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PLEASE DO NOT MERGE Fix minor issues for the terms validation #150

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merged 4 commits into from
Oct 19, 2023
Merged

PLEASE DO NOT MERGE Fix minor issues for the terms validation #150

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c4bf642
fixed error when NT is not available.
ypriverol Oct 12, 2023
9468640
fixed error when NT is not available.
ypriverol Oct 12, 2023
ba64364
black run
ypriverol Oct 12, 2023
03290a0
move to ols4
ypriverol Oct 12, 2023
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17 changes: 11 additions & 6 deletions sdrf_pipelines/sdrf/sdrf_schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,12 @@ def ontology_term_parser(cell_value: str = None):
else:
for name in values:
value_terms = name.split("=")
term[value_terms[0].strip().upper()] = value_terms[1].strip().lower()
if len(value_terms) == 2:
term[value_terms[0].strip().upper()] = value_terms[1].strip().lower()
else:
raise ValueError(
f"Invalid term: {name} after splitting by '=', please check the prefix (e.g. AC, NT, " f"TA..)"
)
return term


Expand Down Expand Up @@ -109,8 +114,8 @@ def default_message(self):
@staticmethod
def validate_ontology_terms(cell_value, labels):
"""
Check if a cell value is in a list of labels or list of strings
:param cell_value: string line in cell
Check if a cell value is in a list of labels or list of string
:param cell_value: line in a cell
:param labels: list of labels
:return:
"""
Expand All @@ -124,7 +129,7 @@ def validate(self, series: pd.Series) -> pd.Series:
"""
Validate if the term is present in the provided ontology. This method looks in the provided
ontology _ontology_name
:param series: return the series that do not match the criteria
:param series: return series that do not match the criteria
:return:
"""
terms = [ontology_term_parser(x) for x in series.unique()]
Expand Down Expand Up @@ -165,7 +170,7 @@ def __new__(cls, ordered: bool = False, min_columns: int = 0) -> Any:
def validate(self, panda_sdrf: sdrf = None) -> typing.List[LogicError]:
errors = []

# Check minimum number of columns
# Check the minimum number of columns
if check_minimum_columns(panda_sdrf, self._min_columns):
error_message = (
"The number of columns in the SDRF ({}) is smaller than the number of mandatory fields ({})".format(
Expand All @@ -179,7 +184,7 @@ def validate(self, panda_sdrf: sdrf = None) -> typing.List[LogicError]:
if error_mandatory is not None:
errors.append(error_mandatory)

# Check the columns order
# Check the column order
error_columns_order = self.validate_columns_order(panda_sdrf)
if error_columns_order is not None:
errors.extend(error_columns_order)
Expand Down
14 changes: 7 additions & 7 deletions sdrf_pipelines/zooma/ols.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@

import requests

OLS = "https://www.ebi.ac.uk/ols"
OLS = "https://www.ebi.ac.uk/ols4"

__all__ = ["OlsClient"]

Expand Down Expand Up @@ -45,7 +45,7 @@ def _concat_str_or_list(input_str):
def _dparse(iri):
"""
Double url encode the IRI, which is required
@:param iri IRI in the OLS
@:param iri in the OLS
"""
return urllib.parse.quote_plus(urllib.parse.quote_plus(iri))

Expand All @@ -70,7 +70,7 @@ def __init__(self, ols_base=None, ontology=None, field_list=None, query_fields=N

def besthit(self, name, **kwargs):
"""
select first element of the /search API response
select a first element of the /search API response
"""
search_resp = self.search(name, **kwargs)
if search_resp:
Expand All @@ -82,8 +82,8 @@ def get_term(self, ontology, iri):
"""
Gets the data for a given term
Args:
ontology: The name of the ontology
iri: The IRI of a term
ontology: The name of the ontology
iri: The IRI of a term
"""

url = self.ontology_term.format(ontology=ontology, iri=_dparse(iri))
Expand Down Expand Up @@ -117,7 +117,7 @@ def search(
"""
Searches the OLS with the given term

@:param query_fields: By default the search is performed over term labels,
@:param query_fields: By default, the search is performed over term labels,
synonyms, descriptions, identifiers and annotation properties. This option allows
to specify the fields to query, the defaults are
`{label, synonym, description, short_form, obo_id, annotations, logical_description, iri}`
Expand Down Expand Up @@ -196,7 +196,7 @@ def select(self, name, ontology=None, field_list=None):
"""Select terms,
Tuned specifically to support applications such as autocomplete.

.. seealso:: https://www.ebi.ac.uk/ols/docs/api#_select
.. see also:: https://www.ebi.ac.uk/ols4/docs/api#_select
"""
params = {"q": name}
if ontology:
Expand Down