def test_gds_info(self):
gds_info = GDSInfo()
self.assertIsNotNone(gds_info)
self.assertGreater(len(gds_info.keys()), 0)
self.assertGreater(len(gds_info.items()), 0)
self.assertGreater(len(gds_info.values()), 0)
self.assertIsNotNone(gds_info[self.test_sample])
self.assertEqual(gds_info[self.test_sample]['genes'], 9561)
self.assertEqual(int(gds_info[self.test_sample]['sample_count']), 4)
self.assertEqual(len(gds_info[self.test_sample]['subsets']), 2)
def get_gds_model(progress=lambda val: None):
"""
Initialize and return a GDS datasets model.
:param progress: A progress callback.
:rval tuple:
A tuple of (QStandardItemModel, GDSInfo, [GDS])
.. note::
The returned QStandardItemModel's thread affinity is set to
the GUI thread.
"""
progress(1)
info = GDSInfo()
search_keys = ["dataset_id", "title", "platform_organism", "description"]
cache_dir = serverfiles.localpath(DOMAIN)
gds_link = "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc={0}"
pm_link = "http://www.ncbi.nlm.nih.gov/pubmed/{0}"
gds_list = []
def is_cached(gds):
return os.path.exists(
os.path.join(cache_dir, gds["dataset_id"]) + ".soft.gz")
def item(displayvalue, item_values={}):
item = QStandardItem()
item.setData(displayvalue, Qt.DisplayRole)
for role, value in item_values.items():
item.setData(value, role)
return item
def gds_to_row(gds):
#: Text for easier full search.
search_text = " | ".join(
[gds.get(key, "").lower() for key in search_keys])
row = [
item(" " if is_cached(gds) else "", {TextFilterRole: search_text}),
item(gds["dataset_id"],
{gui.LinkRole: gds_link.format(gds["dataset_id"])}),
item(gds["title"]),
item(gds["platform_organism"]),
item(len(gds["samples"])),
item(gds["feature_count"]),
item(gds["gene_count"]),
item(len(gds["subsets"])),
item(
gds.get("pubmed_id", ""), {
gui.LinkRole:
pm_link.format(gds["pubmed_id"])
if gds.get("pubmed_id") else None
})
]
return row
model = QStandardItemModel()
model.setHorizontalHeaderLabels([
"", "ID", "Title", "Organism", "Samples", "Features", "Genes",
"Subsets", "PubMedID"
])
progress(20)
for gds in info.values():
model.appendRow(gds_to_row(gds))
gds_list.append(gds)
progress(50)
if QThread.currentThread() is not QCoreApplication.instance().thread():
model.moveToThread(QCoreApplication.instance().thread())
return model, info, gds_list