update tests

cancervariants · Nov 12, 2024 · a0020e3 · a0020e3
1 parent bc3c13f
commit a0020e3
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Showing 4 changed files with 19 additions and 16 deletions.
diff --git a/src/therapy/etl/guidetopharmacology.py b/src/therapy/etl/guidetopharmacology.py
@@ -74,6 +74,7 @@ def _transform_ligands(self, data: dict) -> None:
                 "PubChem CID",
                 "UniProt ID",
                 "Ensembl ID",
+                "ChEMBL ID",
                 "Ligand Subunit IDs",
                 "Ligand Subunit Name",
                 "Ligand Subunit UniProt IDs",
@@ -114,14 +115,16 @@ def _transform_ligands(self, data: dict) -> None:
                     )
                 if row[10]:
                     associated_with.append(f"{NamespacePrefix.UNIPROT.value}:{row[10]}")
-                if row[16]:
-                    aliases.append(self._process_name(row[16]))  # IUPAC
+                if row[12]:
+                    associated_with.append(f"{NamespacePrefix.CHEMBL.value}:{row[12]}")
                 if row[17]:
-                    # International Non-proprietary Name assigned by the WHO
-                    aliases.append(self._process_name(row[17]))
+                    aliases.append(self._process_name(row[17]))  # IUPAC
                 if row[18]:
+                    # International Non-proprietary Name assigned by the WHO
+                    aliases.append(self._process_name(row[18]))
+                if row[19]:
                     # synonyms
-                    synonyms = row[18].split("|")
+                    synonyms = row[19].split("|")
                     for s in synonyms:
                         if "&" in s and ";" in s:
                             name_code = s[s.index("&") : s.index(";") + 1]
@@ -130,9 +133,9 @@ def _transform_ligands(self, data: dict) -> None:
                                 s = s.replace(name_code, "")
                             s = html.unescape(s)
                         aliases.append(self._process_name(s))
-                if row[20]:
+                if row[21]:
                     associated_with.append(
-                        f"{NamespacePrefix.INCHIKEY.value}:{row[20]}"
+                        f"{NamespacePrefix.INCHIKEY.value}:{row[21]}"
                     )
 
                 if associated_with:

diff --git a/...acology/gtop_ligand_id_mapping_2023.2.tsv → ...acology/gtop_ligand_id_mapping_2024.3.tsv b/...acology/gtop_ligand_id_mapping_2023.2.tsv → ...acology/gtop_ligand_id_mapping_2024.3.tsv
@@ -1,4 +1,4 @@
-"# GtoPdb Version: 2023.2 - published: 2023-08-07"
+"# GtoPdb Version: 2024.3 - published: 2024-10-03"
 "Ligand id"	"Name"	"Species"	"Type"	"PubChem SID"	"PubChem CID"	"ChEMBl ID"	"Chebi ID"	"UniProt id"	"Ensembl ID"	"IUPAC name"	"INN"	"CAS"	"DrugBank ID"	"Drug Central ID"
 "2169"	"arginine vasotocin"	""	"Peptide"	"135652004"	"68649"	""	""	""	""	"L-cysteinyl-L-tyrosyl-(3S)-DL-isoleucyl-L-glutaminyl-L-asparagyl-L-cysteinyl-DL-prolyl-L-arginyl-glycinamide (1->6)-disulfide"	"argiprestocin"	"113-80-4"	""	""
 "240"	"cisapride"	""	"Synthetic organic"	"135650104"	"2769"	"CHEMBL1729"	"CHEBI:151790"	""	""	"4-amino-5-chloro-N-[1-[3-(4-fluorophenoxy)propyl]-3-methoxypiperidin-4-yl]-2-methoxybenzamide"	"cisapride"	"81098-60-4"	"DB00604"	"660"

