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@danbe danbe/zotero.py
Last active Feb 21, 2020

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Library for creating Zotero items from Python. Connects to a local Zotero repository running in Firefox through MozRepl.
# -*- coding: utf-8 -*-
from collections import namedtuple
import json
import urllib.parse
#import telnetlib
import time
import os.path
import filecmp
import random
import string
import requests
try:
import yaml
yamlExists = True
except:
print('yaml is not available, cannot store the protocol to file.')
yamlExists = False
# Library for interacting with a local Zotero library in Firefox
# MozRepl doesn't work anymore, use Zotero Debug Bridge instead
# enter the password you set in the advanced settings for the debug bridge here:
debugBridgePassword="setYourPasswordHere"
# test with curl -X POST -H "Content-Type: application/javascript" --data "await Zotero.Schema.schemaUpdatePromise; return 'hello ' + query.world" "http://127.0.0.1:23119/debug-bridge/execute?foo=bar&baz=quux&world=world&password=debugBridgePassword"
# should print "hello world"
# This library is intended to allow bulk import of existing libraries.
# The user has to find a way to extract the metadata for his library items.
# Possibilities are
# * ISBNs in the filename
# * XMP Metadata (e.g. using cb2bib http://www.molspaces.com/cb2bib/)
# * ...
# For a usage example look at the bottom of this file.
# BSD License
# Configuration
Verbose = True
#####################################################################################################
def makeItem(itemName, itemKeys):
cls= namedtuple(itemName, itemKeys)
cls.__new__.__defaults__ = (None,) * len(itemKeys)
return cls
# Field definitions
# A list of Zotero fields can be found at http://aurimasv.github.io/z2csl/typeMap.xml#map-journalArticle
# Replace creator with creators and delete the other creator fields creatorItems = ['authors', 'creators', 'contributors', 'editors', 'translators', 'seriesEditors', 'reviewedAuthors']
bookKeys='abstractNote accessDate archive archiveLocation callNumber creators date edition extra ISBN language libraryCatalog numberOfVolumes numPages place publisher rights series seriesNumber shortTitle title url volume'.split()
book = makeItem('book', bookKeys)
journalArticleKeys='abstractNote accessDate archive archiveLocation callNumber creators date DOI extra ISSN issue journalAbbreviation language libraryCatalog pages publicationTitle rights series seriesText seriesTitle shortTitle title url volume'.split()
journalArticle = makeItem('journalArticle', journalArticleKeys)
bookSectionKeys = 'abstractNote accessDate archive archiveLocation bookTitle callNumber creators date edition extra ISBN language libraryCatalog numberOfVolumes pages place publisher rights series seriesNumber shortTitle title url volume'.split()
bookSection = makeItem('bookSection', bookSectionKeys)
blogPostKeys = 'abstractNote accessDate blogTitle creators date extra language rights shortTitle title url websiteType'.split()
blogPost = makeItem('blogPost', blogPostKeys)
conferencePaperKeys = 'abstract accessDate archive archiveLocation callNumber conferenceName creators date DOI extra ISBN language libraryCatalog pages place proceedingsTitle publisher rights series shortTitle title url volume'.split()
conferencePaper = makeItem('conferencePaper', conferencePaperKeys)
documentKeys = 'abstract accessDate archive archiveLocation callNumber creators date extra language libraryCatalog publisher rights shortTitle title url'.split()
document = makeItem('document', documentKeys)
presentationKeys = 'abstractNote accessDate creators date extra language meetingName place presentationType rights shortTitle title url'.split()
presentation = makeItem('presentation', presentationKeys)
reportKeys = 'abstractNote accessDate archive archiveLocation callNumber creators date extra institution language libraryCatalog pages place reportNumber reportType rights seriesTitle shortTitle title url'.split()
report = makeItem('report', reportKeys)
thesisKeys = 'abstract accessDate archive archiveLocation callNumber creators date extra language libraryCatalog numPages place rights shortTitle thesisType title university url'.split()
thesis = makeItem('thesis', thesisKeys)
webpageKeys = 'abstractNote accessDate creators date extra language rights shortTitle title url websiteTitle websiteType'.split()
webpage = makeItem('webpage', webpageKeys)
#####################################################################################################
#####################################################################################################
# Class Definitions, these classes represent Zotero items
#book = namedtuple('book', bookKeys)
#book.__new__.__defaults__ = (None,) * len(bookKeys)
#journalArticle = namedtuple('journalArticle', journalArticleKeys)
#journalArticle.__new__.__defaults__ = (None,)*len(journalArticleKeys)
#####################################################################################################
# Different types of creators
class creator(object):
'''Base class for all creators'''
def __init__(self, first, last):
self.first = first
self.last = last
def __str__(self):
return '%s(%s, %s)' % (self.__class__.__name__, self.first, self.last)
class author(creator): pass
class bookAuthor(creator): pass
class contributor(creator): pass
class commenter(creator): pass
class editor(creator): pass
class presenter(creator): pass
class translator(creator): pass
class seriesEditor(creator): pass
class reviewedAuthor(creator): pass
# Not all creators are allowed for all items
allowedCreators = {
book:[author, contributor, editor, seriesEditor, translator],
conferencePaper:[author, contributor, editor, seriesEditor, translator],
bookSection:[author, bookAuthor, contributor, editor, seriesEditor, translator],
journalArticle:[author, contributor, editor, reviewedAuthor, translator],
document:[author, contributor, editor, reviewedAuthor, translator],
blogPost:[author, commenter, contributor],
presentation:[contributor, presenter],
report:[author, contributor, seriesEditor, translator],
thesis:[author, contributor],
webpage:[author, contributor, translator],
}
######################################################################################################
from unidecode import unidecode
def printd(*x):
if Verbose: #
print(list(unidecode(str(xx)) for xx in x))
class JSVariable(object):
'''Create a variable that lives in the javascript namespace'''
