From 75a1d2c12dd5d4f929863d0793b7a71e28d68ba6 Mon Sep 17 00:00:00 2001
From: Charles Tapley Hoyt <cthoyt@gmail.com>
Date: Tue, 26 Nov 2024 11:41:04 +0100
Subject: [PATCH] Update code

---
 build.py                |  39 +++--
 docs/_data/manifest.yml | 314 +++++++++++++++++++++++-----------------
 2 files changed, 209 insertions(+), 144 deletions(-)

diff --git a/build.py b/build.py
index 5cfafde..184f56f 100644
--- a/build.py
+++ b/build.py
@@ -24,24 +24,24 @@
 from textwrap import dedent
 from typing import TypedDict
 
+import bioontologies.version
+import bioregistry
+import bioregistry.version
 import click
 import pystow.utils
 import yaml
+from bioontologies.robot import convert
 from more_click import verbose_option
 from tabulate import tabulate
 from tqdm import tqdm
 from tqdm.contrib.logging import logging_redirect_tqdm
 from typing_extensions import NotRequired
+
 import pyobo.constants
 import pyobo.version
 from pyobo import Obo
 from pyobo.sources import ontology_resolver
 
-import bioontologies.version
-import bioregistry
-import bioregistry.version
-from bioontologies.robot import convert
-
 BASE_PURL = "https://w3id.org/biopragmatics/resources"
 HERE = Path(__file__).parent.resolve()
 DATA = HERE.joinpath("docs", "_data")
@@ -163,15 +163,19 @@ def _get_summary(obo: Obo) -> dict:
             len(values) for term in terms for values in term.relationships.values()
         ),
         "properties": sum(
-            len(values) for term in terms for values in term.properties.values()
+            len(values)
+            for term in terms
+            for dd in [term.annotations_literal, term.annotations_object]
+            for values in dd.values()
         ),
         "synonyms": sum(len(term.synonyms) for term in terms),
-        "xrefs": sum(len(term.xrefs) for term in terms),
+        "mappings": sum(len(term.get_mappings(include_xrefs=True)) for term in terms),
         "alts": sum(len(term.alt_ids) for term in terms),
         "parents": sum(len(term.parents) for term in terms),
         "references": sum(len(term.provenance) for term in terms),
         "definitions": sum(term.definition is not None for term in terms),
         "version": obo.data_version,
+        "license": bioregistry.get_license(obo.ontology),
     }
     return rv
 
@@ -253,7 +257,7 @@ def _make(
     _write_nodes(names_path, obo, prefix)
     _, rv["nodes"] = _prepare_artifact(prefix, names_path, has_version, ".tsv.gz")
 
-    sssom_df = pyobo.get_sssom_df(obo, names=False)
+    sssom_df = pyobo.get_mappings_df(obo, names=False)
     sssom_df.to_csv(sssom_path, sep="\t", index=False)
     _, rv["sssom"] = _prepare_artifact(prefix, sssom_path, has_version, ".sssom.tsv.gz")
 
@@ -306,20 +310,25 @@ def _make(
 
     # Write a README file, so anyone who navigates there can see what's going on
     summary = sorted((k, v) for k, v in rv["summary"].items() if k != "version")
-    text = dedent(f"""\
+    text = (
+        dedent(f"""\
 # {bioregistry.get_name(prefix)}
 
 {bioregistry.get_description(prefix)}
 
+**License**: {bioregistry.get_license(prefix) or '_unlicensed_'}
+
 ## PURLs
 
-{tabulate(purls_table_rows, headers=['Artifact', 'Download PURL', 'Versioned Download PURL'], tablefmt="github")}
+{tabulate(purls_table_rows, headers=['Artifact', 'Download PURL', 'Latest Versioned Download PURL'], tablefmt="github")}
 
 ## Summary
 
 {tabulate(summary, headers=['field', 'count'], tablefmt='github')}
 
 """).strip()
+        + "\n"
+    )
     readme_path.write_text(text)
 
     return rv
@@ -330,8 +339,8 @@ def _make(
 @click.option("-m", "--minimum")
 @click.option("--no-convert", is_flag=True)
 @click.option("-x", "--xvalue", help="Select a specific ontology", multiple=True)
-@click.option("-w", "--no-force", is_flag=True)
-def main(minimum: str | None, xvalue: list[str], no_convert: bool, no_force: bool):
+@click.option("--force/--no-force")
+def main(minimum: str | None, xvalue: list[str], no_convert: bool, force: bool):
     """Build the PyOBO examples."""
     if xvalue:
         for prefix in xvalue:
@@ -345,6 +354,10 @@ def main(minimum: str | None, xvalue: list[str], no_convert: bool, no_force: boo
     else:
         prefixes = PREFIXES
 
