class IRIDA(IRIDAQueryLayout):
#baseURL = "https://irida.corefacility.ca/irida-public-test/irida-api/"
#baseURL = "https://irida.corefacility.ca/staging/api/"
#baseURL = "http://localhost:48888/irida/api/"
baseURL = "http://129.173.66.114:48888/irida/api/"
#clientId = "gengis"
clientId = ""
# THIS NEEDS TO BE HIDDEN
clientSecret = ""
#clientSecret = "bledjijitFeOpEerichFeatsatHowGheibwenecWijWifciek/"
username = ""
password = ""
service = ""
token = ""
selectedTaxon = set()
# this will be a 1:1 mapping of Project Name to Unique ID
projectMap = {}
obs = []
phylo = ""
def __init__(self,parent=None):
IRIDAQueryLayout.__init__(self,parent)
self.GBIFGeneric = GBIFGeneric()
self.login = Login(self)
#self.credentials = Credentials()
self.SetIcon(wx.Icon(GenGIS.mainWindow.GetExeDir() + "images/CrazyEye.ico",wx.BITMAP_TYPE_ICO))
self.m_Add.SetBitmapLabel(wx.Image(GenGIS.mainWindow.GetExeDir() + "images/green_arrow_down.png",wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.m_Add.SetBitmapHover(wx.Image(GenGIS.mainWindow.GetExeDir() + "images/green_arrow_down_hover.png",wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.m_Remove.SetBitmapLabel(wx.Image(GenGIS.mainWindow.GetExeDir() + "images/red_arrow_up.png",wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.m_Remove.SetBitmapHover(wx.Image(GenGIS.mainWindow.GetExeDir() + "images/red_arrow_up_hover.png",wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.m_IDList.Clear()
self.m_Search.Enable(False)
self.m_Calc.Enable(False)
#fix to expand summary box enough to print two lines of text properly
#Map Data
if GenGIS.layerTree.GetNumMapLayers() > 0 :
self.m_AddData.Enable()
borders = GenGIS.layerTree.GetMapLayer(0).GetController().GetMapBorders()
#check if geographic coordinates are used or some other measure; only geographic are compatible
geographic = GenGIS.StudyController.IsUsingGeographic(GenGIS.study.GetController())
projected = GenGIS.StudyController.IsUsingProjection(GenGIS.study.GetController())
if(not (geographic or projected)):
wx.MessageBox("Geographic coordinates are not being used in the current map file. Only geographic coordinates are compatible with MG-RAST. Geographic range will need to be manually set, and any returned data will not display correctly.","Warning")
self.m_AddData.Disable()
credential = Credentials(self,False)
credential.OnCredentialClose("fake")
# By this point the active credential should be loaded.
if self.clientId and self.clientSecret:
self.login.ShowModal()
def ReLogin(self, event):
self.login.ShowModal()
# Bring the main IRIDA instance back to the foreground after running login.
self.Raise()
def SetClientID(self,ID):
self.clientId = ID
def SetClientSecret(self,secret):
self.clientSecret = secret
def HandleLinks(self, result, type):
response = {}
if type == 'label':
response['label'] = '';
links = result[type]
for val in links:
if type=='links':
response[val['rel']] = val['href']
elif type == 'label':
response['label'] = response['label'] + val
else:
if 'name' in val:
response[val['name']] = val
elif 'sampleName' in val:
response[val['sampleName']] = val
return response
def ngs_request(self, url, oauth_service, access_token,debug=False):
session = oauth_service.get_session(access_token)
# the raw json being fetched
response = session.get(url)
# print response.text
if debug:
print response.text
result = json.loads(response.text)
return result
def newick_request( self, url, oauth_service, access_token, debug = False):
session = oauth_service.get_session(access_token)
# the raw newick being fetched
response = session.request("GET",url, True,headers={'Accept':'text/plain'})
if debug:
print response.text
return response.text
def decoder(self,returnDict):
# NEEDS A WAY TO DETECT BAD PASSWORD
# print returnDict
# if "Error report" in returnDict:
# print "error occured"
# return {}
iridaDict = ast.literal_eval(returnDict)
if "error" in iridaDict.keys():
wx.MessageBox(iridaDict['error_description'], iridaDict['error'])
return None
return iridaDict
def GetOauthService(self):
oauth_service = OAuth2Service(
client_id = self.clientId,
client_secret = self.clientSecret,
name="irida",
access_token_url = self.baseURL + "oauth/token",
base_url=self.baseURL)
return oauth_service
def GetParams(self):
params = {'data' : {'grant_type' : 'password',
'client_id' : self.clientId,
'client_secret' : self.clientSecret,
'username' : self.username,
'password' : self.password}}
return params
def GetToken(self):
oauth_service = self.GetOauthService()
params = self.GetParams()
try:
# print "sandwich"
access_token = oauth_service.get_access_token(decoder = self.decoder,**params)
# print "banana"
except:
return None, None
session = oauth_service.get_session(access_token)
return oauth_service, access_token
# Type is either RESOURCES or LINKS
def GetResponse(self, url, oauth_service, access_token, type, debug=False):
result = self.ngs_request(url, oauth_service, access_token, debug)
if debug:
print "#########\n\n",result,"\n\n#########"
response = {}
try:
# parse out the response from the server
response = self.HandleLinks(result['resource'],type)
except ValueError:
print "Server replied but reponse is in an unsupported format."