def __init__(self, zoteroObject, name, initialValue = -9999, initFromFunctionCall=None, bindingType = 'var', gensym = True):
# create variable
value = initialValue
self.zoteroObject = zoteroObject
self.name = name
if gensym: # normal case
self.jsname = zoteroObject.gensym(name)
else: # use this for debugging
self.jsname = self.name
if bindingType == 'let':
raise Exception('let binding not working yet')
# the let binding works, but the readback doesn't. as all variables are gensym'ed, it doesn't matter
self.zoteroObject.let_binding(self.jsname, value)
elif bindingType == 'var':
self.zoteroObject.var_binding(self.jsname, value)
else:
raise Exception('bindingType must be let or var', bindingType)
if initFromFunctionCall != None: # immediately set the new variable by executing the function call
self.setVariableFromFunctionCall(initFromFunctionCall)
# TODO: always use JSON format for all returns?
@property
def value(self):
return self.zoteroObject.getVariable(self.jsname)
@value.setter
def value(self, value):
return self.zoteroObject.setVariable(self.jsname, str(value).encode('unicode_escape'))
def setVariableFromFunctionCall(self, functionCallString):
'''Execute the function call and assign the result to the variable
Example: setVariableFromFunctionCall("new Zotero.Item('note')") '''
return self.zoteroObject.setVariableFromFunctionCall(self.jsname, functionCallString)
def attributeAccess(self, attributeString):
'''Execute the function or attribute on the variable and return the result
example: attributeAccess(".setNote('{text}');".format(text=text))
Needs leading . '''
self.zoteroObject.writeToRepl(self.jsname + attributeString)
return self.zoteroObject.readFromRepl()
class ZoteroError(Exception): pass
class zoteroTransaction(object):
def __init__(self, zoteroObject):
self.zoteroObject = zoteroObject
def __enter__(self):
return
self.zoteroObject.sendToZotero(code='Zotero.DB.beginTransaction();')
# TODO: this does not work
# ...: data = "Zotero.DB.beginTransaction()"
# ...: r = requests.post(url, data = data, headers=headers)
# ...: print(r.text)
# debug-bridge failed: TypeError: Zotero.DB.beginTransaction is not a function
# anonymous@chrome://zotero-debug-bridge/content/debug-bridge.js line 33 > AsyncFunction:3:1
def __exit__(self, type, value, traceback):
if type == None and value == None and traceback == None:
#ODO: remove this when transactions work
#self.zoteroObject.sendToZotero(code='Zotero.DB.commitTransaction();')
printd('Committing Transaction')
else:
#self.zoteroObject.sendToZotero(code='Zotero.DB.rollbackTransaction();')
printd('Rolling Back Transaction')
return False # re-raise exception
class zotero(object):
def __init__(self):
pass
def __enter__(self):
self.open()
return self
def __exit__(self, type, value, traceback):
self.close()
if type == None and value == None and traceback == None:
pass
else:
print('Zotero Error')
return False
def __del__(self):
self.close()
def open(self):
if not self.testZoteroConnection():
print('No connection to Zotero')
raise Exception('No connection')
#printd( self.telnet.read_until(b"repl>", 10))
def close(self):
#self.telnet.close()
pass
def gensym(self, name = '', symbolLength = 10):
'Create a random symbol name, use this for javascript variables to avoid accidental capture'
return name + ''.join(random.choice(string.ascii_letters) for _ in range(symbolLength))
def introduceJSVariable(self, name, initialValue = -9999):
'''Introduce a let-binding in the JS namespace'''
return JSVariable(self, name, initialValue)
def var_binding(self, name, value):
'''introduce a let-binding in JS, name is assumed to be a bytestring and the value should be .encode('unicode_escape')'''
# TODO: deal with strings properly, "abc" -> b"\'abc\'" etc. 123 -> b'123'
# TODO: is it better to call a toJSON function here????
# this needs to be recursive
if type(value) == bytes:
print('Argument should be a string or a number, not a bytes string')
1/0
value = json.dumps(value).encode('unicode_escape')
if type(name) != bytes:
name = name.encode('ascii')
cmd = b"var %b = %b ;" % (name, value)
print('var variable introduction', cmd)
self.telnet.write(cmd)
ret=self.telnet.read_until(b"repl>", 1)
retp=self.telnet.read_until(b"repl>", 1)
self.telnet.write(b"%b;" % name)
retn=self.telnet.read_until(b"repl>", 1)
print("var-binding", ret, retp, retn)
print(self.getVariable(name), self.getVariableJSON(name))
if not ret.endswith(b"repl>"):
raise IOError('Error executing {command}. Did not get repl>. Got: {ret}'.format(command=name, ret=repr(ret)))
return ret.decode('utf-8')
def getVariable(self, name):
'''Get a variable from MozRepl'''
if type(name) != bytes:
name = name.encode('ascii')
cmd = name + b';'
print('getVariable', cmd)
self.telnet.write(cmd)
ret=self.telnet.read_until(b"repl>", 1)
if not ret.endswith(b"repl>"):
raise IOError('Error executing {command}. Did not get repl>. Got: {ret}'.format(command=name, ret=repr(ret)))
# ret starts with space
ret = ret[1:-len(b"\nrepl>")]
return ret.decode('utf-8')
def setVariable(self, name, value):
self.zoteroObject.writeToRepl('%s = %s;' % (variable, functionCall))
def cleanTelnetQueue(self):
'''Read as much as possible'''
ret = b''
while True:
x = self.telnet.read_eager()
if x == b'':
break
ret += x
return ret
def getVariableJSON(self, name):
'''Get a variable as JSON '''
ret = self.sendToZotero(code='return ' + name)
return json.loads(ret)
if False: # TODO: remove old code
print('cleaning before ', self.cleanTelnetQueue())
if type(name) != bytes:
name = name.encode('ascii')
self.telnet.write(b'var jsonitems = JSON.stringify(' + name + b');')
time.sleep(0.1)
# get rid of b'repl> '
print('cleaning 3', self.cleanTelnetQueue())
self.telnet.write(b'jsonitems;')
time.sleep(0.1)
#print('cleaning', self.cleanTelnetQueue())
ret=self.telnet.read_until(b"repl>", 10)
if not ret.endswith(b"repl>"):
raise IOError('Error executing {command}. Did not get repl>. Got: {ret}'.format(command=name, ret=repr(ret)))
# ret starts with space
print('returned string \n')
print(ret)
ret = ret[1:-len(b"repl>")].decode('utf-8').strip('"') # TODO: probably only strip one level of quotation marks??
#ret = ret.replace('\\"','"') # something changed in MozRepl, quotes escaped ", i.e. \\"
return json.loads(ret.strip('\n"'))
def testZoteroConnection(self):
'Test if the Zotero Debug Bridge is working'
rtext = self.sendToZotero(variables={'world':'world'}, code="await Zotero.Schema.schemaUpdatePromise; return 'hello ' + query.world")
if rtext=='"hello world"':
print('Connection to Zotero is working')
return True
else:
print('ERROR: Connection to Zotero not working')
return False
return r.text
