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Commit 5c6bdc51 authored by Romain Loth's avatar Romain Loth
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finish up service modules refacto

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README.md
View file @ 5c6bdc51
......@@ -164,7 +164,7 @@ More info in `doc/` directory
This project was developed over several years with 3 main development phases.
Scholars statistics and directory structure originally developed by D. Chavalarias (scholars data exploration in the `php_library` folder).
Graph extraction logic originally developed by [S. Castillo](https://github.com/PkSM3/) (SubsetExtractor in the `dbdatapi` module)
Graph extraction logic originally developed by [S. Castillo](https://github.com/PkSM3/) (BipartiteExtractor in the `dbdatapi` module)
Ports to python3+MySQL, user registration and merge of the various layers into one deployable docker by [R. Loth](https://github.com/rloth/)
##### Copyright
......
services/db_to_tina_api/README.md deleted 100644 → 0
View file @ 7e7aefbb
#### Structure
- `extractDataCustom.py`: starting from a query or a scholar's id, retrieves all related kw+neighbors data from DB, and builds a graph's json with the metadata and custom html in node's `content` property
- `converter.py`: normalizes country names and codes
#### Requirements
see global documentation
(this module no longer need to be ran independantly, now part of main run.sh)
#### History
Several modules related to graph community region extraction and graph force atlas layout have been moved to `graph_manipulation_unused` dir, because they are replaced by a client-side FA2 in tinawebJS.
Extraction logic originally developed by [S. Castillo](https://github.com/PkSM3/)
python3 port and merge with regcomex into ../comex_main_backend by [R. Loth](https://github.com/rloth/)
Copyright 2014-2016 ISCPIF/CNRS - UPS 3611
services/dbdatapi.py
View file @ 5c6bdc51
......@@ -18,11 +18,11 @@ from traceback import format_tb
if __package__ == 'services':
from services.tools import mlog, REALCONFIG
from services.dbcrud import connect_db
from services.text.converter import CountryConverter
from services.text.utils import CountryConverter
else:
from tools import mlog, REALCONFIG
from dbcrud import connect_db
from text.converter import CountryConverter
from text.utils import CountryConverter
FIELDS_FRONTEND_TO_SQL = {
......@@ -219,7 +219,16 @@ def find_scholar(some_key, some_str_value, cmx_db = None):
class SubsetExtractor:
class BipartiteExtractor:
"""
JSON FILTERS => SQL SELECT => scholars subset
||
VV
keywords
||
VV
neighboors
"""
def __init__(self,dbhost):
self.connection=connect(
......
services/main.py
View file @ 5c6bdc51
......@@ -25,11 +25,11 @@ __status__ = "Dev"
# ============== imports ==============
from re import sub, match
from re import sub
from os import path
from json import dumps
from datetime import timedelta
from urllib.parse import urlparse, urljoin, unquote
from urllib.parse import unquote
from flask import Flask, render_template, request, \
redirect, url_for, session
from flask_login import fresh_login_required, login_required, \
......@@ -42,9 +42,8 @@ if __package__ == 'services':
from services import tools, dbcrud, dbdatapi
from services.user import User, login_manager, \
doors_login, doors_register
from services.dbdatapi import SubsetExtractor
# TODO move sanitize there
# from services.text import keywords, sanitize
from services.dbdatapi import BipartiteExtractor
from services.text.utils import sanitize
else:
# when this script is run directly
print("*** comex services (dev server mode) ***")
......@@ -52,8 +51,8 @@ else:
import tools, dbcrud, dbdatapi
from user import User, login_manager, \
doors_login, doors_register
from db_to_tina_api.extractDataCustom import MyExtractor
# from text import keywords, sanitize
from dbdatapi import BipartiteExtractor
from text.utils import sanitize
# ============= app creation ============
config = tools.REALCONFIG
......@@ -162,6 +161,9 @@ def unauthorized():
)
def reroute(function_name_str):
return redirect(url_for(function_name_str, _external=True))
# ============= views =============
......@@ -180,18 +182,10 @@ def rootindex():
"rootindex.html"
)
# # /test_base
# @app.route('/test_base')
# def test_base():
# return render_template(
# "base_layout.html"
# )
# /services/
@app.route(config['PREFIX']+'/')
def services():
return redirect(url_for('login', _external=True))
return reroute('login')
# /services/api/aggs
@app.route(config['PREFIX'] + config['API_ROUTE'] + '/aggs')
......@@ -226,7 +220,7 @@ def graph_api():
(original author S. Castillo)
"""
if 'qtype' in request.args:
graphdb = SubsetExtractor(config['SQL_HOST'])
graphdb = BipartiteExtractor(config['SQL_HOST'])
scholars = graphdb.getScholarsList(
request.args['qtype'],
tools.restparse(
......@@ -269,7 +263,7 @@ def user_api():
# /services/user/
@app.route(config['PREFIX'] + config['USR_ROUTE']+'/', methods=['GET'])
def user():
