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nbndialog.py
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nbndialog.py
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# -*- coding: utf-8 -*-
"""
/***************************************************************************
NBNDialog
A QGIS plugin
FSC QGIS plugin for biological recorders
-------------------
begin : 2014-02-17
copyright : (C) 2014 by Rich Burkmar, Field Studies Council
email : [email protected]
***************************************************************************/
/***************************************************************************
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
***************************************************************************/
"""
from . import ui_nbn
import os.path
import os
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from PyQt5.QtNetwork import *
from PyQt5.QtWidgets import *
from qgis.core import *
from qgis.gui import *
from qgis.utils import *
import urllib
import json
import hashlib, uuid
import shutil
import csv
import zipfile
from io import BytesIO
import re
import datetime
import random
from . import osgr
from . import envmanager
from . import filedialog
class NBNDialog(QWidget, ui_nbn.Ui_nbn):
displayNBNCSVFile = pyqtSignal(basestring)
def __init__(self, iface, dockwidget):
QWidget.__init__(self)
ui_nbn.Ui_nbn.__init__(self)
self.setupUi(self)
self.canvas = iface.mapCanvas()
self.iface = iface
self.pathPlugin = "%s%s%%s" % ( os.path.dirname( __file__ ), os.path.sep )
self.treeNodesExact = {}
self.treeNodesFuzzy = {}
# Get a reference to an osgr object and an osgrLayer object
self.osgr = osgr.osgr()
# Load the environment stuff
self.env = envmanager.envManager()
self.pbSpeciesWMS.clicked.connect(self.WMSFetchSpecies)
self.butTaxonSearch.clicked.connect(self.taxonSearch)
self.leTaxonSearch.returnPressed.connect(self.taxonSearch)
self.butClearLast.clicked.connect(self.removeMap)
self.butClear.clicked.connect(self.removeMaps)
self.butHelp.clicked.connect(self.helpFile)
self.butGithub.clicked.connect(self.github)
#self.pbRefreshDatasets.clicked.connect(self.refreshDatasets)
self.pbRefreshDatasets.clicked.connect(self.refreshProviders)
self.pbRefreshSpeciesLists.clicked.connect(self.refreshSpeciesLists)
self.pbUncheckAll.clicked.connect(self.uncheckAll)
self.pbUncheckAllSpeciesList.clicked.connect(self.uncheckAllSpeciesList)
self.twProviders.itemClicked.connect(self.providersClick)
self.twSpeciesLists.itemClicked.connect(self.speciesListClick)
self.twTaxa.itemClicked.connect(self.taxaTwClick)
self.cbStartYear.stateChanged.connect(self.checkFilters)
self.cbEndYear.stateChanged.connect(self.checkFilters)
self.pbBuffer.clicked.connect(self.generateBuffer)
self.pbClearLastBuffer.clicked.connect(self.removeBuffer)
self.rbGR.toggled.connect(self.bufferEnableDisable)
self.rbEN.toggled.connect(self.bufferEnableDisable)
self.pbDownload.clicked.connect(self.downloadNBNObservations)
self.pbClearFilters.clicked.connect(self.clearAllFilters)
self.pbClearTaxonFilters.clicked.connect(self.clearTaxonFilters)
self.pbBrowseNbnOutputFolder.clicked.connect(self.browseNbnOutputFolder)
self.twDownloaded.itemDoubleClicked.connect(self.downloadClicked)
self.twTaxa.itemDoubleClicked.connect(self.selectTaxa)
self.lwTaxa.itemDoubleClicked.connect(self.removeTaxa)
self.cbShowAllMetadata.stateChanged.connect(self.showHideMetadataColumns)
# Map canvas events
self.canvas.extentsChanged.connect(self.mapExtentsChanged)
self.canvas.selectionChanged.connect(self.checkMapSelectionFilter)
self.iface.currentLayerChanged.connect(self.checkMapSelectionFilter)
