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rdf-mover.py
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rdf-mover.py
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# Steve Baskauf 2017-07-05 Freely available under a GNU GPLv3 license.
# By its nature, this software overwrites and deletes data, so use at your own risk.
# See https://github.com/baskaufs/guid-o-matic/blob/master/rdf-mover.md for usage notes.
#libraries for GUI interface
import tkinter
from tkinter import *
from tkinter import ttk
import tkinter.scrolledtext as tkst
import csv #library to read/write/parse CSV files
import requests #library to do HTTP communication
root = Tk()
# this sets up the characteristics of the window
root.title("RDF data mover")
mainframe = ttk.Frame(root, padding="3 3 12 12")
mainframe.grid(column=0, row=0, sticky=(N, W, E, S))
mainframe.columnconfigure(0, weight=1)
mainframe.rowconfigure(0, weight=1)
#set up array of labels, text entry boxes, and buttons
repoText = StringVar()
ttk.Label(mainframe, textvariable=repoText).grid(column=3, row=3, sticky=(W, E))
repoText.set('Github repo path')
githubRepoBox = ttk.Entry(mainframe, width = 25, textvariable = StringVar())
githubRepoBox.grid(column=4, row=3, sticky=W)
githubRepoBox.insert(END, 'VandyVRC/tcadrt/')
subpathText = StringVar()
ttk.Label(mainframe, textvariable=subpathText).grid(column=3, row=4, sticky=(W, E))
subpathText.set('Github repo subpath')
repoSubpathBox = ttk.Entry(mainframe, width = 25, textvariable = StringVar())
repoSubpathBox.grid(column=4, row=4, sticky=W)
repoSubpathBox.insert(END, '')
basexUriText = StringVar()
ttk.Label(mainframe, textvariable=basexUriText).grid(column=3, row=5, sticky=(W, E))
basexUriText.set('BaseX API URI root')
basexUriBox = ttk.Entry(mainframe, width = 50, textvariable = StringVar())
basexUriBox.grid(column=4, row=5, sticky=W)
basexUriBox.insert(END, 'http://yourservername.com/gom/rest/')
databaseText = StringVar()
ttk.Label(mainframe, textvariable=databaseText).grid(column=3, row=6, sticky=(W, E))
databaseText.set('Database name')
databaseBox = ttk.Entry(mainframe, width = 20, textvariable = StringVar())
databaseBox.grid(column=4, row=6, sticky=W)
databaseBox.insert(END, 'building')
passwordText = StringVar()
ttk.Label(mainframe, textvariable=passwordText).grid(column=3, row=7, sticky=(W, E))
passwordText.set('BaseX database pwd')
passwordBox = ttk.Entry(mainframe, width = 15, textvariable = StringVar(), show='*')
passwordBox.grid(column=4, row=7, sticky=W)
passwordBox.insert(END, '[pwd]')
def gitToBaseButtonClick():
dataToBasex(githubRepoBox.get(), repoSubpathBox.get(), databaseBox.get(), basexUriBox.get(), passwordBox.get())
gitToBaseButton = ttk.Button(mainframe, text = "Transfer from Github to BaseX", width = 30, command = lambda: gitToBaseButtonClick() )
gitToBaseButton.grid(column=4, row=8, sticky=W)
emptyText = StringVar()
ttk.Label(mainframe, textvariable=emptyText).grid(column=3, row=9, sticky=(W, E))
emptyText.set(' ')
dumpUriText = StringVar()
ttk.Label(mainframe, textvariable=dumpUriText).grid(column=3, row=10, sticky=(W, E))
dumpUriText.set('Graph dump URI root')
dumpUriBox = ttk.Entry(mainframe, width = 50, textvariable = StringVar())
dumpUriBox.grid(column=4, row=10, sticky=W)
dumpUriBox.insert(END, 'http://yourservername.com/gom/dump/')
endpointUriText = StringVar()
ttk.Label(mainframe, textvariable=endpointUriText).grid(column=3, row=11, sticky=(W, E))
endpointUriText.set('SPARQL endpoint URI')
endpointUriBox = ttk.Entry(mainframe, width = 50, textvariable = StringVar())
endpointUriBox.grid(column=4, row=11, sticky=W)
endpointUriBox.insert(END, 'https://sparql.vanderbilt.edu/sparql')
pwd2Text = StringVar()
ttk.Label(mainframe, textvariable=pwd2Text).grid(column=3, row=12, sticky=(W, E))
pwd2Text.set('Endpoint password')
passwordBox2 = ttk.Entry(mainframe, width = 15, textvariable = StringVar(), show='*')
passwordBox2.grid(column=4, row=12, sticky=W)
passwordBox2.insert(END, '[pwd]')
graphNameText = StringVar()
ttk.Label(mainframe, textvariable=graphNameText).grid(column=3, row=13, sticky=(W, E))
graphNameText.set('Graph name')