def sendToZotero(self, variables={}, code=''):
'set the variables variables and then run the code'
url = "http://127.0.0.1:23119/debug-bridge/execute?" + urllib.parse.urlencode({**variables, **{'password':debugBridgePassword}})
headers = {"Content-Type":"application/javascript"}
data = b"await Zotero.Schema.schemaUpdatePromise; " + code.encode('utf-8')
print('data', data)
r = requests.post(url, data = data, headers=headers)
print(r)
print(r.request)
r.raise_for_status()
return r.text
def writeToRepl(self, msg):
'This function was a layer that encapsulated the telnet calls.'
raise DeprecationWarning('Do not use telnet anymore')
#return self.telnet.write(msg.encode('ascii'))
def readFromRepl(self, timeout=1):
ret=self.telnet.read_until(b"repl>", timeout)
ret = ret[1:-len("\nrepl>")].decode('utf-8')
return ret
def createVariableFromFunctionCall(self, variable, functionCall):
self.writeToRepl('var %s = %s;' % (variable, functionCall))
ret = self.readFromRepl()
return ret
def setVariableFromFunctionCall(self, variable, functionCall):
self.writeToRepl('%s = %s;' % (variable, functionCall))
ret = self.readFromRepl()
return ret
def executeFunction(self, functionCall):
self.writeToRepl('%s;' % (functionCall))
ret = self.readFromRepl()
return ret
# TODO: this function has to go, replace by more specific functions that do direct error handling
def execute(self, cmd, timeout=10, noCheck=False):
print('cmd before ', cmd.encode('utf-8'))
printd( 'executing %s ' % cmd)
# execute will do some rudimentary error checks
# These checks are probably very specific not only to MozRepl, but also
# to the commands used.
self.telnet.write(cmd.encode('unicode_escape'))
print('executed command, trying to read')
time.sleep(0.1)
ret=self.telnet.read_until(b"repl>", timeout)
if not ret.endswith(b"repl>"):
raise IOError('Error executing {command}. Did not get repl>. Got: {ret}. If you got a number at the end, like repl1>, it means another repl is running. Better restart mozrepl in that case.'.format(command=cmd, ret=repr(ret)))
else:
print('Readback from command', repr(ret))
# first value returned = spc
ret = ret[1:-len("\nrepl>")].decode('utf-8')
if ret.startswith('[object Promise]'):
print('We are dealing with a promise, trying to resolve')
#self.telnet.write(b'var jsonitems = JSON.stringify(' + name.encode('ascii') + b');')
#self.telnet.write(b'resolved = ret.then(function(result) {return JSON.stringify(result)})')
self.telnet.write(b'resolved = ret.get()')
ret2=self.telnet.read_until(b"repl>", timeout)
resolved = self.getVariable('resolved')
print('After resolving', ret2)
print('resolved', resolved)
if noCheck == True:
return ret
returnOK = False
# Some commands return an empty string, no way to do error checking
# There might be a more generic way, but better be on the safe side
printd('stripped cmd', cmd.strip())
if ( cmd.strip() in [
'var item = new Zotero.Item;',
'var creator = new Zotero.Creator;',
'var itemID = item.save();',
'var file = Components.classes["@mozilla.org/file/local;1"].createInstance(Components.interfaces.nsILocalFile);',
'Zotero.DB.beginTransaction();',
'Zotero.DB.commitTransaction();',
'Zotero.DB.rollbackTransaction();',
'var tags = item.getTags();',
'var item = new Zotero.Item(\'note\');',
'var notes = item.getNotes();',
'var items = ZoteroPane.getSelectedItems();',
'var att_ids = item.getAttachments(false);',
]
) and ret == '':
returnOK = True
elif ( cmd.startswith('var item = Zotero.Items.get(') or
cmd.startswith('file.initWithPath(') or
cmd.startswith('var creator = item.getCreator(') or
cmd.startswith('var attachment = Zotero.Items.get(') or
cmd.startswith('var note = Zotero.Items.get(')
) and ret == '':
returnOK = True
# These items might have an equal sign
elif (cmd.startswith('item.setNote(') or \
cmd.startswith('item.setField("url"')) and \
ret=='true':
returnOK = True
elif '=' in cmd and '(' not in cmd: # no functions allowed
# for other assignments, the RHS is returned. Check that this is true.
RHS = cmd.split('=')[-1]
RHS = RHS.strip(' ;')
printd('cmd', cmd, cmd[:5])
printd('rhs', RHS, RHS[:5], str(RHS), type(RHS))
printd('ret', ret, type(ret))
printd('ret=rhs', RHS==ret)
# RHS has backslash escaped
if RHS != ret:
raise IOError('Error executing {command}. Looks like assignment, but RHS was not returned. Got: >{ret}<'.format(command=repr(cmd), ret=repr(ret)))
else:
returnOK = True
elif len(cmd) > 100 and ret.endswith('....> ....> true'):
# Long commands end with ....> ....> true. Length where this occurs has not been
# verified
returnOK = True
elif len(cmd) > 50 and ret.endswith('....> true'):
# Long commands end with ....> ....> true. Length where this occurs has not been
# verified
returnOK = True
# Commands returning a number
elif cmd.endswith('.save();') or \
cmd.startswith('Zotero.Attachments.linkFromFile(') :
try:
id = int(ret)
except ValueError:
raise IOError('Error executing {command}. Could not convert to int Got: >{ret}<'.format(command=cmd, ret=repr(ret)))
else:
returnOK = True
elif cmd.startswith('item.addTag('):
try:
if ret != 'false':
# addTag returns false if the tag was not added. This is the case if the tag already exists
pass
except ValueError:
raise IOError('Error executing {command}. Could not convert to int Got: >{ret}<'.format(command=cmd, ret=repr(ret)))
else:
returnOK = True
elif cmd.startswith('ret = Zotero.Attachments.importFromFile(file,') and \
int(cmd[:-1].split(',')[1]) + 1 <= int(ret): # returns ID of newly created file item.
# This seems (sometimes) to be be one more than the ID of the file item we pass in
# sometimes a bit more
print(1234, cmd)
print(cmd)
print(int(cmd[:-1].split(',')[1]))
print(int(ret))
returnOK = True
elif ret in ['true']: # generic case
returnOK = True
else:
raise IOError('Error executing {command}. Did not return true. Got: >{ret}<'.format(command=cmd, ret=repr(ret)))
if returnOK != True:
raise Exception('This should not happen, must have overlooked a case.')
return ret
def addItem(self, item, attachmentList=[], tags = [], notes=[], attachmentMode='import'):
'''Add an item (book, journalArticle) to Zotero database, attachments
will be linked to avoid loosing the original data'''
attachmentList = list(map(os.path.abspath, attachmentList))
# Check that all attachments exist
for f in attachmentList:
if not os.path.isfile(f):
raise Exception('File %s not found!' % f)
# Tags without a type will get type 0
tags = [(str(t[0]), t[1]) if type(t)==tuple else (str(t),0) for t in tags]
# This dict will hold all data item data together with the itemID and
# IDs of attachments
# The idea is to store this with the original data to have a link
# folder -> zoteroDB
addReport = {}