# Make a coordinate translator. Also need global references to OSGB and canvas CRSs since
# they cannot be retrieved from a translator object.
self.canvasCrs = self.canvas.mapSettings().destinationCrs()
self.osgbCrs = QgsCoordinateReferenceSystem("EPSG:27700")
self.transformCrs = QgsCoordinateTransform(self.canvas.mapSettings().destinationCrs(), QgsCoordinateReferenceSystem("EPSG:27700"), QgsProject.instance())
# Inits
self.layers = []
self.buffers = []
self.tvks = {} #Initialise tvk dictionary
self.butClearLast.setIcon(QIcon( self.pathPlugin % "images/removelayer.png" ))
self.butClear.setIcon(QIcon( self.pathPlugin % "images/removelayers.png" ))
self.pbSpeciesWMS.setIcon(QIcon( self.pathPlugin % "images/nbngridmap.png" ))
self.pbDownload.setIcon(QIcon( self.pathPlugin % "images/nbndownload.png" ))
self.butTaxonSearch.setIcon(QIcon( self.pathPlugin % "images/speciesinventory.png" ))
self.pbBuffer.setIcon(QIcon( self.pathPlugin % "images/buffer.png" ))
self.pbClearLastBuffer.setIcon(QIcon( self.pathPlugin % "images/bufferclear.png" ))
self.sbPointSize.setValue(6)
self.mcbWMSColour.setColor(QColor('#cd3844'))
self.butHelp.setIcon(QIcon( self.pathPlugin % "images/info.png" ))
self.butGithub.setIcon(QIcon( self.pathPlugin % "images/github.png" ))
self.twTaxa.setHeaderLabel("Matching taxa")
self.guiFile = None
self.infoFile = os.path.join(os.path.dirname( __file__ ), "infoNBNTool.txt")
self.readProviderFile()
self.readSpeciesListFile()
self.datasetSelectionChanged()
self.speciesListSelectionChanged()
self.checkFilters()
self.bufferEnableDisable()
self.lblMetadata.setText("")
self.defaultColumns = []
self.cbShowAllMetadata.setEnabled(False)
self.WMSType = self.enum(species=1, dataset=2, designation=3)
# Populate the download reason combobox
self.cboDownloadReason.addItem("Reason for download", -99)
url = 'https://logger.nbnatlas.org/service/logger/reasons'
res = self.restRequest(url)
self.reasonTips = {}
if not res is None:
jsonData = json.loads(res.data())
for reason in jsonData:
if not reason["deprecated"]:
splitName = reason["name"].split("|")
self.cboDownloadReason.addItem(splitName[0], reason["id"])
tip = ""
if len(splitName) > 1:
tip = splitName[1]
self.reasonTips[reason["id"]] = tip
self.cboDownloadReason.currentIndexChanged.connect(self.downloadReasonChanged)
def downloadReasonChanged(self):
if self.cboDownloadReason.currentData() != -99:
self.cboDownloadReason.setToolTip(self.reasonTips[self.cboDownloadReason.currentData()])
else:
self.cboDownloadReason.setToolTip("Specify a reason for NBN download")
def browseNbnOutputFolder(self):
#Reload env
self.env.loadEnvironment()
dlg = QFileDialog
if os.path.exists(self.leNbnOutputFolder.text()):
strInitPath = self.leNbnOutputFolder.text()
else:
strInitPath = ""
folderName = dlg.getExistingDirectory(self, "Browse for NBN download folder", strInitPath)
if folderName:
self.leNbnOutputFolder.setText(folderName)
self.leNbnOutputFolder.setToolTip(folderName)
def showEvent(self, ev):
# Load the environment stuff
self.env = envmanager.envManager()
# Set the download folder if set in env file
self.leNbnOutputFolder.setText(self.env.getEnvValue("nbn.downloadfolder"))
return QWidget.showEvent(self, ev)
def enum(self, **enums):
return type('Enum', (), enums)
def logMessage(self, strMessage, level=Qgis.Info):
QgsMessageLog.logMessage(strMessage, "NBN Tool", level)
def infoMessage(self, strMessage):
self.iface.messageBar().pushMessage("Info", strMessage, level=Qgis.Info)
def warningMessage(self, strMessage):
self.iface.messageBar().pushMessage("Warning", strMessage, level=Qgis.Warning)
def errorMessage(self, strMessage):
self.iface.messageBar().pushMessage("Error", strMessage, level=Qgis.Critical)
def uncheckAll(self):
for iProvider in range(self.twProviders.topLevelItemCount()):