diff --git a/tests/data/guidetopharmacology/gtop_ligands_2023.2.tsv b/tests/data/guidetopharmacology/gtop_ligands_2023.2.tsv
diff --git a/tests/data/guidetopharmacology/gtop_ligands_2024.3.tsv b/tests/data/guidetopharmacology/gtop_ligands_2024.3.tsv
@@ -0,0 +1,8 @@
+"# GtoPdb Version: 2024.3 - published: 2024-10-03"
+"Ligand ID"	"Name"	"Species"	"Type"	"Approved"	"Withdrawn"	"Labelled"	"Radioactive"	"PubChem SID"	"PubChem CID"	"UniProt ID"	"Ensembl ID"	"ChEMBL ID"	"Ligand Subunit IDs"	"Ligand Subunit Name"	"Ligand Subunit UniProt IDs"	"Ligand Subunit Ensembl IDs"	"IUPAC name"	"INN"	"Synonyms"	"SMILES"	"InChIKey"	"InChI"	"GtoImmuPdb"	"GtoMPdb"	"Antibacterial"
+"2169"	"arginine vasotocin"	""	"Peptide"	""	""	""	""	"135652004"	"68649"	""	""	""	""	""	""	""	"L-cysteinyl-L-tyrosyl-(3S)-DL-isoleucyl-L-glutaminyl-L-asparagyl-L-cysteinyl-DL-prolyl-L-arginyl-glycinamide (1->6)-disulfide"	"argiprestocin"	"[Arg<sup>8</sup>]vasotocin|AVT"	"CC[C@@H](C1NC(=O)[C@H](Cc2ccc(cc2)O)NC(=O)[C@@H](N)CSSC[C@H](NC(=O)[C@@H](NC(=O)[C@@H](NC1=O)CCC(=O)N)CC(=O)N)C(=O)N1CCCC1C(=O)N[C@H](C(=O)NCC(=O)N)CCCN=C(N)N)C"	"OXDZADMCOWPSOC-ICBIOJHSSA-N"	"InChI=1S/C43H67N15O12S2/c1-3-21(2)34-41(69)53-26(12-13-31(45)60)37(65)55-28(17-32(46)61)38(66)56-29(20-72-71-19-24(44)35(63)54-27(39(67)57-34)16-22-8-10-23(59)11-9-22)42(70)58-15-5-7-30(58)40(68)52-25(6-4-14-50-43(48)49)36(64)51-18-33(47)62/h8-11,21,24-30,34,59H,3-7,12-20,44H2,1-2H3,(H2,45,60)(H2,46,61)(H2,47,62)(H,51,64)(H,52,68)(H,53,69)(H,54,63)(H,55,65)(H,56,66)(H,57,67)(H4,48,49,50)/t21-,24-,25-,26-,27-,28-,29-,30?,34?/m0/s1"	""	""	""
+"240"	"cisapride"	""	"Synthetic organic"	"yes"	"yes"	""	""	"135650104"	"2769"	""	""	"CHEMBL1729"	""	""	""	""	"4-amino-5-chloro-N-[1-[3-(4-fluorophenoxy)propyl]-3-methoxypiperidin-4-yl]-2-methoxybenzamide"	"cisapride"	"Prepulsid&reg;|Propulsid&reg;"	"COC1CN(CCCOc2ccc(cc2)F)CCC1NC(=O)c1cc(Cl)c(cc1OC)N"	"DCSUBABJRXZOMT-UHFFFAOYSA-N"	"InChI=1S/C23H29ClFN3O4/c1-30-21-13-19(26)18(24)12-17(21)23(29)27-20-8-10-28(14-22(20)31-2)9-3-11-32-16-6-4-15(25)5-7-16/h4-7,12-13,20,22H,3,8-11,14,26H2,1-2H3,(H,27,29)"	""	""	""
+"5343"	"cisplatin"	""	"Inorganic"	"yes"	""	""	""	"178102005"	"441203"	""	""	"CHEMBL11359"	""	""	""	""	""	"cisplatin"	"Platinol&reg;"	""	""	""	""	""	""
+"3303"	"L745870"	""	"Synthetic organic"	""	""	""	""	"178100340"	"5311200"	""	""	"CHEMBL267014"	""	""	""	""	"3-[[4-(4-chlorophenyl)piperazin-1-yl]methyl]-1H-pyrrolo[2,3-b]pyridine"	""	"L 745870|L-745,870"	"Clc1ccc(cc1)N1CCN(CC1)Cc1c[nH]c2c1cccn2"	"OGJGQVFWEPNYSB-UHFFFAOYSA-N"	"InChI=1S/C18H19ClN4/c19-15-3-5-16(6-4-15)23-10-8-22(9-11-23)13-14-12-21-18-17(14)2-1-7-20-18/h1-7,12H,8-11,13H2,(H,20,21)"	""	""	""
+"2804"	"phenobarbital"	""	"Synthetic organic"	"yes"	""	""	""	"135650817"	"4763"	""	""	"CHEMBL40"	""	""	""	""	"5-ethyl-5-phenyl-1,3-diazinane-2,4,6-trione"	"phenobarbital"	"fenobarbital|Luminal&reg;|phenobarb|phenobarbital sodium|phenobarbitone|phenylethylbarbiturate"	"CCC1(C(=O)NC(=O)NC1=O)c1ccccc1"	"DDBREPKUVSBGFI-UHFFFAOYSA-N"	"InChI=1S/C12H12N2O3/c1-2-12(8-6-4-3-5-7-8)9(15)13-11(17)14-10(12)16/h3-7H,2H2,1H3,(H2,13,14,15,16,17)"	""	""	""
+"5260"	"rolipram"	""	"Synthetic organic"	""	""	""	""	"178101944"	"5092"	""	""	"CHEMBL63"	""	""	""	""	"4-[3-(cyclopentyloxy)-4-methoxyphenyl]pyrrolidin-2-one"	"rolipram"	"(&plusmn;)-rolipram|(R,S)-rolipram"	"COc1ccc(cc1OC1CCCC1)C1CNC(=O)C1"	"HJORMJIFDVBMOB-UHFFFAOYSA-N"	"InChI=1S/C16H21NO3/c1-19-14-7-6-11(12-9-16(18)17-10-12)8-15(14)20-13-4-2-3-5-13/h6-8,12-13H,2-5,9-10H2,1H3,(H,17,18)"	"yes"	""	""