Refactor converter generation code

exports/contexts/bioregistry.epm.json

@@ -26168,14 +26168,12 @@
         "uri_prefix": "http://arabidopsis.org/servlets/TairObject?accession=AASequence:",
         "uri_prefix_synonyms": [
             "TAIR.PROTEIN:",
-            "http://arabidopsis.org/servlets/TairObject?accession=",
             "http://bio2rdf.org/tair.protein:",
             "http://bioregistry.io/tair.protein:",
             "http://identifiers.org/tair.protein/",
             "http://identifiers.org/tair.protein/AASequence:",
             "http://identifiers.org/tair.protein:",
             "http://n2t.net/tair.protein:",
-            "https://arabidopsis.org/servlets/TairObject?accession=",
             "https://arabidopsis.org/servlets/TairObject?accession=AASequence:",
             "https://bio2rdf.org/tair.protein:",
             "https://bioregistry.io/tair.protein:",

exports/contexts/bioregistry.rpm.json

@@ -3167,7 +3167,6 @@
     "http://aps.unmc.edu/AP/database/query_output.php?ID=": "apd",
     "http://ar5iv.org/abs/": "arxiv",
     "http://arabidopsis.info/StockInfo?NASC_id=": "nasc",
-    "http://arabidopsis.org/servlets/TairObject?accession=": "tair.protein",
     "http://arabidopsis.org/servlets/TairObject?accession=AASequence:": "tair.protein",
     "http://arabidopsis.org/servlets/TairObject?accession=Gene:": "tair.gene",
     "http://arabidopsis.org/servlets/TairObject?type=locus&name=": "tair.locus",
@@ -10733,7 +10732,6 @@
     "https://aps.unmc.edu/AP/database/query_output.php?ID=": "apd",
     "https://ar5iv.org/abs/": "arxiv",
     "https://arabidopsis.info/StockInfo?NASC_id=": "nasc",
-    "https://arabidopsis.org/servlets/TairObject?accession=": "tair.protein",
     "https://arabidopsis.org/servlets/TairObject?accession=AASequence:": "tair.protein",
     "https://arabidopsis.org/servlets/TairObject?accession=Gene:": "tair.gene",
     "https://arabidopsis.org/servlets/TairObject?type=locus&name=": "tair.locus",

exports/contexts/obo.epm.json

@@ -22771,14 +22771,12 @@
         "prefix": "tair.protein",
         "uri_prefix": "http://arabidopsis.org/servlets/TairObject?accession=AASequence:",
         "uri_prefix_synonyms": [
-            "http://arabidopsis.org/servlets/TairObject?accession=",
             "http://bio2rdf.org/tair.protein:",
             "http://bioregistry.io/tair.protein:",
             "http://identifiers.org/tair.protein/",
             "http://identifiers.org/tair.protein/AASequence:",
             "http://identifiers.org/tair.protein:",
             "http://n2t.net/tair.protein:",
-            "https://arabidopsis.org/servlets/TairObject?accession=",
             "https://arabidopsis.org/servlets/TairObject?accession=AASequence:",
             "https://bio2rdf.org/tair.protein:",
             "https://bioregistry.io/tair.protein:",

src/bioregistry/__init__.py

@@ -127,7 +127,6 @@
     write_registry,
 )
 from .uri_format import (  # noqa:F401
-    get_extended_prefix_map,
     get_pattern_map,
     get_prefix_map,
     get_uri_format,

src/bioregistry/data/bioregistry.json

@@ -95986,8 +95986,7 @@
       "namespaceEmbeddedInLui": false,
       "pattern": "^Gene:\\d{7}$",
       "prefix": "tair.gene",
-      "sampleId": "Gene:2200934",
-      "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+      "sampleId": "Gene:2200934"
     },
     "n2t": {
       "description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus.",
@@ -95996,8 +95995,7 @@
       "name": "The Arabidopsis Information Resource (TAIR) Gene",
       "namespaceEmbeddedInLui": false,
       "pattern": "^Gene:\\d{7}$",
-      "prefix": "tair.gene",
-      "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+      "prefix": "tair.gene"
     },
     "part_of": "tair",
     "pattern": "^\\d{7}$",
@@ -96012,8 +96010,7 @@
       "prefix": "tair.gene",
       "pubmed_ids": [
         "12444417"
-      ],
-      "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+      ]
     },
     "publications": [
       {
@@ -96133,8 +96130,7 @@
       "namespaceEmbeddedInLui": false,
       "pattern": "^AASequence:\\d{10}$",
       "prefix": "tair.protein",
-      "sampleId": "AASequence:1009107926",
-      "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+      "sampleId": "AASequence:1009107926"
     },
     "n2t": {
       "description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept",
@@ -96143,8 +96139,7 @@
       "name": "The Arabidopsis Information Resource (TAIR) Protein",
       "namespaceEmbeddedInLui": false,
       "pattern": "^AASequence:\\d{10}$",
-      "prefix": "tair.protein",
-      "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+      "prefix": "tair.protein"
     },
     "pattern": "^\\d{10}$",
     "prefixcommons": {
@@ -96158,8 +96153,7 @@
       "prefix": "tair.protein",
       "pubmed_ids": [
         "12444417"
-      ],
-      "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+      ]
     },
     "publications": [
       {

