Add ontology and terms inside a software #29
Description
Hi @geektortoise,
Is it possible to add new ontology from a software?
Here part of my codes:
import sys
import numpy as np
import os
from shapely.geometry import shape, box, Polygon,Point
from shapely import wkt
from glob import glob
from tifffile import imread
from cytomine import Cytomine, models, CytomineJob
from cytomine.models import Annotation, AnnotationTerm, AnnotationCollection, ImageInstanceCollection, Job
from cytomine.models.ontology import Ontology, OntologyCollection, Term, RelationTerm, TermCollection
from PIL import Image
import argparse
import json
import logging
def main(argv):
with CytomineJob.from_cli(argv) as conn:
print(conn.parameters)
conn.job.update(status=Job.RUNNING, progress=0, statusComment="Initialization...")
base_path = "{}".format(os.getenv("HOME")) # Mandatory for Singularity
working_path = os.path.join(base_path,str(conn.job.id))
ontology = Ontology("classPNcells"+str(conn.parameters.cytomine_id_project)).save()
#Algorithm goes here
#.....
#.....
if cellclass==1:
print("Positive (H: ", str(hue), ", V: ", str(val))
id_terms=Term("PositiveCell", ontology.id, "#FF0000").save()
elif cellclass==2:
print("Negative (H: ", str(hue), ", V: ", str(val))
id_terms=Term("NegativeCell", ontology.id, "#00FF00").save()
cytomine_annotations = AnnotationCollection()
cytomine_annotations.append(Annotation(location=roi_geometry,
id_image=id_image,#conn.parameters.cytomine_id_image,
id_project=conn.parameters.cytomine_id_project,
id_terms=[id_terms]))
print(".",end = '',flush=True)
#Send Annotation Collection (for this ROI) to Cytomine server in one http request
ca = cytomine_annotations.save()
conn.job.update(status=Job.TERMINATED, progress=100, statusComment="Finished.")
if __name__ == "__main__":
main(sys.argv[1:])
The input is:
python3 classifypncell.py --cytomine_host "http://localhost-core" --cytomine_public_key "xxxxx" --cytomine_private_key "xxxxxx" --cytomine_id_project "44890" --cytomine_id_software "48284" --cytomine_id_images "44902" --cytomine_id_roi_term "1486"
And the log:
[2021-05-19 21:43:48,738][INFO] [GET] [currentuser] CURRENT USER - 61 : admin | 200 OK
[2021-05-19 21:43:48,906][INFO] [GET] [project] 44890 : Test_classifyPNcells | 200 OK
[2021-05-19 21:43:48,961][INFO] [GET] [software] 48284 : classify_PN_cells_test | 200 OK
[2021-05-19 21:43:49,082][INFO] [GET] [software_parameter collection] 7 objects | 200 OK
[2021-05-19 21:43:49,449][INFO] [POST] [job] 50694 : classify_PN_cells_test : 33 | 200 OK
[2021-05-19 21:43:49,492][INFO] [GET] [user] 50700 : JOB[admin ], 2021-05-19 13:43:49:381 | 200 OK
[2021-05-19 21:43:49,535][INFO] [GET] [currentuser] CURRENT USER - 50700 : JOB[admin ], 2021-05-19 13:43:49:381 | 200 OK
[2021-05-19 21:43:49,536][INFO] Job (id:50694) status update: "None" (status: RUNNING, progress: 0%)
[2021-05-19 21:43:49,634][INFO] [PUT] [job] 50694 : classify_PN_cells_test : 33 | 200 OK
[2021-05-19 21:43:49,743][INFO] [POST] [jobparameter] 50707 : cytomine_id_images | 200 OK
[2021-05-19 21:43:49,813][INFO] [POST] [jobparameter] 50713 : cytomine_id_roi_term | 200 OK
[2021-05-19 21:43:49,814][INFO] Job (id:50694) status update: "Initialization..." (status: RUNNING, progress: 0%)
[2021-05-19 21:43:49,898][INFO] [PUT] [job] 50694 : classify_PN_cells_test : 33 | 200 OK
[2021-05-19 21:43:50,471][INFO] [POST] [ontology] None : classPNcells44890 | 500 Internal Server Error
[2021-05-19 21:43:50,654][INFO] [GET] [ontology collection] 0 objects | 200 OK
[ontology collection] 0 objects
[2021-05-19 21:43:50,748][INFO] [GET] [term collection] 3 objects | 200 OK
[term collection] 3 objects
[2021-05-19 21:43:51,088][INFO] [GET] [imageinstance collection] 1 objects | 200 OK
[44902]
[2021-05-19 21:43:51,088][INFO] Job (id:50694) status update: "Running PN classification on image (1/1)." (status: RUNNING, progress: 0%)
[2021-05-19 21:43:51,159][INFO] [PUT] [job] 50694 : classify_PN_cells_test : 33 | 200 OK
[2021-05-19 21:43:51,370][INFO] [GET] [annotation collection] 1 objects | 200 OK
[annotation collection] 1 objects
----------------------------Cells------------------------------
ROI Geometry from Shapely: POLYGON ((5 505, 621 505, 621 0, 5 0, 5 505))
ROI Bounds
(5.0, 0.0, 621.0, 505.0)
roi_png_filename: /home/wshmunirah/50694/44890/44902/44918/44918.png
[2021-05-19 21:43:54,455][INFO] File downloaded successfully from http://localhost-core/api/userannotation/44918/alphamask.png with parameters {'bits': 8, 'complete': True}
hue: 199.8789470500792
val: 200.5944437181143
Positive (H: 199.8789470500792 , V: 200.5944437181143
[2021-05-19 21:43:54,800][INFO] Job (id:50694) status update: "'bool' object has no attribute 'id'" (status: FAILED, progress: 0%)
[2021-05-19 21:43:54,900][INFO] [PUT] [job] 50694 : classify_PN_cells_test : 33 | 200 OK
Traceback (most recent call last):
File "classifypncell.py", line 226, in
main(sys.argv[1:])
File "classifypncell.py", line 204, in main
id_terms=Term("PositiveCell", ontology.id, "#FF0000").save()
It seems like the error is caused by 500 Internal Server Error when adding the new Ontology, hence ontology.id is not defined. I tried using the example add_ontology.py and it worked like charm. Is there anything I missed here? I have updated to the latest Cytomine release 3.0.3.
Thank you.