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update gene set name validation to match latest requirements (#2117)

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This commit is contained in:
Bruce Martin
2021-03-22 14:54:12 -07:00
committed by GitHub
parent 8d932fb47d
commit a89362c1ad
2 changed files with 59 additions and 12 deletions
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local_server/data_common/data_adaptor.py
+8 -9
View File
@@ -276,11 +276,11 @@ class DataAdaptor(metaclass=ABCMeta):
Rules:
0. all geneset names must be unique.
1. All geneset names must be legal, meaning:
1. All geneset names must be comprised of legal characters, meaning:
* no leading or trailing white space
* no multi-space runs
* character set matches: [A-Z][a-z][0-9][ .()-]
Generates hard error.
* no tab, vertical tab, newline or return
Where "space" means ASCII 32. Generates hard error.
2. Gene symbols must be part of the current var_index. If symbol not in var_index,
will generate a warning and the symbol removed.
3. Duplicate gene symbols are silently de-duped.
@@ -299,19 +299,18 @@ class DataAdaptor(metaclass=ABCMeta):
raise KeyError("All geneset names must be unique.")
# 1. check gene set character set and format
legal_name = re.compile(r"^(\w|[ .()-])+$")
illegal_name = re.compile(r"^\s| |[\v\t\r\n]|\s$")
for name in geneset_names:
if type(name) != str or len(name) == 0:
raise KeyError("Geneset names must be non-null string.")
if name[0] in " \t\n\r" or name[-1] in " \t\n\r" or not legal_name.match(name) or " " in name:
if illegal_name.search(name):
messagefn(
"Error: "
f"Geneset name {name} is not valid. Only alphanumeric and limited special characters (-_.) "
"and space are allowed. Leading, trailing, and multiple spaces within a name are not allowed."
f"Geneset name {name} "
"is not valid. Leading, trailing, and multiple spaces within a name are not allowed."
)
raise KeyError(
"Geneset name is not valid, only alphanumeric and limited special characters (-_.) "
"and space are allowed. Leading, trailing, and multiple spaces within a name are not allowed."
"Geneset name is not valid. Leading, trailing, and multiple spaces within a name are not allowed."
)
# 2. & 3. check for duplicate gene symbols, and those not present in the dataset. They will
local_server/test/unit/common/test_api.py
+51 -3
View File
@@ -568,8 +568,26 @@ summary test,,PIGU,\r
result = self.session.put(url, json=test1)
self.assertEqual(result.status_code, HTTPStatus.NOT_FOUND)
test2 = {"tid": 4, "genesets": [{"geneset_name": "foobar", "genes": []}]}
test2_response = {"tid": 4, "genesets": [{"geneset_name": "foobar", "geneset_description": "", "genes": []}]}
test2 = {
"tid": 4,
"genesets": [
{"geneset_name": "foobar", "genes": []},
{"geneset_name": "contains a space", "genes": []},
{"geneset_name": "contains_weird_characters: #$%^&*()_+=-!@<>,./?';:\"[]{}|\\", "genes": []},
],
}
test2_response = {
"tid": 4,
"genesets": [
{"geneset_name": "foobar", "geneset_description": "", "genes": []},
{"geneset_name": "contains a space", "geneset_description": "", "genes": []},
{
"geneset_name": "contains_weird_characters: #$%^&*()_+=-!@<>,./?';:\"[]{}|\\",
"geneset_description": "",
"genes": [],
},
],
}
result = self.session.put(url, json=test2)
self.assertEqual(result.status_code, HTTPStatus.OK)
result = self.session.get(url, headers={"Accept": "application/json"})
@@ -629,7 +647,37 @@ summary test,,PIGU,\r
# illegal geneset_name
test_case(
{"tid": tid + 1, "genesets": [{"geneset_name": "&quot;", "genes": []}]},
{"tid": tid + 1, "genesets": [{"geneset_name": " foo", "genes": []}]},
HTTPStatus.BAD_REQUEST,
original_data,
)
test_case(
{"tid": tid + 1, "genesets": [{"geneset_name": "foo ", "genes": []}]},
HTTPStatus.BAD_REQUEST,
original_data,
)
test_case(
{"tid": tid + 1, "genesets": [{"geneset_name": "f oo", "genes": []}]},
HTTPStatus.BAD_REQUEST,
original_data,
)
test_case(
{"tid": tid + 1, "genesets": [{"geneset_name": "f\too", "genes": []}]},
HTTPStatus.BAD_REQUEST,
original_data,
)
test_case(
{"tid": tid + 1, "genesets": [{"geneset_name": "f\roo", "genes": []}]},
HTTPStatus.BAD_REQUEST,
original_data,
)
test_case(
{"tid": tid + 1, "genesets": [{"geneset_name": "f\noo", "genes": []}]},
HTTPStatus.BAD_REQUEST,
original_data,
)
test_case(
{"tid": tid + 1, "genesets": [{"geneset_name": "f\voo", "genes": []}]},
HTTPStatus.BAD_REQUEST,
original_data,
)