addReport['itemType'] = item.__class__.__name__
addReport['itemData'] = dict((field,getattr(item, field)) for field in item._fields)
try:
with zoteroTransaction(self): # TODO: the transaction doesn't work.
# the alternative is to calll return await Zotero.DB.executeTransaction(async () => {...})
# the problem is that this does not work with the context manager.
# Add item
itemID = self.addItemBase(item)
print(itemID)
addReport['itemID'] = itemID
# Confirm that the data was written correctly
print('Item verification disabled')
addReport['verified'] = True# self.verifyItem(item, itemID)
addReport['attachments'] = []
# Add attachments and verify each one
for attachment in attachmentList:
attachmentID = self.attachFile(itemID, attachment, mode=attachmentMode)
addReport['attachments']+=[{attachment:attachmentID}]
print('Skipping attachment verification')
#self.verifyAttachment(attachment, attachmentID, itemID)
# Add tags
self.addTags(tags, itemID)
#self.verifyTags(tags, itemID)
print('Skipping tags verification')
addReport['tags'] = True# tags
# Add notes
for note in notes:
self.addNote(text=note, parent=itemID)
# Verify notes
print('Skipping note verification')
addReport['notes'] = True#self.verifyNotes(notes, itemID)
except:
print('Failed to add item')
raise
else:
print('Successfully added and verified item.')
return addReport
def getUrlToAttachedFile(self, attachmentID):
attachmentURLValue = self.getVariableJSON(f'Zotero.Items.get({attachmentID}).getLocalFileURL()')
print('attachmentURL', attachmentURLValue)
url = urllib.parse.unquote(attachmentURLValue.strip('"'))
return url
def verifyAttachment(self, path, attachmentID, parentID):
printd('Verifying attachment %s' %path)
printd( 'attachmentID %s' % attachmentID)
self.execute('var attachment = Zotero.Items.get({attachmentID});'.format(attachmentID=attachmentID))
ID= int(self.getVariable('attachment.getID()'))
exists = self.getVariable('attachment.exists()')
#type=self.getVariable('attachment.getType()')
isAttachment = self.getVariable('attachment.isAttachment()')
savedFilename = self.getVariable('attachment.getFilename()')[1:-1]
isFileAttachment = self.getVariable('attachment.isFileAttachment()')
attachmentPath = self.getVariable('attachment.attachmentPath;')[1:-1]
urlToAttachedFile = self.getUrlToAttachedFile(attachmentID)
sourceItemID = int(self.getVariable('attachment._sourceItemID;'))
self.execute('var item = Zotero.Items.get({ID});'.format(ID=parentID))
# getAttachments => 2860,2861,2862 - {0: 2860, 1: 2861, 2: 2862}
attachmentsOfParent = list(map(int, self.getVariable('item.getAttachments();').split('-')[0].split(',')))
# This does not work for bmp and png
#fileExists = self.getVariable('attachment._fileExists;')
# imported item
if (attachmentPath.startswith('storage:') and
urlToAttachedFile.startswith('file:///') and
exists == 'true' and
ID == attachmentID and
isFileAttachment == 'true' and
attachmentPath[len('storage:'):] == os.path.basename(path) and
sourceItemID == parentID and
attachmentID in attachmentsOfParent and
filecmp.cmp(path, urlToAttachedFile[len('file:///'):], shallow=True)):
print('Successfully compared file', urlToAttachedFile)
# linked item
elif (exists == 'true' and
ID == attachmentID and
isAttachment == 'true' and
savedFilename == os.path.basename(path) and
isFileAttachment == 'true' and
os.path.abspath(attachmentPath) == path and
sourceItemID == parentID and
attachmentID in attachmentsOfParent):
pass
else:
raise Exception('Could not verify file fileExists={exists}, attachmentPath={attachmentPath}, path={path}, ID={ID}, attachmentID={attachmentID}, savedFilename={savedFilename}, sourceItemID={sourceItemID}, parentID={parentID}'.format(**locals()))
return dict(urlToAttachedFile=urlToAttachedFile)
def addItemBase(self, item):
'''Add item without attachments, notes etc.
this wil be part of a transaction, if the creation fails,0'''
code = 'return await Zotero.DB.executeTransaction(async () => {'
code+='var item = new Zotero.Item;'
code+='item.setType(Zotero.ItemTypes.getID(\'{itemType}\'));'.format(itemType = item.__class__.__name__)
creatorcode = ''
for field in item._fields:
if getattr(item, field) == None: # Default value, nothing to do
continue
# Add creators
if field == 'creators':
for creatorNumber, creator in enumerate(getattr(item, field)):
if creator.__class__ not in allowedCreators[item.__class__]:
raise Exception('Creator %s not allowed for %s' % (creator.__class__.__name__, item.__class__.__name__))
# TODO: Create new Creator, or search for existing ones?
creatorcode+=f'{{firstName:"{creator.first}", lastName:"{creator.last}", creatorType:"{creator.__class__.__name__}"}},'
# code+='var creator = Zotero.Creator;'
# code+='creator.firstName = "{first}";'.format(first=creator.first)
# code+='creator.lastName = "{last}";'.format(last=creator.last)
# code+= "creator.save();"
# code+="item.setCreator({creatorNumber}, creator, '{creatorType}');".format(creatorType=creator.__class__.__name__, creatorNumber=creatorNumber)
# Add fields
else:
code+=f'item.setField("{field}", {json.dumps(getattr(item, field))});'#.format(field=field, fieldValue=getattr(item, field))
if creatorcode != '':
creatorcode = 'item.setCreators([ ' + creatorcode + ']);'
code += creatorcode
code += 'return item.save()})'
print('addItemBaseCode\n', code, '\n')
return self.sendToZotero(code=code)
return int(self.getVariable('item.save()'))
def verifyItem(self, item, itemID):
'''Verify that the item corresponds to the one referenced by the id'''
self.execute('var item = Zotero.Items.get({itemID});'.format(itemID=itemID))
creatorNumber = -1
for field in item._fields:
if field == 'creators':
for creatorNumber, creator in enumerate(getattr(item, field)):
self.execute("var creator = item.getCreator({creatorNumber});".format(creatorNumber=creatorNumber))
savedFirst = self.getVariable('creator.ref.firstName;')[1:-1]
savedLast = self.getVariable('creator.ref.lastName;')[1:-1]
savedID = self.getVariable('creator.creatorTypeID;')
if savedFirst == creator.first and \
savedLast == creator.last and \
savedID == self.getVariable('Zotero.CreatorTypes.getID("{creatorType}");'.format(creatorType = creator.__class__.__name__)):
printd('Successfully verified creator %s %s (%s)' % (savedFirst, savedLast, creator.__class__.__name__))
else:
raise Exception('Creator Name does not match. (%s %s %s) != (%s %s %s) '\
% (savedFirst, savedLast, savedID,
creator.first, creator.last, creator.__class__.__name__))
else:
# All values are stored as strings, remove double quotes
savedValue = self.getVariable('item.getField("{field}")'.format(field=field)).strip('"')
