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Update mdv app #9

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edb7bbb
Try to use text16 datatype for link column
will-moore Nov 23, 2023
ab37f2e
Load MDV projects from URL like project/ANN_ID/ to work with updated MDV
will-moore Nov 24, 2023
b9d1c05
try to support get_view and get_data URLs
will-moore Nov 24, 2023
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20 changes: 12 additions & 8 deletions omero_mdv/urls.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,23 +18,27 @@
re_path(r'^datasets_info/(?P<projectid>[0-9]+)/$', views.datasets_info, name='mdv_datasets_info'),

# MDV viewer
re_path(r"^config/(?P<configid>[0-9]+)/json/$", views.config_json, name='mdv_config_json'),
re_path(r"^project/(?P<configid>[0-9]+)/json/$", views.config_json, name='mdv_config_json'),
# save configs, so a config ID is the FileAnnotation ID for JSON
re_path(r"^config/(?P<configid>[0-9]+)/datasources.json$", views.datasources, name='mdv_datasources'),
re_path(r"^project/(?P<configid>[0-9]+)/datasources.json$", views.datasources, name='mdv_datasources'),
# list configs
re_path(r'^open/$', views.list_mdv_configs, name="open_mdv"),
# delete config
re_path(r'^delete_mdv_config/$', views.delete_mdv_config, name="delete_mdv_config"),

re_path(r"^config/(?P<configid>[0-9]+)/state.json$", views.state, name='mdv_state'),
re_path(r"^config/(?P<configid>[0-9]+)/views.json$", views.views, name='mdv_views'),
re_path(r"^project/(?P<configid>[0-9]+)/state.json$", views.state, name='mdv_state'),
re_path(r"^project/(?P<configid>[0-9]+)/views.json$", views.views, name='mdv_views'),
# Not sure why we need get_view AND views.json?
re_path(r"^project/(?P<configid>[0-9]+)/get_view$", views.views, name='mdv_get_views'),
# get_data
re_path(r"^project/(?P<configid>[0-9]+)/get_data$", views.table_bytes, name='mdv_get_data'),

# We name a table datasource mdv_config_ID, so we use that ID (ignore configid for now)
re_path(r"^config/(?P<configid>[0-9]+)/mdv_config_(?P<tableid>[0-9]+).json$", views.table_cols_byte_offsets),
re_path(r"^config/(?P<configid>[0-9]+)/mdv_config_(?P<tableid>[0-9]+).b$", views.table_bytes),
re_path(r"^project/(?P<configid>[0-9]+)/mdv_config_(?P<tableid>[0-9]+).json$", views.table_cols_byte_offsets),
re_path(r"^project/(?P<configid>[0-9]+)/mdv_config_(?P<tableid>[0-9]+).gz$", views.table_bytes),

re_path(r"^config/(?P<configid>[0-9]+)/thumbnail/(?P<imageid>[0-9]+).png$", views.thumbnail),
re_path(r"^config/(?P<configid>[0-9]+)/image/(?P<imageid>[0-9]+).png$", views.image),
re_path(r"^project/(?P<configid>[0-9]+)//thumbnail/(?P<imageid>[0-9]+).png$", views.thumbnail),
re_path(r"^project/(?P<configid>[0-9]+)//image/(?P<imageid>[0-9]+).png/$", views.image),

# POST here when user hits "Save" button on MDV
re_path(r"^meths/execute_project_action/$", views.save_view),
Expand Down
7 changes: 5 additions & 2 deletions omero_mdv/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -487,8 +487,11 @@ def marshal_mdv_column(colname, kvp_by_id, primary_key_ids, bytes_offset):

byte_count = len(get_column_bytes(kvp_data))

if datatype == "text" and max_value_count > 1:
datatype = "multitext"
if datatype == "text":
if max_value_count > 1:
datatype = "multitext"
elif len(vals) > 256:
datatype = "text16"
col = {
"name": colname,
"datatype": datatype,
Expand Down
54 changes: 38 additions & 16 deletions omero_mdv/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -325,7 +325,7 @@ def get_column(name):

# redirect to app, with absolute config URL...
url = reverse("mdv_index")
config_url = f"config/{ann_id}/"
config_url = f"project/{ann_id}/"

return HttpResponseRedirect("%s?dir=%s" % (url, config_url))

