Some of the single quotes in the synonyms column of the compound reference file are not escaped.

[jeevangelista]

Example CID: 5337997

['Nifuroxazide', '965-52-6', 'Nifuroxazid', 'Dicoferin', 'Diarlidan', 'UNII-PM5LI0P38J', 'PM5LI0P38J', 'MLS000069620', 'Ercefuryl', 'BENZOIC ACID, p-HYDROXY-, (5-NITROFURFURYLIDENE)HYDRAZIDE', 'Nifuroxazida', 'Nifuroxazidum', '4-hydroxy-N-[(E)-(5-nitro-2-furyl)methyleneamino]benzamide', 'Ercefurol', 'RC-27109', 'SMR000058185', '4-hydroxy-N-[(E)-(5-nitrofuran-2-yl)methylideneamino]benzamide', '4-Hydroxy-N'-((5-nitrofuran-2-yl)methylene)benzohydrazide', 'Benzoic acid, 4-hydroxy-, 2-[(5-nitro-2-furanyl)methylene]hydrazide', 'Nifuroxazidum [INN-Latin]', 'Nifuroxazida [INN-Spanish]', 'CCRIS 5490', 'RC 27109', 'p-Hydroxybenzoic acid (5-nitrofurfurylidene)hydrazide', 'R.C. 27-109', 'EINECS 213-522-0', 'BRN 1352180', 'Diaryl', 'Nifuroxazide [INN:BAN:DCF]', 'MFCD00079482', '4-Hydroxy-N'-(5-nitrofurfuryliden)benzhydrazid', 'Prestwick_874', '(Nitro-5' furfurylidene-2') hydroxy-4 benzhydrazide', 'Nifuroxazide (INN)', 'Opera_ID_40', '(Nitro-5' furfurylidene-2') hydroxy-4 benzhydrazide [French]', 'Prestwick2_000555', 'Prestwick3_000555', 'BSPBio_000629', 'SCHEMBL542542', 'SCHEMBL543480', 'p-Hydroxybenzoic acid 5-nitrofurfurylidene hydrazide', 'ARONIS016368', 'BPBio1_000693', 'CHEMBL244888', 'SCHEMBL14608895', 'CHEBI:94556', 'CHEBI:135136', 'HMS1569P11', 'HMS2096P11', 'HMS3713P11', 'Pharmakon1600-01505788', 'HY-B1436', 'ZINC7997719', 'BDBM50396177', 'NSC759261', 's4182', 'STK091243', 'STL454990', 'AKOS000483758', 'AC-8713', 'CCG-213989', 'CS-4918', 'DB13855', 'NSC 759261', 'NSC-759261', 'AS-13310', 'H868', 'BIM-0014420.P001', 'SBI-0014420.P002', 'AB00513861', 'SJ000287313', 'D07111', 'AB00513861_02', 'AB00513861_03', 'Nifuroxazide, VETRANAL(TM), analytical standard', '4-hydroxy-2'-(5-nitrofurfurylidene)benzohydrazide', '965N526', 'A845610', 'W-100139', 'BRD-K68188368-001-03-7', '4-Dydroxy-N-[(E)-(5-nitro-2-furyl)methyleneamino]benzamide', '4-hydroxy-N'-[(1E)-(5-nitro-2-furyl)methylene]benzohydrazide', 'Nifuroxazide, European Pharmacopoeia (EP) Reference Standard', '4-hydroxy-N'-[(E)-(5-nitrofuran-2-yl)methylidene]benzohydrazide', '4-hydroxy-N-[(E)-(5-nitrofuran-2-yl)methylidene]benzenecarbohydrazonic acid', 'Benzoic acid, 4-hydroxy-, [(1E)-(5-nitro-2-furanyl)methylene]hydrazide']

[abradyIGS]

Replicated; fixing and pushing an update, stand by

[abradyIGS]

This issue has now tested as "fixed" -- marking "answered," but please reopen and report if you find otherwise.

Ontology files and the submission prep script have all been updated and published here: please overwrite local copies and try again.

Note: the master C2M2 JSON schema has also updated (to match previous development schema): it is here and an up-to-date copy needs to be included with submissions during prep with the script.

