Merge branch 'master' of github.com:DDMAL/Rodan

Conflicts:
	rodan/jobs/neon/module_loader.py

requirements.txt

@@ -1,54 +1,39 @@
-Django==1.5.1
-Fabric==1.6.0
-Markdown==2.3.1
-PIL==1.1.7
-PyYAML==3.10
-South==0.7.6
-Spawning==0.9.7
-Werkzeug==0.8.3
-amqp==1.0.10
+Django==1.7b3
+Pillow==2.4.0
+Werkzeug==0.9.4
+amqp==1.4.5
 amqplib==1.0.2
 anyjson==0.3.3
-background-estimation==2.2.0pre2
-billiard==2.7.3.23
-border-removal==2.2.0pre2
-celery==3.0.17
-distribute==0.6.35
-django-celery==3.0.17
-django-celery-transactions==0.1.3
-django-extensions==1.1.1
+backports.ssl-match-hostname==3.4.0.2
+billiard==3.3.0.17
+celery==3.1.11
+django-extensions==1.3.5
 django-filter==0.7
-django-guardian==1.1.0.beta
-django-picklefield==0.3.0
-django-uuidfield==0.4.0
-djangorestframework==2.3.6
-eventlet==0.12.1
-flower==0.4.3
+django-guardian==1.2.0
+django-picklefield==0.3.1
+django-uuidfield==0.5.0
+djangorestframework==2.3.13
+ecdsa==0.11
+eventlet==0.14.0
+flower==0.6.0
 ## FIXME: could not find svn URL in dependency_links for this package:
 flup==1.0.3.dev-20110405
-gamera==3.4.0
-greenlet==0.4.0
-ipython==0.13.1
-jsonfield==0.9.13
-kombu==2.5.8
-lxml==3.2.1
-lyric-extraction==2.2.0pre2
+greenlet==0.4.2
+ipython==2.0.0
+jsonfield==0.9.20
+kombu==3.0.16
+lxml==3.3.5
 mimeparse==0.1.3
-musicstaves==1.3.8
-paramiko==1.10.0
-psycopg2==2.4.6
-py==1.4.13
-pycrypto==2.6
-pyparsing==1.5.6
-pypng==0.0.15
-pytest==2.3.4
-python-dateutil==2.1
-pytz==2013b
+paramiko==1.13.0
+psycopg2==2.5.2
+pybagit==1.5.1
+pycrypto==2.6.1
+pyparsing==2.0.2
+pypng==0.0.16
+python-dateutil==2.2
+pytz==2014.2
 readline==6.2.4.1
-rodan-plugins==3.0.1
-six==1.3.0
-solrpy==0.9.5
-ssh==1.8.0
-staffline-removal==2.2.0pre2
-tornado==3.0
+six==1.6.1
+solrpy==0.9.6
+tornado==3.2.1
 wsgiref==0.1.2

rodan/__init__.py

@@ -0,0 +1,5 @@
+from __future__ import absolute_import
+
+# This will make sure the app is always imported when
+# Django starts so that shared_task will use this app.
+from .celery import app as celery_app

rodan/admin/admin.py

@@ -9,10 +9,7 @@
 from rodan.models.runjob import RunJob
 from rodan.models.job import Job
 from rodan.models.result import Result
-from rodan.models.classifier import Classifier
-from rodan.models.pageglyphs import PageGlyphs
 from rodan.models.resultspackage import ResultsPackage
-from rodan.models.classifiersetting import ClassifierSetting
 
 # from rodan.models.rodanuser import RodanUser
 
@@ -51,22 +48,10 @@ class WorkflowRunAdmin(admin.ModelAdmin):
     list_display = ('workflow', 'run', 'created')
 
 
-class ClassifierAdmin(admin.ModelAdmin):
-    list_display = ('name',)
-
-
-class PageGlyphsAdmin(admin.ModelAdmin):
-    list_display = ('uuid', 'classifier')
-
-
 class ResultsPackageAdmin(admin.ModelAdmin):
     list_display = ('uuid', 'workflow_run', 'created')
 
