PATH = '/CercalSystem/'
CERCDB = PSDB(URL, PATH)
def getVaric(iid):
df = CERCDB.getFile(iid)
doc = deserialize(df)
var = doc.getElements('Fiducial', {"Style":"spheres"})
return var
records = CERCDB.get(PATH)
doc = nmpml.blankDocument()
for rec in records:
if 'afferent' in rec['metadata']['anatomy_type']:
iid = rec['id']
print iid
els = getVaric(iid)
if not els:
print("warning, no varicosities in record %s. Skipping record" % iid)
continue
elif len(els)>1:
print("warning, duplicate varicosities in record %s. Using first element" % (iid,))
el = els[0]
el.sever()
el.setName("v"+iid)
metas = CERCDB.getInfo(iid)['metadata']
for k in metas:
el.setAttrib('meta_'+k, metas[k])
doc.newElement(el)
io.write(doc, 'varric.mat', format='.mat')
class DBTool(BaseGui):
def __init__(self, parent, **opts):
BaseGui.__init__(self, parent, title="Database Tool", menus=["Connection", "Get", "Put"], pycommand=True)
controls = [
["Connection", "Choose Data Store", self.selectDB],
["Get", "List All Entries", self.list],
["Get", "Show Details", self.infoprint],
["Get", "Search", self.do_search],
["Get", "Download Single File", self.download],
["Get", "Download Several Files", self.downloadGroup],
["Put", "Upload Current File", self.upload],
]
self.fillMenus(controls)
self.mainSizer = wx.BoxSizer(wx.VERTICAL)
self.main.SetSizer(self.mainSizer)
self.main.SetAutoLayout(True)
self.SetAutoLayout(True)
self.mainSizer.Add(wx.StaticText(self.main, -1, "Connected To:"), 1, wx.GROW | wx.ALL | wx.ALIGN_CENTRE, 5)
self.dbid = wx.StaticText(self.main, -1, "")
self.mainSizer.Add(self.dbid, 1, wx.GROW | wx.ALL | wx.ALIGN_CENTRE, 5)
self.dbreccount = wx.StaticText(self.main, -1, "0 Records")
self.mainSizer.Add(self.dbreccount, 1, wx.GROW | wx.ALL | wx.ALIGN_CENTRE, 5)
self.selectDB(None, URLS[0], "/CercalSystem/")
self.doc = self.Parent.document
self.SetSize(wx.Size(500, 200))
def getMetas(self):
conflict = []
metas = {}
for e in self.doc.elements:
m = dict([(k[5:], e.attrib(k)) for k in e.attributes if k.startswith("meta_")])
for k in m:
if k in conflict:
continue
elif not k in metas:
metas[k] = m[k]
elif metas[k] != m[k]:
del (metas[k])
conflict.append(k)
return metas
def classList(self, url):
z = Resource(url)
d = z.get("/Class/")
cl = ["/" + a["id"] + "/" for a in d if not a.get("core")]
return cl
def selectDB(self, event, url=None, clas="/CercalSystem/"):
if not url:
if len(URLS) == 1:
self.report("Only one datastore available. Using it")
url = URLS[0]
else:
d = self.askParam([{"Name": "Select Database Site", "Type": "List", "Value": URLS}])
if not d:
return
url = d[0]
if not clas or type(clas) == int:
cl = self.classList(url)
if len(cl) == 1:
clas = cl[0]
elif type(clas) == int:
clas = cl[clas]
else:
d = self.askParam([{"Name": "Select Database Table", "Type": "List", "Value": cl}])
if not d:
return
clas = d[0]
self.rest = PSDB(url, clas)
self.dbid.SetLabel("%s%s" % (url, clas))
n = len(self.list(None))
self.dbreccount.SetLabel("%i records" % n)
def list(self, event):
ids = self.rest.getIDList()
if event == None:
return ids
self.report("\n".join(ids))
def upload(self, event):
groups = self.doc.getElements("Group")
groups = [g for g in groups if g.attrib("DBrecord")]
if any(groups):
self.report("found existing records. Committing them to the DB")
for g in groups:
self.report(g.name())
self.upload_group(g)
else:
self.report("no existing DB groups. Uploading whole file as new record")
self.upload_doc()
def upload_group(self, g):
m = dict([(k[5:], g.attrib(k)) for k in g.attributes if k.startswith("meta_")])
name = g.name()
self.do_upload(name, g, m)
def upload_doc(self):
m = self.getMetas()
name = "%s_%s_%s" % (m["length"][0].upper(), str(m["class"]), str(m["slide_number"]))
self.do_upload(name, self.doc, m)
def do_upload(self, name, doc, meta):
name = name.replace(".", "_")
s = serialize(None, doc)
self.rest.addOrUpdate(name, meta, s)
self.report("sent")
def infoprint(self, event):
ids = self.list(None)
d = self.askParam([{"Name": "Which Record?", "Type": "List", "Value": ids}])
if not d:
return
print self.rest.getInfo(d[0])
def do_search(self, event):
j = self.rest.get(self.rest.path)
import ccbcv.yogo
reload(ccbcv.yogo)
s = ccbcv.yogo.SearchGui(self, j)
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 downloadGroup(self, event=None, records=None):
if not records:
ids = self.list(None)
d = self.askParam([{"Name": "Which Record?", "Type": "Select", "Value": ids}])
if not d:
return
records = d[0]
for r in records:
self.download(None, r, True, False)
self.Parent.update_all(element=self.Parent.document, action="rebuild")