Expand All @@ -340,13 +340,14 @@ def get_webclient_links_column(image_ids, bytes_offset):
values.append(f"{url}?show=image-{iid}")
indices.append(index)

byte_count = len(get_column_bytes(indices))
byte_count = len(get_column_bytes(indices, np.int16))

col = {
"name": WEBCLIENT_LINK,
"field": WEBCLIENT_LINK,
"is_url": True,
"datatype": "text",
# text16 allows up to 65536 values instead of 256
"datatype": "text16",
"values": values,
"bytes": [bytes_offset, bytes_offset + byte_count],
"data": indices,
Expand Down Expand Up @@ -454,17 +455,25 @@ def table_cols_byte_offsets(request, configid, conn=None, **kwargs):
@login_required()
def table_bytes(request, configid, conn=None, **kwargs):

range_header = request.headers['Range']
m = re.search('(\d+)-(\d*)', range_header)
g = m.groups()
print("table_bytes....")
col_names = None
if request.method == "POST":
json_data = json.loads(request.body)
print("table_data POST", json_data)
col_names = [col["name"] for col in json_data.get("columns")]
print("col_names", col_names)

byte1 = int(g[0]) if g[0] else None
byte2 = int(g[1]) if g[1] else None
# range_header = request.headers['Range']
# m = re.search('(\d+)-(\d*)', range_header)
# g = m.groups()

if byte1 is None or byte2 is None:
raise Http404(
"No byte 'Range' in request Header: got `%s-%s`" % (byte1, byte2))
size = byte2 - byte1
# byte1 = int(g[0]) if g[0] else None
# byte2 = int(g[1]) if g[1] else None

# if byte1 is None or byte2 is None:
# raise Http404(
# "No byte 'Range' in request Header: got `%s-%s`" % (byte1, byte2))
# size = byte2 - byte1

# get data from config...
config_json = _config_json(conn, configid)
Expand All @@ -475,7 +484,9 @@ def table_bytes(request, configid, conn=None, **kwargs):
column_bytes = None
# find the column that has the correct byte1 (used as column ID)
for col in config_json["columns"]:
if col["bytes"][0] == byte1:
# if col["bytes"][0] == byte1:
if col["name"] in col_names:
print("col", col["name"])
# handle omero tables, load table below
if "omero_table_file_id" in col:
tableid = col.get("omero_table_file_id")
Expand All @@ -484,9 +495,10 @@ def table_bytes(request, configid, conn=None, **kwargs):
dtype = None
if col["datatype"] == "text":
dtype = np.int8
elif col["datatype"] == "multitext":
elif col["datatype"] in ("multitext", "text16"):
dtype = np.int16
column_bytes = get_column_bytes(col["data"], dtype)

break

if tableid is not None:
Expand All @@ -500,8 +512,9 @@ def table_bytes(request, configid, conn=None, **kwargs):
finally:
t.close()

print("bytes!", len(column_bytes))
rsp = HttpResponse(column_bytes, content_type="application/octet-stream")
rsp['Content-Range'] = 'bytes {0}-{1}/{2}'.format(byte1, byte2, size)
# rsp['Content-Range'] = 'bytes {0}-{1}/{2}'.format(byte1, byte2, size)
rsp['Accept-Ranges'] = 'bytes'
return rsp

Expand Down Expand Up @@ -539,6 +552,12 @@ def views(request, configid, conn=None, **kwargs):
# Load
config_json = _config_json(conn, configid)

# Handle POST to project/ID/get_view...
view_name = None
if request.method == "POST":
json_data = json.loads(request.body)
view_name = json_data.get("view")

# If views exist, simply return them...
if "views" in config_json:
rsp = {}
Expand All @@ -562,6 +581,9 @@ def views(request, configid, conn=None, **kwargs):
ds[datasourceId] = ds_info
view_config["dataSources"] = ds
rsp[view_id] = view_config

if view_name is not None and view_name in rsp:
rsp = rsp[view_name]
return JsonResponse(rsp)

# create a default view...
Expand All @@ -583,7 +605,7 @@ def add_default_charts(config_json, charts=[], add_table=True,
column_names = []
columns = config_json["columns"]
# Don't add webclient-link column into Table
column_names = [col["name"] for col in columns if col["name"] != WEBCLIENT_LINK]
column_names = [col["name"] for col in columns] # if col["name"] != WEBCLIENT_LINK]
image_col = None
for idx, col in enumerate(columns):
if col["name"].lower() == "image":
Expand Down