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editor.py
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#!/usr/bin/python
# -*- coding: utf-8 -*-
#print("Content-type:text/html\r\n\r\n")
from six import iteritems
import cgi, cgitb
import os, shutil, io
import sys, traceback
from modules.logintools import login
import urllib
from modules.gitdox_sql import *
from modules.gitdox_git import *
from modules.reorder_sgml import reorder
from modules.configobj import ConfigObj
import requests
from requests.auth import HTTPBasicAuth
import platform, re
from paths import ether_url, get_menu, get_nlp_credentials
from modules.ether import make_spreadsheet, delete_spreadsheet, sheet_exists, get_socialcalc, ether_to_sgml, \
build_meta_tag, get_ether_stylesheets, get_file_list, postprocess_sgml, merge_entities, get_pos_list
from modules.renderer import render
import modules.redis_cache as cache
# Support IIS site prefix on Windows
if platform.system() == "Windows":
prefix = "transc\\"
else:
prefix = ""
# Read configuration
scriptpath = os.path.dirname(os.path.realpath(__file__)) + os.sep
userdir = scriptpath + "users" + os.sep
templatedir = scriptpath + "templates" + os.sep
config = ConfigObj(userdir + 'config.ini')
project = config["project"]
editor_help_link = config["editor_help_link"]
# Captions and API URLs for NLP buttons
xml_nlp_button = config["xml_nlp_button"]
spreadsheet_nlp_button = config["spreadsheet_nlp_button"]
ner_nlp_button = config["ner_nlp_button"]
xml_nlp_api = config["xml_nlp_api"]
spreadsheet_nlp_api = config["spreadsheet_nlp_api"]
code_2fa = None
def harvest_meta(sgml):
"""
Get metadata key value pairs from <meta> element in imported SGML file
:param sgml: TT SGML as string
:return: dictionary of key value pairs
"""
sgml = sgml.replace("\r","").strip()
meta = {}
if not sgml.startswith("<meta "):
return meta
else:
metatag = re.search(r'<meta ([^\n]*)>',sgml).group(1)
matches = re.findall(r'([^ =>]+?)="([^"]+)"',metatag)
for match in matches:
meta[match[0].strip()] = match[1].strip().replace("<","<").replace(">",">")
return meta
def serialize_file(text_content,file_name):
f=open(prefix+file_name,'w')
f.write(text_content)#.encode("utf8"))
f.close()
def get_user_list():
user_list=[]
scriptpath = os.path.dirname(os.path.realpath(__file__)) + os.sep
userdir = scriptpath + "users" + os.sep
return get_file_list(userdir,"ini",forbidden=["admin","default","config"],hide_extension=True)
def load_page(user,admin,theform):
global ether_url
global code_2fa
if theform.getvalue("2fa"):
code_2fa = theform.getvalue("2fa")
else:
code_2fa = ""
max_id = generic_query("SELECT MAX(id) AS max_id FROM docs","")[0][0]
if not max_id: # This is for the initial case after init db
max_id = 0
text_content = ""
repo_name = ""
corpus = ""
status = ""
assignee = ""
mode = "xml"
schema = ""
doc_id = "" # Should only remain so if someone navigated directly to editor.py
docname = ""
enable_entities = False if "enable_entities" not in config else config["enable_entities"]
old_docname, old_corpus, old_repo, old_status, old_assignee, old_mode, old_schema = ["", "", "", "", "", "", ""]
if int(admin) > 0:
git_username, git_token, git_2fa = get_git_credentials(user, admin, code_2fa)
else:
git_username, git_token, git_2fa = (None, None, None)
# dict of variables we'll need to render the html
render_data = {}
if theform.getvalue('id'):
doc_id = theform.getvalue('id')
if int(doc_id) > int(max_id):
# Creating new doc case, assign some default values
docname = "new_document"
repo_name = "account/repo_name"
status = "editing"
assignee = "default_user"
corpus = "default_corpus"
schema = ""
text_content = ""
# If one of the four forms is edited or we're cloning a doc, then we create the doc, otherwise nothing happens (user cannot fill in nothing and create the doc)
if theform.getvalue('edit_docname') and user != "demo":
