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Commit b79f438f authored by Romain Loth's avatar Romain Loth
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WIP2 comex_shared DB (luid and hashtags in create/update user)

parent ae898647
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Showing with 199 additions and 129 deletions
doc/table_specifications.md
View file @ b79f438f
......@@ -11,7 +11,7 @@ CREATE TABLE scholars (
-- local uid necessary for users who still have no doors_uid
luid int(15) not null auto_increment unique primary key,
-- doors uid common to all lab's services
doors_uid char(36) not null unique,
doors_uid char(36) unique,
last_modified_date char(24) not null,
email varchar(255) not null unique,
country varchar(60) not null,
......
services/db.py
View file @ b79f438f
......@@ -19,7 +19,8 @@ else:
# sorted columns as declared in DB, as a tuple
USER_COLS = [
# NAME, NOT NULL, N or MAXCHARS (if applicable)
("doors_uid", True, 36),
("luid", True, 15),
("doors_uid", False, 36),
("last_modified_date", True, 24),
("email", True, 255),
("country", True, 60),
......@@ -31,7 +32,6 @@ USER_COLS = [
("position", False, 30),
("hon_title", False, 30),
("interests_text", False, 1200),
("community_hashtags", False, 350),
("gender", False, 1),
("job_looking_date", False, 24),
("home_url", False, 120),
......@@ -49,14 +49,15 @@ ORG_COLS = [
FIELDS_FRONTEND_TO_SQL = {
"keywords": "keywords.kwstr",
"tags": "hashtags.htstr",
"countries": "scholars.country",
"gender": "scholars.gender",
"organizations": "affiliations.org",
"laboratories": "affiliations.team_lab",
"tags": "scholars.community_hashtags",
# new
"gender": "scholars.gender",
"cities": "affiliations.org_city",
"linked": "linked_ids.ext_id_type"
}
......@@ -139,7 +140,7 @@ def get_field_aggs(a_field, hapax_threshold=int(REALCONFIG['HAPAX_THRESHOLD'])):
FROM scholars
-- 0 or 1
LEFT JOIN linked_ids
ON scholars.doors_uid = linked_ids.uid
ON scholars.luid = linked_ids.uid
GROUP BY %(col)s
) AS allcounts
%(filter)s
......@@ -153,8 +154,8 @@ def get_field_aggs(a_field, hapax_threshold=int(REALCONFIG['HAPAX_THRESHOLD'])):
FROM scholars
-- 0 or many
LEFT JOIN sch_kw
ON scholars.doors_uid = sch_kw.uid
JOIN keywords
ON scholars.luid = sch_kw.uid
LEFT JOIN keywords
ON sch_kw.kwid = keywords.kwid
GROUP BY %(col)s
) AS allcounts
......@@ -162,6 +163,21 @@ def get_field_aggs(a_field, hapax_threshold=int(REALCONFIG['HAPAX_THRESHOLD'])):
ORDER BY occs DESC
""" % {'col': sql_col, 'filter': where_clause}
elif sql_tab == 'hashtags':
stmt = """
SELECT * FROM (
SELECT %(col)s AS x, COUNT(*) AS occs
FROM scholars
-- 0 or many
LEFT JOIN sch_ht
ON scholars.luid = sch_ht.uid
LEFT JOIN hashtags
ON sch_ht.htid = hashtags.htid
GROUP BY %(col)s
) AS allcounts
%(filter)s
ORDER BY occs DESC
""" % {'col': sql_col, 'filter': where_clause}
mlog("DEBUGSQL", "get_field_aggs STATEMENT:\n-- SQL\n%s\n-- /SQL" % stmt)
......@@ -179,6 +195,9 @@ def get_field_aggs(a_field, hapax_threshold=int(REALCONFIG['HAPAX_THRESHOLD'])):
def get_full_scholar(uid):
"""
uid : str
local user id aka luid
Autonomous function to be used by User class
=> Retrieves one line from *scholars* table, with joined optional concatenated *affiliations*, *keywords* and *linked_ids*
=> Parse it all into a structured python user info dict
......@@ -195,7 +214,7 @@ def get_full_scholar(uid):
one_usr_stmt = """
SELECT
sch_n_aff_n_kws.*,
sch_n_aff_n_kws_n_hts.*,
-- linked_ids info condensed
-- (format : "type1:ID1,type2:ID2,...")
