def _test_parsing_context(self):
"""
Create a small csv file, use populate_metadata.py to parse and
attach to Plate. Then query to check table has expected content.
"""
ctx = ParsingContext(self.client, self.plate, file=self.csvName)
ctx.parse()
ctx.write_to_omero()
# Get file annotations
anns = self.get_plate_annotations()
# Only expect a single annotation which is a 'bulk annotation'
assert len(anns) == 1
tableFileAnn = anns[0]
assert unwrap(tableFileAnn.getNs()) == NSBULKANNOTATIONS
fileid = tableFileAnn.file.id.val
# Open table to check contents
r = self.client.sf.sharedResources()
t = r.openTable(OriginalFileI(fileid), None)
cols = t.getHeaders()
rows = t.getNumberOfRows()
assert rows == self.rowCount * self.colCount
for hit in range(rows):
rowValues = [col.values[0] for col in t.read(range(len(cols)),
hit, hit+1).columns]
assert len(rowValues) == 4
if "a1" in rowValues:
assert "Control" in rowValues
elif "a2" in rowValues:
assert "Treatment" in rowValues
else:
assert False, "Row does not contain 'a1' or 'a2'"
def populate_metadata(client, conn, script_params):
object_id = long(script_params["IDs"])
file_id = long(script_params["File_ID"])
original_file = get_original_file(
conn, script_params["Data_Type"], object_id, file_id)
provider = DownloadingOriginalFileProvider(conn)
file_handle = provider.get_original_file_data(original_file)
if script_params["Data_Type"] == "Plate":
omero_object = PlateI(long(object_id), False)
else:
omero_object = ScreenI(long(object_id), False)
ctx = ParsingContext(client, omero_object, "")
ctx.parse_from_handle(file_handle)
ctx.write_to_omero()
def testPopulateMetadataPlate(self):
"""
Create a small csv file, use populate_metadata.py to parse and
attach to Plate. Then query to check table has expected content.
"""
csvName = "testCreate.csv"
self.createCsv(csvName)
rowCount = 1
colCount = 2
plate = self.createPlate(rowCount, colCount)
ctx = ParsingContext(self.client, plate, csvName)
ctx.parse()
ctx.write_to_omero()
# Delete local temp file
os.remove(csvName)
# Get file annotations
query = """select p from Plate p
left outer join fetch p.annotationLinks links
left outer join fetch links.child
where p.id=%s""" % plate.id.val
qs = self.client.sf.getQueryService()
plate = qs.findByQuery(query, None)
anns = plate.linkedAnnotationList()
# Only expect a single annotation which is a 'bulk annotation'
assert len(anns) == 1
tableFileAnn = anns[0]
assert unwrap(tableFileAnn.getNs()) == NSBULKANNOTATIONS
fileid = tableFileAnn.file.id.val
# Open table to check contents
r = self.client.sf.sharedResources()
t = r.openTable(OriginalFileI(fileid), None)
cols = t.getHeaders()
rows = t.getNumberOfRows()
assert rows == rowCount * colCount
for hit in range(rows):
rowValues = [col.values[0] for col in t.read(range(len(cols)),
hit, hit+1).columns]
assert len(rowValues) == 4
if "a1" in rowValues:
assert "Control" in rowValues
elif "a2" in rowValues:
assert "Treatment" in rowValues
else:
assert False, "Row does not contain 'a1' or 'a2'"
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()
def populate_metadata(client, conn, script_params):
object_id = int(script_params["IDs"])
file_id = int(script_params["File_ID"])
original_file = get_original_file(conn, script_params["Data_Type"],
object_id, file_id)
provider = DownloadingOriginalFileProvider(conn)
file_handle = provider.get_original_file_data(original_file)
if script_params["Data_Type"] == "Plate":
omero_object = PlateI(int(object_id), False)
else:
omero_object = ScreenI(int(object_id), False)
ctx = ParsingContext(client, omero_object, "")
ctx.parse_from_handle(file_handle)
ctx.write_to_omero()
def testPopulateMetadataPlate(self):
"""
Create a small csv file, use populate_metadata.py to parse and
attach to Plate. Then query to check table has expected content.