return redirect(url_for('login', _external=True))
return reroute('login')
# /services/user/login/
......@@ -380,7 +374,7 @@ def login():
elif user.empty:
mlog('DEBUG',"empty user redirected to profile")
# we go straight to empty profile for the person to create infos
return(redirect(url_for('profile', _external=True)))
return reroute('profile')
# normal call, normal user
else:
......@@ -388,7 +382,7 @@ def login():
next_url = request.args.get('next', None)
if not next_url:
return(redirect(url_for('profile', _external=True)))
return reroute('profile')
else:
next_url = unquote(next_url)
mlog("DEBUG", "login with next_url:", next_url)
......@@ -404,7 +398,7 @@ def login():
else:
# server name is different than ours
# in next_url so we won't go there
return(redirect(url_for('rootindex', _external=True)))
return reroute('rootindex')
# /services/user/logout/
......@@ -412,7 +406,7 @@ def login():
def logout():
logout_user()
mlog('INFO', 'logged out previous user')
return redirect(url_for('rootindex', _external=True))
return reroute('rootindex')
# /services/user/profile/
@app.route(config['PREFIX'] + config['USR_ROUTE'] + '/profile/', methods=['GET', 'POST'])
......@@ -458,7 +452,8 @@ def profile():
"executing DELETE scholar's data at the request of user %s" % str(the_id_to_delete))
logout_user()
dbcrud.rm_scholar(the_id_to_delete)
return(redirect(url_for('rootindex', _external=True)))
return reroute('rootindex')
else:
......@@ -863,53 +858,11 @@ def read_record_from_request(request):
if hasattr(request, "files") and 'pic_file' in request.files and request.files['pic_file']:
new_fname = tools.pic_blob_to_filename(request.files['pic_file'])
clean_records['pic_fname'] = new_fname
mlog("DEBUG", "new_fname", new_fname)
mlog("INFO", "new_fname", new_fname)
return clean_records
# TODO move to text submodules
def sanitize(value, specific_type=None):
"""
simple and radical: leaves only alphanum and '@' '.' '-' ':' ',' '(', ')', '#', ' '
One of the main goals is to remove ';'
POSS better
args:
@value: any string to santize
@specific_type: None or 'url' or 'date'
"""
vtype = type(value)
str_val = str(value)
clean_val = sub(r'^\s+', '', str_val)
clean_val = sub(r'\s+$', '', clean_val)
if not specific_type:
san_val = sub(r'[^\w@\.:,()# -]', '_', clean_val)
elif specific_type == "sbool":
# DB uses int(0) or int(1)
if match('^[01]$',clean_val):
san_val = int(clean_val)
else:
san_val = 0
# NB san_val_bool = bool(san_val)
elif specific_type == "surl":
san_val = sub(r'[^\w@\.: -/]', '_', clean_val)
elif specific_type == "sdate":
san_val = sub(r'[^0-9/-:]', '_', clean_val)
if vtype not in [int, str]:
raise ValueError("Value has an incorrect type %s" % str(vtype))
else:
# cast back to orginal type
san_typed_val = vtype(san_val)
return san_typed_val
########### MAIN ###########
# this can only be used for debug
# (in general use comex-run.sh to run the app)
......
services/text/keywords.py
View file @ 5c6bdc51
# TODO a keywords class gathering to factorize all cleanup and split operations
services/text/converter.py → services/text/utils.py
View file @ 5c6bdc51
from sqlite3 import connect, Row
from re import sub, match
if __package__ == "services.text":
from services.tools import mlog
......@@ -6,6 +7,48 @@ else:
from tools import mlog
def sanitize(value, specific_type=None):
"""
simple and radical: leaves only alphanum and '@' '.' '-' ':' ',' '(', ')', '#', ' '
One of the main goals is to remove ';'
POSS better
args:
@value: any string to santize
@specific_type: None or 'url' or 'date'
"""
vtype = type(value)
str_val = str(value)
clean_val = sub(r'^\s+', '', str_val)
clean_val = sub(r'\s+$', '', clean_val)
if not specific_type:
san_val = sub(r'[^\w@\.:,()# -]', '_', clean_val)
elif specific_type == "sbool":
# DB uses int(0) or int(1)
if match('^[01]$',clean_val):
san_val = int(clean_val)
else:
san_val = 0
# NB san_val_bool = bool(san_val)
elif specific_type == "surl":
san_val = sub(r'[^\w@\.: -/]', '_', clean_val)
elif specific_type == "sdate":
san_val = sub(r'[^0-9/-:]', '_', clean_val)
if vtype not in [int, str]:
raise ValueError("Value has an incorrect type %s" % str(vtype))
else:
# cast back to orginal type
san_typed_val = vtype(san_val)
return san_typed_val
class CountryConverter:
def __init__(self,dbname,dbtable,dbcolumnID,dbcolumnName):
......
services/tools.py
View file @ 5c6bdc51
......@@ -124,6 +124,18 @@ read_config()
# ============================ other tools =====================================
from urllib.parse import urlparse, urljoin, unquote
def is_safe_url(target, host_url):
"""
Checks if url is ok for redirects
cf. http://flask.pocoo.org/snippets/62/
"""
ref_url = urlparse(host_url)
test_url = urlparse(urljoin(host_url, target))
return (test_url.scheme in ('http', 'https')
and ref_url.netloc == test_url.netloc)
def re_hash(userinput, salt="verylonverylongverylonverylongverylonverylong"):
"""
Build the captcha's verification hash server side
......
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