Update to biaflows-utilities

Author: bpavie

Dockerfile

@@ -7,22 +7,22 @@ RUN apt-get update && apt-get install openjdk-8-jdk -y && apt-get clean
 # ---------------------------------------------------------------------------------------------------------------------
 # Install Cytomine python client (annotation exporter, compute metrics, helpers,...)
 RUN git clone https://github.com/cytomine-uliege/Cytomine-python-client.git && \
-    cd /Cytomine-python-client && git checkout tags/v2.3.0.poc.1 && pip install . && \
+    cd /Cytomine-python-client && git checkout v2.7.3 && pip install . && \
     rm -r /Cytomine-python-client
 
 # ---------------------------------------------------------------------------------------------------------------------
 # Install Neubias-W5-Utilities (annotation exporter, compute metrics, helpers,...)    
 # It will get DiademMetric.jar and JSAP-2.1.jar files to compute DIADEM metric
 RUN apt-get update && apt-get install libgeos-dev -y && apt-get clean
-RUN git clone https://github.com/Neubias-WG5/neubiaswg5-utilities.git && \
-    cd /neubiaswg5-utilities/ && git checkout tags/v0.8.8 && pip install .
+RUN git clone https://github.com/Neubias-WG5/biaflows-utilities.git && \
+    cd /biaflows-utilities/ && git checkout tags/v0.9.1 && pip install .
 
 # install utilities binaries
-RUN chmod +x /neubiaswg5-utilities/bin/*
-RUN cp /neubiaswg5-utilities/bin/* /usr/bin/
+RUN chmod +x /biaflows-utilities/bin/*
+RUN cp /biaflows-utilities/bin/* /usr/bin/
 
 # cleaning
-RUN rm -r /neubiaswg5-utilities    
+RUN rm -r /biaflows-utilities    
 
 
 # --------------------------------------------------------------------------------------------

wrapper.py

@@ -3,13 +3,13 @@
 import glob
 from subprocess import call
 from cytomine.models import Job
-from neubiaswg5 import CLASS_TRETRC
-from neubiaswg5.helpers import NeubiasJob, prepare_data, upload_data, upload_metrics
+from biaflows import CLASS_TRETRC
+from biaflows.helpers import BiaflowsJob, prepare_data, upload_data, upload_metrics
 from workflow import workflow 
 
 def main(argv):
     # 0. Initialize Cytomine client and job
-    with NeubiasJob.from_cli(argv) as nj:
+    with BiaflowsJob.from_cli(argv) as nj:
         nj.job.update(status=Job.RUNNING, progress=0, statusComment="Initialisation...")
         problem_cls = CLASS_TRETRC
         is_2d = False