twiProvider = self.twProviders.topLevelItem(iProvider)
twiProvider.setCheckState(0, Qt.Unchecked)
for iDataset in range(twiProvider.childCount()):
twiDataset = twiProvider.child(iDataset)
twiDataset.setCheckState(0, Qt.Unchecked)
self.datasetSelectionChanged()
def uncheckAllSpeciesList(self):
for iListType in range(self.twSpeciesLists.topLevelItemCount()):
twiListType = self.twSpeciesLists.topLevelItem(iListType)
for iSpeciesList in range(twiListType.childCount()):
twiSpeciesList = twiListType.child(iSpeciesList)
twiSpeciesList.setCheckState(0, Qt.Unchecked)
self.speciesListSelectionChanged()
def bufferEnableDisable(self):
gr = self.rbGR.isChecked()
en = self.rbEN.isChecked()
self.lePointBufferGR.setEnabled(gr)
self.sbEasting.setEnabled(en)
self.sbNorthing.setEnabled(en)
self.rbBritishEN.setEnabled(en)
self.rbIrishEN.setEnabled(en)
def generateBuffer(self):
gridType = ""
if self.rbGR.isChecked():
#Get grid mid point of GR
gridRef = self.lePointBufferGR.text().strip()
ret = self.osgr.enFromGR(gridRef)
if ret[0] == 0:
self.warningMessage(ret[3])
return
sName = gridRef
easting = ret[0]
northing = ret[1]
gridType = ret[4]
else:
easting = self.sbEasting.value()
northing = self.sbNorthing.value()
if self.rbBritishEN.isChecked():
gridType = "os"
else:
gridType= "irish"
sName = str(easting) + "/" + str(northing) + " (" + gridType + ")"
sName = sName + " " + str(self.sbBuffer.value()) + "m"
geom = self.osgr.circleGeom(easting, northing, self.sbBuffer.value())
# Create layer
if gridType == "os":
epsg = "27700"
else:
epsg = "29903"
self.vl = QgsVectorLayer("Polygon?crs=epsg:" + epsg, sName, "memory")
self.pr = self.vl.dataProvider()
self.buffers.append(self.vl.id())
# Symbology
props = { 'color' : '255,0,0,100', 'color_border' : '0,0,0,200', 'style' : 'solid', 'style_border' : 'solid' }
s = QgsFillSymbol.createSimple(props)
self.vl.setRenderer( QgsSingleSymbolRenderer( s ) )
# Add geometry to layer
fet = QgsFeature()
fet.setGeometry(geom)
# Needs an attribute otherwise it cannot be selected and geometry functions fail
#self.pr.addAttributes([QgsField("id", QVariant.Int)])
#attrs=[random.randrange(1, 100000)]
##attrs=[1]
#fet.setAttributes(attrs)
self.vl.startEditing()
self.vl.addFeatures([fet])
self.vl.commitChanges()
self.vl.updateExtents()
# Add to map layer registry
QgsProject.instance().addMapLayer(self.vl)
# Zoom to buffer extent
self.iface.actionZoomToLayer().trigger()
self.checkMapSelectionFilter()
def taxaTwClick(self, twItem, iCol):
#If current item is checked, uncheck all others
#Only one taxon can be checked.
for twiKey in self.treeNodesExact:
if not self.treeNodesExact[twiKey] == twItem and self.treeNodesExact[twiKey].checkState(0) == Qt.Checked:
self.treeNodesExact[twiKey].setCheckState(0, Qt.Unchecked)
for twiKey in self.treeNodesFuzzy:
if not self.treeNodesFuzzy[twiKey] == twItem and self.treeNodesFuzzy[twiKey].checkState(0) == Qt.Checked:
self.treeNodesFuzzy[twiKey].setCheckState(0, Qt.Unchecked)
self.checkFilters()
def datasetSelectionChanged(self):
iChecked = 0
for iProvider in range(self.twProviders.topLevelItemCount()):
twiProvider = self.twProviders.topLevelItem(iProvider)
for iDataset in range(twiProvider.childCount()):
twiDataset = twiProvider.child(iDataset)
if twiDataset.checkState(0) == Qt.Checked:
iChecked += 1
if iChecked == 0:
self.lblDatasetFilter.setText("No datasets selected.")
else:
self.lblDatasetFilter.setText(str(iChecked) + " datasets selected.")
self.checkFilters()
def speciesListSelectionChanged(self):
iChecked = 0
for iType in range(self.twSpeciesLists.topLevelItemCount()):
twiType = self.twSpeciesLists.topLevelItem(iType)
for iList in range(twiType.childCount()):
twiList = twiType.child(iList)
if twiList.checkState(0) == Qt.Checked:
iChecked += 1
if iChecked == 0:
self.lblSpeciesListFilter.setText("No species lists selected.")