sys.exit(1)
return response
# Formates a lat/lon into one string with 2 decimal places
def FormatLocation(self, value):
lat = value['latitude']
lon = value['longitude']
if lat != None and lon != None:
loc = '%.2f_%.2f'%(float(lat),float(lon))
return lon,lat,loc
else:
loc = '0_0'
return 0,0,loc
#Given All samples create a set of unique locations and the sequences that belong to them
#Returns a dictionary of this information
def CreateLocations(self, samples):
idNum = 1
idString = 'Loc_'
locations = {}
for sample in samples:
for key, value in sample.items():
lon,lat,loc = self.FormatLocation(value)
id = idString + '%0*d' %(3,idNum)
idNum += 1
if loc in locations:
locations[loc].append(key)
else:
locations[loc] = [id, lon, lat, key]
return locations
def CreateOutText(self, locations, samples):
locationText = ""
sequenceText = ""
locationHeader = "Site ID, Longitude, Latitude\n"
sequencesHeader = ["Sequence ID, Site ID "]
first = True
#first create locations
for key, value in locations.items():
locationText = '%s%s, %s, %s\n' %( locationText, value[0], value[1], value[2] )
locationText = locationHeader + locationText
#then create sequences
for sample in samples:
for key, values in sample.items():
seq = []
#Append Sequence ID
seq.append(key)
#Append Site ID
# seq.append('Seq_%0*d' %(3, idNum) )
lon,lat,loc = self.FormatLocation(values)
seq.append(locations[loc][0])
for i,j in values.items():
if i == 'links':
continue
if first:
sequencesHeader.append(str(i))
seq.append(str(j).replace(',','|'))
first = False
text = ','.join(seq)
sequenceText = sequenceText + text + '\n'
sequenceHeader = ','.join(sequencesHeader)
sequenceText = sequenceHeader + '\n' + sequenceText
return locationText, sequenceText
def OnHelp(self, event):
wx.LaunchDefaultBrowser( 'http://kiwi.cs.dal.ca/GenGIS/index.php/Description_of_GenGIS_plugins#MG-RAST_Query' )
# Close the Plugin
def OnClose(self, event):
if self.login:
self.login.Close()
event.Skip()
# Close the Plugin
def OnOK( self, event ):
self.Close()
# Add Data from Results Table to ID List
def OnAdd(self,event):
i=0
IDCount = self.m_IDList.GetCount()
for index in self.m_Result.GetSelections():
selected = self.m_Result.GetString(index)
split = selected.split(": ")
if (split[0],split[1]) not in self.selectedTaxon:
self.m_IDList.InsertItems(["%s" % selected],IDCount+i)
#add study ID and study location
self.selectedTaxon.add((split[0],split[1]))
i+=1
# Remove Data from ID List
def OnRemove(self,event):
candidates = sorted(self.m_IDList.GetSelections(),reverse=True)
for index in candidates:
selected = self.m_IDList.GetString(index)
split = selected.split(": ")
self.selectedTaxon.remove((split[0],split[1]))
self.m_IDList.Delete(index)
# Retrieves token from IRIDA API.
def AuthorizeToken(self):
if self.username == "" or self.password == "":
wx.MessageBox("Please enter a username and/or password.")
return 0
if self.clientId == "" or self.clientSecret == "":
wx.MessageBox("No Client Credentials have been loaded.")
return -1
try:
self.service, self.token = self.GetToken()
if self.service == None or self.token == None:
wx.MessageBox("Bad username and/or password.")
return 0
except ValueError:
wx.MessageBox("Unable to retrieve token from API at this time. Please try again later.")
return 0
return 1
def InitializeResults(self):
wx.BeginBusyCursor()
result = []
links = self.GetResponse(self.baseURL+'projects/', self.service, self.token,'resources')
if len(links.keys())==0:
wx.MessageBox("No Projects currently stored in IRIDA")
else:
for key,value in links.items():
str = "%s: %s" %(key,value['projectDescription'])
# add mapping for this project
self.projectMap[key] = value['identifier']
result.append(str)
self.m_Result.InsertItems(result,self.m_Result.GetCount())
wx.EndBusyCursor()
def InitializeAnalyses(self):
wx.BeginBusyCursor()
result = []
links = self.GetResponse(self.baseURL+'analysisSubmissions/', self.service, self.token,'resources')
if len(links.keys())==0:
wx.MessageBox("No analyses currently stored in IRIDA")
else:
for key,value in links.items():
str = "%s: %s" %(key,value['label'])
# add mapping for this project
self.projectMap[key] = value['identifier']
result.append(str)
self.m_Result.InsertItems(result,self.m_Result.GetCount())
wx.EndBusyCursor()
def OnSearch(self,event):
wx.BeginBusyCursor()
# Clear the results list
projName = self.m_ProjectName.GetValue()
if projName not in self.projectMap.keys():
wx.EndBusyCursor()
wx.MessageBox("Please enter a valid Project name.")
