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identifiers_form() function does not work well. #35

Description

@136s

When I input expression data to analysis.identifiers_form() function, "Status code returned a value of 415" raises.

The following code shows the difference from using the analysis.identifiers_url() function using the expample of Microarray data.

Reproducible code:

from subprocess import run
from reactome2py import analysis

expression_url = "https://gist.githubusercontent.com/136s/144efdf249c135717a52f2a2c257cd8e/raw/e7633a3c7a17802bf37ab895c65f511610f14d74/Probeset.tsv"

run("curl -O {}".format(expression_url), shell=True)
form_res = analysis.identifiers_form("Probeset.tsv")
print(f"{form_res=}")

url_res = analysis.identifiers_url(expression_url)
print(f"{url_res=}")

results:

Status code returned a value of 415
form_res=None
url_res={'summary': {'token': 'MjAyNDAxMjIwMTM0MjNfOTQ5OQ%3D%3D', 'projection': False, 'interactors': False, 'type': 'EXPRESSION', 'sampleName': 'Probeset', 'text': True, 'includeDisease': True}, 'expression': {'columnNames': ['10h_control', '10h', '14h', '18h', '24h'], 'min': 2.812419, 'max': 13.505858}, 'identifiersNotFound': 34, 'pathwaysFound': 1408, 'pathways': [{'stId': 'R-HSA-5651801', 'dbId': 5651801, 'name': 'PCNA-Dependent Long Patch Base Excision Repair', 'species': {'dbId': 48887, 'taxId': '9606', 'name': 'Homo sapiens'}, 'llp': True, 'entities': {'resource': 'TOTAL', 'total': 23, 'found': 19, 'ratio': 0.001487325400931195, 'pValue': 1.1102230246251565e-16, 'fdr': 7.771561172376096e-16, 'exp': [8.307529157894736, 7.673377315789473, 7.888002789473684, 7.8596394736842115, 7.299411473684212]}, 'reactions': {'resource': 'TOTAL', 'total': 6, 'found': 6, 'ratio': 0.00040752564015485973}, 'inDisease': False}], 'resourceSummary': [{'resource': 'TOTAL', 'pathways': 1408, 'filtered': 1408}, {'resource': 'UNIPROT', 'pathways': 1408, 'filtered': 1408}], 'speciesSummary': [{'dbId': 48887, 'taxId': '9606', 'name': 'Homo sapiens', 'pathways': 1408, 'filtered': 1408}], 'warnings': []}

version:

  • python: 3.11.0
  • reactome2py: 3.0.0

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