 
-class ClassifierSettingAdmin(admin.ModelAdmin):
-    list_display = ('name', 'uuid', 'fitness', 'producer', 'created')
-
-
 # class UserProfileInline(admin.StackedInline):
 #     model = RodanUser
 #     can_delete = False
@@ -88,7 +73,4 @@ class ClassifierSettingAdmin(admin.ModelAdmin):
 admin.site.register(Job, JobAdmin)
 admin.site.register(WorkflowJob, WorkflowJobAdmin)
 admin.site.register(Result)
-admin.site.register(Classifier, ClassifierAdmin)
-admin.site.register(PageGlyphs, PageGlyphsAdmin)
 admin.site.register(ResultsPackage, ResultsPackageAdmin)
-admin.site.register(ClassifierSetting, ClassifierSettingAdmin)

rodan/celery.py

@@ -0,0 +1,15 @@
+from __future__ import absolute_import
+import os
+# set the default Django settings module for the 'celery' program.
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'rodan.settings')
+import django
+django.setup()
+from django.conf import settings
+from celery import Celery
+
+app = Celery('rodan')
+
+# Using a string here means the worker will not have to
+# pickle the object when using Windows.
+app.config_from_object('django.conf:settings')
+app.autodiscover_tasks(lambda: settings.INSTALLED_APPS)

rodan/jobs/__init__.py

@@ -25,129 +25,129 @@
     in the `helpers` directory, since this will automatically offload all thumbnailing to Celery as well.
 """
 
-print "Loading Rodan Jobs"
+print("Loading Rodan Jobs")
 
 try:
     from rodan.jobs.gamera import binarization
     binarization.load_module()
 except ImportError as e:
-    print "Trouble loading the Gamera binarization plugins. Is Gamera installed?"
+    print("Trouble loading the Gamera binarization plugins. Is Gamera installed?")
 
 try:
     from rodan.jobs.gamera import threshold
     threshold.load_module()
 except ImportError as e:
-    print "Trouble loading the Gamera threshold plugins. Is Gamera installed?"
+    print("Trouble loading the Gamera threshold plugins. Is Gamera installed?")
 
 try:
     from rodan.jobs.gamera import image_conversion
     image_conversion.load_module()
 except ImportError as e:
-    print "Trouble loading the Gamera image_conversion plugins. Is Gamera installed?"
+    print("Trouble loading the Gamera image_conversion plugins. Is Gamera installed?")
 
 try:
     from rodan.jobs.gamera import transformation
     transformation.load_module()
 except ImportError as e:
-    print "Trouble loading the Gamera transformation plugins. Is Gamera installed?"
+    print("Trouble loading the Gamera transformation plugins. Is Gamera installed?")
 
 try:
     from rodan.jobs.gamera.toolkits import rodan_plugins
     rodan_plugins.load_module()
 except ImportError as e:
-    print "The Rodan Plugins have not been installed. Skipping."
+    print("The Rodan Plugins have not been installed. Skipping.")
 
 try:
     from rodan.jobs.gamera.toolkits import border_removal
     border_removal.load_module()
 except ImportError as e:
-    print "No Border Removal Toolkit Installed. Skipping."
+    print("No Border Removal Toolkit Installed. Skipping.")
 
 try:
     from rodan.jobs.gamera.toolkits import staff_removal
     staff_removal.load_module()
 except ImportError as e:
-    print "No Staff Removal Toolkit Installed. Skipping."
+    print("No Staff Removal Toolkit Installed. Skipping.")
 
 try:
     from rodan.jobs.gamera.toolkits import background_estimation
     background_estimation.load_module()
 except ImportError as e:
-    print "No Background Estimation Toolkit Installed. Skipping."
+    print("No Background Estimation Toolkit Installed. Skipping.")
 
 try:
     from rodan.jobs.gamera.toolkits import lyric_extraction
     lyric_extraction.load_module()
 except ImportError as e:
-    print "No Lyric Extraction Toolkit Installed. Skipping."
+    print("No Lyric Extraction Toolkit Installed. Skipping.")
 
 try:
     from rodan.jobs.gamera.toolkits import musicstaves
     musicstaves.load_module()
 except ImportError as e:
-    print "No Music Staves Toolkit Installed. Skipping."
+    print("No Music Staves Toolkit Installed. Skipping.")
 