else:
self.lblSpeciesListFilter.setText(str(iChecked) + " species lists selected.")
self.checkFilters()
def refreshProviders(self):
self.twProviders.clear()
url = 'https://registry.nbnatlas.org/ws/dataProvider'
res = self.restRequest(url)
if res is None:
return
responseText = res.data().decode('utf-8')
#responseText = res.data()
# Write the json data to a file
datafile = self.pathPlugin % ("NBNCache%s%s" % (os.path.sep, "providers.json"))
with open(datafile, 'w') as jsonfile:
jsonfile.write(responseText)
# Rebuild dataset tree
self.readProviderFile()
self.datasetSelectionChanged()
def refreshSpeciesLists(self):
self.twSpeciesLists.clear()
url = 'https://lists.nbnatlas.org/ws/speciesList?max=1000'
res = self.restRequest(url)
if res is None:
return
responseText = res.data().decode('utf-8')
# Write the json data to a file
datafile = self.pathPlugin % ("NBNCache%s%s" % (os.path.sep, "species-lists.json"))
with open(datafile, 'w') as jsonfile:
jsonfile.write(responseText)
# Rebuild dataset tree
self.readSpeciesListFile()
self.speciesListSelectionChanged()
def providersClick(self, twi):
if twi.text(2) == "provider" and twi.childCount() == 0:
url = 'https://registry.nbnatlas.org/ws/dataProvider/' + twi.text(1)
res = self.restRequest(url)
if res is None:
return
jsonData = json.loads(res.data())
twi.setExpanded(True)
for dataResource in jsonData["dataResources"]:
QgsMessageLog.logMessage("dataset: " + dataResource["name"], "NBN Tool")
# Create a tree item for the dataset
twiDataset = QTreeWidgetItem(twi)
twiDataset.setText(0, dataResource["name"])
twiDataset.setText(1, dataResource["uid"])
twiDataset.setText(2, "dataset")
twiDataset.setExpanded(False)
twiDataset.setFlags(Qt.ItemIsEnabled | Qt.ItemIsUserCheckable)
twiDataset.setCheckState(0, twi.checkState(0))
elif twi.text(2) == "provider":
#If provider is checked, then check all children
#If provider is unchecked, then uncheck all children
#if twi.checkState(0) == Qt.Checked:
for i in range(0, twi.childCount()):
twi.child(i).setCheckState(0, twi.checkState(0))
else: #dataset
if twi.checkState(0) == Qt.Unchecked:
#If a dataset is unchecked, then uncheck provider
twi.parent().setCheckState(0, Qt.Unchecked)
else:
#If all datasets are checked, then check provider
allChecked = True
for i in range(0, twi.parent().childCount()):
if twi.parent().child(i).checkState(0) == Qt.Unchecked:
allChecked = False
break
if allChecked:
twi.parent().setCheckState(0, Qt.Checked)
else:
twi.parent().setCheckState(0, Qt.Unchecked)
self.datasetSelectionChanged()
def speciesListClick(self):
self.speciesListSelectionChanged()
def readProviderFile(self):
datafile = self.pathPlugin % ("NBNCache%s%s" % (os.path.sep, "providers.json"))
if not os.path.isfile(datafile):
self.infoMessage("NBN Atlas data providers file not found.")
return
try:
with open(datafile) as f:
jsonData = json.load(f)
except:
self.warningMessage("NBN Atlas data providers file failed to load. Use the refresh button to generate a new one.")
return
for jDataset in jsonData:
#Create a new top level tree item for the dataset provider organisation
twiProvider = QTreeWidgetItem(self.twProviders)
twiProvider.setText(0, jDataset["name"])
twiProvider.setText(1, jDataset["uid"])
twiProvider.setText(2, "provider")
twiProvider.setExpanded(False)
twiProvider.setFlags(Qt.ItemIsEnabled | Qt.ItemIsUserCheckable)
twiProvider.setCheckState(0, Qt.Unchecked) # 0 is the column number
self.twProviders.sortItems(0, Qt.AscendingOrder)
def readSpeciesListFile(self):
datafile = self.pathPlugin % ("NBNCache%s%s" % (os.path.sep, "species-lists.json"))
if not os.path.isfile(datafile):
self.infoMessage("NBN Atlas species list file not found.")
return
try:
with open(datafile) as f:
jsonData = json.load(f)
except:
self.warningMessage("NBN Atlas data species list file failed to load. Use the refresh button to generate a new one.")