if getattr(item, field) == None:
# No item specified, maps to empty string in Zotero
expectedValue = ''
else:
expectedValue = getattr(item, field)
if savedValue.strip() != expectedValue.strip(): # Zotero strips whitespace
printd('+++++ expected value')
printd(repr(expectedValue.strip()), len(expectedValue.strip()), expectedValue.encode('utf-8'))
printd('+++++ saved value')
printd(repr(savedValue.strip()), len(savedValue.strip()), savedValue.encode('utf-8'))
for a,b in zip(savedValue.strip(), expectedValue.strip()):
if a != b:
print(a.encode('utf-8'), b.encode('utf-8'))
raise Exception('Retrieved field {field} for item # {itemID}, does not match {expectedValue}'.format(field=field, itemID=itemID, expectedValue=repr(expectedValue)))
else:
printd('Successfully verified {field} = {expectedValue}'.format(field=repr(field), expectedValue=repr(expectedValue)))
printd( '...Successfully verified all fields.')
return True
def addNote(self, text, parent=None):
'''parent=None -> standalone note'''
code="item = new Zotero.Item('note');"
code+=f"item.setNote('{text}');"
if parent!=None:
code+=f'item.parentID = {parent};'
code+='return item.save();' # itemID
print('code\n', code, '\nend\n')
return int(self.sendToZotero(code=code))
def verifyNotes(self, notes, itemID):
raise Exception('Not converted to the new debug bridge yet')
self.execute('var item = Zotero.Items.get({ID});'.format(ID=itemID))
self.execute("var notes = item.getNotes();")
nNotes = int(self.getVariable('notes.length'))
# order of notes not maintained
retrievedNotes = []
for n in range(nNotes):
self.execute('var note = Zotero.Items.get(notes[{n}]);'.format(n=n))
retrievedNotes += [self.getVariable('note.getNote()')[1:-1]]
for retrievedNote, originalNote in zip(sorted(retrievedNotes), sorted(notes)):
if retrievedNote != originalNote:
raise Exception('Notes do not match: original:\n %s \nretrieved:\n %s' % (originalNote, retrievedNote))
else:
return notes
def attachFile(self, sourceItemID, filename, mode='import'):
# single \ -> \\ for MozRepl
filepath=os.path.abspath(filename)
# TODO Zotero Error log has this error Error: The character encoding of the plain text document was not declared. The document will render with garbled text in some browser configurations if the document contains characters from outside the US-ASCII range. The character encoding of the file needs to be declared in the transfer protocol or file needs to use a byte order mark as an encoding signature.
# The same error is logged when file is manually attached through menu, so there is no way to fix it here
#optionsJV = JSVariable(self, 'options', initialValue = {"file":filepath.replace('\\', '\\'*2), "parentItemID":sourceItemID})
#importPromiseJV = JSVariable(self, 'importPromise')
if mode == 'link':
# TODO: not tested
#importPromiseJV.setVariableFromFunctionCall('Zotero.Attachments.linkFromFile(' + optionsJV.jsname + ')')
id = self.sendToZotero(code=f'return Zotero.Attachments.linkFromFile({{"file":{json.dumps(filepath, ensure_ascii=True)}, "parentItemID":{sourceItemID}}})')
elif mode == 'import':
#importPromiseJV.setVariableFromFunctionCall('Zotero.Attachments.importFromFile(' + optionsJV.jsname + ')')
id = self.sendToZotero(code=f'return Zotero.Attachments.importFromFile({{"file":{json.dumps(filepath, ensure_ascii=True)}, "parentItemID":{sourceItemID}}})')
print('attached file, trying to resolve', id)
#outJV = JSVariable(self, 'out')
# TODO: loop till promise is either rejected or fulfilled
#ret=self.telnet.read_until(b"repl>", timeout = 10)
#importPromiseJV.attributeAccess('.then((res) => ' + outJV.jsname + ' = res)')
#print('out.value', outJV.value)
else:
raise Exception('Mode not supporte %s ' % mode)
print('attachment ID', id)
return id
def addTags(self, tags, itemID):
# Add Tags
output=[] # List of javascript commands
#self.setVariableFromFunctionCall('item', 'Zotero.Items.get({ID})'.format(ID=itemID))
#self.setVariableFromFunctionCall('itemID', 'item.save()')
#output+=['var item = Zotero.Items.get({ID});'.format(ID=itemID)]
#output+=["var itemID = item.save();"]
code=f'item = Zotero.Items.get({itemID}); itemID = item.save();'
for tagAndType in tags: # cannot add tags to unsaved item
if type(tagAndType) == str or len(tagAndType) == 1: # no type, using default 0
tag, tagtype = tagAndType, 0
elif len(tagAndType) == 2:
tag, tagtype = tagAndType
else:
raise Exception('Expected a tag or a tag and a tag type, not this', tagAndType)
print('adding', tag, tagtype)
#output+=["item.addTag('{tag}', {tagtype});".format(tag=tag, tagtype=tagtype)]
code += f'if(! item.addTag("{tag}", {tagtype})) {{return false}};'
code += 'return true;'
result = self.sendToZotero(code=code)
if result != 'true':
raise ZoteroError('Could not add tags', tags, itemID)
#for l in output:
# printd( self.execute(l))
def getTags(self, itemID):
self.execute('var item = Zotero.Items.get({ID});'.format(ID=itemID))
self.execute('var tags = item.getTags();')
nTags = int(self.getVariable('tags.length;'))
savedTags = []
for n in range(nTags):
tagName = self.getVariable('tags[{n}].name'.format(n=n))[1:-1]
print('tagName', tagName)
print('tags', self.getVariable('tags'))
try:
tagType = int(self.getVariable('tags[{n}].type'.format(n=n)))
except ValueError: # sometimes tag literal is '', cannot convert to int
tagType = 0
print('Setting tag type to 0')
# order of tags is not preserved
savedTags += [(tagName, tagType)]
return savedTags
def verifyTags(self, tags, itemID):
# Verify tags
self.execute('var item = Zotero.Items.get({ID});'.format(ID=itemID))
self.execute('var tags = item.getTags();')
nTags = int(self.getVariable('tags.length;'))
if nTags != len(tags):
raise Exception('Number of tags does not match %s %s' % (nTags, len(tags)))
savedTags = []
for n in range(nTags):
tagName = self.getVariable('tags[{n}].name'.format(n=n))[1:-1]
tagType = int(self.getVariable('tags[{n}].type'.format(n=n)))
# order of tags is not preserved
savedTags += [(tagName, tagType)]
if sorted(savedTags) != sorted(tags):
raise Exception('Tags do not match %s %s' % (savedTags,tags))
printd('Verified all tags.')
def getSelectedItems(self):
'''Return the items currently selected in the zotero gui'''
items = json.loads(self.sendToZotero(code='return ZoteroPane.getSelectedItems()'))
self.sendToZotero(code='items = ZoteroPane.getSelectedItems()')
itemIDs = [self.getVariableJSON(f'items[{i}].id') for i in range(len(items))]
regularItemP = [self.getVariableJSON(f'items[{i}].isRegularItem()') for i in range(len(items))]
return zip(itemIDs, items, regularItemP)