return
project = projName
if(len(project)==0):
wx.MessageBox("You did not enter a taxon name.")
else:
self.selectedTaxon.clear()
self.selectedTaxon.add((project,"dummy value"))
self.OnCalculate(wx.EVT_BUTTON)
wx.EndBusyCursor()
def OnCalculate( self, event):
self.RetrieveSamples()
# self.RetrievePhylogeny()
# def RetrieveSamples(self,event):
def RetrieveSamples(self):
if(self.selectedTaxon):
#index of which taxon is being used
index = 0
for proj in self.selectedTaxon:
self.m_Progress.WriteText("Retrieving %s...\n" %(proj[0]))
project = self.projectMap[proj[0]]
# projectURL = '%sprojects/%s' %(self.baseURL,project)
projectURL = '%sprojects/%s' %(self.baseURL,3)
self.phylo = self.RetrieveKnownPhylogeny(project)
# print newick
projLink = self.GetResponse(projectURL, self.service, self.token,'links')
sampleURL = projLink['project/samples']
samples = self.GetResponse(sampleURL, self.service, self.token, 'resources')
# obs is just a list of these samples
self.obs.append(samples)
self.m_Progress.WriteText("%s samples retrieved.\n" %(len(samples.keys())))
self.m_Progress.WriteText("Done.\n")
# def RetrievePhylogeny(self,event):
def RetrievePhylogeny(self):
if(self.selectedTaxon):
#index of which taxon is being used
index = 0
for proj in self.selectedTaxon:
self.m_Progress.WriteText("Retrieving %s...\n" %(proj[0]))
project = self.projectMap[proj[0]]
projectURL = '%sanalysisSubmissions/%s' %(self.baseURL,project)
print projectURL
projLink = self.GetResponse(projectURL, self.service, self.token,'links')
analysisURL = projLink['analysis']
print analysisURL
# get samples
'''
sequenceURL = analysisURL + "/sequenceFiles/pairs"
print "pants"
sequenceLink = self.GetResponse(projectURL, self.service, self.token, 'response',True)
print "sandwich"
'''
# get phylogeny
links = self.GetResponse(analysisURL, self.service, self.token, 'links')
newickURL = links['outputFile/tree']
newick = self.newick_request(newickURL, self.service,self.token,True)
# obs is just a list of these samples
# self.obs.append(samples)
self.m_Progress.WriteText("%s samples retrieved.\n" %(len(samples.keys())))
self.m_Progress.WriteText("Done.\n")
def RetrieveKnownPhylogeny(self, identifier):
projectURL = '%sanalysisSubmissions/%s' %(self.baseURL,identifier)
projLink = self.GetResponse(projectURL, self.service, self.token,'links')
analysisURL = projLink['analysis']
# get phylogeny
links = self.GetResponse(analysisURL, self.service, self.token, 'links')
newickURL = links['outputFile/tree']
newick = self.newick_request(newickURL, self.service,self.token)
return newick
def OnAddData(self, event):
if GenGIS.layerTree.GetNumMapLayers() == 0:
wx.MessageBox("This action requires a Map layer. Please load a Map.")
return
if len(self.obs) > 0:
loc = self.CreateLocations(self.obs)
locText, seqText = self.CreateOutText(loc,self.obs)
locArray = locText.split('\n')
seqArray = seqText.split('\n')
locArray.pop()
seqArray.pop()
layerName = "IRIDALayer_%d" % GenGIS.layerTree.GetNumLocationLayers()
GenGIS.mainWindow.OpenLocationsCSVFile(locArray, layerName)
GenGIS.mainWindow.OpenSequenceCSVFile(seqArray, layerName)
print self.phylo
self.phylo = self.phylo.replace("reference:0.00000001,","")
print self.phylo
fh = "phylogeny.nwk"
file = open("phylogeny.nwk",'w')
file.write(self.phylo)
file.close()
GenGIS.mainWindow.OpenTreeFile(fh)
else:
wx.MessageBox("Please make a successful IRIDA query first.")