return
#List types are initialised to known list types so that order can be specified
knownListTypes = ["CONSERVATION_LIST", "SENSITIVE_LIST", "LOCAL_LIST", "COMMON_HABITAT"]
excludeListTypes = ["TEST"]
readListTypes = []
listTypes = []
for speciesList in jsonData["lists"]:
if not speciesList["listType"] in readListTypes and not speciesList["listType"] in excludeListTypes:
readListTypes.append(speciesList["listType"])
for speciesList in knownListTypes:
if speciesList in readListTypes:
listTypes.append(speciesList)
for speciesList in readListTypes:
if not speciesList in listTypes:
listTypes.append(speciesList)
for listType in listTypes:
twiListType = QTreeWidgetItem(self.twSpeciesLists)
twiListType.setText(0, listType.replace("_", " ").capitalize())
for speciesList in jsonData["lists"]:
listType=speciesList["listType"].replace("_", " ").capitalize()
matchItems = self.twSpeciesLists.findItems(listType, Qt.MatchExactly, 0)
if len(matchItems) == 1:
twiList = QTreeWidgetItem(matchItems[0])
twiList.setText(0, speciesList["listName"])
twiList.setText(1, speciesList["dataResourceUid"])
twiList.setFlags(Qt.ItemIsEnabled | Qt.ItemIsUserCheckable)
twiList.setCheckState(0, Qt.Unchecked)
def helpFile(self):
##iface.layerTreeView().setSelectionMode( QAbstractItemView.MultiSelection )
## Select your layers, this time they are not mutually exclusive
#i=0
##QgsProject.instance().layerTreeRoot().
#for layer in self.layers:
# iface.layerTreeView().setCurrentLayer(layer)
# #QgsProject.instance().layerTreeRoot().setCurrentLayer(layer)
# break
##iface.layerTreeView().setSelectionMode( QAbstractItemView.ExtendedSelection )
#return
QDesktopServices().openUrl(QUrl("http://www.fscbiodiversity.uk/qgisnbnatlastool"))
#self.guiFile = filedialog.FileDialog(self.iface, self.infoFile)
#self.guiFile.setVisible(True)
def github(self):
QDesktopServices().openUrl(QUrl("https://github.com/FieldStudiesCouncil/QGIS-Biological-Recording-Tools/issues"))
def taxonSearch(self):
#NBN Atlas search
if self.leTaxonSearch.text() == "":
self.iface.messageBar().pushMessage("No search term specified.", level=Qgis.Info)
return
url = 'https://species-ws.nbnatlas.org/search?q=' + self.leTaxonSearch.text() + '&pageSize=50&fq=taxonomicStatus:accepted'
#url = 'https://species-ws.nbnatlas.org/search?q=' + self.leTaxonSearch.text() + '&pageSize=100'
res = self.restRequest(url)
#self.logMessage(url)
if res is None:
return
responseText = res.data().decode('utf-8')
#self.logMessage(responseText)
jsonData = json.loads(responseText)
jResponseList = jsonData["searchResults"]["results"]
lightGrey = QBrush(QColor(130,130,130,255))
#Tree view
self.twTaxa.clear()
self.treeNodesExact = {}
self.treeNodesFuzzy = {}
#Create top level items for exact and fuzzy matches
twiExact = QTreeWidgetItem(self.twTaxa)
twiExact.setText(0, "Exact match")
twiExact.setExpanded(False)
twiExact.setFlags(Qt.ItemIsEnabled) #By resetting the flags, we take off default isSelectable
twiFuzzy = QTreeWidgetItem(self.twTaxa)
twiFuzzy.setText(0, "Fuzzy match")
twiFuzzy.setExpanded(False)
twiFuzzy.setFlags(Qt.ItemIsEnabled) #By resetting the flags, we take off default isSelectable
for jTaxon in jResponseList:
#QgsMessageLog.logMessage(jTaxon["name"], "NBN Tool")
#Is this a fuzzy match or an exact match?
