Create a set of realistic users, groups, projects, datasets and tags for movie making.

dbPrepForMovies.py

from omero.gateway import BlitzGateway
import omero
from omero.rtypes import rstring
from omero_model_ProjectI import ProjectI
from omero_model_DatasetI import DatasetI
from omero_model_ProjectDatasetLinkI import ProjectDatasetLinkI
from omero_model_ExperimenterI import ExperimenterI
from omero_model_ExperimenterGroupI import ExperimenterGroupI
from omero_model_PermissionsI import PermissionsI
from omero_model_TagAnnotationI import TagAnnotationI
from omero_model_AnnotationAnnotationLinkI import AnnotationAnnotationLinkI

rootpassw = "omero"
# set to actual host before use
host='localhost'
conn = BlitzGateway('root', rootpassw, host=host)
conn.connect()
admin = conn.getAdminService()
uuid = admin.getEventContext().sessionUuid 
uuid = ""            # for real
#uuid = "_"   # for testing the script itself

userpassw = "ome"
passw = rstring(userpassw)
emailsuff = "@example.com"

# Define some groups, users, projects, datasets and tags.

groups = {
    "g1" : {"name":"Nevis Group (Private)",  "perms":"rw----"},
    "g2" : {"name":"Nevis Group (Collab)",  "perms":"rwra--"},
    "g3" : {"name":"Skye Lab", "perms":"rw----"},
    "g4" : {"name":"Skye Teaching Lab", "perms":"rwr---"}
}

users = {
    "u1" : {"name":"ben", "first":"Ben", "last":"Nevis", "groups":["g1","g2"], "owner":["g1","g2"], "admin":True},
    "u2" : {"name":"isla", "first":"Isla", "last":"Skye", "groups":["g3","g4"], "owner":["g3","g4"], "admin":False},
    "u3" : {"name":"glen", "first":"Glen", "last":"Coe", "groups":["g1","g2","g4"], "owner":[], "admin":False},
    "u4" : {"name":"eileen", "first":"Eileen", "last":"Donan", "groups":["g1","g2","g4"], "owner":[], "admin":False},
    "u5" : {"name":"benj", "first":"Ben", "last":"Becula", "groups":["g3","g4"], "owner":["g4"], "admin":False},
    "u6" : {"name":"kay", "first":"Kay", "last":"Prath", "groups":["g3","g4"], "owner":[], "admin":False},
    "u7" : {"name":"kyle", "first":"Kyle", "last":"Lochalsh", "groups":["g3"], "owner":[], "admin":False}
}

projects = {
    "p1" : {"name":"Analysis MCAK - GFP - MCAK cell line", "user":"u1", "group":"g1",
            "datasets":["201126 - siCTL_LPM_M_total", "201126 - siHP1b_LPM_M_total", "201226 - siHP1a_LPM_M_total"]},
    "p2" : {"name":"Analysis_siAllKyotoWT_M", "user":"u1", "group":"g2",
            "datasets":["siAll_Exp1_LPM_M"]},
    "p3" : {"name":"Bod1", "user":"u2", "group":"g3",
            "datasets":["080506_ColdStable","2010-12-21_Bod1_cul3_KLHL22"]},
    "p4" : {"name":"DYRK1A_fragments", "user":"u2", "group":"g3",
            "datasets":["090120", "090121", "090122"]},
    "p5" : {"name":"Embryos", "user":"u3", "group":"g1",
            "datasets":[]},
    "p6" : {"name":"Flp-ln cell lines", "user":"u3", "group":"g2",
            "datasets":["101024-GFP-MCAK_drugs", "101026-sirna"]},
    "p7" : {"name":"Centrosomes", "user":"u4", "group":"g1",
            "datasets":["Fig 2", "Fig 3", "Fig 4"]},
    "p8" : {"name":"Cilia and Centrosomes 201108088", "user":"u4", "group":"g1",
            "datasets":["Fig 4"]},
    "p9" : {"name":"Disease", "user":"u5", "group":"g3",
            "datasets":["201102142-Fig 1", "201102142-Fig 4", "201102142-Fig 6"]},
    "p10" : {"name":"Structural analysis reveals features of the spindle checkpoint kinase", "user":"u5", "group":"g3",
            "datasets":["201110013-Figure 1", "201110013-Figure 4", "201110013-Figure 6", "201110013-Figure 8"]},
    "p11" : {"name":"Timelapse", "user":"u6", "group":"g3",
            "datasets":["200908150-Figure 1", "200908150-Figure 5", "200908150-Figure 6", ]},

    "p12" : {"name":"Term 1", "user":"u5", "group":"g4",
            "datasets":["Week 1", "Week 3", "Week 5", ]},
    "p13" : {"name":"Term 2", "user":"u5", "group":"g4",
            "datasets":["Week 1", "Week 3", "Week 5", ]},
    "p14" : {"name":"Term 3", "user":"u5", "group":"g4",
            "datasets":["Week 1", "Week 3", "Week 5", ]},
    "p15" : {"name":"Publications", "user":"u1", "group":"g2",
            "datasets":["JCB 2010", "Nature 2011", "Cell 2012"]},