+    for prefix in prefixes:
+        if not bioregistry.get_license(prefix):
+            click.secho(f"missing license for `{prefix}`", fg="yellow")
+
     it = [(prefix, ontology_resolver.lookup(prefix)) for prefix in prefixes]
     it = tqdm(it, desc="Making OBO examples")
 
@@ -359,7 +372,7 @@ def main(minimum: str | None, xvalue: list[str], no_convert: bool, no_force: boo
                     prefix=prefix,
                     module=cls,
                     do_convert=not no_convert,
-                    no_force=no_force,
+                    no_force=not force,
                 )
             except Exception as e:
                 tqdm.write(click.style(f"[{prefix}] {e}", fg="red"))
diff --git a/docs/_data/manifest.yml b/docs/_data/manifest.yml
index 07b697f..06fb4af 100644
--- a/docs/_data/manifest.yml
+++ b/docs/_data/manifest.yml
@@ -1,4 +1,4 @@
-date: '2024-11-04'
+date: '2024-11-26'
 resources:
   cgnc:
     nodes:
@@ -24,14 +24,14 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 41332
       parents: 0
-      properties: 0
+      properties: 41332
       references: 0
-      relations: 67353
+      relations: 26021
       synonyms: 27221
       terms: 26021
       version: null
-      xrefs: 41332
   complexportal:
     nodes:
       gzipped: false
@@ -66,14 +66,14 @@ resources:
     summary:
       alts: 0
       definitions: 4841
+      mappings: 9863
       parents: 0
-      properties: 0
+      properties: 19802
       references: 12655
-      relations: 24643
+      relations: 4841
       synonyms: 12156
       terms: 4841
       version: '2024-09-08'
-      xrefs: 9865
   dictybase.gene:
     nodes:
       gzipped: false
@@ -98,6 +98,7 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 0
       parents: 0
       properties: 0
       references: 0
@@ -105,7 +106,6 @@ resources:
       synonyms: 16000
       terms: 14222
       version: null
-      xrefs: 0
   drugcentral:
     nodes:
       gzipped: false
@@ -140,14 +140,14 @@ resources:
     summary:
       alts: 0
       definitions: 3267
+      mappings: 76519
       parents: 0
-      properties: 8620
+      properties: 17913
       references: 0
-      relations: 9293
+      relations: 0
       synonyms: 19053
       terms: 4995
       version: '54'
-      xrefs: 76519
   eccode:
     nodes:
       gzipped: false
@@ -168,11 +168,11 @@ resources:
       version_iri: https://w3id.org/biopragmatics/resources/eccode/2024-10-02/eccode.json
       version_path: eccode/2024-10-02/eccode.json
     owl:
-      gzipped: true
-      iri: https://w3id.org/biopragmatics/resources/eccode/eccode.owl.gz
-      path: eccode/eccode.owl.gz
-      version_iri: https://w3id.org/biopragmatics/resources/eccode/2024-10-02/eccode.owl.gz
-      version_path: eccode/2024-10-02/eccode.owl.gz
+      gzipped: false
+      iri: https://w3id.org/biopragmatics/resources/eccode/eccode.owl
+      path: eccode/eccode.owl
+      version_iri: https://w3id.org/biopragmatics/resources/eccode/2024-10-02/eccode.owl
+      version_path: eccode/2024-10-02/eccode.owl
     sssom:
       gzipped: false
       iri: https://w3id.org/biopragmatics/resources/eccode/eccode.sssom.tsv
@@ -182,14 +182,14 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 0
       parents: 7244
-      properties: 0
+      properties: 254949
       references: 0
-      relations: 259726
+      relations: 4777
       synonyms: 10465
       terms: 8736
       version: '2024-10-02'
-      xrefs: 0
   flybase:
     nodes:
       gzipped: false
@@ -224,6 +224,7 @@ resources:
     summary:
       alts: 0
       definitions: 35702
+      mappings: 0
       parents: 35298
       properties: 0
       references: 0
@@ -231,7 +232,48 @@ resources:
       synonyms: 24869
       terms: 35702
       version: '2024_05'
-      xrefs: 0
+  gtdb:
+    nodes:
+      gzipped: true
+      iri: https://w3id.org/biopragmatics/resources/gtdb/gtdb.tsv.gz
+      path: gtdb/gtdb.tsv.gz
