def _test_bulk_to_map_annotation_context(self):
# self._testPopulateMetadataPlate()
assert len(self.get_well_annotations()) == 0
cfg = os.path.join(
os.path.dirname(__file__), 'bulk_to_map_annotation_context.yml')
fileid = self.get_plate_annotations()[0].file.id.val
ctx = BulkToMapAnnotationContext(
self.client, self.plate, fileid=fileid, cfg=cfg)
ctx.parse()
assert len(self.get_well_annotations()) == 0
ctx.write_to_omero()
was = self.get_well_annotations()
assert len(was) == 2
for ma, wid, wr, wc in was:
assert isinstance(ma, MapAnnotationI)
assert unwrap(ma.getNs()) == NSBULKANNOTATIONS
mv = ma.getMapValueAsMap()
assert mv['Well'] == str(wid)
assert coord2offset(mv['Well Name']) == (wr, wc)
if (wr, wc) == (0, 0):
assert mv['Well Type'] == 'Control'
assert mv['Concentration'] == '0'
else:
assert mv['Well Type'] == 'Treatment'
assert mv['Concentration'] == '10'
def _test_bulk_to_map_annotation_context(self):
# self._testPopulateMetadataPlate()
assert len(self.get_well_annotations()) == 0
cfg = os.path.join(os.path.dirname(__file__),
'bulk_to_map_annotation_context.yml')
fileid = self.get_plate_annotations()[0].file.id.val
ctx = BulkToMapAnnotationContext(self.client,
self.plate,
fileid=fileid,
cfg=cfg)
ctx.parse()
assert len(self.get_well_annotations()) == 0
ctx.write_to_omero()
was = self.get_well_annotations()
assert len(was) == 2
for ma, wid, wr, wc in was:
assert isinstance(ma, MapAnnotationI)
assert unwrap(ma.getNs()) == NSBULKANNOTATIONS
mv = ma.getMapValueAsMap()
assert mv['Well'] == str(wid)
assert coord2offset(mv['Well Name']) == (wr, wc)
if (wr, wc) == (0, 0):
assert mv['Well Type'] == 'Control'
assert mv['Concentration'] == '0'
else:
assert mv['Well Type'] == 'Treatment'
assert mv['Concentration'] == '10'
def populate_data(self, csv, cfg):
row_count = 1
col_count = 6
self.screen, self.plate = self.create_screen(row_count, col_count)
ctx = ParsingContext(self.client, self.screen.proxy(), file=csv)
ctx.parse()
ctx.write_to_omero()
# Get file annotations
anns = self.get_screen_annotations()
# Only expect a single annotation which is a 'bulk annotation'
assert len(anns) == 1
table_file_ann = anns[0]
assert unwrap(table_file_ann.getNs()) == NSBULKANNOTATIONS
fileid = table_file_ann.file.id.val
ctx = BulkToMapAnnotationContext(
self.client, self.screen.proxy(), fileid=fileid, cfg=cfg)
ctx.parse()
ctx.write_to_omero()
class PlateInfo:
def __init__(self, i, platename):
self.i = i
self.name, u, v = re.match("([\w_-]+)_chamber--(U\d\d)--(V\d\d)", r[1]).groups()
self.well = "%s%s" % (u, v)
plateinfos = [PlateInfo(r[0], r[1]) for r in rs]
names_csv = set(df["Plate"])
names_run = set(pm.name for pm in plateinfos)
# Check all plates have an entry in the CSV
missing = names_run.difference(names_csv)
if missing:
msg = "No matching annotations found for:%s\n" % ("\n".join(missing))
if ignore_missing:
warnings.warn(msg)
else:
raise Exception(msg)
links = []
for pm in plateinfos:
r = df.loc[(df["Plate"] == pm.name) & (df["Well"] == pm.well), :]
target = omero.model.PlateI(pm.i, False)
rowkvs = zip(r.columns, r.values.squeeze())
link = BulkToMapAnnotationContext.create_map_annotation([target], rowkvs, ns)
links.extend(link)
ids = us.saveAndReturnIds(links)
print "Created MapAnnotation links: %s" % ids
self.i = i
self.name, u, v = re.match('([\w_-]+)_chamber--(U\d\d)--(V\d\d)',
r[1]).groups()
self.well = "%s%s" % (u, v)
plateinfos = [PlateInfo(r[0], r[1]) for r in rs]
names_csv = set(df['Plate'])
names_run = set(pm.name for pm in plateinfos)
# Check all plates have an entry in the CSV
missing = names_run.difference(names_csv)
if missing:
msg = 'No matching annotations found for:%s\n' % ('\n'.join(missing))
if ignore_missing:
warnings.warn(msg)
else:
raise Exception(msg)
links = []
for pm in plateinfos:
r = df.loc[(df['Plate'] == pm.name) & (df['Well'] == pm.well), :]
target = omero.model.PlateI(pm.i, False)
rowkvs = zip(r.columns, r.values.squeeze())
link = BulkToMapAnnotationContext.create_map_annotation([target], rowkvs,
ns)
links.extend(link)
ids = us.saveAndReturnIds(links)
print 'Created MapAnnotation links: %s' % ids
