Error in fetching metadata

[mfitzp]

Requests to the mapping API now return the error Error in fetching metadata. The same queries work if the IDs are passed with the query parameter (space separated list) rather than as a file, which suggests that the UniProt mapping API is not supporting files anymore.

The example code snippets all pass values via query (for example).

[fbonnardel]

Try bioservices until this package is repared:

from bioservices import UniProt
u = UniProt(verbose=False)
res = u.mapping("P_REFSEQ_AC", "ACC", query='XP_021413590')
for key, values in res.items():
for value in values:
print (value)
res = u.search(value, frmt="tab", limit=3, columns="id, entry name, genes, length", database='uniparc')
#res = u.retrieve(value, frmt='xml', database='uniparc')
print (res)

_valid_columns = [
    # Names & Taxonomy
    'id', 'entry name', 'genes', 'genes(PREFERRED)', 'genes(ALTERNATIVE)',
    'genes(OLN)', 'genes(ORF)', 'organism', 'organism-id', 'protein names',
    'proteome', 'lineage(ALL)', 'lineage-id', 'virus hosts',
    # Sequences
    'fragement', 'sequence', 'length', 'mass', 'encodedon',
    'comment(ALTERNATIVE PRODUCTS)', 'comment(ERRONEOUS GENE MODEL PREDICTION)',
    'comment(ERRONEOUS INITIATION)', 'comment(ERRONEOUS TERMINATION)',
    'comment(ERRONEOUS TRANSLATION)', 'comment(FRAMESHIFT)',
    'comment(MASS SPECTROMETRY)', 'comment(POLYMORPHISM)',
    'comment(RNA EDITING)', 'comment(SEQUENCE CAUTION)',
    'feature(ALTERNATIVE SEQUENCE)', 'feature(NATURAL VARIANT)',
    'feature(NON ADJACENT RESIDUES)',
    'feature(NON STANDARD RESIDUE)', 'feature(NON TERMINAL RESIDUE)',
    'feature(SEQUENCE CONFLICT)', 'feature(SEQUENCE UNCERTAINTY)',
    'version(sequence)',
    # Family and Domains
    'domains', 'domain', 'comment(DOMAIN)', 'comment(SIMILARITY)',
    'feature(COILED COIL)', 'feature(COMPOSITIONAL BIAS)',
    'feature(DOMAIN EXTENT)', 'feature(MOTIF)', 'feature(REGION)',
    'feature(REPEAT)', 'feature(ZINC FINGER)',
    # Function
    'ec', 'comment(ABSORPTION)', 'comment(CATALYTIC ACTIVITY)',
    'comment(COFACTOR)', 'comment(ENZYME REGULATION)', 'comment(FUNCTION)',
    'comment(KINETICS)', 'comment(PATHWAY)', 'comment(REDOX POTENTIAL)',
    'comment(TEMPERATURE DEPENDENCE)', 'comment(PH DEPENDENCE)',
    'feature(ACTIVE SITE)', 'feature(BINDING SITE)', 'feature(DNA BINDING)',
    'feature(METAL BINDING)', 'feature(NP BIND)', 'feature(SITE)',
    # Gene Ontologys
    'go', 'go(biological process)', 'go(molecular function)',
    'go(cellular component)', 'go-id',
    # InterPro
    'interpro',
    # Interaction
    'interactor', 'comment(SUBUNIT)',
    # Publications
    'citation', 'citationmapping',
    # Date of
    'created', 'last-modified', 'sequence-modified', 'version(entry)',
    # Structure
    '3d', 'feature(BETA STRAND)', 'feature(HELIX)', 'feature(TURN)',
    # Subcellular location
    'comment(SUBCELLULAR LOCATION)', 'feature(INTRAMEMBRANE)',
    'feature(TOPOLOGICAL DOMAIN)',
    'feature(TRANSMEMBRANE)',
    # Miscellaneous
    'annotation score', 'score', 'features', 'comment(CAUTION)',
    'comment(TISSUE SPECIFICITY)',
    'comment(GENERAL)', 'keywords', 'context', 'existence', 'tools',
    'reviewed', 'feature', 'families', 'subcellular locations', 'taxonomy',
    'version', 'clusters', 'comments', 'database', 'keyword-id', 'pathway',
    'score',
    # Pathology & Biotech
    'comment(ALLERGEN)', 'comment(BIOTECHNOLOGY)', 'comment(DISRUPTION PHENOTYPE)',
    'comment(DISEASE)', 'comment(PHARMACEUTICAL)', 'comment(TOXIC DOSE)',
    # PTM / Processsing
    'comment(PTM)', 'feature(CHAIN)', 'feature(CROSS LINK)', 'feature(DISULFIDE BOND)',
    'feature(GLYCOSYLATION)', 'feature(INITIATOR METHIONINE)', 'feature(LIPIDATION)',
    'feature(MODIFIED RESIDUE)', 'feature(PEPTIDE)', 'feature(PROPEPTIDE)',
    'feature(SIGNAL)', 'feature(TRANSIT)',
    # Taxonomic lineage
    'lineage(all)', 'lineage(SUPERKINGDOM)', 'lineage(KINGDOM)', 'lineage(SUBKINGDOM)',
    'lineage(SUPERPHYLUM)', 'lineage(PHYLUM)', 'lineage(SUBPHYLUM)', 'lineage(SUPERCLASS)',
    'lineage(CLASS)', 'lineage(SUBCLASS)', 'lineage(INFRACLASS)', 'lineage(SUPERORDER)',
    'lineage(ORDER)', 'lineage(SUBORDER)', 'lineage(INFRAORDER)', 'lineage(PARVORDER)',
    'lineage(SUPERFAMILY)', 'lineage(FAMILY)', 'lineage(SUBFAMILY)', 'lineage(TRIBE)',
    'lineage(SUBTRIBE)', 'lineage(GENUS)', 'lineage(SUBGENUS)', 'lineage(SPECIES GROUP)',
    'lineage(SPECIES SUBGROUP)', 'lineage(SPECIES)', 'lineage(SUBSPECIES)', 'lineage(VARIETAS)',
    'lineage(FORMA)',
    # Taxonomic identifier
    'lineage-id(all)', 'lineage-id(SUPERKINGDOM)', 'lineage-id(KINGDOM)', 'lineage-id(SUBKINGDOM)',
    'lineage-id(SUPERPHYLUM)', 'lineage-id(PHYLUM)', 'lineage-id(SUBPHYLUM)', 'lineage-id(SUPERCLASS)',
    'lineage-id(CLASS)', 'lineage-id(SUBCLASS)', 'lineage-id(INFRACLASS)', 'lineage-id(SUPERORDER)',
    'lineage-id(ORDER)', 'lineage-id(SUBORDER)', 'lineage-id(INFRAORDER)', 'lineage-id(PARVORDER)',
    'lineage-id(SUPERFAMILY)', 'lineage-id(FAMILY)', 'lineage-id(SUBFAMILY)', 'lineage-id(TRIBE)',
    'lineage-id(SUBTRIBE)', 'lineage-id(GENUS)', 'lineage-id(SUBGENUS)', 'lineage-id(SPECIES GROUP)',
    'lineage-id(SPECIES SUBGROUP)', 'lineage-id(SPECIES)', 'lineage-id(SUBSPECIES)', 'lineage-id(VARIETAS)',
    'lineage-id(FORMA)',
    # Cross-references
    'database(db_abbrev)', 'database(EMBL)']