if jTaxon["name"].lower() == self.leTaxonSearch.text().lower() or jTaxon["commonNameSingle"].lower() == self.leTaxonSearch.text().lower():
treeNodes = self.treeNodesExact
twiParent = twiExact
else:
treeNodes = self.treeNodesFuzzy
twiParent = twiFuzzy
try:
tKingdom = jTaxon["kingdom"]
if tKingdom is None:
tKingdom = ""
except:
tKingdom = ""
try:
tPhylum = jTaxon["phylum"]
if tPhylum is None:
tPhylum = ""
except:
tPhylum = ""
try:
tClass = jTaxon["class"]
if tClass is None:
tClass = ""
except:
tClass = ""
try:
tOrder = jTaxon["order"]
if tOrder is None:
tOrder = ""
except:
tOrder = ""
try:
tFamily = jTaxon["family"]
if tFamily is None:
tFamily = ""
except:
tFamily = ""
try:
tGenus = jTaxon["genus"]
if tFamily is None:
tGenus = ""
except:
tGenus = ""
if 'commonNameSingle' in jTaxon and jTaxon["commonNameSingle"] != "":
tName = jTaxon["name"] + " (" + jTaxon["commonNameSingle"] + ")"
else:
tName = jTaxon["name"]
if tKingdom != "" and not tKingdom in(treeNodes.keys()):
#Create a new top level tree item for the taxon group
twiKingdom = QTreeWidgetItem(twiParent)
twiKingdom.setText(0, tKingdom + ' (Kingdom)')
twiKingdom.setExpanded(True)
twiKingdom.setForeground(0, lightGrey)
twiKingdom.setFlags(Qt.ItemIsEnabled) #By resetting the flags, we take off default isSelectable
twiKingdom.setIcon(0, QIcon( self.pathPlugin % "images/taxonomy20x16.png" ))
try:
twiKingdom.setToolTip(0, jTaxon["kingdomGuid"])
except:
pass
#Add to dictionary
treeNodes[tKingdom] = twiKingdom
elif tKingdom != "":
twiKingdom = treeNodes[tKingdom]
if tKingdom != "":
twiParent = twiKingdom
if tPhylum != "" and not tPhylum in(treeNodes.keys()):
#Create a new top level tree item for the taxon group
twiPhylum = QTreeWidgetItem(twiParent)
twiPhylum.setText(0, tPhylum + ' (Phylum)')
twiPhylum.setExpanded(True)
twiPhylum.setForeground(0, lightGrey)
twiPhylum.setFlags(Qt.ItemIsEnabled) #By resetting the flags, we take off default isSelectable
twiPhylum.setIcon(0, QIcon( self.pathPlugin % "images/taxonomy20x16.png" ))
try:
twiPhylum.setToolTip(0, jTaxon["phylumGuid"])
except:
pass
#self.twTaxa.addTopLevelItem(twiPhylum)
#Add to dictionary
treeNodes[tPhylum] = twiPhylum
elif tPhylum != "":
twiPhylum = treeNodes[tPhylum]
if tPhylum != "":
twiParent = twiPhylum
if tClass != "" and not tClass in(treeNodes.keys()):
#Create a new top level tree item for the taxon group
twiClass = QTreeWidgetItem(twiParent)
twiClass.setText(0, tClass + ' (Class)')
twiClass.setExpanded(True)
twiClass.setForeground(0, lightGrey)
twiClass.setFlags(Qt.ItemIsEnabled) #By resetting the flags, we take off default isSelectable
twiClass.setIcon(0, QIcon( self.pathPlugin % "images/taxonomy20x16.png" ))
try:
twiClass.setToolTip(0, jTaxon["classGuid"])
except:
pass
#self.twTaxa.addTopLevelItem(twiClass)
#Add to dictionary
treeNodes[tClass] = twiClass
elif tClass != "":
twiClass = treeNodes[tClass]
if tClass != "":
twiParent = twiClass
if tOrder != "" and not tOrder in(treeNodes.keys()):
#Create a new top level tree item for the taxon group
twiOrder = QTreeWidgetItem(twiParent)
twiOrder.setText(0, tOrder + ' (Order)')
twiOrder.setExpanded(True)
twiOrder.setForeground(0, lightGrey)
twiOrder.setFlags(Qt.ItemIsEnabled) #By resetting the flags, we take off default isSelectable
twiOrder.setIcon(0, QIcon( self.pathPlugin % "images/taxonomy20x16.png" ))
try:
twiOrder.setToolTip(0, jTaxon["orderGuid"])
except:
pass
#self.twTaxa.addTopLevelItem(twiOrder)
#Add to dictionary
treeNodes[tOrder] = twiOrder
elif tOrder != "":
twiOrder = treeNodes[tOrder]
if tOrder != "":
twiParent = twiOrder
if tFamily != "" and not tFamily in(treeNodes.keys()):
