_CURIE",
"bacdive": "manubot.cite.curie.Handler_CURIE",
"bacmap.biog": "manubot.cite.curie.Handler_CURIE",
"bacmap.map": "manubot.cite.curie.Handler_CURIE",
"bactibase": "manubot.cite.curie.Handler_CURIE",
"bao": "manubot.cite.curie.Handler_CURIE",
"bartoc": "manubot.cite.curie.Handler_CURIE",
"bbkg": "manubot.cite.curie.Handler_CURIE",
"bbtp": "manubot.cite.curie.Handler_CURIE",
"bcgo": "manubot.cite.curie.Handler_CURIE",
"bcio": "manubot.cite.curie.Handler_CURIE",
"bco": "manubot.cite.curie.Handler_CURIE",
"bcrc": "manubot.cite.curie.Handler_CURIE",
"bcrj": "manubot.cite.curie.Handler_CURIE",
"bdgp.est": "manubot.cite.curie.Handler_CURIE",
"bdgp.insertion": "manubot.cite.curie.Handler_CURIE",
"bdsc": "manubot.cite.curie.Handler_CURIE",
"beetlebase": "manubot.cite.curie.Handler_CURIE",
"begdb": "manubot.cite.curie.Handler_CURIE",
"bei_resources": "manubot.cite.curie.Handler_CURIE",
"beiresources": "manubot.cite.curie.Handler_CURIE",
"bfo": "manubot.cite.curie.Handler_CURIE",
"bgee.family": "manubot.cite.curie.Handler_CURIE",
"bgee.gene": "manubot.cite.curie.Handler_CURIE",
"bgee.organ": "manubot.cite.curie.Handler_CURIE",
"bgee.stage": "manubot.cite.curie.Handler_CURIE",
"bibo": "manubot.cite.curie.Handler_CURIE",
"bido": "manubot.cite.curie.Handler_CURIE",
"bigg.compartment": "manubot.cite.curie.Handler_CURIE",
"bigg.metabolite": "manubot.cite.curie.Handler_CURIE",
"bigg.model": "manubot.cite.curie.Handler_CURIE",
"bigg.reaction": "manubot.cite.curie.Handler_CURIE",
"bila": "manubot.cite.curie.Handler_CURIE",
"bind": "manubot.cite.curie.Handler_CURIE",
"bindingdb": "manubot.cite.curie.Handler_CURIE",
"biocarta.pathway": "manubot.cite.curie.Handler_CURIE",
"biocatalogue.service": "manubot.cite.curie.Handler_CURIE",
"biocyc": "manubot.cite.curie.Handler_CURIE",
"biogrid": "manubot.cite.curie.Handler_CURIE",
"biogrid.interaction": "manubot.cite.curie.Handler_CURIE",
"biolegend": "manubot.cite.curie.Handler_CURIE",
"biolink": "manubot.cite.curie.Handler_CURIE",
"biomagresbank": "manubot.cite.curie.Handler_CURIE",
"biomd": "manubot.cite.curie.Handler_CURIE",
"biominder": "manubot.cite.curie.Handler_CURIE",
"biomodels.db": "manubot.cite.curie.Handler_CURIE",
"biomodels.kisao": "manubot.cite.curie.Handler_CURIE",
"biomodels.teddy": "manubot.cite.curie.Handler_CURIE",
"biomodels.vocabulary": "manubot.cite.curie.Handler_CURIE",
"bionumbers": "manubot.cite.curie.Handler_CURIE",
"biopixie": "manubot.cite.curie.Handler_CURIE",
"bioportal": "manubot.cite.curie.Handler_CURIE",
"bioproject": "manubot.cite.curie.Handler_CURIE",
"bioregistry": "manubot.cite.curie.Handler_CURIE",
"bioregistry.collection": "manubot.cite.curie.Handler_CURIE",
"bioregistry.registry": "manubot.cite.curie.Handler_CURIE",
"bioregistry.schema": "manubot.cite.curie.Handler_CURIE",
"biorxiv": "manubot.cite.curie.Handler_CURIE",
"biosample": "manubot.cite.curie.Handler_CURIE",
"biosamples": "manubot.cite.curie.Handler_CURIE",
"biosimulations": "manubot.cite.curie.Handler_CURIE",
"biosimulators": "manubot.cite.curie.Handler_CURIE",
"biostudies": "manubot.cite.curie.Handler_CURIE",
"biosystems": "manubot.cite.curie.Handler_CURIE",
"biotools": "manubot.cite.curie.Handler_CURIE",
"biozil": "manubot.cite.curie.Handler_CURIE",
"birdbase": "manubot.cite.curie.Handler_CURIE",
"birnlex": "manubot.cite.curie.Handler_CURIE",
"biro": "manubot.cite.curie.Handler_CURIE",
"bitbucket": "manubot.cite.curie.Handler_CURIE",
"bitterdb.cpd": "manubot.cite.curie.Handler_CURIE",
"bitterdb.rec": "manubot.cite.curie.Handler_CURIE",
"bko": "manubot.cite.curie.Handler_CURIE",
"bmrb": "manubot.cite.curie.Handler_CURIE",
"bmrb.restraint": "manubot.cite.curie.Handler_CURIE",
"bold.taxonomy": "manubot.cite.curie.Handler_CURIE",
"bootstrep": "manubot.cite.curie.Handler_CURIE",
"bpdb": "manubot.cite.curie.Handler_CURIE",
"brenda": "manubot.cite.curie.Handler_CURIE",
"brenda.ligand": "manubot.cite.curie.Handler_CURIE",
"brenda.ligandgroup": "manubot.cite.curie.Handler_CURIE",
"broad": "manubot.cite.curie.Handler_CURIE",
"bs": "manubot.cite.curie.Handler_CURIE",
"bspo": "manubot.cite.curie.Handler_CURIE",
"bto": "manubot.cite.curie.Handler_CURIE",
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