src/bioregistry/data/external/miriam/processed.json

@@ -9440,8 +9440,7 @@
     "namespaceEmbeddedInLui": false,
     "pattern": "^Gene:\\d{7}$",
     "prefix": "tair.gene",
-    "sampleId": "Gene:2200934",
-    "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+    "sampleId": "Gene:2200934"
   },
   "tair.locus": {
     "deprecated": false,
@@ -9476,8 +9475,7 @@
     "namespaceEmbeddedInLui": false,
     "pattern": "^AASequence:\\d{10}$",
     "prefix": "tair.protein",
-    "sampleId": "AASequence:1009107926",
-    "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+    "sampleId": "AASequence:1009107926"
   },
   "tarbase": {
     "deprecated": false,

src/bioregistry/data/external/n2t/processed.json

@@ -5460,8 +5460,7 @@
     "homepage": "http://arabidopsis.org/index.jsp",
     "name": "The Arabidopsis Information Resource (TAIR) Gene",
     "namespaceEmbeddedInLui": false,
-    "pattern": "^Gene:\\d{7}$",
-    "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+    "pattern": "^Gene:\\d{7}$"
   },
   "tair.locus": {
     "description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.",
@@ -5478,8 +5477,7 @@
     "homepage": "http://arabidopsis.org/index.jsp",
     "name": "The Arabidopsis Information Resource (TAIR) Protein",
     "namespaceEmbeddedInLui": false,
-    "pattern": "^AASequence:\\d{10}$",
-    "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+    "pattern": "^AASequence:\\d{10}$"
   },
   "tarbase": {
     "description": "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used.",

src/bioregistry/data/external/prefixcommons/processed.json

@@ -10795,8 +10795,7 @@
     "prefix": "tair.gene",
     "pubmed_ids": [
       "12444417"
-    ],
-    "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+    ]
   },
   "tair.locus": {
     "description": "The locus name",
@@ -10823,8 +10822,7 @@
     "prefix": "tair.protein",
     "pubmed_ids": [
       "12444417"
-    ],
-    "uri_format": "http://arabidopsis.org/servlets/TairObject?accession=$1"
+    ]
   },
   "tao": {
     "bioportal": "1110",

src/bioregistry/external/miriam.py

@@ -27,6 +27,9 @@
     "4503",
     "6vts",
 }
+SKIP_URI_FORMATS = {
+    "http://arabidopsis.org/servlets/TairObject?accession=$1",
+}
 
 
 def get_miriam(force_download: bool = False, force_process: bool = False):
@@ -91,7 +94,8 @@
     else:
         primary, *rest = resources
     rv["homepage"] = primary["homepage"]
-    rv[URI_FORMAT_KEY] = primary[URI_FORMAT_KEY]
+    if URI_FORMAT_KEY in primary:
+        rv[URI_FORMAT_KEY] = primary[URI_FORMAT_KEY]
 
     extras = []
     for provider in rest:
@@ -113,14 +117,17 @@
 
 
 def _preprocess_resource(resource):
-    return {
+    rv = {
         "official": resource["official"],
         "homepage": resource["resourceHomeUrl"],
         "code": resource["providerCode"],
-        URI_FORMAT_KEY: resource["urlPattern"].replace("{$id}", "$1"),
         "name": resource["name"],
         "description": resource["description"],
     }
+    uri_format = resource["urlPattern"].replace("{$id}", "$1")
+    if uri_format not in SKIP_URI_FORMATS:
+        rv[URI_FORMAT_KEY] = uri_format
+    return rv
 
