Ci tests

Former-commit-id: 9ef16855

.gitlab-ci.yml

@@ -6,7 +6,6 @@ variables:
 
 stages:
   - download_data
-  - test_prefactor
   - validate_cwl_scripts
   - test_steps
   - integration_test
@@ -29,13 +28,6 @@ download_data:
     paths:
     - data
 
-test_prefactor:
-  stage: test_prefactor
-  needs: ["download_data"]
-  script:
-     - cd data
-     - ls -l
-
 validate_scripts:
   stage: validate_cwl_scripts
   script:
@@ -46,24 +38,24 @@ blsmooth:
   allow_failure: true
   needs: ["download_data"]
   script:
-    - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/blsmooth.cwl test_jobs/blsmooth.json
+    - cwltool --no-container steps/blsmooth.cwl test_jobs/blsmooth.json
 
 find_skymodel_cal:
   stage: test_steps
   allow_failure: true
   needs: ["download_data"]
   script:
-    - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/find_skymodel_cal.cwl test_jobs/find_skymodel_cal.json
+    - cwltool --no-container --preserve-environment PYTHONPATH steps/find_skymodel_cal.cwl test_jobs/find_skymodel_cal.json
 
 check_ateam_separation:
   stage: test_steps
   allow_failure: true
   needs: ["download_data"]
   script:
-    - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/check_ateam_separation.cwl test_jobs/check_ateam_separation.json
+    - cwltool --no-container steps/check_ateam_separation.cwl test_jobs/check_ateam_separation.json
 
 prefactor_calibrator:
   stage: integration_test
   needs: ["download_data"]
   script:
-    - cwltool --no-container workflows/HBA_calibrator.cwl test_jobs/HBA_calibrator.json
+    - cwltool --no-container --preserve-environment PYTHONPATH --preserve-environment PREFACTOR_DATA_ROOT workflows/HBA_calibrator.cwl test_jobs/HBA_calibrator.json

Docker/Dockerfile_ci

-FROM lofareosc/prefactor3-cwl
-SHELL ["/bin/bash", "-c"]
-
-#ADD L570745_uv_first10.MS.tar.xz /data
-#ADD skymodels.tar.gz /data/skymodels
-ADD test_data/A-Team_lowres.sourcedb /data/A-Team_lowres.sourcedb
-ADD test_data/example.h5 /data/example.h5
-ADD test_data/calibration.h5  /data/calibration.h5
-ADD test_data/L570745_SB001_uv_MODEL.MS /data/L570745_SB001_uv_MODEL.MS
-ADD test_data/L570745_SB001_uv_CORRECTED_DATA.MS /data/L570745_SB001_uv_CORRECTED_DATA.MS
-ADD test_data/L570745_SB002_uv_CORRECTED_DATA.MS /data/L570745_SB002_uv_CORRECTED_DATA.MS
-ADD test_data/L570745_SB003_uv_CORRECTED_DATA.MS /data/L570745_SB003_uv_CORRECTED_DATA.MS

steps/check_ateam_separation.cwl

@@ -19,7 +19,7 @@ inputs:
       position: 2
       prefix: '--outputimage'
   - id: min_separation
-    type: int
+    type: int?
     inputBinding:
       position: 1
       prefix: '--min_separation'

test_jobs/blsmooth.json

@@ -3,5 +3,5 @@
             "class": "Directory",
             "path": "../data/L570745_SB003_uv_first10.MS"
         },
-    "do_smooth": true
+    "do_smooth": false
 }