graphNameBox = ttk.Entry(mainframe, width = 50, textvariable = StringVar())
graphNameBox.grid(column=4, row=13, sticky=W)
graphNameBox.insert(END, 'http://example.org/building')
def baseToTripleButtonClick():
dataToTriplestore(dumpUriBox.get(), databaseBox.get(), endpointUriBox.get(), graphNameBox.get(), passwordBox2.get())
baseToTripleButton = ttk.Button(mainframe, text = "Transfer from BaseX to Triplestore", width = 30, command = lambda: baseToTripleButtonClick() )
baseToTripleButton.grid(column=4, row=14, sticky=W)
ttk.Label(mainframe, textvariable=emptyText).grid(column=3, row=15, sticky=(W, E))
def dropGraphButtonClick():
dropGraph(endpointUriBox.get(), graphNameBox.get(), passwordBox2.get())
dropGraphButton = ttk.Button(mainframe, text = "Drop (delete) graph", width = 30, command = lambda: dropGraphButtonClick() )
dropGraphButton.grid(column=4, row=16, sticky=W)
ttk.Label(mainframe, textvariable=emptyText).grid(column=3, row=17, sticky=(W, E))
logText = StringVar()
ttk.Label(mainframe, textvariable=logText).grid(column=3, row=18, sticky=(W, E))
logText.set('Action log')
#scrolling text box hacked from https://www.daniweb.com/programming/software-development/code/492625/exploring-tkinter-s-scrolledtext-widget-python
edit_space = tkst.ScrolledText(master = mainframe, width = 100, height = 25)
# the padx/pady space will form a frame
edit_space.grid(column=4, row=18, padx=8, pady=8)
edit_space.insert(END, '')
def updateLog(message):
edit_space.insert(END, message + '\n')
edit_space.see(END) #causes scroll up as text is added
root.update_idletasks() # causes updated to log window, see https://stackoverflow.com/questions/6588141/update-a-tkinter-text-widget-as-its-written-rather-than-after-the-class-is-fini
def generateFilenameList(coreDoc):
filenameList = [{'name': 'namespace','tag': 'namespaces'},{'name': coreDoc + '-column-mappings','tag': 'column-index'},{'name': coreDoc + '-classes','tag': 'base-classes'}]
return filenameList
def getCsvObject(httpPath, fileName, fieldDelimiter):
# retrieve remotely from GitHub
uri = httpPath + fileName
r = requests.get(uri)
updateLog(str(r.status_code) + ' ' + uri)
body = r.text
csvData = csv.reader(body.splitlines()) # see https://stackoverflow.com/questions/21351882/reading-data-from-a-csv-file-online-in-python-3
return csvData
# XML creation functions hacked from http://code.activestate.com/recipes/577423-convert-csv-to-xml/
def buildGenericXml(rootElementName, csvData):
xmlData = ''
xmlData = xmlData + '<' + rootElementName + '>' + "\n"
rowNum = 0
for row in csvData:
if rowNum == 0:
tags = row
# replace spaces w/ underscores in tag names
for i in range(len(tags)):
tags[i] = tags[i].replace(' ', '_')
else:
xmlData = xmlData + '<record>' + "\n"
for i in range(len(tags)):
xmlData = xmlData + ' ' + '<' + tags[i] + '>' + escapeBadXmlCharacters(row[i]) + '</' + tags[i] + '>' + "\n"
xmlData = xmlData + '</record>' + "\n"
rowNum +=1
xmlData = xmlData + '</' + rootElementName + '>' + "\n"
return xmlData
def escapeBadXmlCharacters(dirtyString):
ampString = dirtyString.replace('&','&')
ltString = ampString.replace('<','<')
cleanString = ltString.replace('>','>')
return cleanString
def buildLinkedMetadataXml(httpPath, csvData, fieldDelimiter):
xmlData = '<?xml version="1.0" encoding="UTF-8" ?>' + '\n'
xmlData = xmlData + '<linked-metadata>' + "\n"
rowNum = 0
for row in csvData:
if rowNum == 0:
tags = row
else:
xmlData = xmlData + '<file>' + "\n"
xmlData = xmlData + ' ' + '<link_column>' + row[tags.index('link_column')] + '</link_column>' + "\n"
xmlData = xmlData + ' ' + '<link_property>' + row[tags.index('link_property')] + '</link_property>' + "\n"
xmlData = xmlData + ' ' + '<suffix1>' + row[tags.index('suffix1')] + '</suffix1>' + "\n"
xmlData = xmlData + ' ' + '<link_characters>' + row[tags.index('link_characters')] + '</link_characters>' + "\n"
xmlData = xmlData + ' ' + '<suffix2>' + row[tags.index('suffix2')] + '</suffix2>' + "\n"
xmlData = xmlData + ' ' + '<class>' + row[tags.index('class')] + '</class>' + "\n"
fileName = row[tags.index('filename')]
fileNameRoot = fileName[0:fileName.find('.')]