if docname != 'new_document':
if doc_id > max_id:
create_document(doc_id, docname, corpus, status, assignee, repo_name, text_content)
max_id = doc_id
else:
update_docname(doc_id, docname)
if theform.getvalue('edit_filename') and user != "demo":
repo_name = theform.getvalue('edit_filename')
if repo_name != 'account/repo_name':
if doc_id > max_id:
create_document(doc_id, docname, corpus, status, assignee, repo_name, text_content)
max_id = doc_id
else:
update_filename(doc_id, repo_name)
if theform.getvalue('edit_corpusname') and user != "demo":
corpus = theform.getvalue('edit_corpusname')
if corpus != 'default_corpus':
if doc_id > max_id:
create_document(doc_id, docname, corpus, status, assignee, repo_name, text_content)
max_id = doc_id
else:
update_corpus(doc_id, corpus)
if theform.getvalue('edit_status') and user != "demo":
status = theform.getvalue('edit_status')
if status != 'editing':
if doc_id > max_id:
create_document(doc_id, docname, corpus, status, assignee, repo_name, text_content)
max_id = doc_id
else:
update_status(doc_id, status)
if theform.getvalue('edit_assignee') and user != "demo":
assignee = theform.getvalue('edit_assignee')
if assignee != "default_user":
if doc_id > max_id:
create_document(doc_id, docname, corpus, status, assignee, repo_name, text_content)
max_id = doc_id
else:
update_assignee(doc_id, assignee)
# cloning metadata from an existing doc into a new doc
if theform.getvalue('source_doc'):
source_meta = get_doc_meta(theform.getvalue('source_doc'))
if doc_id > max_id:
create_document(doc_id, docname, corpus, status, assignee, repo_name, text_content)
max_id = doc_id
for meta in source_meta:
m_key, m_val = meta[2:4]
save_meta(int(doc_id), m_key, m_val)
cache.invalidate_by_doc(doc_id, "meta")
else:
# Get previous values from DB
old_docname, old_corpus, old_repo, old_status, old_assignee, old_mode, old_schema = get_doc_info(doc_id)
# Assume new values are same, overwrite with different form values and update DB if new values found
docname, corpus, repo_name, status, assignee, mode, schema = old_docname, old_corpus, old_repo, old_status, old_assignee, old_mode, old_schema
docname = old_docname
# Handle switch to spreadsheet mode if NLP spreadsheet service is called
if theform.getvalue('nlp_spreadsheet') == "do_nlp_spreadsheet" and mode == "xml" and user != "demo":
data_to_process = generic_query("SELECT content FROM docs WHERE id=?",(doc_id,))[0][0]
api_call = spreadsheet_nlp_api
if api_call != "":
nlp_user, nlp_password = get_nlp_credentials()
data = {"data":data_to_process, "lb":"line", "format":"sgml_no_parse"}
resp = requests.post(api_call, data, auth=HTTPBasicAuth(nlp_user,nlp_password))
sgml = resp.text.encode("utf8")
postproc = config["nlp_postprocessing"] if "nlp_postprocessing" in config else None
sgml = postprocess_sgml(sgml,postproc)
else:
sgml = data_to_process.encode("utf8")
out, err = make_spreadsheet(sgml, ether_url + "_/gd_" + corpus + "_" + docname, "sgml")
mode = "ether"
# handle copying metadata
if theform.getvalue('source_doc'):
source_meta = get_doc_meta(theform.getvalue('source_doc'))
existing_meta_keys = [x[2] for x in get_doc_meta(doc_id)]
# don't overwrite existing keys
meta_to_write = [x for x in source_meta if x[2] not in existing_meta_keys]
for meta in meta_to_write:
m_key, m_val = meta[2], meta[3]
save_meta(int(doc_id), m_key, m_val)
cache.invalidate_by_doc(doc_id, "meta")
if theform.getvalue('edit_docname'):
docname = theform.getvalue('edit_docname')
elif old_docname != "":
docname = old_docname
if theform.getvalue('edit_corpusname'):
corpus = theform.getvalue('edit_corpusname')
elif old_corpus != "":
corpus = old_corpus
if theform.getvalue('id'):
if int(doc_id) <= int(max_id):
# After clicking edit in landing page, editing existing doc case, get the values from the db. pull the content from db to be displayed in the editor window.