"""
csvName = "testCreate.csv"
self.createCsv(csvName)
rowCount = 1
colCount = 2
plate = self.createPlate(rowCount, colCount)
ctx = ParsingContext(self.client, plate, csvName)
ctx.parse()
ctx.write_to_omero()
# Delete local temp file
os.remove(csvName)
# Get file annotations
query = """select p from Plate p
left outer join fetch p.annotationLinks links
left outer join fetch links.child
where p.id=%s""" % plate.id.val
qs = self.client.sf.getQueryService()
plate = qs.findByQuery(query, None)
anns = plate.linkedAnnotationList()
# Only expect a single annotation which is a 'bulk annotation'
assert len(anns) == 1
tableFileAnn = anns[0]
assert unwrap(tableFileAnn.getNs()) == NSBULKANNOTATIONS
fileid = tableFileAnn.file.id.val
# Open table to check contents
r = self.client.sf.sharedResources()
t = r.openTable(OriginalFileI(fileid), None)
cols = t.getHeaders()
rows = t.getNumberOfRows()
assert rows == rowCount * colCount
for hit in range(rows):
rowValues = [
col.values[0]
for col in t.read(range(len(cols)), hit, hit + 1).columns
]
assert len(rowValues) == 4
if "a1" in rowValues:
assert "Control" in rowValues
elif "a2" in rowValues:
assert "Treatment" in rowValues
else:
assert False, "Row does not contain 'a1' or 'a2'"
def populate_metadata(client, conn, script_params):
object_ids = script_params["IDs"]
object_id = object_ids[0]
file_ann_id = None
if "File_Annotation" in script_params:
file_ann_id = long(script_params["File_Annotation"])
data_type = script_params["Data_Type"]
original_file = get_original_file(conn, data_type, object_id, file_ann_id)
provider = DownloadingOriginalFileProvider(conn)
file_handle = provider.get_original_file_data(original_file)
if data_type == "Plate":
omero_object = PlateI(long(object_id), False)
else:
omero_object = ScreenI(long(object_id), False)
ctx = ParsingContext(client, omero_object, "")
ctx.parse_from_handle(file_handle)
ctx.write_to_omero()
return "Table data populated for %s: %s" % (data_type, object_id)
def _test_parsing_context(self):
"""
Create a small csv file, use populate_metadata.py to parse and
attach to Plate. Then query to check table has expected content.
"""
ctx = ParsingContext(self.client, self.plate, file=self.csvName)
ctx.parse()
ctx.write_to_omero()
# Get file annotations
anns = self.get_plate_annotations()
# Only expect a single annotation which is a 'bulk annotation'
assert len(anns) == 1
tableFileAnn = anns[0]
assert unwrap(tableFileAnn.getNs()) == NSBULKANNOTATIONS
fileid = tableFileAnn.file.id.val
# Open table to check contents
r = self.client.sf.sharedResources()
t = r.openTable(OriginalFileI(fileid), None)
cols = t.getHeaders()
rows = t.getNumberOfRows()
assert rows == self.rowCount * self.colCount
for hit in range(rows):
rowValues = [
col.values[0]
for col in t.read(range(len(cols)), hit, hit + 1).columns
]
assert len(rowValues) == 4
if "a1" in rowValues:
assert "Control" in rowValues
elif "a2" in rowValues:
assert "Treatment" in rowValues
else:
assert False, "Row does not contain 'a1' or 'a2'"
# ===================================================
orig_table_file = conn.getObject(
"OriginalFile", attributes={'name': tablename}) # if name is unique
savedTable = conn.c.sf.sharedResources().openTable(orig_table_file._obj)
print "Opened table with row-count:", savedTable.getNumberOfRows()
# Populate a table on a Plate from a csv file
# ===========================================
colNames = "Well, Well Type, Concentration\n"
csvLines = [
colNames,
"A1, Control, 0\n",
"A2, Treatment, 5\n",
"A3, Treatment, 10\n"]
with open('data.csv', 'w') as csvData:
csvData.writelines(csvLines)
plate = conn.getObject("Plate", plateId)
target_object = plate._obj
client = conn.c
ctx = ParsingContext(client, target_object, 'data.csv')
ctx.parse()
ctx.write_to_omero()
os.remove('data.csv')
# Close connection
# ================
# When you are done, close the session to free up server resources.
conn._closeSession()
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()
# ===================================================
orig_table_file = conn.getObject(
"OriginalFile", attributes={'name': table_name}) # if name is unique
saved_table = resources.openTable(orig_table_file._obj)
print("Opened table with row-count:", saved_table.getNumberOfRows())
saved_table.close()
# Populate a table on a Plate from a csv file
# ===========================================
col_names = "Well, Well Type, Concentration\n"
csv_lines = [
col_names,
"A1, Control, 0\n",
"A2, Treatment, 5\n",
"A3, Treatment, 10\n"]
with open('data.csv', 'w') as csv_data:
csv_data.writelines(csv_lines)
plate = conn.getObject("Plate", plateId)
target_object = plate._obj
client = conn.c
ctx = ParsingContext(client, target_object, 'data.csv')
ctx.parse()
ctx.write_to_omero()
os.remove('data.csv')
# Close connection
# ================
# When you are done, close the session to free up server resources.
conn.close()