def OnExportData(self,event):
if (len(self.obs) > 0):
fileTypes = 'Loc and Seq Files (*.csv)|*.csv'
dlg = wx.FileDialog(self, "Save plot", "", "", fileTypes, wx.SAVE)
if dlg.ShowModal()==wx.ID_OK:
filename = dlg.GetFilename()
dir = dlg.GetDirectory()
file_split = filename.split(".",1)
OUTLfile = os.path.join(dir,file_split[0]+"_locs.csv")
OUTSfile = os.path.join(dir,file_split[0]+"_seqs.csv")
loc = self.CreateLocations(self.obs)
locText, seqText = self.CreateOutText(loc,self.obs)
self.GBIFGeneric.WRITEEXPORT(OUTLfile , locText )
self.GBIFGeneric.WRITEEXPORT(OUTSfile, seqText )
def SetToken(self,tok):
self.token = tok
def OnCredentials(self,event):
credentials = Credentials(self)
credentials.Show()
def OnCredentialClose(self,active):
# self.credential = active
self.clientId = active.GetID()
self.clientSecret = active.GetSecret()
class GBIFQuery(GBIFQueryLayout):
# Global variables to store queried information
__obs__ = []
__selectedTaxon__ = set()
__description__ = ""
masterKeys = set()
def __init__(self, parent=None):
MaxLon, MinLon, MaxLat, MinLat = 180, -180, 90, -90
self.GBIFSpecific = GBIFSpecific()
self.GBIFGeneric = GBIFGeneric()
GBIFQueryLayout.__init__(self, parent)
self.SetIcon(
wx.Icon(GenGIS.mainWindow.GetExeDir() + "images/CrazyEye.ico",
wx.BITMAP_TYPE_ICO))
self.m_Compass.SetIcon(
wx.Icon(
GenGIS.mainWindow.GetExeDir() +
"images/GBIF_compass_small.png", wx.BITMAP_TYPE_PNG))
self.m_Add.SetBitmapLabel(
wx.Image(
GenGIS.mainWindow.GetExeDir() + "images/green_arrow_down.png",
wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.m_Add.SetBitmapHover(
wx.Image(
GenGIS.mainWindow.GetExeDir() +
"images/green_arrow_down_hover.png",
wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.m_Remove.SetBitmapLabel(
wx.Image(GenGIS.mainWindow.GetExeDir() + "images/red_arrow_up.png",
wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.m_Remove.SetBitmapHover(
wx.Image(
GenGIS.mainWindow.GetExeDir() +
"images/red_arrow_up_hover.png",
wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.graphicalElementIds = []
self.__selectedTaxon__ = set()
self.__obs__ = []
self.m_IDList.Clear()
#fix to expand summary box enough to print two lines of text properly
self.m_Summary.SetLabel("\n\n")
#No Map Data
self.m_AddData.Disable()
#Map Data
if GenGIS.layerTree.GetNumMapLayers() > 0:
self.m_AddData.Enable()
borders = GenGIS.layerTree.GetMapLayer(
0).GetController().GetMapBorders()
#check if geographic coordinates are used or some other measure; only geographic are compatible
geographic = GenGIS.StudyController.IsUsingGeographic(
GenGIS.study.GetController())
projected = GenGIS.StudyController.IsUsingProjection(
GenGIS.study.GetController())
if (not (geographic or projected)):
wx.MessageBox(
"Geographic coordinates are not being used in the current map file. Only geographic coordinates are compatible with MG-RAST. Geographic range will need to be manually set, and any returned data will not display correctly.",
"Warning")
self.m_AddData.Disable()
self.m_MinLat.SetValue(str(MinLat))
self.m_MaxLat.SetValue(str(MaxLat))
self.m_MinLon.SetValue(str(MinLon))
self.m_MaxLon.SetValue(str(MaxLon))
else:
#Text boxes hate non String types. use int to round, and string to make them fit the container
# if projected coordinates but not geographic, a conversion may be possible
if (projected and not geographic):
convTop = self.GBIFGeneric.SpecialUTMConversion(
borders.x1, borders.y1)
convBottom = self.GBIFGeneric.SpecialUTMConversion(
borders.dx, borders.dy)
borders.x1 = convTop.easting
borders.y1 = convTop.northing
borders.dx = convBottom.easting
borders.dy = convBottom.northing
#limiting borders
self.m_MinLat.SetValue(
str("%.1f" %
self.GBIFGeneric.BorderTest(MinLat, borders.y1, max)))
self.m_MaxLat.SetValue(
str("%.1f" %
self.GBIFGeneric.BorderTest(MaxLat, borders.dy, min)))
self.m_MinLon.SetValue(
str("%.1f" %
self.GBIFGeneric.BorderTest(MinLon, borders.x1, max)))
self.m_MaxLon.SetValue(
str("%.1f" %
self.GBIFGeneric.BorderTest(MaxLon, borders.dx, min)))
# Query GBIF for Taxa in Lat/Lon Boundary
def OnSearch(self, event):
wx.BeginBusyCursor()
# Clear the results list
self.m_Result.Clear()
taxon = self.m_TaxonName.GetLineText(0)
taxon = taxon.split()
if (len(taxon) == 0):
wx.MessageBox("You did not enter a taxon name.")
