def comments_userA(request, userA, groupA):
"""
Returns new OMERO Comments
"""
comments = []
ctx = {'omero.group': str(groupA.id.val)}
for text in ["Test Comment", "Another comment userA"]:
comment = CommentAnnotationI()
comment.textValue = rstring(text)
comments.append(comment)
comments = get_update_service(userA).saveAndReturnArray(comments, ctx)
comments.sort(cmp_id)
return comments
def comments_userA(request, userA, groupA):
"""
Returns new OMERO Comments
"""
comments = []
ctx = {'omero.group': str(groupA.id.val)}
for text in ["Test Comment", "Another comment userA"]:
comment = CommentAnnotationI()
comment.textValue = rstring(text)
comments.append(comment)
comments = get_update_service(userA).saveAndReturnArray(comments, ctx)
comments.sort(cmp_id)
return comments
def fileset_with_images_and_annotations(request, gatewaywrapper):
gatewaywrapper.loginAsAuthor()
update_service = gatewaywrapper.gateway.getUpdateService()
fileset = create_fileset()
comment_annotation = CommentAnnotationI()
comment_annotation.ns = rstring("comment_annotation")
comment_annotation.textValue = rstring("textValue")
long_annotation = LongAnnotationI()
long_annotation.ns = rstring("long_annotation")
long_annotation.longValue = rlong(1L)
fileset.linkAnnotation(comment_annotation)
fileset.linkAnnotation(long_annotation)
fileset = update_service.saveAndReturnObject(fileset)
return gatewaywrapper.gateway.getObject("Fileset", fileset.id.val)
def fileset_with_images_and_annotations(request, gatewaywrapper):
gatewaywrapper.loginAsAuthor()
update_service = gatewaywrapper.gateway.getUpdateService()
fileset = create_fileset()
comment_annotation = CommentAnnotationI()
comment_annotation.ns = rstring('comment_annotation')
comment_annotation.textValue = rstring('textValue')
long_annotation = LongAnnotationI()
long_annotation.ns = rstring('long_annotation')
long_annotation.longValue = rlong(1L)
fileset.linkAnnotation(comment_annotation)
fileset.linkAnnotation(long_annotation)
fileset = update_service.saveAndReturnObject(fileset)
return gatewaywrapper.gateway.getObject('Fileset', fileset.id.val)
def rename_fileset(client, mrepo, fileset, new_dir, ctx=None):
"""
Loads each OriginalFile found under orig_dir and
updates its path field to point at new_dir. Files
are not yet moved.
"""
from omero.constants.namespaces import NSFSRENAME
from omero.model import CommentAnnotationI
from omero.model import FilesetAnnotationLinkI
tomove = []
tosave = []
query = client.sf.getQueryService()
update = client.sf.getUpdateService()
orig_dir = fileset.templatePrefix.val
def parse_parent(dir):
"""
Note that final elements are empty
"""
parts = dir.split("/")
parpath = "/".join(parts[0:-2]+[""])
parname = parts[-2]
logname = parts[-2] + ".log"
return parpath, parname, logname
orig_parpath, orig_parname, orig_logname = parse_parent(orig_dir)
new_parpath, new_parname, new_logname = parse_parent(new_dir)
for entry in contents(mrepo, orig_dir, ctx):
ofile = query.get("OriginalFile", entry.id, ctx)
path = ofile.path.val
if entry.level == 0:
tomove.append((orig_dir, new_dir))
assert orig_parpath in path
repl = path.replace(orig_parpath, new_parpath)
ofile.name = rstring(new_parname)
else:
assert orig_dir in path
repl = path.replace(orig_dir, new_dir)
ofile.path = rstring(repl)
tosave.append(ofile)
fileset.templatePrefix = rstring(new_dir)
# TODO: placing the fileset at the end of this list
# causes ONLY the fileset to be updated !!
tosave.insert(0, fileset)
# Add an annotation to the fileset as well so
# we can detect if something's gone wrong.
link = FilesetAnnotationLinkI()
link.parent = fileset.proxy()
link.child = CommentAnnotationI()
link.child.ns = rstring(NSFSRENAME)
link.child.textValue = rstring("previous=%s" % orig_dir)
tosave.insert(1, link)
# And now move the log file as well:
log = get_logfile(query, fileset.id.val)
if log is not None:
target = new_parpath + new_logname
source = orig_parpath + orig_logname
tomove.append((source, target))
log.path = rstring(new_parpath)
log.name = rstring(new_logname)
tosave.append(log)
# Done. Save in one transaction and return tomove
update.saveAndReturnArray(tosave, ctx)
return tomove
def add_annotations(o):
'''
Annotation
BasicAnnotation
BooleanAnnotation
BooleanAnnotationI
NumericAnnotation
DoubleAnnotation
DoubleAnnotationI
LongAnnotation
LongAnnotationI
TermAnnotation
TermAnnotationI
TimestampAnnotation
TimestampAnnotationI
ListAnnotation
ListAnnotationI
MapAnnotation
MapAnnotationI
TextAnnotation
CommentAnnotation
CommentAnnotationI
TagAnnotation
TagAnnotationI
XmlAnnotation
XmlAnnotationI
TypeAnnotation
FileAnnotation
FileAnnotationI
'''
annotation = BooleanAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('boolean_annotation')
annotation.boolValue = rbool(True)
o.linkAnnotation(annotation)
annotation = CommentAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('comment_annotation')
annotation.textValue = rstring('text_value')
o.linkAnnotation(annotation)
annotation = DoubleAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('double_annotation')
annotation.doubleValue = rdouble(1.0)
o.linkAnnotation(annotation)
annotation = LongAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('long_annotation')
annotation.longValue = rlong(1L)
o.linkAnnotation(annotation)
annotation = MapAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('map_annotation')
annotation.setMapValue([NamedValue('a', '1'), NamedValue('b', '2')])
o.linkAnnotation(annotation)
annotation = TagAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('tag_annotation')
annotation.textValue = rstring('tag_value')
o.linkAnnotation(annotation)
annotation = TermAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('term_annotation')
annotation.termValue = rstring('term_value')
o.linkAnnotation(annotation)
annotation = TimestampAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('timestamp_annotation')
annotation.timeValue = rtime(1)
o.linkAnnotation(annotation)
annotation = XmlAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('xml_annotation')
annotation.textValue = rstring('<xml_value></xml_value>')
o.linkAnnotation(annotation)