class ISHFetcher:
''' A downloader object for Section Data Sets
Methods
-------
find_id_ish:
Returns the ids of Section Data Sets (a single gene experiment) sorted by qc time
download_grid_all:
Dowloads all the expression energy 3d density file (200um grid) that satisfy the query
download_grid_recent:
Dowloads the most recently qc-ed expression energy 3d density file (200um grid) that satisfy the query
Attributes
----------
rma:
Rma Api instance
gda
GridData Api instance
res
results of the find_id_ish query
'''
def __init__(self) -> None:
self.rma = RmaApi()
self.gda = GridDataApi()
self.res = None # type: List
def find_id_ish(self,
gene: str,
sag_or_cor: str = "sagittal",
adu_or_dev: str = "adult",
time_point: str = "P56") -> List:
"""Returns the ids of Section Data Sets (a single gene experiment)
Args
----
gene: str
the gene to search for
sag_or_cor: str (accepts * wild cards)
`coronal` or `sagittal` or `*`
adu_or_dev: str (accepts * wild cards)
`adult`, `development`, `both`
time_point: str (it will be autmatically wildcarded)
e.g. "P56", "E", "E13", "P"
Returns
-------
list of ids:
sorted by most_recent to mose ancient
"""
if adu_or_dev == "adult" and "E" in time_point:
raise ValueError("there is not adult with age %s" % time_point)
if adu_or_dev == "adult":
adu_or_dev = "Mouse"
elif adu_or_dev == "development":
adu_or_dev = "DevMouse"
elif adu_or_dev == "both":
adu_or_dev = "*Mouse"
else:
raise ValueError("adu_or_dev='%s' is not valid" % adu_or_dev)
criteria = [
"[failed$eq'false']",
"reference_space[name$li'*%s*']" % time_point,
"products[abbreviation$li'%s']" % adu_or_dev,
"plane_of_section[name$li'%s']" % sag_or_cor,
"genes[acronym$eq'%s']" % gene
]
# include='reference_space',
self.res = self.rma.model_query("SectionDataSet",
criteria=','.join(criteria),
only=["id", "qc_date"],
num_rows='all')
if isinstance(self.res, str):
raise ValueError("Bad query! Server returned :\n%s" % self.res)
if self.res == []:
return []
qc_date = []
for i in self.res:
if i["qc_date"] is None:
qc_date.append('')
else:
qc_date.append(i["qc_date"])
ix = np.argsort(qc_date)
ix = ix[::-1]
results = []
for i in ix:
results.append(int(self.res[i]["id"]))
return results
def download_grid_all(self,
gene: str,
folder: str = '../data',
sag_or_cor: str = "sagittal",
adu_or_dev: str = "adult",
time_point: str = "P56") -> None:
"""Dowloads all the files
Args
----
gene: str
the gene to search for
sag_or_cor: str (accepts * wild cards)
`coronal` or `sagittal` or `*`
adu_or_dev: str (accepts * wild cards)
`adult`, `development`, `both`
time_point: str (it will be autmatically wildcarded)
e.g. "P56", "E", "E13", "P"
"""
ids = self.find_id_ish(gene,
sag_or_cor=sag_or_cor,
adu_or_dev=adu_or_dev,
time_point=time_point)
for idd in ids:
self.gda.download_expression_grid_data(
idd,
path=os.path.join(
folder,
"%s_%s_%s_%s.zip" % (gene, sag_or_cor, time_point, idd)))
def download_grid_recent(self,
gene: str,
folder: str = '../data',
sag_or_cor: str = "sagittal",
adu_or_dev: str = "adult",
time_point: str = "P56") -> Union[str, bool]:
"""Dowloads the most recently qc-ed file among the ones available
Args
----
gene: str
the gene to search for
sag_or_cor: str (accepts * wild cards)
`coronal` or `sagittal` or `*`
adu_or_dev: str (accepts * wild cards)
`adult`, `development`, `both`
time_point: str (it will be autmatically wildcarded)
e.g. "P56", "E", "E13", "P"
Returns
-------
output_path: output_path or bool
if the download was successfull returns the path to the file otherwise False
"""
ids = self.find_id_ish(gene,
sag_or_cor=sag_or_cor,
adu_or_dev=adu_or_dev,
time_point=time_point)
try:
idd = ids[0]
output_path = os.path.join(
folder,
"%s_%s_%s_%s.zip" % (gene, sag_or_cor, time_point, idd))
self.gda.download_expression_grid_data(idd, path=output_path)
return output_path
except IndexError:
logging.warn("Experiment %s was never performed" % gene)
return False