[jeevangelista]

I'm still getting a CastError here:

[CastError('Field "synonyms" can't cast value "["26239-55-4", "N-(2-Acetamido)iminodiacetic acid", "2,2'-((2-Amino-2-oxoethyl)azanediyl)diacetic acid", "ADA", "Glycine, N-(2-amino-2-oxoethyl)-N-(carboxymethyl)-", "Carbamoylmethylaminodiacetic acid", "2,2'-[(2-amino-2-oxoethyl)imino]diacetic acid", "N-(Carbamoylmethyl)iminodiacetic acid", "N-Carbamoylmethyliminodi(acetic acid)", "MFCD00008031", "UNII-5C4R3O704E", "N-(2-Acetamido)-2-iminodiacetic acid", "(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID", "2-[(2-amino-2-oxoethyl)-(carboxymethyl)amino]acetic acid", "5C4R3O704E", "N-[2-Acetamido]iminodiacetic acid", "N-[2-ACETAMIDO]-2-IMINODIACETIC ACID", "ADA buffer", "EINECS 247-530-0", "a d a", "bmse000146", "N-(2-amino-2-oxoethyl)-N-(carboxymethyl)glycine", "SCHEMBL233033", "2-[(carbamoylmethyl)(carboxymethyl)amino]acetic acid", "ADA, >=98% (titration)", "DTXSID4067191", "CHEBI:43960", "n-(2-acetamide)iminodiacetic acid", "N-(2-Acetamido)imidodiacetic acid", "n-(-2-acetamido)iminodiacetic acid", "n-(2-acetamido)-iminodiacetic acid", "ZINC2545127", "BBL023210", "s6310", "STL355999", "ADA, BioXtra, >=98% (titration)", "AKOS005267103", "AKOS025395625", "AC-8316", "ADA, BioUltra, >=99.0% (T)", "DB02810", "MCULE-7776883622", "ADA, Vetec(TM) reagent grade, >=98%", "AS-12375", "SY048625", "A0699", "FT-0621892", "Iminodiacetic acid, N-(2-amino-2-oxoethyl)-", "D70536", "2,2'-(2-amino-2-oxoethylazanediyl)diacetic acid", "2,2\'-[(2-amino-2-oxoethyl)imino]diacetic acid", "W-107186", "acetic acid, 2,2'-[(2-amino-2-oxoethyl)imino]bis-", "Q27093765"]" for type "array" with format "default"')]

[abradyIGS]

Sorry -- we had other issues with single quotes being inappropriate delimiters for JSON strings, which was fixed, and I rolled my response above into the fix for that -- but what you quote above is a spec-compliant JSON string array, and none of our software is going to have any problem with it.

Single quotes are inconsistently escaped within the double-quoted names, but this is irrelevant: the only characters JSON requires escape sequences for inside double-quoted strings are the double-quote characters themselves. All other escape-like sequences are ignored by spec-compliant software and treated as string literals.

Note also that the single-quote-escape inconsistency is something we imported directly from the PubChem labels and is not an artifact of our processing. See this page, section 3.4.2, and search for a backslash: what you quote above, with one \' sequence in one of the listed synonyms, but with other (unescaped) single quotes present, matches the inconsistency in the synonyms as submitted by the depositor.

[abradyIGS]

[just so i can try to avoid falling on my face again this week -- i'm correct in thinking that CastError was not generated by CFDE software, right? if i'm wrong and it was, please let me know which bit so i can go yell at it]

[jeremyjyang]

Today I get this cfde-submit error which seems relevant to this discussion:

[DEBUG] cfde_submit.validation::validate_user_submission() Validating TableSchema in BDBag '/home/data/CFDE/data/drugpages2021/submission_output.zip'
Validation error in compound.tsv
Type error in the cell "["Chloropyramine", "Halopyramine", "Chlorpyramine", "Anaphylline", "59-32-5", "Suprastin", "Avapena", "Synopen", "Synpen", "Chlorneoantergan", "Chloropyribenzamine", "Chlorpyraminum", "Allergan S", "Synopen R", "Chloroneoantergan", "Chloropyramine [INN:BAN:DCF]", "UNII-2K3L8O9SOV", "NSC 241038", "N-(p-Chlorobenzyl)-N',N'-dimethyl-N-(2-pyridyl)ethylenediamine", "2K3L8O9SOV", "2-((p-Chlorobenzyl)(2-(dimethylamino)ethyl)amino)pyridine", "Ethylenediamine, N-(p-chlorobenzyl)-N',N'-dimethyl-N-(2-pyridyl)-", "N'-[(4-chlorophenyl)methyl]-N,N-dimethyl-N'-pyridin-2-ylethane-1,2-diamine", "Pyridine, 2-((p-chlorobenzyl)(2-(dimethylamino)ethyl)amino)-", "1,2-Ethanediamine, N-[(4-chlorophenyl)methyl]-N',N'-dimethyl-N-2-pyridinyl-", "p-Chlorbenzyl-.alpha.-pyridyl-dimethyl-aethylendiamin", "2-[(p-Chlorobenzyl)[2-(dimethylamino)ethyl]amino]pyridine", "Chloropyraminum", "Cloropiramina", "N-(4-Chlorobenzyl)-N',N'-dimethyl-N-(pyridin-2-yl)ethane-1,2-diamine", "Chloropyraminum [INN-Latin]", "Cloropiramina [INN-Spanish]", "NCGC00016672-01", "NCGC00016672-04", "EINECS 200-421-1", "CAS-6170-42-9", "BRN 0257085", "Pyridine, 2-[(p-chlorobenzyl)[2-(dimethylamino)ethyl]amino]-", "Chloropyramine (INN)", "p-Chlorbenzyl-alpha-pyridyl-dimethyl-aethylendiamin [German]", "N-((4-CHLOROPHENYL)METHYL)-N',N'-DIMETHYL-N-2-PYRIDINYL-1,2-ETHANEDIAMINE", "Prestwick0_000807", "Prestwick1_000807", "Prestwick2_000807", "Prestwick3_000807", "SCHEMBL30021", "BSPBio_000673", "p-Chlorbenzyl-alpha-pyridyl-dimethyl-aethylendiamin", "SPBio_002594", "BPBio1_000741", "2-((p-Chlorobenzyl)(2-dimethylaminoethyl)amino)pyridine", "CHEMBL1194287", "CHEBI:94767", "DTXSID50207729", "1H-Indole, 2-(2-bromophenyl)-", "NSC241038", "STL483421", "ZINC20148995", "AKOS024323312", "WLN: T6NJ BN2N1&1&1R DG", "DB08800", "MCULE-5568455528", "NSC-241038", "NCGC00016672-02", "NCGC00016672-07", "SBI-0207051.P001", "D07195", "170C429", "Q729863", "2-[(p-Chlorobenzyl)[2-(dimethylamino)ethyl]pyridine", "BRD-K83257731-003-03-7", "BRD-K83257731-003-14-4", "1, N-[(4-chlorophenyl)methyl]-N',N'-dimethyl-N-2-pyridinyl-", "2-[(4-CHLOROBENZYL)[2-(DIMETHYLAMINO)ETHYL]AMINO]PYRIDINE", "N,N-Dimethyl-N'-(p-chlorobenzyl)-N'-(2-pyridyl)ethylenediamine", "N-[(4-chlorophenyl)methyl]-N-[2-(dimethylamino)ethyl]pyridin-2-amine", "1,2-Ethanediamine, N-((4-chlorophenyl)methyl)-N',N'-dimethyl-N-2-pyridinyl- (9CI)", "N'-[(4-chlorophenyl)methyl]-N,N-dimethyl-N'-(2-pyridinyl)ethane-1,2-diamine", "N'-[(4-chlorophenyl)methyl]-N,N-dimethyl-N'-pyridin-2-ylethane-1,2-diamine"]" in row "1349" and field "synonyms" at position "4": type is "array/default"

[abradyIGS]

@jeremyjyang i'm moving this last issue to the helpdesk; as soon as i can figure out how to add you as a watcher, you should get an email

@jeevangelista after some further reading, i think i have to tweak one more thing to process these [censored] backslashes properly; stand by for another fix attempt, and sorry for confusion in earlier replies

[abradyIGS]

[FYI: I tried to port this to JIRA and I think I failed, but if anyone can actually access the ticket here, please let me know: it would help with internal access-management debugging]

@jeremyjyang @jeevangelista Please download the latest prep script, compound and substance tables from here: if either of your respective issues remains unsolved by this update, please attach your submission TSVs [somewhere on github I can get to?] for immediate followup (and email [email protected] so I can fold further developments more effectively into our issue tracker).

PS. Also be sure to grab the latest JSON schema file for inclusion with your submission; we removed some uniqueness constraints (relevant to @jeremyjyang at minimum) on 4/8.