def download(self, event=None, record=None, append=True, refresh=True):
if not record:
ids = self.list(None)
d = self.askParam([{"Name": "Which Record?", "Type": "List", "Value": ids}])
if not d:
return
record = d[0]
df = self.rest.getFile(record)
doc = deserialize(df)
if not append:
self.Parent.newDoc(doc)
else:
m = self.rest.getInfo(record)["metadata"]
m = dict([("meta_" + k, m[k]) for k in m])
m["Name"] = record
m["DBrecord"] = self.rest.path
m["DBurl"] = self.rest.url
m["color"] = (255, 255, 255)
group = createElement("Group", m)
self.Parent.document.newElement(group)
for e in doc.elements[:]:
e.move(group)
if refresh:
self.Parent.update_all(element=self.Parent.document, action="rebuild")
def run(self):
doc=self.send('get object')
self.doc=mzip.deserialize(doc)
print 'client registered'
while not self.abort:
self.doJob()
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with
# this program; if not, write to the Free Software Foundation, Inc., 59 Temple
# Place, Suite 330, Boston, MA 02111-1307 USA
#
from mien.interface.cellview3D import CellViewer
import wx, os, sys, tempfile
from mien.parsers.mzip import deserialize
sys.path.append("/home/gic/mienblocks")
from ccbcv.rest import PSDB
URL = 'http://cercus.cns.montana.edu:8090'
PATH = '/CercalCellAfferent/'
CERCDB = PSDB(URL, PATH)
os.environ['DISPLAY'] = 'localhost:1.0'
record = sys.argv[1]
wxapp = wx.PySimpleApp()
x = CellViewer()
x.Show(True)
df = CERCDB.getFile(record)
doc = deserialize(df)
x.newDoc(doc)
fid, fname=tempfile.mkstemp('.png')
x.graph.screenShot(fname)
CERCDB.putFile(record, open(fname,'rb').read(), "snapshot", 'image/png')
os.unlink(fname)
def dbscript(lfn):
"""The first argument should be a command. Allowed commands are:
add, set, del, list, info, pull, metas, file
add takes a list of file names to add to the db.
set takes a DB id, meta tag, and value, and sets the indicated
tag on the indicated object to the value
del deletes the listed DB ids. The first ID may be "all" to
clear the db.
list takes no arguments and prints a list of ids of the db entries
info takes a list of ids and prints detailed info about each
pull takes a db id and a file name, and downloads the datafile
associated to the id into the named file.
metas list all the defined metadata tags in the db
file takes a db id, an attribute name (e.g. image) and a file name
downloads the named file attribute into the named file
"""
cmd = lfn[0]
PATH = "/CercalSystem/"
CERCDB = PSDB(URL, PATH)
CERCDB.auth("gic", "graham")
if cmd == "del":
lfn = lfn[1:]
if lfn and lfn[0] == "all":
lfn = CERCDB.getIDList()
for name in lfn:
CERCDB.delete(name)
print "deleted entry %s" % name
elif cmd == "add":
for fn in lfn[1:]:
doc = io.read(fn)
groups = doc.getElements("Group", depth=1)
groups = [g for g in groups if g.attrib("DBrecord")]
if groups:
for grp in groups:
print ("Commiting db group %s from %s" % (grp.name(), fn))
m = dict([(k[5:], grp.attrib(k)) for k in grp.attributes if k.startswith("meta_")])
name = grp.name()
name = name.replace(".", "_")
s = serialize(None, grp)
if grp.attrib("DBurl") == URL and grp.attrib("DBrecord") == PATH:
db = CERCDB
else:
db = PSDB(grp.attrib("DBurl"), grp.attrib("DBrecord"))
db.addOrUpdate(name, m, s)
else:
m = db_getmetas(doc)
if "dbid" in m:
name = m["dbid"]
del (m["dbid"])
else:
name = "%s_%s_%s" % (m["length"][0].upper(), str(m["class"]), str(m["slide_number"]))
print "commiting %s as %s" % (fn, name)
s = serialize(None, doc)
CERCDB.addOrUpdate(name, m, s)
elif cmd == "set":
iid = lfn[1]
tag = lfn[2]
val = lfn[3]
nmd = {tag: val}
CERCDB.update(iid, nmd)
elif cmd == "list":
for iid in CERCDB.getIDList():
print (iid)
elif cmd == "info":
l = CERCDB.get(CERCDB.path)
lidd = dict([(e["id"], e) for e in l])
for id_ in lfn[1:]:
e = lidd.get(id_, "No such entry")
print (e)
elif cmd == "pull":
record = lfn[1]
fname = lfn[2]
df = CERCDB.getFile(record)
doc = deserialize(df)
doc = io.write(doc, fname, format="guess")
elif cmd == "metas":
l = CERCDB.get(CERCDB.path)
metas = set([])
for e in l:
md = e["metadata"]
for k in md:
metas.add(k)
for k in metas:
print (k)
elif cmd == "file":
record = lfn[1]
fpath = lfn[2]
fname = lfn[3]
df = CERCDB.getFile(record, fpath)
open(fname, "wb").write(df)
def getVaric(iid):
df = CERCDB.getFile(iid)
doc = deserialize(df)
var = doc.getElements('Fiducial', {"Style":"spheres"})
return var