else:
minLatitude = float(self.m_MinLat.GetValue())
maxLatitude = float(self.m_MaxLat.GetValue())
minLongitude = float(self.m_MinLon.GetValue())
maxLongitude = float(self.m_MaxLon.GetValue())
result = self.GBIFSpecific.GETTAXRESULT(taxon, self.m_Result)
self.m_Result.InsertItems(result, 0)
wx.EndBusyCursor()
# Create Sequence and Location files for selected Taxa
def OnCalculate(self, event):
self.m_Summary.SetLabel("\n")
records, distLocations = 0, 0
self.__obs__ = []
self.__conversions__ = []
self.__description__ = ""
wx.BeginBusyCursor()
if (self.__selectedTaxon__):
minLatitude = float(self.m_MinLat.GetValue())
maxLatitude = float(self.m_MaxLat.GetValue())
minLongitude = float(self.m_MinLon.GetValue())
maxLongitude = float(self.m_MaxLon.GetValue())
self.m_Progress.WriteText("Starting...\n")
for tax in self.__selectedTaxon__:
obs, self.masterKeys, records = self.GBIFSpecific.GETOBSENTIRERANGE(
tax[0], minLatitude, maxLatitude, minLongitude,
maxLongitude, self.m_Progress)
self.__obs__.append(obs)
distLocations += len(obs)
self.m_Progress.WriteText("Done.\n")
else:
wx.MessageBox("Please select some Taxa.")
summaryText = ("%d records retrieved.\n%d distinct locations." %
(records, distLocations))
f = self.m_Summary.GetFont()
dc = wx.WindowDC(self.m_Summary)
dc.SetFont(f)
aSize = dc.GetMultiLineTextExtent(summaryText)
aSize = wx.Size(aSize[0], aSize[1])
self.m_Summary.SetSize(aSize)
self.m_Summary.SetLabel(summaryText)
wx.EndBusyCursor()
# Present the number of locations a user is about to query
# Used as a check by the user to know they aren't going to produce way too much data.
def OnPreCalculate(self, event):
wx.BeginBusyCursor()
self.m_Progress.WriteText("Retrieving record counts.\n")
self.m_Summary.SetLabel("\n")
if (self.__selectedTaxon__):
count = 0
for tax in self.__selectedTaxon__:
count += self.GBIFSpecific.GETCOUNT(tax[1].split(), tax[0],
self.m_Progress)
self.m_Summary.SetLabel(
"There were %d records for the given location." % count)
else:
wx.MessageBox("Please select some Taxa.")
wx.EndBusyCursor()
# Redirects User to Wiki page for this plugin
def OnHelp(self, event):
wx.LaunchDefaultBrowser(
'http://kiwi.cs.dal.ca/GenGIS/index.php/Description_of_GenGIS_plugins#GBIF_Query'
)
# Adds Data to GenGIS
def OnAddData(self, event):
if (len(self.__obs__) > 0):
OUTLText, OUTSText = self.GBIFGeneric.GETTEXT(
self.__obs__, self.masterKeys)
OUTLArray = self.GBIFGeneric.CPPOUT(OUTLText)
OUTSArray = self.GBIFGeneric.CPPOUT(OUTSText)
OUTLArray.pop()
OUTSArray.pop()
layerName = "GBIFLayer_%d" % GenGIS.layerTree.GetNumLocationSetLayers(
)
GenGIS.mainWindow.OpenLocationsCSVFile(OUTLArray, layerName)
GenGIS.mainWindow.OpenSequenceCSVFile(OUTSArray, layerName)
#Get the number of last location layer added (the gbif one)
numLocationLayers = GenGIS.layerTree.GetNumLocationSetLayers()
locationSetLayer = GenGIS.layerTree.GetLocationSetLayer(
numLocationLayers - 1)
else:
wx.MessageBox("Please make a successful GBIF Query first.")
# Exports Location and Sequence Data to a location of the users choice
def OnExportData(self, event):
if (len(self.__obs__) > 0):
fileTypes = 'Loc and Seq Files (*.csv)|*.csv'
dlg = wx.FileDialog(self, "Save plot", "", "", fileTypes, wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetFilename()
dir = dlg.GetDirectory()
file_split = filename.split(".", 1)
#creates the directories
OUTLfile = os.path.join(dir, file_split[0] + "_locs.csv")
OUTSfile = os.path.join(dir, file_split[0] + "_seqs.csv")
OUTLText, OUTSText = self.GBIFGeneric.GETTEXT(
self.__obs__, self.masterKeys)
self.GBIFGeneric.WRITEEXPORT(OUTLfile, OUTLText)
self.GBIFGeneric.WRITEEXPORT(OUTSfile, OUTSText)
dlg.Destroy()
else:
wx.MessageBox("Please make a successful GBIF Query first.")