def getAttachmentInfo(self, itemID):
self.sendToZotero(code = 'item = Zotero.Items.get(%s);' % itemID)
regularItem = self.getVariableJSON('item.isRegularItem()')
if not regularItem:
print('Item', itemID, 'is not a regular item, no attachments')
return None
self.sendToZotero(code='att_ids = item.getAttachments(false);')
attachment_ids = self.getVariableJSON('att_ids')
attachments = [self.getVariableJSON(f'Zotero.Items.get(att_ids[{i}])') for i in range(len(attachment_ids))]
fileURLs = list(self.getUrlToAttachedFile(aid) for aid in attachment_ids)
return zip(attachment_ids, attachments, fileURLs)
def getZoteroDir(self):
"Return the top level directory that contains the Storage directory "
return self.getVariableJSON('Zotero.DataDirectory')['dir']
###############################################################################
# Usage examples
# Create a series of items
def itemCreationTest():
with zotero() as z:
# First create a standalone note (unrelated to next entry)
z.addNote(text='This is the text of a standalone note', parent=None)
# Create library item without unicode first
book0 = book(
abstractNote='''This is the abstract''',
accessDate='2013-01-01',
archive='Archive',
archiveLocation='Archive Location',
callNumber='Call 1234',
creators=[
#author('Иван Иванович', 'Иванов'),
author('Author First 2', 'Author Last 2'),
author('Author First 3', 'Author Last 3'),
contributor('Contributor First 1', 'Contributor Last 1'),
contributor('Contributor First 2', 'Contributor Last 2'),
contributor('Contributor First 3', 'Contributor Last 3'),
editor('Editor First 1', 'Editor Last 1'),
editor('Editor First 2', 'Editor Last 2'),
editor('Editor First 3', 'Editor Last 3'),
seriesEditor('S. Editor First 1', 'S. Editor Last 1'),
seriesEditor('S. Editor First 2', 'S. Editor Last 2'),
seriesEditor('S. Editor First 3', 'S. Editor Last 3'),
translator('Translator First 1', 'Translator Last 1'),
translator('Translator First 2', 'Translator Last 2'),
translator('Translator First 3', 'Translator Last 3'),
],
date='1234-12-34',
edition='1st Edition',
#extra='Extras', # Default value None -> ''
ISBN='12345678x',
language='SomeLanguage',
libraryCatalog='library catalog',
numberOfVolumes='10 Volumes',
numPages='3141',
place='Publisher place',
publisher='Publisher',
rights='Rights',
series='Series',
seriesNumber='Series Number 1',
shortTitle='A short title',
title='Item with file attachments',
url='http://a.b.c',
volume='12')
# Add the book to the library
# Attachments are linked or imported, see mode argument of attachFile
report = z.addItem(
book0,
# to test, add files to folder. If not, comment out next line
attachmentMode='import', # the default
attachmentList=['book toc.pdf', 'book chapter 2.pdf', 'Test.png'],
tags=['defaultTag_type0', ('tag2', 0), ('tag_type_1', 1)],
notes=['A simple text note.', 'another note'])
# Create library item and populate the fields
book1 = book(
abstractNote='''
This is a long abstract with some unicode content.
По оживлённым берегам
Громады стройные теснятся
Дворцов и башен; корабли
Толпой со всех концов земли
К богатым пристаням стремятся;
子曰:「學而時習之,不亦說乎?有朋自遠方來,不亦樂乎?
人不知而不慍,不亦君子乎?」
有子曰:「其為人也孝弟,而好犯上者,鮮矣;
不好犯上,而好作亂者,未之有也。君子務本,本立而道生。
孝弟也者,其為仁之本與!」
''',
accessDate='2013-01-01',
archive='Archive',
archiveLocation='Archive Location',
callNumber='Call 1234',
creators=[
author('Иван Иванович', 'Иванов'),
author('AAuthor First 2', 'Author Last 2'),
author('Author First 3', 'Author Last 3'),
contributor('Contributor First 1', 'Contributor Last 1'),
contributor('Contributor First 2', 'Contributor Last 2'),
contributor('Contributor First 3', 'Contributor Last 3'),
editor('Editor First 1', 'Editor Last 1'),
editor('Editor First 2', 'Editor Last 2'),
editor('Editor First 3', 'Editor Last 3'),
seriesEditor('S. Editor First 1', 'S. Editor Last 1'),
seriesEditor('S. Editor First 2', 'S. Editor Last 2'),
seriesEditor('S. Editor First 3', 'S. Editor Last 3'),
translator('Translator First 1', 'Translator Last 1'),
translator('Translator First 2', 'Translator Last 2'),
translator('Translator First 3', 'Translator Last 3'),
],
date='1234-12-34',
edition='1st Edition',
#extra='Extras', # Default value None -> ''
ISBN='12345678x',
language='Русский',
libraryCatalog='library catalog',
numberOfVolumes='10 Volumes',
numPages='3141',
place='Publisher place',
publisher='Publisher',
rights='Rights',
series='Series',
seriesNumber='Series Number 1',
shortTitle='A short title',
title='Item with linked attachments',
url='http://a.b.c',
volume='12')
# Add the book to the library
# Attachments are linked or imported, see mode argument of attachFile
report = z.addItem(
book1,
# to test, add files to folder. If not, comment out next line
attachmentMode='link', # 'import' is the default
attachmentList=['book toc.pdf', 'book chapter 2.pdf', 'Test.png', 'sample-bitmap.png'],
tags=['defaultTag_type0', ('tag2', 0), ('tag_type_1', 1)],
notes=[ 'A simple text note.',
'A note with unicode Без муки нет науки.',
# A note with html
'<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en"> <head> <title>HTML Note</title> <style type="text/css" media="all"> </style> </head> <body> <h1>Heading 1 (h1)</h1> <h2>Heading 2 (h2)</h2> <h3>Heading 3 (h3)</h3> <h4>Heading 4 (h4)</h4> <h5>Heading 5 (h5)</h5> <h6>Heading 6 (h6)</h6> </body> </html>'
])
if yamlExists: # save report for each entry
with open('report.yaml', 'w') as f:
printd( yaml.dump(report))
yaml.dump(report, f)
# Add an article
article = journalArticle(
abstractNote='This is a long abstract for an article. It has some unicode'*5,
accessDate='2013-09-09',
archive='Article archive',
archiveLocation='Nowhere',
callNumber='123 Article',
creators=[
author('Иван Иванович', 'Иванов'),
author('AAuthor First 2', 'Author Last 2'),
author('Author First 3', 'Author Last 3'),
contributor('Contributor First 1', 'Contributor Last 1'),
contributor('Contributor First 2', 'Contributor Last 2'),
contributor('Contributor First 3', 'Contributor Last 3'),
editor('Editor First 1', 'Editor Last 1'),
editor('Editor First 2', 'Editor Last 2'),
editor('Editor First 3', 'Editor Last 3'),
reviewedAuthor('Reviewed Author First 1', 'Reviewed AuthorLast 1'),
reviewedAuthor('Reviewed Author First 2', 'Reviewed AuthorLast 2'),
reviewedAuthor('Reviewed Author First 3', 'Reviewed AuthorLast 3'),
translator('Translator First 1', 'Translator Last 1'),
translator('Translator First 2', 'Translator Last 2'),
translator('Translator First 3', 'Translator Last 3'),
],
date='1234-45-79',
DOI='10.1.1.168.4008',
extra='Extra notes for article',
#ISSN='',
issue='Issue 4',
journalAbbreviation='ABC',