#Create a new top level tree item for the taxon group
twiFamily = QTreeWidgetItem(twiParent)
twiFamily.setText(0, tFamily + ' (Family)')
twiFamily.setExpanded(True)
twiFamily.setForeground(0, lightGrey)
twiFamily.setFlags(Qt.ItemIsEnabled) #By resetting the flags, we take off default isSelectable
twiFamily.setIcon(0, QIcon( self.pathPlugin % "images/taxonomy20x16.png" ))
try:
twiFamily.setToolTip(0, jTaxon["familyGuid"])
except:
pass
#self.twTaxa.addTopLevelItem(twiFamily)
#Add to dictionary
treeNodes[tFamily] = twiFamily
elif tFamily != "":
twiFamily = treeNodes[tFamily]
if tFamily != "":
twiParent = twiFamily
if tGenus != "" and not tGenus in(treeNodes.keys()):
#Create a new top level tree item for the taxon group
twiGenus = QTreeWidgetItem(twiParent)
twiGenus.setText(0, tGenus + ' (Genus)')
twiGenus.setExpanded(True)
twiGenus.setForeground(0, lightGrey)
twiGenus.setFlags(Qt.ItemIsEnabled) #By resetting the flags, we take off default isSelectable
twiGenus.setIcon(0, QIcon( self.pathPlugin % "images/taxonomy20x16.png" ))
try:
twiGenus.setToolTip(0, jTaxon["genusGuid"])
except:
pass
#Add to dictionary
treeNodes[tGenus] = twiGenus
elif tGenus != "":
twiGenus = treeNodes[tGenus]
if tGenus != "":
twiParent = twiGenus
#Create a child tree item for the preferred TVK group
twiPTVK = QTreeWidgetItem(twiParent)
twiPTVK.setData(0, Qt.ToolTipRole, jTaxon["guid"])
twiPTVK.setText(0, tName)
twiPTVK.setIcon(0, QIcon( self.pathPlugin % "images/Taxon20x16.png" ))
#twiPTVK.setFlags(Qt.ItemIsEnabled | Qt.ItemIsUserCheckable)
#twiPTVK.setFlags(Qt.ItemIsEnabled)
#twiPTVK.setCheckState(0, Qt.Unchecked) # 0 is the column number
twiPTVK.setExpanded(True)
#self.twTaxa.addTopLevelItem(twiPTVK)
#Add to dictionary
treeNodes[jTaxon["guid"]] = twiPTVK
if twiExact.childCount() > 0:
twiExact.setExpanded(True)
elif twiFuzzy.childCount() > 0:
twiFuzzy.setExpanded(True)
def datasetsSelected(self):
for iProvider in range(self.twProviders.topLevelItemCount()):
twiProvider = self.twProviders.topLevelItem(iProvider)
if twiProvider.checkState(0) == Qt.Checked:
return True
for iDataset in range(twiProvider.childCount()):
twiDataset = twiProvider.child(iDataset)
if twiDataset.checkState(0) == Qt.Checked:
return True
return False
def selectedSpeciesLists(self):
speciesLists = []
for iListType in range(self.twSpeciesLists.topLevelItemCount()):
twiListType = self.twSpeciesLists.topLevelItem(iListType)
for iSpeciesList in range(twiListType.childCount()):
twiSpeciesList = twiListType.child(iSpeciesList)
if twiSpeciesList.checkState(0) == Qt.Checked:
speciesLists.append(twiSpeciesList.text(1))
if len(speciesLists) > 0:
return speciesLists
else:
return None
def getSelectedTVK(self):
if self.lwTaxa.count() == 0:
self.logMessage("No taxa selected")
return None
else:
i = 0
tvks = []
while i < self.lwTaxa.count():
lwi = self.lwTaxa.item(i)
tvks.append(lwi.toolTip())
i += 1
self.logMessage("Taxa selected: " + str(len(tvks)))
return tvks
def makeFilterQuery(self):
#Filters
fq = ''
#Taxon
tvks = self.getSelectedTVK()
if not tvks is None:
if fq == '':
fq = "&fq="
else:
fq = fq + '+AND+'
if len(tvks) == 1:
fq = fq + 'lsid:' + tvks[0]
else:
fq = fq + '(lsid:' + tvks[0]
i = 1
while i < len(tvks):
fq = fq + '+OR+lsid:' + tvks[i]
i += 1
fq = fq + ')'
#Year filter
startYear = None
endYear = None
if self.cbStartYear.checkState() == Qt.Checked:
startYear = self.sbStartYear.value()
if self.cbEndYear.checkState() == Qt.Checked:
endYear = self.sbEndYear.value()
# Year validity check
if not startYear is None and not endYear is None:
if startYear > endYear:
self.infoMessage("End year, if specified, must come after start year (or be equal to it), if specified.")