# Add Data from Results Table to ID List
def OnAdd(self, event):
i = 0
IDCount = self.m_IDList.GetCount()
for index in self.m_Result.GetSelections():
selected = self.m_Result.GetString(index)
split = selected.split(" | ")
if (int(split[0]), split[1]) not in self.__selectedTaxon__:
self.m_IDList.InsertItems(["%s" % selected], IDCount + i)
self.__selectedTaxon__.add((int(split[0]), split[1]))
i += 1
# Remove Data from ID List
def OnRemove(self, event):
candidates = sorted(self.m_IDList.GetSelections(), reverse=True)
for index in candidates:
selected = self.m_IDList.GetString(index)
split = selected.split(" | ")
self.__selectedTaxon__.remove((int(split[0]), split[1]))
self.m_IDList.Delete(index)
# Close the Plugin
def OnClose(self, event):
# remove plotted lines
for id in self.graphicalElementIds:
GenGIS.graphics.RemoveLine(id)
GenGIS.viewport.Refresh()
event.Skip()
# Close the Plugin
def OnOK(self, event):
self.Close()
def OnLatEnter(self, event):
str = event.GetString()
str2 = re.sub('[^\d\.\-]', '', str)
if str2 and str != "-":
str3 = float(str2)
if str3 > 90:
str2 = str2[:-1]
elif str3 < -90:
str2 = str2[:-1]
event.GetClientData().SetValue(str2)
event.GetClientData().SetInsertionPoint(len(str2))
def OnLonEnter(self, event):
str = event.GetString()
str2 = re.sub('[^\d\.\-]', '', str)
if str2 and str != "-":
str3 = float(str2)
if str3 > 180:
str2 = str[:-1]
elif str3 < -180:
str2 = str[:-1]
event.GetClientData().SetValue(str2)
event.GetClientData().SetInsertionPoint(len(str2))
class MGRastQuery(MGRASTQueryLayout):
# Global variables to store queried information
__obs__ = []
__selectedTaxon__ = set()
__description__ = ""
__options__ = ""
__metaVals__ = {}
__TAXON__ = [
"Domain", "Phylum", "Class", "Order", "Family", "Genus", "Species",
"Strain"
]
def __init__(self, parent=None):
self.__options__ = Options()
self.MGRastSpecific = MGRastSpecific()
MGRASTQueryLayout.__init__(self, parent)
self.GBIFGeneric = GBIFGeneric()
self.SetIcon(
wx.Icon(GenGIS.mainWindow.GetExeDir() + "images/CrazyEye.ico",
wx.BITMAP_TYPE_ICO))
self.m_Add.SetBitmapLabel(
wx.Image(
GenGIS.mainWindow.GetExeDir() + "images/green_arrow_down.png",
wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.m_Add.SetBitmapHover(
wx.Image(
GenGIS.mainWindow.GetExeDir() +
"images/green_arrow_down_hover.png",
wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.m_Remove.SetBitmapLabel(
wx.Image(GenGIS.mainWindow.GetExeDir() + "images/red_arrow_up.png",
wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.m_Remove.SetBitmapHover(
wx.Image(
GenGIS.mainWindow.GetExeDir() +
"images/red_arrow_up_hover.png",
wx.BITMAP_TYPE_PNG).ConvertToBitmap())
self.m_Compass.SetIcon(
wx.Icon(
GenGIS.mainWindow.GetExeDir() +
"images/GBIF_compass_small.png", wx.BITMAP_TYPE_PNG))
MaxLon, MinLon, MaxLat, MinLat = 180, -180, 90, -90
self.m_IDList.Clear()
#fix to expand summary box enough to print two lines of text properly
self.m_Summary.SetLabel("\n\n")
#Map Data
if GenGIS.layerTree.GetNumMapLayers() > 0:
self.m_AddData.Enable()
borders = GenGIS.layerTree.GetMapLayer(
0).GetController().GetMapBorders()
#check if geographic coordinates are used or some other measure; only geographic are compatible
geographic = GenGIS.StudyController.IsUsingGeographic(
GenGIS.study.GetController())
projected = GenGIS.StudyController.IsUsingProjection(
GenGIS.study.GetController())
if (not (geographic or projected)):
wx.MessageBox(
"Geographic coordinates are not being used in the current map file. Only geographic coordinates are compatible with MG-RAST. Geographic range will need to be manually set, and any returned data will not display correctly.",
"Warning")
self.m_AddData.Disable()
self.m_MinLat.SetValue(str(MinLat))
self.m_MaxLat.SetValue(str(MaxLat))
self.m_MinLon.SetValue(str(MinLon))
self.m_MaxLon.SetValue(str(MaxLon))
else:
#Text boxes hate non String types. use int to round, and string to make them fit the container
# if projected coordinates but not geographic, a conversion may be possible
if (projected and not geographic):
convTop = self.GBIFGeneric.SpecialUTMConversion(
borders.x1, borders.y1)
convBottom = self.GBIFGeneric.SpecialUTMConversion(
borders.dx, borders.dy)
borders.x1 = convTop.easting
borders.y1 = convTop.northing
borders.dx = convBottom.easting
borders.dy = convBottom.northing
#limiting borders
self.m_MinLat.SetValue(
str("%.1f" %
self.GBIFGeneric.BorderTest(MinLat, borders.y1, max)))
self.m_MaxLat.SetValue(
str("%.1f" %
self.GBIFGeneric.BorderTest(MaxLat, borders.dy, min)))
self.m_MinLon.SetValue(
str("%.1f" %
self.GBIFGeneric.BorderTest(MinLon, borders.x1, max)))
self.m_MaxLon.SetValue(
str("%.1f" %
self.GBIFGeneric.BorderTest(MaxLon, borders.dx, min)))
# Query GBIF for Taxa in Lat/Lon Boundary
def OnSearch(self, event):
wx.BeginBusyCursor()
# Clear the results list
self.m_Result.Clear()
searchType = self.__options__.GetSearchType()
taxon = self.m_TaxonName.GetLineText(0)
taxon = taxon.split()
if (len(taxon) == 0):
wx.MessageBox("You did not enter a taxon name.")