+      version_iri: https://w3id.org/biopragmatics/resources/gtdb/220/gtdb.tsv.gz
+      version_path: gtdb/220/gtdb.tsv.gz
+    obo:
+      gzipped: true
+      iri: https://w3id.org/biopragmatics/resources/gtdb/gtdb.obo.gz
+      path: gtdb/gtdb.obo.gz
+      version_iri: https://w3id.org/biopragmatics/resources/gtdb/220/gtdb.obo.gz
+      version_path: gtdb/220/gtdb.obo.gz
+    obograph:
+      gzipped: false
+      iri: https://w3id.org/biopragmatics/resources/gtdb/gtdb.json
+      path: gtdb/gtdb.json
+      version_iri: https://w3id.org/biopragmatics/resources/gtdb/220/gtdb.json
+      version_path: gtdb/220/gtdb.json
+    owl:
+      gzipped: false
+      iri: https://w3id.org/biopragmatics/resources/gtdb/gtdb.owl
+      path: gtdb/gtdb.owl
+      version_iri: https://w3id.org/biopragmatics/resources/gtdb/220/gtdb.owl
+      version_path: gtdb/220/gtdb.owl
+    sssom:
+      gzipped: false
+      iri: https://w3id.org/biopragmatics/resources/gtdb/gtdb.sssom.tsv
+      path: gtdb/gtdb.sssom.tsv
+      version_iri: https://w3id.org/biopragmatics/resources/gtdb/220/gtdb.sssom.tsv
+      version_path: gtdb/220/gtdb.sssom.tsv
+    summary:
+      alts: 0
+      definitions: 0
+      mappings: 596859
+      parents: 3581154
+      properties: 4178013
+      references: 0
+      relations: 0
+      synonyms: 0
+      terms: 4178013
+      version: '220'
   hgnc:
     nodes:
       gzipped: false
@@ -266,14 +308,14 @@ resources:
     summary:
       alts: 0
       definitions: 43882
+      mappings: 260015
       parents: 43882
-      properties: 44134
+      properties: 295301
       references: 34994
-      relations: 402851
+      relations: 151684
       synonyms: 105217
       terms: 43882
       version: '2024-10-01'
-      xrefs: 260015
   hgnc.genegroup:
     nodes:
       gzipped: false
@@ -308,6 +350,7 @@ resources:
     summary:
       alts: 0
       definitions: 730
+      mappings: 0
       parents: 1885
       properties: 0
       references: 1612
@@ -315,7 +358,6 @@ resources:
       synonyms: 1160
       terms: 1815
       version: '2024-10-01'
-      xrefs: 0
   interpro:
     nodes:
       gzipped: false
@@ -350,6 +392,7 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 0
       parents: 8976
       properties: 46035
       references: 0
@@ -357,7 +400,6 @@ resources:
       synonyms: 0
       terms: 46035
       version: '102.0'
-      xrefs: 0
   kegg.genome:
     nodes:
       gzipped: false
@@ -392,6 +434,7 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 0
       parents: 0
       properties: 0
       references: 0
@@ -399,7 +442,6 @@ resources:
       synonyms: 0
       terms: 10682
       version: '112.0'
-      xrefs: 0
   mesh:
     nodes:
       gzipped: false
@@ -434,6 +476,7 @@ resources:
     summary:
       alts: 0
       definitions: 30613
+      mappings: 0
       parents: 42021
       properties: 0
       references: 0
@@ -441,39 +484,48 @@ resources:
       synonyms: 634143
       terms: 354471
       version: '2024'
-      xrefs: 0
   mgi:
     nodes:
       gzipped: false
       iri: https://w3id.org/biopragmatics/resources/mgi/mgi.tsv
       path: mgi/mgi.tsv
+      version_iri: https://w3id.org/biopragmatics/resources/mgi/6.24/mgi.tsv
+      version_path: mgi/6.24/mgi.tsv
     obo:
       gzipped: true
       iri: https://w3id.org/biopragmatics/resources/mgi/mgi.obo.gz
       path: mgi/mgi.obo.gz
+      version_iri: https://w3id.org/biopragmatics/resources/mgi/6.24/mgi.obo.gz
+      version_path: mgi/6.24/mgi.obo.gz
     obograph:
       gzipped: true
       iri: https://w3id.org/biopragmatics/resources/mgi/mgi.json.gz
       path: mgi/mgi.json.gz
+      version_iri: https://w3id.org/biopragmatics/resources/mgi/6.24/mgi.json.gz
+      version_path: mgi/6.24/mgi.json.gz
     owl:
       gzipped: true
       iri: https://w3id.org/biopragmatics/resources/mgi/mgi.owl.gz
       path: mgi/mgi.owl.gz
+      version_iri: https://w3id.org/biopragmatics/resources/mgi/6.24/mgi.owl.gz
