def test_stage_object_fetch(self, history_id):
job = {"input1": "randomstr"}
inputs, datasets = stage_inputs(self.galaxy_interactor,
history_id,
job,
use_path_paste=False)
dataset = datasets[0][0]
content = self.dataset_populator.get_history_dataset_content(
history_id=history_id, dataset=dataset)
self.assertEqual(content, '"randomstr"')
def test_composite_datatype_stage_upload1(self, history_id):
job = {
"input1": {
"class": "File",
"format": "velvet",
"composite_data": [
"test-data/simple_line.txt",
"test-data/simple_line_alternative.txt",
"test-data/simple_line_x2.txt",
]
}
}
inputs, datsets = stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False, use_fetch_api=False)
def test_newlines_stage_fetch(self, history_id):
job = {
"input1": {
"class": "File",
"format": "txt",
"path": "test-data/simple_line_no_newline.txt",
}
}
inputs, datasets = stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False)
dataset = datasets[0][0]
content = self.dataset_populator.get_history_dataset_content(
history_id=history_id,
dataset=dataset
)
# By default this appends the newline.
self.assertEqual(content, "This is a line of text.\n")
def test_composite_datatype_pbed_stage_fetch(self, history_id):
job = {
"input1": {
"class":
"File",
"format":
"pbed",
"composite_data": [
"test-data/rgenetics.bim",
"test-data/rgenetics.bed",
"test-data/rgenetics.fam",
],
}
}
inputs, datsets = stage_inputs(self.galaxy_interactor,
history_id,
job,
use_path_paste=False)
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
def test_composite_datatype_stage_fetch(self, history_id):
job = {
"input1": {
"class":
"File",
"format":
"velvet",
"composite_data": [
"test-data/simple_line.txt",
"test-data/simple_line_alternative.txt",
"test-data/simple_line_x2.txt",
]
}
}
inputs, datsets = stage_inputs(self.galaxy_interactor,
history_id,
job,
use_path_paste=False)
self.dataset_populator.wait_for_history(history_id, assert_ok=True)
def test_newlines_stage_fetch_configured(self, history_id):
job = {
"input1": {
"class": "File",
"format": "txt",
"path": "test-data/simple_line_no_newline.txt",
"dbkey": "hg19",
}
}
inputs, datasets = stage_inputs(self.galaxy_interactor,
history_id,
job,
use_path_paste=False,
to_posix_lines=False)
dataset = datasets[0][0]
content = self.dataset_populator.get_history_dataset_content(
history_id=history_id, dataset=dataset)
# By default this appends the newline.
self.assertEqual(content, "This is a line of text.")
details = self.dataset_populator.get_history_dataset_details(
history_id=history_id, dataset=dataset)
assert details["genome_build"] == "hg19"