language='Language',
libraryCatalog='No Catalog',
pages='1234564645',
publicationTitle='Some Example Article',
rights='Unknown',
series='Article Series',
seriesText='Series Text',
seriesTitle='Series Title',
shortTitle='A short title',
title='The real title',
url='citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.168.4008',
volume='Vol 123')
report = z.addItem(
article,
attachmentList=['book toc.pdf', 'book chapter 2.pdf'],# 'cover1.png', 'cover2.bmp'],
tags=['tag1_0', ('tag2_0', 0), ('tag3_1', 1)],
notes=['A simple text note.', 'Без муки нет науки.',
'<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en"> <head> <title>HTML Note</title> <style type="text/css" media="all"> </style> </head> <body> <h1>Heading 1 (h1)</h1> <h2>Heading 2 (h2)</h2> <h3>Heading 3 (h3)</h3> <h4>Heading 4 (h4)</h4> <h5>Heading 5 (h5)</h5> <h6>Heading 6 (h6)</h6> </body> </html>'])
def interfaceTest():
'''Get currently selected items and their attachments '''
with zotero() as z:
selectedItems = z.getSelectedItems()
for itemID, item, isRegularItem in selectedItems:
print('#' * 5)
printd(itemID, item, isRegularItem)
attachments = z.getAttachmentInfo(itemID)
if attachments != None:
for ID, att, fileURL in attachments:
print('Attachments', ID, att, fileURL)
def testZoteroConnection():
'''Make sure the debug bridge is working'''
with zotero() as z:
z.testZoteroConnection()
if __name__=='__main__':
testZoteroConnection()
interfaceTest() # get currently selected item
itemCreationTest() # add a few items to Zotero
# Zotero Org-Note
# Taking notes for Zotero in Org-mode
# Advantages:
# - pdf articles found with notes will be interleaved
# - much nicer editing
# - can paste images
# - active code through org-babel
# - notes stay in Zotero folder for syncing
# - very lightweight, low overhead.
# - can be used with org-ref or zotxt
# - keep track of notes through one big index file
# TODO:
# - rewrite this file and relevant parts of zotero.py in elisp
# - bidirectionally update tags (tags in emacs <-> zotero)
# - reindex item after saving in emacs. (after-save-hook)
# - store information in zotero-readable note,0
# - make index file nicer, sort by date, title, tags etc?
# - create list of files in order they are addressed
# - put all notes in index file itself?
# - add a link from each note back to the appropriate index file
# - see if org-noter [https://github.com/weirdNox/org-noter] is better than interleave mode
# License: BSD
# Mode of operation
# Select item to edit in Zotero pane
# run this program, it will
# - create a note template with link to pdfs for interleaving if it doesn't exist
# - attach the template to Zotero item through js api
# - open item in emacs
# - update the master index file
import zotero
import json
import os.path
import subprocess
import datetime
# master index file. Each entry gets a new * heading in this file with a link to it
indexFileName = 'notesIndex.org'
def addToIndex(indexFilePath, notesFileLocation, itemInfo, filesToInterleave, tags):
print('notes file location', notesFileLocation)
print('indexFilePath', indexFilePath, os.path.abspath(indexFilePath))
with open(indexFilePath, 'a+', encoding='utf-8') as f:
f.seek(0)
indexContent = f.read()
relativeNotesFileLocation = os.path.relpath(notesFileLocation, os.path.dirname(indexFilePath)).replace('\\', '/')
# TODO: for debug, add index every time
# remove False to not do this
if False and relativeNotesFileLocation in indexContent: # already have an index
return # TODO: on each edit, add a subsection with the date.
# unfortunately tags can only be set on the title line, not as properties
filetags = ':'.join(t for t, tagtype in tags if tagtype in [0]) # just use user tags
filetags = filetags.replace(' ', '_')
f.write('* %s :%s:\n' % (itemInfo['title'], filetags))
f.write('[[file:%s]]\n' % relativeNotesFileLocation)
f.write(':PROPERTIES:\n')
f.write(':AUTHOR:' + '; '.join([c.get('lastName', '') + ', ' + c.get('firstName', '') for c in itemInfo['creators']]) + '\n')
f.write(':END:\n')
f.write(datetime.datetime.now().strftime('[%Y-%m-%d %W %a]\n'))
with zotero.zotero() as zotinst:
items = list(zotinst.getSelectedItems())
if len(items) != 1:
print('Select exactly 1 item')
exit()
itemID, itemInfo, regularItem = items[0]
if not regularItem:
print('Select a regular item, not an attachment')
exit()
print(itemID)
print(json.dumps(itemInfo).encode('utf-8', 'ignore'))
tags = zotinst.getTags(itemID)
attInfo = list(zotinst.getAttachmentInfo(itemID))
# find pdf attachments for interleaving
filesToInterleave = [] # (title, filename)
for attID, attachment, fileURL in attInfo:
name, ext = os.path.splitext(fileURL)
print(fileURL)
if ext != '.pdf':
continue
_, relativePath = fileURL.split('Zotero/storage')
relativePath = '..' + relativePath
filesToInterleave.append((attachment['title'], relativePath))
# check if org-file exists
for attID, attachment, fileURL in attInfo:
print(attID, json.dumps(attachment , sort_keys=True, indent=4, separators=(',', ': ')), fileURL)
if attachment["title"] == 'notes.org':
print('found existing org file, re-using')
# TODO: update tags from database
break
else: # no attachments or no notes.org
print('No existing org file, creating new')
filename = 'notes.org' # TODO: move into temp folder
with open(filename, 'w', encoding='utf-8') as f:
f.write('''#+Title: {title}
#+AUTHOR: {authors}
#+FILETAGS: :{filetags}:
:BIBINFO:
{bibinfo}
:END:\n'''.format(title = itemInfo['title'],
authors = '; '.join([c.get('lastName', '') + ', ' + c.get('firstName', '') for c in itemInfo['creators']]),
bibinfo = json.dumps(itemInfo , sort_keys=True, indent=4, separators=(',', ': ')),
filetags = ':'.join(t for t,_ in tags) ))
if len(filesToInterleave) == 1:
f.write('Attachment: %s\n#+INTERLEAVE_PDF: %s\n' % filesToInterleave[0])
elif len(filesToInterleave) > 1:
for title, relativePath in filesToInterleave:
f.write('* Attachment %s\n:PROPERTIES:\n:INTERLEAVE_PDF: %s\n:END:\n' % (title, relativePath))
# TODO: do we need to set mime type of file manually?
attID = zotinst.attachFile(itemID, filename, mode='import')
#verifiedAttInfo = zotinst.verifyAttachment(filename, attID, itemID)
zotinst.addTags(['notes.org'], itemID)
notesFileLocation = zotinst.getUrlToAttachedFile(attID)[len('file:///'):]
addToIndex(zotinst.getZoteroDir() + '\\..\\ZoteroAnnotations\\' + indexFileName, notesFileLocation, itemInfo, filesToInterleave, tags)
print('Starting Emacs')
subprocess.Popen(['emacsclientw', '--create-frame', notesFileLocation, '--alternate-editor=runemacs'])
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danbe commented Feb 8, 2020