 ##########
 
 try:
     from rodan.jobs.diva import to_jpeg2000
     to_jpeg2000.load_module()
 except ImportError as e:
-    print "No Diva JPEG2000 converter Installed. Skipping. ", e
+    print("No Diva JPEG2000 converter Installed. Skipping. {0}".format(e))
 
 try:
     from rodan.jobs.gamera.custom.poly_mask import module_loader
     module_loader.load_module()
 except ImportError as e:
-    print "Custom Poly Mask job not installed. Skipping", e
+    print("Custom Poly Mask job not installed. Skipping".format(e))
 
 try:
     from rodan.jobs.gamera.custom.border_removal import module_loader
     module_loader.load_module()
 except ImportError as e:
-    print "Custom Border Removal job not installed. Skipping", e
+    print("Custom Border Removal job not installed. Skipping. {0}".format(e))
 
 try:
     from rodan.jobs.gamera.custom.segmentation import module_loader
     module_loader.load_module()
 except ImportError as e:
-    print "Custom Segmentation job not installed. Skipping", e
+    print("Custom Segmentation job not installed. Skipping. {0}".format(e))
 
 try:
     from rodan.jobs.gamera.custom.neume_classification import module_loader
     module_loader.load_module()
 except ImportError as e:
-    print "Custom Classification job not installed. Skipping", e
+    print("Custom Classification job not installed. Skipping. {0}".format(e))
 
 try:
     from rodan.jobs.gamera.custom.staff_removal import module_loader
     module_loader.load_module()
 except ImportError as e:
-    print "Custom RT Staff Removal job not installed. Skipping", e
+    print("Custom RT Staff Removal job not installed. Skipping. {0}".format(e))
 
 try:
     from rodan.jobs.gamera.custom.pitch_finding import module_loader
     module_loader.load_module()
 except ImportError as e:
-    print "Custom Pitch Finding job not installed. Skipping", e
+    print("Custom Pitch Finding job not installed. Skipping. {0}".format(e))
 
 try:
     from rodan.jobs.neon import module_loader
     module_loader.load_module()
 except ImportError as e:
-    print "Custom Pitch Correction job not installed. Skipping", e
+    print("Custom Pitch Correction job not installed. Skipping. {0}".format(e))
 
-
-## Periodic Tasks
 try:
-    from rodan.jobs.periodic_tasks.classifier_ga_optimization import OptimizeAllClassifiersTask
+    from rodan.jobs.gamera.custom.pixel_segment import module_loader
+    module_loader.load_module()
 except ImportError as e:
-    print "Classifier optimization periodic task not installed. Skipping", e
+    print("Custom Pixel Segment job not installed. Skipping. {0}".format(e))
+
 
 #Development
 try:
     from rodan.jobs.util.devdummyjobs import load_wfjobuuid
     load_wfjobuuid()
 except ImportError as e:
-    print "DEV: The dummy job could not be loaded properly. Skipping"
+    print("DEV: The dummy job could not be loaded properly. Skipping")
     print e

rodan/jobs/base.py

@@ -2,8 +2,8 @@
 from rodan.models.runjob import RunJob, RunJobStatus
 from rodan.jobs.util import taskutil
 
-class RodanJob(Task):
 
+class RodanJob(Task):
     def run_task(self, result_id, runjob_id, *args, **kwargs):
         """
         This is where all the execution code of a job goes.

rodan/jobs/gamera/custom/border_removal/celery_task.py

@@ -2,8 +2,8 @@
 from rodan.jobs.gamera import argconvert
 from gamera.core import init_gamera
 from gamera.toolkits.border_removal.plugins.border_removal import border_removal
-import Image
-import ImageDraw
+from PIL import Image
+from PIL import ImageDraw
 from gamera.plugins.pil_io import from_pil