else:
minLatitude = float(self.m_MinLat.GetValue())
maxLatitude = float(self.m_MaxLat.GetValue())
minLongitude = float(self.m_MinLon.GetValue())
maxLongitude = float(self.m_MaxLon.GetValue())
if searchType == "study":
self.__selectedTaxon__.clear()
# test data for multiple study search mgm4440037.3 mgm4440055.3 mgm4440064.3
for tax in taxon:
self.__selectedTaxon__.add(("dummy value", tax))
self.OnCalculate(wx.EVT_BUTTON)
else:
matches = self.MGRastSpecific.GETTAXRESULT(
taxon, searchType, minLatitude, maxLatitude, minLongitude,
maxLongitude, self.m_Summary)
if matches:
self.m_Result.InsertItems(matches, 0)
wx.EndBusyCursor()
# Create Sequence and Location files for selected Taxa
######################
#
# CAN NOT PERFORM MORE THAN ONE QUERY PER SECOND
#
######################
def OnCalculate(self, event):
self.MGRastSpecific.RESETSEQUENCE()
self.__obs__ = []
self.__metaVals__ = {}
sequence = {}
self.m_Summary.SetLabel("\n")
records, distLocations = 0, 0
searchType = self.__options__.GetSearchType()
additFields = "%s%s%s%s%s%s%s" % (
self.__options__.GetFilterLevel(),
self.__options__.GetFilterSource(),
self.__options__.GetGroupLevel(), self.__options__.GetHitType(),
self.__options__.GetIdentity(), self.__options__.GetLength(),
self.__options__.GetSource())
if (self.__selectedTaxon__):
self.m_Progress.WriteText("Starting...\n")
#index of which taxon is being used
index = 0
for tax in self.__selectedTaxon__:
startTime = time.time()
obs, metaVals, taxonLength = self.MGRastSpecific.GETOBS(
tax[1], searchType, additFields, self.m_Progress)
# Some sort of error occured trying to get that object, skip to next one
if not obs:
self.SetFocus()
continue
taxonomy = []
for i in range(0, taxonLength):
if i < len(self.__TAXON__):
taxonomy.append(self.__TAXON__[i])
else:
taxonomy[i].append("Level_%s" % i)
self.__TAXON__ = taxonomy
if obs:
self.__obs__.append(obs)
if sequence:
self.__sequences__.append(sequence)
# add all unique key/val pairs from json files
for key, value in metaVals.iteritems():
if key in self.__metaVals__:
self.__metaVals__[key][index] = value
else:
list = [''] * len(self.__selectedTaxon__)
list[index] = value
self.__metaVals__[key] = list
index += 1
if (time.time() - startTime) < 1:
sleep.time(1)
# Now query again for the Sequence to that study
if self.__options__.GetSequence():
fileTypes = 'Sequence data files (*.fasta)|*.fasta'
dlg = wx.FileDialog(self, "Save plot", "", "", fileTypes,
wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetFilename()
dir = dlg.GetDirectory()
file_split = filename.split(".", 1)
outFile = ("%s/%s_sequenceData.fasta.gz" %
(dir, file_split[0]))
self.MGRastSpecific.GETSEQUENCES(tax[1], self.m_Progress,
outFile)
else:
wx.MessageBox("Please select some Taxa.")
self.m_Progress.WriteText("Done\n")
# Redirects User to Wiki page for this plugin
def OnHelp(self, event):
wx.LaunchDefaultBrowser(
'http://kiwi.cs.dal.ca/GenGIS/index.php/Description_of_GenGIS_plugins#MG-RAST_Query'
)
# Adds Data to GenGIS
def OnAddData(self, event):
# check required data has been loaded
if GenGIS.layerTree.GetNumMapLayers() == 0:
wx.MessageBox(
"This action requires a Map layer. Please load a Map.")
