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
Exemplo n.º 3
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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)
Exemplo n.º 4
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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)
Exemplo n.º 5
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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
Exemplo n.º 6
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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)