+      version_path: mgi/6.24/mgi.owl.gz
     sssom:
       gzipped: false
       iri: https://w3id.org/biopragmatics/resources/mgi/mgi.sssom.tsv
       path: mgi/mgi.sssom.tsv
+      version_iri: https://w3id.org/biopragmatics/resources/mgi/6.24/mgi.sssom.tsv
+      version_path: mgi/6.24/mgi.sssom.tsv
     summary:
       alts: 0
-      definitions: 719749
+      definitions: 719756
+      mappings: 168405
       parents: 0
-      properties: 0
+      properties: 111831
       references: 0
-      relations: 1042386
-      synonyms: 259738
-      terms: 719749
-      version: null
-      xrefs: 168405
+      relations: 930562
+      synonyms: 259761
+      terms: 719756
+      version: '6.24'
   mirbase:
     nodes:
       gzipped: false
@@ -508,6 +560,7 @@ resources:
     summary:
       alts: 0
       definitions: 38589
+      mappings: 8814
       parents: 0
       properties: 0
       references: 0
@@ -515,7 +568,6 @@ resources:
       synonyms: 1441
       terms: 38589
       version: '22.1'
-      xrefs: 8814
   mirbase.family:
     nodes:
       gzipped: false
@@ -550,6 +602,7 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 0
       parents: 0
       properties: 0
       references: 0
@@ -557,7 +610,6 @@ resources:
       synonyms: 0
       terms: 19907
       version: '22.1'
-      xrefs: 0
   mirbase.mature:
     nodes:
       gzipped: false
@@ -592,6 +644,7 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 0
       parents: 0
       properties: 0
       references: 0
@@ -599,7 +652,6 @@ resources:
       synonyms: 7179
       terms: 49168
       version: '22.1'
-      xrefs: 0
   npass:
     nodes:
       gzipped: false
@@ -634,6 +686,7 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 103085
       parents: 0
       properties: 0
       references: 0
@@ -641,7 +694,6 @@ resources:
       synonyms: 22501
       terms: 96420
       version: '2.0'
-      xrefs: 103085
   pathbank:
     nodes:
       gzipped: false
@@ -676,14 +728,14 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 110242
       parents: 0
-      properties: 110242
+      properties: 220484
       references: 0
-      relations: 2565795
+      relations: 2455553
       synonyms: 0
       terms: 110242
       version: '2.0'
-      xrefs: 110242
   pfam:
     nodes:
       gzipped: false
@@ -718,6 +770,7 @@ resources:
     summary:
       alts: 0
       definitions: 23794
+      mappings: 0
       parents: 10923
       properties: 0
       references: 0
@@ -725,7 +778,6 @@ resources:
       synonyms: 0
       terms: 23794
       version: '37.1'
-      xrefs: 0
   pfam.clan:
     nodes:
       gzipped: false
@@ -760,6 +812,7 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 0
       parents: 0
       properties: 0
       references: 0
@@ -767,7 +820,6 @@ resources:
       synonyms: 0
       terms: 751
       version: '37.1'
-      xrefs: 0
   pombase:
     nodes:
       gzipped: false
@@ -802,14 +854,14 @@ resources:
     summary:
       alts: 0
       definitions: 12684
+      mappings: 0
       parents: 12684
-      properties: 12684
+      properties: 23473
       references: 0
-      relations: 23473
+      relations: 12684
       synonyms: 2620
       terms: 12684
       version: '2024-11-01'
-      xrefs: 0
   reactome:
     nodes:
       gzipped: false
@@ -844,6 +896,7 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 0
       parents: 22675
       properties: 0
       references: 0
@@ -851,49 +904,48 @@ resources:
       synonyms: 0
       terms: 22537
       version: '90'
-      xrefs: 0
   rgd:
     nodes:
       gzipped: false
       iri: https://w3id.org/biopragmatics/resources/rgd/rgd.tsv
       path: rgd/rgd.tsv
-      version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-10-25/rgd.tsv
-      version_path: rgd/2024-10-25/rgd.tsv
+      version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-11-22/rgd.tsv
+      version_path: rgd/2024-11-22/rgd.tsv
     obo:
       gzipped: false
