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 __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 GBIF. 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
self.m_MinLat.SetValue(str(max(MinLat,borders.y1)))
self.m_MaxLat.SetValue(str(min(MaxLat,borders.dy)))
self.m_MinLon.SetValue(str(max(MinLon,borders.x1)))
self.m_MaxLon.SetValue(str(min(MaxLon,borders.dx)))
def __init__(self): self.GBIFGeneric = GBIFGeneric() self.__description__ = set() self.__warnings__=[0,0] self.__uniqueNodeList__=set()
class GBIFQuery(GBIFQueryLayout):
# Global variables to store queried information
__obs__ = []
__selectedTaxon__= set()
__description__=""
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 GBIF. 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
self.m_MinLat.SetValue(str(max(MinLat,borders.y1)))
self.m_MaxLat.SetValue(str(min(MaxLat,borders.dy)))
self.m_MinLon.SetValue(str(max(MinLon,borders.x1)))
self.m_MaxLon.SetValue(str(min(MaxLon,borders.dx)))
# 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,recs,distLocs,description= self.GBIFSpecific.GETOBSENTIRERANGE(tax[1].split(),tax[0],minLatitude,maxLatitude,minLongitude,maxLongitude,self.m_Progress)
self.__obs__.append(obs)
self.__description__+="%s\n" % description
records += recs
distLocations +=distLocs
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__):
minLatitude= self.GBIFGeneric.roundCoord(self.m_MinLat.GetValue())
maxLatitude= self.GBIFGeneric.roundCoord(self.m_MaxLat.GetValue())
minLongitude= self.GBIFGeneric.roundCoord(self.m_MinLon.GetValue())
maxLongitude= self.GBIFGeneric.roundCoord(self.m_MaxLon.GetValue())
count=0
for tax in self.__selectedTaxon__:
count+=self.GBIFSpecific.GETCOUNT(tax[1].split(),tax[0],minLatitude,maxLatitude,minLongitude,maxLongitude,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/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__)
OUTLArray=self.GBIFGeneric.CPPOUT(OUTLText)
OUTSArray=self.GBIFGeneric.CPPOUT(OUTSText)
# Removing some Gridding based artifacts, may become useful again in the future.
#OUTLArray.insert(0,"Site ID,Latitude,Longitude,Richness,Cell ID,Taxon,Genus")
OUTLArray.insert(0,"Site ID,Latitude,Longitude,Cell ID,Taxon,Genus")
#OUTSArray.insert(0,"Sequence ID,Site ID,CellLat,CellLong,Taxon,Genus,TrueLat,TrueLong,Count,AllRecords")
OUTSArray.insert(0,"Sequence ID,Site ID,Taxon,Genus,TrueLat,TrueLong,Count,AllRecords")
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)
locationSetLayer.SetDescription(self.__description__)
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 = ("%s/%s_locs.csv" % (dir,file_split[0]))
OUTSfile = ("%s/%s_seqs.csv" % (dir,file_split[0]))
OUTDfile = ("%s/%s_source.txt" % (dir,file_split[0]))
OUTLText, OUTSText = self.GBIFGeneric.GETTEXT(self.__obs__)
# Removing some Gridding based artifacts, may become useful again in the future.
# self.GBIFGeneric.WRITEEXPORT(OUTLfile,OUTLText,"Site ID,Latitude,Longitude,Richness,Cell ID,Taxon,Genus\n")
self.GBIFGeneric.WRITEEXPORT(OUTLfile,OUTLText,"Site ID,Latitude,Longitude,Cell ID,Taxon,Genus\n")
# self.GBIFGeneric.WRITEEXPORT(OUTSfile,OUTSText,"Sequence ID,Site ID,CellLat,CellLong,Taxon,Genus,TrueLat,TrueLong,Count,AllRecords\n")
self.GBIFGeneric.WRITEEXPORT(OUTSfile,OUTSText,"Sequence ID,Site ID,Taxon,Genus,TrueLat,TrueLong,Count,AllRecords\n")
description = self.__description__.encode('utf-8')
self.GBIFGeneric.WRITEEXPORT(OUTDfile,description,"")
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))
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)))
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 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 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()