if theform.getvalue('edit_docname'):
docname = theform.getvalue('edit_docname')
if docname != old_docname and user != "demo":
update_docname(doc_id,docname)
if theform.getvalue('edit_filename'):
repo_name=theform.getvalue('edit_filename')
if repo_name != old_repo and user != "demo":
update_filename(doc_id,repo_name)
if theform.getvalue('edit_corpusname'):
corpus = theform.getvalue('edit_corpusname')
if corpus != old_corpus and user != "demo":
update_corpus(doc_id,corpus)
if theform.getvalue('edit_status'):
status = theform.getvalue('edit_status')
if status != old_status and user != "demo":
update_status(doc_id,status)
if theform.getvalue('edit_assignee'):
assignee = theform.getvalue('edit_assignee')
if assignee != old_assignee and user != "demo":
update_assignee(doc_id,assignee)
if theform.getvalue('edit_mode'):
mode = theform.getvalue('edit_mode')
if mode != old_mode and user != "demo":
update_mode(doc_id,mode)
if theform.getvalue('nlp_spreadsheet') == "do_nlp_spreadsheet": # mode has been changed to spreadsheet via NLP
update_mode(doc_id, "ether")
mode = "ether"
if old_docname != docname or old_corpus != corpus:
old_sheet_name = "gd" + "_" + old_corpus + "_" + old_docname
if sheet_exists(ether_url, old_sheet_name): # Check if there is an ether sheet to copy
old_socialcalc = get_socialcalc(ether_url, old_sheet_name)
out, err = make_spreadsheet(old_socialcalc, ether_url + "_/gd_" + corpus + "_" + docname, "socialcalc")
if out == "OK":
delete_spreadsheet(ether_url,old_sheet_name)
text_content = generic_query("SELECT content FROM docs WHERE id=?",(doc_id,))[0][0]
# In the case of reloading after hitting 'save', either create new doc into db, or update db
# CodeMirror sends the form with its code content in it before 'save' so we just display it again
if theform.getvalue('code'):
text_content = theform.getvalue('code')
text_content = text_content.replace("\r","")
text_content = re.sub(r'&(?!(#[xX][0-9a-fA-F]+|#\d+|[lg]t|amp|apos|quot);)',r'&',text_content) # Escape unescaped XML &
text_content = unicode(text_content.decode("utf8"))
if user != "demo":
if int(doc_id)>int(max_id):
create_document(doc_id, docname,corpus,status,assignee,repo_name,text_content)
else:
save_changes(doc_id,text_content)
cache.invalidate_by_doc(doc_id, "xml")
render_data["sent_mode"] = "text"
if theform.getvalue("sent_mode"):
render_data["sent_mode"] = theform.getvalue('sent_mode')
if theform.getvalue('entity_sgml') and enable_entities: # Save entity editor output
entity_sgml = theform.getvalue('entity_sgml')
ether_sgml = ether_to_sgml(get_socialcalc(ether_url, "gd" + "_" + corpus + "_" + docname),doc_id)
if len(entity_sgml.strip()) > 0:
word_anno = config["DEFAULT_SGML_TOK_ATTR"] if config["DEFAULT_SGML_TOK_ATTR"].lower() != "none" else None
other_annos = [a.split(":")[0] for a in config["entity_annos"].split(";")] if ":" in config["entity_annos"] else None
merged_sgml = merge_entities(ether_sgml, entity_sgml, merge_anno="entity", word_anno=word_anno,
other_annos=other_annos)
if not merged_sgml: # merged_sgml = False means token counts don't match, can't merge
render_data["entity_save_message"] = "Failed to save entities: token counts do not match with spreadsheet!"
render_data["entity_save_color"] = "red"
render_data["entity_save_icon"] = "ban"
else:
merged_sgml = merged_sgml.replace("&", "&")
out, err = make_spreadsheet(merged_sgml, ether_url + "_/gd_" + corpus + "_" + docname, "sgml")
render_data["entity_save_message"] = "Saved merged entity annotations to spreadsheet"
render_data["entity_save_color"] = "green"
render_data["entity_save_icon"] = "floppy-o"
if mode == "xml":
render_data["xml_mode"] = True
else:
render_data["xml_mode"] = False
# Get GitHub repo info
git_status=False
git_last_commit = False
repo_name = generic_query("SELECT filename FROM docs WHERE id=?", (doc_id,))
if len(repo_name) > 0:
repo_name = repo_name[0][0]
else:
repo_name = ""
file_name = generic_query("SELECT name FROM docs WHERE id=?", (doc_id,))
if len(file_name) > 0:
file_name = file_name[0][0]
else:
file_name = ""
if "/" in repo_name:
repo_info = repo_name.split('/')
git_account, git_repo = repo_info[0], repo_info[1]
else:
repo_info = git_repo = git_account = repo_name
# Get path for this document's serialized file in the repo
if len(repo_info) > 2:
subdir = '/'.join(repo_info[2:]) + "/"
else:
subdir = ""
if mode == "xml":
file_name = file_name.replace(" ","_") + ".xml"
else:
file_name = file_name.replace(" ","_") + "_ether.sgml"
saved_file = subdir + file_name
commit_message = ""
if theform.getvalue('commit_msg'):
commit_message = theform.getvalue('commit_msg')
if theform.getvalue('push_git') == "push_git":
