adapt nims1 to use nimsdata2

apache.conf

@@ -1,28 +1,20 @@
-WSGIDaemonProcess nims processes=4 threads=16 maximum-requests=1000 display-name=%{GROUP}
+WSGIDaemonProcess nims user=nims group=nims processes=2 threads=4 maximum-requests=1000 display-name=%(GROUP)
+
 <Directory /var/local/nims>
  WSGIApplicationGroup %{GLOBAL}
  WSGIProcessGroup nims
 </Directory>
 
-Redirect /nimsgears /nims
-WSGIScriptAlias /nims /var/local/nims/nimsgears/public/nims.wsgi
+WSGIScriptAlias /nims /var/local/nims/nimsgears/public/nims.wsgi
 
-Alias /nims/images /var/local/nims/nimsgears/public/images
-Alias /nims/css /var/local/nims/nimsgears/public/css
-Alias /nims/javascript /var/local/nims/nimsgears/public/javascript
-Alias /nims/static /var/local/nims/nimsgears/public/static
+Alias /nims/images /var/local/nims/nimsgears/public/images
+Alias /nims/css /var/local/nims/nimsgears/public/css
+Alias /nims/javascript /var/local/nims/nimsgears/public/javascript
 
 <IfModule mime_module>
  AddType application/octet-stream .7 .bvec .bval .dcm .dat
 </IfModule>
 
-<Directory /run/shm/nimslinks>
- Order allow,deny
- Allow from all
- Options Indexes FollowSymLinks
- AllowOverride AuthConfig
-</Directory>
-
 <Location /nims/auth>
  AuthType WebAuth
  Require valid-user

nimsgears/controllers/root.py

@@ -11,7 +11,7 @@
 from tg.i18n import ugettext as _, lazy_ugettext as l_
 import webob.exc
 
-import nimsdata
+import nimsdata.medimg.nimsmontage
 import nimsutil
 from nimsgears.model import *
 
@@ -89,7 +89,7 @@ def pyramid(self, **kwargs):
  ds = Dataset.get(kwargs['dataset_id'])
  if user.has_access_to(ds):
  db_file = os.path.join(store_path, ds.relpath, ds.filenames[0])
- return dict(zip(['dataset_id', 'tile_size', 'x_size', 'y_size'], (ds.id,) + nimsdata.nimsmontage.get_info(db_file)))
+ return dict(zip(['dataset_id', 'tile_size', 'x_size', 'y_size'], (ds.id,) + nimsdata.medimg.nimsmontage.get_info(db_file)))
 
  @expose('nimsgears.templates.qa_report', render_params={'doctype': None})
  def qa_report(self, **kwargs):
@@ -156,7 +156,7 @@ def pyramid_tile(self, *args):
  response.etag = args[0]
  response.cache_control = 'max-age = 86400'
  response.last_modified = ds.updatetime
- return nimsdata.nimsmontage.get_tile(os.path.join(store_path, ds.relpath, ds.filenames[0]), z, x, y)
+ return nimsdata.medimg.nimsmontage.get_tile(os.path.join(store_path, ds.relpath, ds.filenames[0]), z, x, y)
 
  @expose(content_type='application/octet-stream')
  def file(self, **kwargs):

nimsgears/controllers/search.py

@@ -10,7 +10,7 @@
 import numpy
 import datetime
 
-import nimsdata
+import nimsdata.medimg.dcm.mr.generic_mr
 from nimsgears.model import *
 from nimsgears.controllers.nims import NimsController
 
@@ -97,7 +97,7 @@ def index(self):
  epoch_columns = [('Group', 'col_sunet'), ('Experiment', 'col_exp'), ('Date & Time', 'col_datetime'),
  ('Exam', 'col_exam'), ('Type Scan', 'col_scantype'), ('Description', 'col_desc')]
  dataset_columns = [('Data Type', 'col_type')]
- scantype_values = [''] + sorted(nimsdata.nimsmrdata.scan_types.all)
+ scantype_values = [''] + sorted(nimsdata.medimg.dcm.mr.generic_mr.scan_types.all)
  psd_names_tuples = DBSession.query(Epoch.psd).distinct(Epoch.psd)
  psd_values = [''] + sorted([elem[0] for elem in psd_names_tuples])
  return dict(page='search',

nimsgears/model/nims.py

@@ -293,7 +293,7 @@ def __unicode__(self):
 class Job(Entity):
 
  timestamp = Field(DateTime, default=datetime.datetime.now)
- status = Field(Enum(u'pending', u'running', u'done', u'failed', u'abandoned', name=u'job_status'))
+ status = Field(Enum(u'pending', u'running', u'done', u'failed', u'abandoned', 'rerun', name=u'job_status'))
  task = Field(Enum(u'find', u'proc', u'find&proc', name=u'job_task'))
  needs_rerun = Field(Boolean, default=False)
  progress = Field(Integer)
@@ -509,13 +509,13 @@ def __unicode__(self):
 
