def test_drop_cmd(conn):
"""Test drop command of VQL language
The following tables are tested:
- selections
- wordsets
"""
# Create a selection named "subset"
conn.execute("INSERT INTO selections (name) VALUES ('subset')")
assert "subset" in [
i["name"]
for i in conn.execute("SELECT name FROM selections").fetchall()
]
ret = command.drop_cmd(conn, feature="selections", name="subset")
assert "subset" not in [
i["name"]
for i in conn.execute("SELECT name FROM selections").fetchall()
]
assert ret["success"]
# Create wordset
test_file = "examples/gene.txt"
wordset_name = "bouzniouf"
command.import_cmd(conn, "wordsets", wordset_name, test_file)
command.drop_cmd(conn, feature="wordsets", name=wordset_name)
assert wordset_name not in [
i["name"]
for i in conn.execute("SELECT name FROM wordsets").fetchall()
]
def test_show_cmd(conn):
"""Test SHOW command of VQL language
Test the following tables:
- samples
- selections
- fields
- wordsets
- WORDSETS (UPPER CASE name)
- truc (wrong table) => VQLSyntaxError expected
"""
# Test samples
result = list(command.execute(conn, "SHOW samples"))
print("Found samples:", result)
assert len(result) == 2
found_sample_names = {sample["name"] for sample in result}
expected_sample_names = {"NORMAL", "TUMOR"}
assert expected_sample_names == found_sample_names
# Test selections
# Create a selection
command.create_cmd(conn, source="variants", target="A")
result = list(command.execute(conn, "SHOW selections"))
print("Found selections:", result)
assert len(result) == 2
# Test fields
result = list(command.execute(conn, "SHOW fields"))
print("Found fields:", result)
# Just test keys of the first item
assert result[0].keys() == {
'id', 'name', 'category', 'type', 'description'
}
# Test wordsets
# Create a wordset
# Test import of word set
test_file = "examples/gene.txt"
wordset_name = "bouzniouf"
command.import_cmd(conn, "wordsets", wordset_name, test_file)
result = list(command.execute(conn, "SHOW wordsets"))
print("Found wordsets in lower case:", result)
assert len(result) == 1
expected_wordset = {'name': 'bouzniouf', 'count': 2}
assert expected_wordset == result[0]
# Test WORDSETS
result = list(command.execute(conn, "SHOW WORDSETS"))
print("Found WORDSETS in upper case:", result)
assert len(result) == 1
expected_wordset = {'name': 'bouzniouf', 'count': 2}
assert expected_wordset == result[0]
# Test wrong table
# Exception is expected
with pytest.raises(vql.VQLSyntaxError, match=r".*truc doesn't exists.*"):
list(command.execute(conn, "SHOW truc"))
def test_import_cmd(conn):
"""Test import wordset from file (import_cmd is for word sets only FOR NOW)
Import from a kindly external file with 2 genes.
"""
# Test import of word set
test_file = "examples/gene.txt"
wordset_name = "boby"
command.import_cmd(conn, "wordsets", wordset_name, test_file)
for record in conn.execute("SELECT * FROM wordsets"):
item = dict(record)
assert item["name"] == wordset_name
def import_wordset(self, words, wordset_name):
"""Import given words into a new wordset in database
Warnings:
There is NO CHECK on manual user's inputs! Except during DB insertion.
Args:
words(list): List of words to be inserted
wordset_name(str): Name of the word set
Returns:
(boolean): Status of the wordset creation
"""
# Dump the list in a temporary file
_, filename = tempfile.mkstemp()
with open(filename, "w") as file:
[file.write(word + "\n") for word in words]
# Import the content of the temp file in DB
result = import_cmd(self.conn, "wordsets", wordset_name, filename)
if not result["success"]:
LOGGER.error(result)
QMessageBox.critical(
self,
self.tr("Error while importing set"),
self.tr("Error while importing set '%s'") % wordset_name,
)
os.remove(filename)
return result["success"]