       iri: https://w3id.org/biopragmatics/resources/rgd/rgd.obo
       path: rgd/rgd.obo
-      version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-10-25/rgd.obo
-      version_path: rgd/2024-10-25/rgd.obo
+      version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-11-22/rgd.obo
+      version_path: rgd/2024-11-22/rgd.obo
     obograph:
       gzipped: false
       iri: https://w3id.org/biopragmatics/resources/rgd/rgd.json
       path: rgd/rgd.json
-      version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-10-25/rgd.json
-      version_path: rgd/2024-10-25/rgd.json
+      version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-11-22/rgd.json
+      version_path: rgd/2024-11-22/rgd.json
     owl:
       gzipped: true
       iri: https://w3id.org/biopragmatics/resources/rgd/rgd.owl.gz
       path: rgd/rgd.owl.gz
-      version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-10-25/rgd.owl.gz
-      version_path: rgd/2024-10-25/rgd.owl.gz
+      version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-11-22/rgd.owl.gz
+      version_path: rgd/2024-11-22/rgd.owl.gz
     sssom:
       gzipped: false
       iri: https://w3id.org/biopragmatics/resources/rgd/rgd.sssom.tsv
       path: rgd/rgd.sssom.tsv
-      version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-10-25/rgd.sssom.tsv
-      version_path: rgd/2024-10-25/rgd.sssom.tsv
+      version_iri: https://w3id.org/biopragmatics/resources/rgd/2024-11-22/rgd.sssom.tsv
+      version_path: rgd/2024-11-22/rgd.sssom.tsv
     summary:
       alts: 0
-      definitions: 50930
+      definitions: 51054
+      mappings: 103906
       parents: 0
-      properties: 0
-      references: 124411
-      relations: 141023
-      synonyms: 139111
+      properties: 79013
+      references: 124654
+      relations: 61331
+      synonyms: 139322
       terms: 61331
-      version: '2024-10-25'
-      xrefs: 104518
+      version: '2024-11-22'
   rhea:
     nodes:
       gzipped: false
@@ -928,98 +980,98 @@ resources:
     summary:
       alts: 0
       definitions: 0
+      mappings: 19627
       parents: 69210
-      properties: 0
+      properties: 165016
       references: 0
-      relations: 762437
+      relations: 597421
       synonyms: 0
       terms: 67880
       version: '135'
-      xrefs: 19627
   sgd:
     nodes:
       gzipped: false
       iri: https://w3id.org/biopragmatics/resources/sgd/sgd.tsv
       path: sgd/sgd.tsv
-      version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-3-1/sgd.tsv
-      version_path: sgd/R64-3-1/sgd.tsv
+      version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-5-1/sgd.tsv
+      version_path: sgd/R64-5-1/sgd.tsv
     obo:
       gzipped: false
       iri: https://w3id.org/biopragmatics/resources/sgd/sgd.obo
       path: sgd/sgd.obo
-      version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-3-1/sgd.obo
-      version_path: sgd/R64-3-1/sgd.obo
+      version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-5-1/sgd.obo
+      version_path: sgd/R64-5-1/sgd.obo
     obograph:
       gzipped: false
       iri: https://w3id.org/biopragmatics/resources/sgd/sgd.json
       path: sgd/sgd.json
-      version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-3-1/sgd.json
-      version_path: sgd/R64-3-1/sgd.json
+      version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-5-1/sgd.json
+      version_path: sgd/R64-5-1/sgd.json
     owl:
       gzipped: false
       iri: https://w3id.org/biopragmatics/resources/sgd/sgd.owl
       path: sgd/sgd.owl
-      version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-3-1/sgd.owl
-      version_path: sgd/R64-3-1/sgd.owl
+      version_iri: https://w3id.org/biopragmatics/resources/sgd/R64-5-1/sgd.owl
+      version_path: sgd/R64-5-1/sgd.owl
     sssom:
       gzipped: false
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@@ -1054,99 +1106,99 @@ resources:
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