  @classmethod
  def from_mrfile(cls, mrfile):
- subj_code, group_name, exp_name = nimsutil.parse_patient_id(mrfile.patient_id, ResearchGroup.all_ids())
+ subj_code, group_name, exp_name = nimsutil.parse_patient_id__(mrfile.subj_code, mrfile.group_name, mrfile.project_name, ResearchGroup.all_ids())
  query = cls.query.join(Experiment, cls.experiment).filter(Experiment.name == exp_name)
  query = query.join(ResearchGroup, Experiment.owner).filter(ResearchGroup.gid == group_name)
  if subj_code:
  subject = query.filter(cls.code==subj_code).first()
  elif mrfile.subj_firstname and mrfile.subj_lastname:
- subject = query.filter(cls.firstname==mrfile.subj_firstname).filter(cls.lastname==mrfile.subj_lastname).filter(cls.dob==mrfile.subj_dob).first()
+ subject = query.filter(cls.firstname==unicode(mrfile.subj_firstname)).filter(cls.lastname==unicode(mrfile.subj_lastname)).filter(cls.dob==mrfile.subj_dob).first()
  else:
  subject = None
  if not subject:
@@ -525,8 +525,8 @@ def from_mrfile(cls, mrfile):
  experiment=experiment,
  person=Person(),
  code=subj_code[:31] or experiment.next_subject_code,
- firstname=mrfile.subj_firstname[:63],
- lastname=mrfile.subj_lastname[:63],
+ firstname=(unicode(mrfile.subj_firstname) or u'')[:63],
+ lastname=(unicode(mrfile.subj_lastname) or u'')[:63],
  dob=mrfile.subj_dob,
  )
  return subject
@@ -605,7 +605,7 @@ def from_mrfile(cls, mrfile):
  # central authority and/or querying the schedule database. But for now,
  # just let the operator be None if the user isn't already in the system.
  operator = User.by_uid(unicode(mrfile.operator), create=False)
- session = Session(uid=uid, exam=mrfile.exam_no, subject=subject, operator=operator)
+ session = Session(uid=uid, exam=mrfile.exam_no if isinstance(mrfile.exam_no, int) else 0, subject=subject, operator=operator)
  return session
 
  @classmethod
@@ -708,13 +708,13 @@ def from_mrfile(cls, mrfile):
  epoch = cls.query.filter_by(uid=uid).filter_by(acq=mrfile.acq_no).first()
  if not epoch:
  session = Session.from_mrfile(mrfile)
- if session.timestamp is None or session.timestamp > mrfile.timestamp:
+ if session.timestamp is None or (mrfile.timestamp is not None and session.timestamp > mrfile.timestamp):
  session.timestamp = mrfile.timestamp
  epoch = cls(
  session = session,
  timestamp = mrfile.timestamp,
- duration = datetime.timedelta(0, mrfile.duration),
- prescribed_duration = datetime.timedelta(0, mrfile.prescribed_duration),
+ duration = datetime.timedelta(0, mrfile.duration or 0),
+ prescribed_duration = datetime.timedelta(0, mrfile.prescribed_duration or 0),
  uid = uid,
  series = mrfile.series_no,
  acq = mrfile.acq_no,
@@ -758,11 +758,11 @@ def toplevel_query(cls):
 
  @property
  def name(self):
- return '%d_%d_%d' % (self.session.exam, self.series, self.acq)
+ return '%d_%d%s' % (self.session.exam, self.series, '_%d' % self.acq if self.acq is not None else '')
 
  @property
  def dirname(self):
- return '%d_%d_%s' % (self.series, self.acq, self.description)
+ return '%d%s_%s' % (self.series, '_%d' % self.acq if self.acq is not None else '', self.description)
 
  @property
  def contains_trash(self):