 
 @click.command()

src/bioregistry/external/n2t.py

@@ -26,6 +26,9 @@
     "merops": "issue with miriam having duplicate prefixes for this resource",  # FIXME
     "hgnc.family": "issue with miriam having duplicate prefixes for this resource",  # FIXME
 }
+SKIP_URI_FORMATS = {
+    "http://arabidopsis.org/servlets/TairObject?accession=$1",
+}
 
 
 def get_n2t(force_download: bool = False):
@@ -53,7 +56,7 @@
 def _process(record):
     rv = {
         "name": record.get("name"),
-        URI_FORMAT_KEY: record["redirect"].replace("$id", "$1") if "redirect" in record else None,
+        URI_FORMAT_KEY: _get_uri_format(record),
         "description": record.get("description"),
         "homepage": record.get("more"),
         "pattern": record.get("pattern"),
@@ -63,6 +66,16 @@
     return {k: v for k, v in rv.items() if v is not None}
 
 
+def _get_uri_format(record):
+    raw_redirect = record.get("redirect")
+    if raw_redirect is None:
+        return None
+    uri_format = raw_redirect.replace("$id", "$1")
+    if uri_format in SKIP_URI_FORMATS:
+        return None
+    return uri_format
+
+
 @click.command()
 def main():
     """Reload the N2T data."""

src/bioregistry/external/prefixcommons.py

@@ -85,6 +85,11 @@
 }
 #: These contain synonyms with mismatches
 DISCARD_SYNONYMS = {"biogrid", "cath", "zfa"}
+SKIP_URI_FORMATS = {
+    "http://purl.obolibrary.org/obo/$1",
+    "http://www.ebi.ac.uk/ontology-lookup/?termId=$1",
+    "http://arabidopsis.org/servlets/TairObject?accession=$1",
+}
 
 
 def get_prefixcommons(force_download: bool = False, force_process: bool = False):
@@ -147,10 +152,7 @@
     uri_format = rv.pop("uri_format", None)
     if uri_format:
         uri_format = uri_format.replace("$id", "$1").replace("[?id]", "$1").replace("$d", "$1")
-        if uri_format not in {
-            "http://purl.obolibrary.org/obo/$1",
-            "http://www.ebi.ac.uk/ontology-lookup/?termId=$1",
-        }:
+        if uri_format not in SKIP_URI_FORMATS:
             rv["uri_format"] = uri_format
 
     uri_rdf_formats = _get_uri_formats(rv, "rdf_uri_prefix")
@@ -191,9 +193,12 @@
             continue
         if "$1" in uri_format or "[?id]" in uri_format:  # FIXME check if these come at the end
             continue
-        rv.append(f"{uri_format}$1")
+        uri_format = f"{uri_format}$1"
+        if uri_format in SKIP_URI_FORMATS:
+            continue
+        rv.append(uri_format)
     return rv
 
 
 if __name__ == "__main__":
-    print(len(get_prefixcommons(force_process=True)))  # noqa:T201
+    print(len(get_prefixcommons(force_process=True, force_download=True)))  # noqa:T201

src/bioregistry/record_accumulator.py

@@ -18,9 +18,14 @@
 )
 
 import curies
+from curies import Converter
 
 from bioregistry import Resource
 
+__all__ = [
+    "get_converter",
+]
+
 logger = logging.getLogger(__name__)
 prefix_blacklist = {"bgee.gene"}
 uri_prefix_blacklist = {
@@ -33,6 +38,7 @@
     "http://www.ncbi.nlm.nih.gov/nuccore/",
     "https://www.ebi.ac.uk/ena/data/view/",
     "http://www.ebi.ac.uk/ena/data/view/",
+    "http://arabidopsis.org/servlets/TairObject?accession=",
 }
 prefix_resource_blacklist = {
     ("orphanet", "http://www.orpha.net/ORDO/Orphanet_"),  # biocontext is wrong
@@ -103,6 +109,28 @@ def _iterate_prefix_prefix(resource: Resource, *extras: str):
 #  (e.g., uniprot.isoform and uniprot)
 
 
+def get_converter(
+    resources: List[Resource],
+    prefix_priority: Optional[Sequence[str]] = None,
+    uri_prefix_priority: Optional[Sequence[str]] = None,
+    include_prefixes: bool = False,
+    strict: bool = False,
+    blacklist: Optional[Collection[str]] = None,
+    remapping: Optional[Mapping[str, str]] = None,
+) -> Converter:
+    """Generate a converter from resources."""
+    records = get_records(
+        resources,
+        prefix_priority=prefix_priority,
+        uri_prefix_priority=uri_prefix_priority,
+        include_prefixes=include_prefixes,
+        strict=strict,
+        blacklist=blacklist,
+        remapping=remapping,
+    )
+    return curies.Converter(records)
+
+
 def get_records(  # noqa: C901
     resources: List[Resource],
     prefix_priority: Optional[Sequence[str]] = None,