return None
#Set filter string for year range
if not startYear is None or not endYear is None:
if startYear is None:
startYear = 1600
if endYear is None:
endYear = datetime.datetime.now().year
if fq == '':
fq = "&fq="
else:
fq = fq + '+AND+'
fq = fq + 'year:[' + str(startYear) + '+TO+' + str(endYear) + ']'
#Species lists
if not self.selectedSpeciesLists() is None:
if fq == '':
fq = "&fq="
else:
fq = fq + '+AND+'
guids = self.selectedSpeciesLists()
if len(guids) == 1:
fq = fq + 'species_list_uid:' + guids[0]
else:
fq = fq + '(species_list_uid:' + guids[0]
i = 1
while i < len(guids):
fq = fq + '+OR+species_list_uid:' + guids[i]
i += 1
fq = fq + ')'
#Dataset providers and datasets
iDatasetCount = 0
providers = []
datasets = []
for iProvider in range(self.twProviders.topLevelItemCount()):
twiProvider = self.twProviders.topLevelItem(iProvider)
if twiProvider.checkState(0) == Qt.Checked:
providers.append(twiProvider.text(1))
else:
for iDataset in range(twiProvider.childCount()):
twiDataset = twiProvider.child(iDataset)
if twiDataset.checkState(0) == Qt.Checked:
datasets.append(twiDataset.text(1))
fqd=''
#Providers
if len(providers) == 1:
fqd = fqd + 'data_provider_uid:' + providers[0]
elif len(providers) > 1:
fqd = fqd + 'data_provider_uid:('
iProvider = 0
for uid in providers:
if iProvider == 0:
fqd = fqd + uid
else:
fqd = fqd + '+OR+' + uid
iProvider+=1
fqd = fqd + ')'
#Join provider and dataset portion if necessary
if len(datasets) > 0 and len(providers) > 0:
fqd = fqd + '+OR+'
#Datasets (where not all datasets for a provider wanted)
if len(datasets) == 1:
fqd = fqd + 'data_resource_uid:' + datasets[0]
elif len(datasets) > 1:
fqd = fqd + 'data_resource_uid:('
iDataset = 0
for uid in datasets:
if iDataset == 0:
fqd = fqd + uid
else:
fqd = fqd + '+OR+' + uid
iDataset+=1
fqd = fqd + ')'
if len(datasets) > 0 and len(providers) > 0:
fqd = '(' + fqd + ')'
if len(fqd) > 0:
if fq == '':
fq = "&fq="
else:
fq = fq + '+AND+'
fq = fq + fqd
#Return filter query
self.logMessage("fq: " + fq)
return fq
def getLayerName(self):
layerName = ""
#Taxon
tvks = self.getSelectedTVK()
if not tvks is None:
if len(tvks) == 1:
taxon = self.taxonDetails(tvks[0])
layerName += " " + taxon["taxonConcept"]["nameString"]
else:
layerName += " multiple taxa"
#Year filters
startYear = None
endYear = None
if self.cbStartYear.checkState() == Qt.Checked:
startYear = self.sbStartYear.value()
if self.cbEndYear.checkState() == Qt.Checked:
endYear = self.sbEndYear.value()
if not startYear is None and not endYear is None:
if startYear == endYear:
layerName += " " + str(startYear)
else:
layerName += " " + str(startYear) + "-" + str(endYear)
elif not startYear is None:
layerName += " " + str(startYear) + "-"
elif not endYear is None:
layerName += " -" + str(endYear)
#Provider filters
providers = []
datasets = []
for iProvider in range(self.twProviders.topLevelItemCount()):
twiProvider = self.twProviders.topLevelItem(iProvider)
if twiProvider.checkState(0) == Qt.Checked:
providers.append(twiProvider.text(1))
else:
for iDataset in range(twiProvider.childCount()):
twiDataset = twiProvider.child(iDataset)
if twiDataset.checkState(0) == Qt.Checked:
datasets.append(twiDataset.text(1))
if len(providers) == 1:
layerName += " provider-" + providers[0]
elif len(providers) > 1:
layerName += " providers-several"