self.Close()
return
taxonLevels = ','.join(str(i) for i in self.__TAXON__)
if (len(self.__obs__) > 0):
OUTLText, OUTSText = self.MGRastSpecific.GETTEXT(
self.__obs__, self.__metaVals__)
OUTLArray = self.GBIFGeneric.CPPOUT(OUTLText)
OUTSArray = self.GBIFGeneric.CPPOUT(OUTSText)
metKey = ','.join(sorted(self.__metaVals__.keys()))
OUTLArray.insert(0,
"Site ID,Latitude,Longitude,Cell ID,%s" % metKey)
OUTSArray.insert(
0,
"Sequence ID,Site ID,CellLat,CellLong,Richness,%s,Taxonomy" %
taxonLevels)
OUTLArray.pop()
OUTSArray.pop()
layerName = "MGRASTLayer_%d" % GenGIS.layerTree.GetNumLocationLayers(
)
GenGIS.mainWindow.OpenLocationsCSVFile(OUTLArray, layerName)
GenGIS.mainWindow.OpenSequenceCSVFile(OUTSArray, layerName)
#Get the number of last location layer added (the gbif one)
numLocationLayers = GenGIS.layerTree.GetNumLocationSetLayers()
locationSetLayer = GenGIS.layerTree.GetLocationSetLayer(
numLocationLayers - 1)
# locationSetLayer.SetDescription(self.__description__)
else:
wx.MessageBox("Please make a successful MG-RAST Query first.")
# Exports Location and Sequence Data to a location of the users choice
def OnExportData(self, event):
if (len(self.__obs__) > 0):
taxonLevels = ','.join(str(i) for i in self.__TAXON__)
fileTypes = 'Loc and Seq Files (*.csv)|*.csv'
dlg = wx.FileDialog(self, "Save plot", "", "", fileTypes, wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetFilename()
dir = dlg.GetDirectory()
file_split = filename.split(".", 1)
#creates the directories
OUTLfile = os.path.join(dir, file_split[0] + "_locs.csv")
OUTSfile = os.path.join(dir, file_split[0] + "_seqs.csv")
OUTLText, OUTSText = self.MGRastSpecific.GETTEXT(
self.__obs__, self.__metaVals__)
# metKey = ','.join(str(x) for x in self.__metaKeys__)
metKey = ','.join(sorted(self.__metaVals__.keys()))
# print metKey
self.GBIFGeneric.WRITEEXPORT(
OUTLfile, OUTLText,
"Site ID,Latitude,Longitude,Cell ID,%s\n" % metKey)
self.GBIFGeneric.WRITEEXPORT(
OUTSfile, OUTSText,
"Sequence ID,Site ID,CellLat,CellLong,Richness,%s,Taxonomy\n"
% taxonLevels)
# if self.__options__.GetSequence():
# self.MGRastSpecific.WRITESEQUENCES(dir,file_split[0],self.__sequences__)
dlg.Destroy()
else:
wx.MessageBox("Please make a successful MG-RAST Query first.")
# Add Data from Results Table to ID List
def OnAdd(self, event):
i = 0
IDCount = self.m_IDList.GetCount()
for index in self.m_Result.GetSelections():
selected = self.m_Result.GetString(index)
split = selected.split(" | ")
if (split[0], split[1]) not in self.__selectedTaxon__:
self.m_IDList.InsertItems(["%s" % selected], IDCount + i)
#add study ID and study location
self.__selectedTaxon__.add((split[0], split[1]))
i += 1
# Remove Data from ID List
def OnRemove(self, event):
candidates = sorted(self.m_IDList.GetSelections(), reverse=True)
for index in candidates:
selected = self.m_IDList.GetString(index)
split = selected.split(" | ")
self.__selectedTaxon__.remove((split[0], split[1]))
self.m_IDList.Delete(index)
# Close the Plugin
def OnClose(self, event):
self.__options__.Close()
event.Skip()
# Close the Plugin
def OnOK(self, event):
self.Close()
self.__options__.Close()
def OnLatEnter(self, event):
str = event.GetString()
str2 = re.sub('[^\d\.\-]', '', str)
if str2 and str != "-":
str3 = float(str2)
if str3 > 90:
str2 = str2[:-1]
elif str3 < -90:
str2 = str2[:-1]
event.GetClientData().SetValue(str2)
event.GetClientData().SetInsertionPoint(len(str2))
def OnLonEnter(self, event):
str = event.GetString()
str2 = re.sub('[^\d\.\-]', '', str)
if str2 and str != "-":
str3 = float(str2)
if str3 > 180:
str2 = str[:-1]
elif str3 < -180:
str2 = str[:-1]
event.GetClientData().SetValue(str2)
event.GetClientData().SetInsertionPoint(len(str2))
def OnOptions(self, event):
self.__options__.Show()