csvSubData = getCsvObject(httpPath, fileNameRoot + '-classes.csv', ',')
xmlData = xmlData + buildGenericXml('classes', csvSubData)
csvSubData = getCsvObject(httpPath, fileNameRoot + '-column-mappings.csv', ',')
xmlData = xmlData + buildGenericXml('mapping', csvSubData)
csvSubData = getCsvObject(httpPath, fileName, fieldDelimiter) # metadata file may have a different delimiter than comma
xmlData = xmlData + buildGenericXml('metadata', csvSubData)
xmlData = xmlData + '</file>' + "\n"
rowNum +=1
xmlData = xmlData + '</linked-metadata>' + "\n"
return xmlData
def writeDatabaseFile(databaseWritePath, filename, body, pwd):
uri = databaseWritePath + '/' + filename
hdr = {'Content-Type' : 'application/xml'}
r = requests.put(uri, auth=('admin', pwd), headers=hdr, data = body.encode('utf-8'))
updateLog(str(r.status_code) + ' ' + uri + '\n')
updateLog(r.text + '\n')
def dataToBasex(githubRepo, repoSubpath, database, basexServerUri, pwd):
databaseWritePath = basexServerUri + database
# first must do a PUT to the database URI to create it if it doesn't exist
r = requests.put(databaseWritePath, auth=('admin', pwd) )
updateLog('create XML database')
updateLog(str(r.status_code) + ' ' + databaseWritePath + '\n')
httpReadPath = 'https://raw.githubusercontent.com/' + githubRepo + 'master/' + repoSubpath + database + '/'
# must open the configuration/constants file separately in order to discover the core document and separator character
updateLog('read constants')
csvData = getCsvObject(httpReadPath, 'constants.csv', ',')
# pull necessary constants out of the CSV object
rowNum = 0
for row in csvData: # only one row of data below headers
if rowNum == 0:
tags = row
else:
coreDocFileName = row[tags.index('coreClassFile')]
fieldDelimiter = row[tags.index('separator')]
rowNum +=1
# find the file name without extension
coreDocRoot = coreDocFileName[0:coreDocFileName.find('.')]
# write the configuration data; not sure why csvData wasn't preserved to this point ???
updateLog('read configuration')
tempCsvData = getCsvObject(httpReadPath, 'constants.csv', ',')
body = '<?xml version="1.0" encoding="UTF-8" ?>' + '\n' + buildGenericXml('constants', tempCsvData)
updateLog('write configuration')
writeDatabaseFile(databaseWritePath, 'constants.xml', body, pwd)
# write each of the various associated files
nameList = generateFilenameList(coreDocRoot)
for name in nameList:
updateLog('read file')
csvData = getCsvObject(httpReadPath, name['name'] + '.csv', ',')
body = '<?xml version="1.0" encoding="UTF-8" ?>' + '\n' + buildGenericXml(name['tag'], csvData)
updateLog('write file')
writeDatabaseFile(databaseWritePath, name['name'] + '.xml', body, pwd)
# The main metadata file must be handled separately, since may have a non-standard file extension or delimiter
updateLog('read core metadata')
csvData = getCsvObject(httpReadPath, coreDocFileName, fieldDelimiter)
body = '<?xml version="1.0" encoding="UTF-8" ?>' + '\n' + buildGenericXml('metadata', csvData)
updateLog('write core metadata')
writeDatabaseFile(databaseWritePath, coreDocRoot + '.xml', body, pwd)
# The linked class data has a different format and must be handled separately
updateLog('read linked metadata')
csvData = getCsvObject(httpReadPath, 'linked-classes.csv', ',')
body = buildLinkedMetadataXml(httpReadPath, csvData, fieldDelimiter)
updateLog('write linked metadata')
writeDatabaseFile(databaseWritePath, 'linked-classes.xml', body, pwd)
updateLog('Ready')
def dataToTriplestore(dumpUri, database, endpointUri, graphName, pwd):
updateCommand = 'LOAD <' + dumpUri + database + '> INTO GRAPH <' + graphName + '>'
updateLog('update SPARQL endpoint into graph ' + graphName)
# SPARQL Update requires HTTP POST
hdr = {'Content-Type' : 'application/sparql-update'}
r = requests.post(endpointUri, auth=('admin', pwd), headers=hdr, data = updateCommand)
updateLog(str(r.status_code) + ' ' + r.url + '\n')
updateLog(r.text + '\n')
updateLog('Ready')
def dropGraph(endpointUri, graphName, pwd):
updateCommand = 'DROP GRAPH <' + graphName + '>'
updateLog('drop graph ' + graphName)
# SPARQL Update requires HTTP POST
hdr = {'Content-Type' : 'application/sparql-update'}
r = requests.post(endpointUri, auth=('admin', pwd), headers=hdr, data = updateCommand)
updateLog(str(r.status_code) + ' ' + r.url + '\n')
updateLog(r.text + '\n')
updateLog('Ready')
def main():
root.mainloop()
if __name__=="__main__":
main()