    "p16" : {"name":"Analysis MCAK - GFP - MCAK cell line", "user":"u5", "group":"g3",
            "datasets":["201126 - siCTL_LPM_M_total", "201126 - siHP1b_LPM_M_total", "201226 - siHP1a_LPM_M_total"]},
    "p17" : {"name":"Analysis_siAllKyotoWT_M", "user":"u5", "group":"g3",
            "datasets":["siAll_Exp1_LPM_M"]}
}

datasets = {
    "d1" : {"name":"Importin-beta negatively regulates multiple aspects of mitosis", "user":"u4", "group":"g1"},
    "d2" : {"name":"Importin-beta negatively regulates multiple aspects of mitosis", "user":"u6", "group":"g3"}
}

tagsets = {
    "t1" : {"user":"u1", "group":"g1", "tagset":"Phases", "tags":["G2phase","Sphase","Interphase","Prometaphase","Metaphase","Anaphase","Telophase","G1phase"]},
    "t2" : {"user":"u1", "group":"g1", "tagset":None, "tags":["Mitosis","Meiosis","Cytokinesis","Postmitotic"]},
    "t3" : {"user":"u1", "group":"g2", "tagset":"Category", "tags":["Primary","Secondary","Junk"]},
    "t4" : {"user":"u2", "group":"g3", "tagset":None, "tags":["Sphase","Interphase","Prometaphase","Metaphase","Anaphase","Telophase"]},
    "t5" : {"user":"u2", "group":"g3", "tagset":"Phases", "tags":["Mitosis","Meiosis","Cytokinesis","Postmitotic"]},
    "t6" : {"user":"u5", "group":"g4", "tagset":"Assignment", "tags":["1","2","3","5","6"]}
}

# existing groups
userGroup = admin.lookupGroup("user")  # all users need to be in 'user' group to do anything! 
systemGroup = admin.lookupGroup("system")  # admin users need to be in 'system' group

####################
# Create groups
####################

for gr in groups.values():
    group = ExperimenterGroupI()
    group.name = rstring(gr["name"] + uuid)
    group.details.permissions = PermissionsI(gr["perms"])
    gr["id"] = admin.createGroup(group)
    gr["group"] = admin.getGroup(gr["id"])

####################
# Create users
####################

for usr in users.values():
    # Create an experimenter object
    user = ExperimenterI()
    user.omeName = rstring(usr["name"] + uuid)
    user.firstName = rstring(usr["first"])
    user.lastName = rstring(usr["last"])
    user.email = rstring(usr["name"] + emailsuff)
    # Set default to first group
    default = groups[usr["groups"][0]]["group"]
    # Create list of groups
    glist = [userGroup]
    for gr in usr["groups"]:
        glist.append(groups[gr]["group"])
    if usr["admin"]:
        glist.append(systemGroup)
    # Create experimenter
    usr["id"] = admin.createExperimenterWithPassword(user, passw, default, glist)
    usr["user"] = admin.getExperimenter(usr["id"])
    # Make owner
    for o in usr["owner"]:
        admin.setGroupOwner(groups[o]["group"], usr["user"])
    
conn.seppuku()

####################
# Create P/Ds
####################

for proj in projects.values():
    conn = BlitzGateway(users[proj["user"]]["name"] + uuid, userpassw, host=host)
    conn.connect()
    update = conn.getUpdateService()

    project = ProjectI()
    project.setName(rstring(proj["name"] + uuid))
    project = update.saveAndReturnObject(project,{'omero.group':str(groups[proj["group"]]["id"])})

    links = []
    for dset in proj["datasets"]:
        dataset = DatasetI()
        dataset.setName(rstring(dset + uuid))
        dataset = update.saveAndReturnObject(dataset,{'omero.group':str(groups[proj["group"]]["id"])})
        l = ProjectDatasetLinkI()
        l.setChild(dataset)
        l.setParent(project)
        links.append(l)
    if links:
        update.saveAndReturnArray(links,{'omero.group':str(groups[proj["group"]]["id"])})

    conn.seppuku()

####################
# Create Datasets
####################

for dset in datasets.values():
    conn = BlitzGateway(users[dset["user"]]["name"] + uuid, userpassw, host=host)
    conn.connect()
    update = conn.getUpdateService()

    dataset = DatasetI()
    dataset.setName(rstring(dset["name"] + uuid))
    dataset = update.saveAndReturnObject(dataset,{'omero.group':str(groups[dset["group"]]["id"])})

    conn.seppuku()

####################
# Create Tags
####################

for tset in tagsets.values():
    conn = BlitzGateway(users[tset["user"]]["name"] + uuid, userpassw, host=host)
    conn.connect()
    update = conn.getUpdateService()

    tagList = []
    for name in tset["tags"]:
        tag = TagAnnotationI()
        tag.setTextValue(rstring(name + uuid))
        tagList.append(tag)
    tagList = update.saveAndReturnArray(tagList,{'omero.group':str(groups[tset["group"]]["id"])})

    if tset["tagset"]:
        tag = TagAnnotationI()
        tag.setTextValue(rstring(tset["tagset"] + uuid))
        tag.setNs(rstring(omero.constants.metadata.NSINSIGHTTAGSET))
        tag = update.saveAndReturnObject(tag,{'omero.group':str(groups[tset["group"]]["id"])})
        links = []
        for child in tagList:
            l = AnnotationAnnotationLinkI()
            l.setChild(child)
            l.setParent(tag)
            links.append(l)
        update.saveAndReturnArray(links,{'omero.group':str(groups[tset["group"]]["id"])})

    conn.seppuku()