This library provides a local interface to a Zotero installation. A Zotero account is not necessary.

The library provides the following functionality:

  1. Create Zotero items from scratch (see function itemCreationTest())
  2. Add attachments (link to file or stored copy of file)
  3. Query a running Zotero instance for the currently selected item. (see function interfaceTest())

The reason for writing library was to import existing articles into Zotero. It is easy to read e.g. RIS files or a folder structure, create the corresponding objects, and add them to Zotero. All transactions are done locally.

To get started, first install MozRepl (https://github.com/bard/mozrepl/wiki) into the Zotero standalone client via Tools | Add-ons (don't install it into Firefox).
MozRepl has to be started manually, to start automatically with zotero, set extensions.mozrepl.autoStart. (https://forums.zotero.org/discussion/29885/mozrepl-in-zotero-standalone)

Assuming MozRepl runs on port 4242, you can now connect to Zotero through telnet localhost:4242, which could be helpful for debugging.
Note: MozRepl will have different prompts if multiple connections are made. Running both a telnet shell and this library will cause errors.

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danbe commented Feb 8, 2020

The file zotero_orgnote.py is an example use case for an org-mode (https://orgmode.org/) workflow.
It is still work in progress, but it shows how the main library can be used.

For an overview what org-mode can do for scientific programming: https://kitchingroup.cheme.cmu.edu/blog/2017/05/26/Org-mode-and-ipython-enhancements-in-scimax/

Org-mode also has a package (https://github.com/rudolfochrist/interleave) that allow to annotate pdf documents side-by-side. The annotations can contain images, LaTeX formulas, source code, which can be executed in place, and much more.
A similar package is https://github.com/weirdNox/org-noter

The file zotero_orgnote.py integrates org-mode and Zotero.

  1. Select an item to be annotated in Zotero
  2. Run zotero_orgnote.py

The program will then:

  • get the selected item from Zotero
  • if it doesn't exist yet, create an .org template file
  • copy title, authors etc. into the .org file
  • get attachments from Zotero and create links in .org file
  • attach the .org file to the original Zotero item
  • open the .org file in Emacs.

Using interleave-mode, it is now possible to read the attached pdfs and directly annotate them. The file resides in the Zotero/storage folder as an attachment, so it can be opened through Zotero directly.

Currently the attachments to the .org file (such as images, formulas etc.) are stored in a subfolder. It will break the Zotero synchronization. WebDAV will work. A better solution is to add all files directly to the attachment folder.

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danbe commented Feb 19, 2020

As of Zotero 5.0.82 MozRepl is not working anymore.
Revision 4 of zotero.py now uses the Zotero Debug Bridge.
First, install the Debug Bridge by following instructions at https://github.com/retorquere/zotero-better-bibtex/tree/master/test/fixtures/debug-bridge
Don't forget to set the password by setting a variable extensions.zotero.debug-bridge.password to your password.
Set the variable debugBridgePassword in zotero.py to the same password.

When you run zotero.py, it will first check the connection. You can also use curl, as described in zotero.py.

Run the file zotero.py on the command line to create a few test items in your library. You will have to create some test files to import, or comment out the lines with the files to attach: attachmentList=['book toc.pdf', 'book chapter 2.pdf', 'Test.png', 'sample-bitmap.png'].

Note: this is a very quick version that only replaces the core parts of MozRepl. It works for me, but there is still a lot of old code that needs to be cleaned up in the future. All functions that call telnet routines need to be modified.

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