# The user will indicate the subdir in the repo_name stored in the db.
# Therefore, a file may be associated with the target repo subdir zangsir/coptic-xml-tool/uploaded_commits,
# and that is fine, but we will need to make this uploaded_commits subdir first to create our file.
if not os.path.isdir(prefix + subdir) and subdir != "":
dirs = subdir.split(os.sep)[:-1]
path_so_far = ""
for dirname in dirs:
if not os.path.isdir(prefix + path_so_far + dirname + os.sep):
os.mkdir(prefix + path_so_far + dirname + os.sep, 0o755)
path_so_far += dirname + os.sep
if mode == "xml":
text_content = generic_query("SELECT content FROM docs WHERE id=?", (doc_id,))[0][0]
serializable_content = build_meta_tag(doc_id) + text_content.strip() + "\n</meta>\n"
serializable_content = serializable_content.encode('utf8')
else: # (mode == "ether")
text_content = ether_to_sgml(get_socialcalc(ether_url, "gd" + "_" + corpus + "_" + docname),doc_id, config="tt_sgml")
serializable_content = text_content
serialize_file(serializable_content, saved_file)
git_status = push_update_to_git(git_username, git_token, saved_file, git_account, git_repo, commit_message)
# File system cleanup
if subdir == "":
# Delete a file
os.remove(prefix+file_name)
else:
# Delete a subdirectory
shutil.rmtree(prefix+subdir)
if theform.getvalue('nlp_xml') == "do_nlp_xml" and mode == "xml":
api_call = xml_nlp_api
if api_call != "":
nlp_user, nlp_password = get_nlp_credentials()
data = {"data":text_content, "format":"pipes"}
resp = requests.post(api_call, data, auth=HTTPBasicAuth(nlp_user,nlp_password))
text_content=resp.text
# Get last commit info
if not (git_account=="account" and git_repo == "repo_name"): # Check this is not the fake default repo name
try:
git_last_commit = get_last_commit(git_username, int(admin), git_account, git_repo, saved_file)
except:
git_last_commit = ""
# Editing options
# Docname
# Filename
status_list = open(prefix+"status.tab").read().replace("\r","").split("\n")
render_data['status_options'] = [{'text': x, 'selected': x == status} for x in status_list]
render_data['assignee_options'] = [{'text': x, 'selected': x == assignee} for x in get_user_list()]
available_modes = ["xml", "ether"]
if enable_entities:
available_modes.append("entities")
render_data['mode_options'] = [{'text': x, 'selected': x == mode} for x in available_modes]
render_data['nlp_service'] = {'xml_button_html': xml_nlp_button.decode("utf8"),
'spreadsheet_button_html': spreadsheet_nlp_button.decode("utf8"),
'disabled': user == "demo" or mode == "ether",
"ner_button_html": ner_nlp_button.decode("utf8")}
render_data['git_2fa'] = git_2fa == "true"
if git_status:
render_data['git_commit_response'] = git_status.replace('<','').replace('>','')
if git_last_commit:
render_data['git_last_commit'] = git_last_commit
# prepare embedded editor html
if str(enable_entities).lower() == "true":
render_data['entity_mode'] = True
if mode == "ether":
render_data['ether_mode'] = True
ether_url += "gd_" + corpus + "_" + docname
render_data['ether_url'] = ether_url # .replace("http","https") # fix AZ
render_data['ether_stylesheets'] = get_ether_stylesheets()
if "file" in theform and user != "demo":
fileitem = theform["file"]
if len(fileitem.filename) > 0:
# strip leading path from file name to avoid directory traversal attacks
fn = os.path.basename(fileitem.filename)
if fn.endswith(".xls") or fn.endswith(".xlsx"):
make_spreadsheet(fileitem.file.read(),ether_url + "_/gd_" + corpus + "_" + docname,"excel")
else:
sgml = fileitem.file.read()
meta_key_val = harvest_meta(sgml)
make_spreadsheet(sgml,ether_url + "_/gd_" + corpus + "_" + docname)
for (key, value) in iteritems(meta_key_val):
key = key.replace("@","_")
save_meta(int(doc_id),key.decode("utf8"),value.decode("utf8"))
cache.invalidate_by_doc(doc_id, "meta")
else:
render_data['ether_mode'] = False
if mode == "entities" and enable_entities:
render_data['entity_mode'] = True
ether_name = "_".join(["gd", corpus, docname])
#ether_url = ether_url.replace("https","http") # fix AZ
soc = get_socialcalc(ether_url, ether_name)
tt_string = ether_to_sgml(soc, doc_id, config="tt_sgml")
tt_string = reorder(tt_string,priorities=[config["DEFAULT_SGML_SENT_TAG"],"entity",config["NER_POS_COL"],str(config["DEFAULT_SGML_TOK_ATTR"])])
base_template = io.open("templates" + os.sep + "spannotator_template.html",encoding="utf8").read().replace('"','"')
if 'entity_annos' in config:
base_template = base_template.replace("%%entity_annos%%", config["entity_annos"]) # optional key-value annotations
base_template = base_template.replace("%%DEFAULT_SGML_SENT_TAG%%",config["DEFAULT_SGML_SENT_TAG"]).replace("%%DEFAULT_SGML_TOK_ATTR%%",config["DEFAULT_SGML_TOK_ATTR"])
import_disabled = "" if int(admin) > 1 else ' disabled="disabled" style="background-color: #6f6f6f"'
base_template = base_template.replace("%%DISABLE_IMPORT%%",import_disabled)
if "NER_POS_COL" in config and "NER_POS_FILTER" in config:
pos_list = get_pos_list(tt_string,config["NER_POS_COL"])
render_data["NER_POS_FILTER"] = config["NER_POS_FILTER"]
render_data["NER_POS_LIST"] = pos_list
render_data["show_ner"] = True
else:
render_data["show_ner"] = False
tt_escaped = tt_string.decode("utf8").replace('"',"%%quot%%").replace('\n','\\n').replace("<","%%lt%%").replace(">","%%gt%%")
base_template = base_template.replace("%%DOC_TT_STRING%%",tt_escaped)
entity_links = get_doc_entities(doc_id)
entity_list = []
if entity_links is not None:
for row in entity_links:
words, etype, eref = row
entity_list.append(words + "+" + etype + "+" + eref)
base_template = base_template.replace("%%DOC_ENTITY_LIST%%","|".join(entity_list).replace('"',"%%quot%%"))
all_entity_links = get_entity_options()
all_entity_list = []
if all_entity_links is not None:
for row in all_entity_links:
etype, eref = row
all_entity_list.append(etype + "+" + eref)
base_template = base_template.replace("%%ALL_ENTITY_LIST%%","|".join(all_entity_list))
render_data['spannotator_template'] = base_template
# stop here if no doc selected
if doc_id:
render_data['doc_is_selected'] = len(doc_id) != 0
else:
return render("editor", render_data)
render_data['id'] = doc_id
render_data['mode'] = mode
render_data['schema'] = schema
render_data['docname'] = docname
render_data['corpusname'] = corpus
render_data['text_content'] = text_content
render_data['repo'] = repo_name
render_data["admin_gt_zero"] = int(admin) > 0
render_data["admin_eq_three"] = admin == "3"
# handle clone meta button, and allow github pushing
if int(admin) > 0:
doc_list = generic_query("SELECT id,corpus,name,status,assignee_username,mode FROM docs ORDER BY corpus, name COLLATE NOCASE",())
render_data["docs"] = []
for doc in doc_list:
doc_vars = {}
doc_vars["id"] = str(doc[0])
doc_vars["corpus"] = doc[1]
doc_vars["name"] = doc[2]
render_data['docs'].append(doc_vars)
render_data["can_save"] = not (int(admin) < 3)
render_data["editor_help_link_html"] = editor_help_link
render_data["first_load"] = len(theform.keys()) == 1
return render("editor", render_data)
def open_main_server():
thisscript = os.environ.get('SCRIPT_NAME', '')
action = None
theform = cgi.FieldStorage()
#print(theform)
scriptpath = os.path.dirname(os.path.realpath(__file__)) + os.sep
userdir = scriptpath + "users" + os.sep
action, userconfig = login(theform, userdir, thisscript, action)
user = userconfig["username"]
admin = userconfig["admin"]
print("Content-type:text/html\n\n")
try:
print(load_page(user, admin, theform).encode("utf8"))
except Exception as e:
print("""<html><body><h1>Loading Error</h1>
<p>For some reason, this page failed to load.</p>
<p>Please send this to your system administrator:</p>
<pre>""")
traceback.print_exc(e, file=sys.stdout)
print("""</pre></body></html>""")
if __name__ == "__main__":
open_main_server()