......@@ -205,49 +224,68 @@ def get_full_scholar(uid):
COUNT(linked_ids.ext_id) AS linked_ids_nb
FROM (
SELECT
sch_n_aff.*,
-- kws info condensed
COUNT(keywords.kwid) AS keywords_nb,
-- GROUP_CONCAT(keywords.kwid) AS kwids,
GROUP_CONCAT(keywords.kwstr) AS keywords
SELECT
sch_n_aff_n_kws.*,
-- hts info condensed
COUNT(hashtags.htid) AS hashtags_nb,
-- GROUP_CONCAT(hashtags.htid) AS htids,
GROUP_CONCAT(hashtags.htstr) AS hashtags
FROM (
FROM (
SELECT
scholars.*,
-- for debug replace scholars.* by
-- scholars.doors_uid,
-- scholars.email,
-- scholars.last_modified_date,
-- scholars.initials,
sch_n_aff.*,
affiliations.*
-- kws info condensed
COUNT(keywords.kwid) AS keywords_nb,
-- GROUP_CONCAT(keywords.kwid) AS kwids,
GROUP_CONCAT(keywords.kwstr) AS keywords
FROM scholars
FROM (
SELECT
-- scholars.*,
-- for debug replace scholars.* by
scholars.luid,
scholars.doors_uid,
scholars.email,
-- scholars.last_modified_date,
-- scholars.initials,
LEFT JOIN affiliations
ON scholars.affiliation_id = affiliations.affid
affiliations.*
FROM scholars
LEFT JOIN affiliations
ON scholars.affiliation_id = affiliations.affid
GROUP BY luid
) AS sch_n_aff
GROUP BY doors_uid
-- two step JOIN for keywords
LEFT JOIN sch_kw
ON sch_kw.uid = luid
LEFT JOIN keywords
ON sch_kw.kwid = keywords.kwid
GROUP BY luid
) AS sch_n_aff
) AS sch_n_aff_n_kws
-- two step JOIN for keywords
LEFT JOIN sch_kw
ON sch_n_aff.doors_uid = sch_kw.uid
LEFT JOIN keywords
ON sch_kw.kwid = keywords.kwid
GROUP BY doors_uid
-- also two step JOIN for hashtags
LEFT JOIN sch_ht
ON sch_ht.uid = luid
LEFT JOIN hashtags
ON sch_ht.htid = hashtags.htid
GROUP BY luid
) AS sch_n_aff_n_kws
) AS sch_n_aff_n_kws_n_hts
LEFT JOIN linked_ids
ON linked_ids.uid = sch_n_aff_n_kws.doors_uid
ON linked_ids.uid = luid
-- WHERE our user UID
WHERE doors_uid = "%s"
GROUP BY doors_uid
WHERE luid = "%s"
GROUP BY luid
""" % str(uid)
mlog("DEBUGSQL", "DB get_full_scholar STATEMENT:\n-- SQL\n%s\n-- /SQL" % one_usr_stmt)
......@@ -289,16 +327,17 @@ def get_full_scholar(uid):
# post-treatments
# ---------------
# 1/ split concatenated kw lists and check correct length
if urow_dict['keywords_nb'] == 0:
urow_dict['keywords'] = []
else:
kws_array = urow_dict['keywords'].split(',')
if len(kws_array) != urow_dict['keywords_nb']:
raise ValueError("Can't correctly split keywords for user %s" % uid)
# 1/ split concatenated kw an ht lists and check correct length
for toktype in ['keywords', 'hashtags']:
if urow_dict[toktype+'_nb'] == 0:
urow_dict[toktype] = []
else:
urow_dict['keywords'] = kws_array
tokarray = urow_dict[toktype].split(',')
if len(tokarray) != urow_dict[toktype+'_nb']:
raise ValueError("Can't correctly split %s for user %s" % (toktype, uid))
else:
urow_dict[toktype] = tokarray
# 2/ also split and parse all linked_ids
if urow_dict['linked_ids_nb'] == 0:
......@@ -326,21 +365,21 @@ def get_full_scholar(uid):
return urow_dict
def save_scholar(uid, date, safe_recs, reg_db, uactive=True, update_flag=False):
def save_scholar(safe_recs, reg_db, uactive=True, update_luid=None):
"""
For new registration:
-> add to *scholars* table
-> add to *scholars* table, return new local uid
For profile change (just toggle update_flag to True)
For profile change (just pass previous local uid in update_luid)
-> *update* scholars table
see also COLS variable and doc/table_specifications.md
"""
# we already have the first two columns
db_tgtcols = ['doors_uid', 'last_modified_date']
db_qstrvals = ["'"+str(uid)+"'", "'"+str(date)+"'"]
actual_len_dbg = 2
# column names and column quoted values
db_tgtcols = []
db_qstrvals = []
actual_len_dbg = 0
# REMARK:
# => In theory should be possible to execute(statment, values) to insert all
......@@ -353,8 +392,7 @@ def save_scholar(uid, date, safe_recs, reg_db, uactive=True, update_flag=False):
# ------------- -----------
# and then we execute(full_statmt) :-)
for colinfo in USER_COLS[2:]:
for colinfo in USER_COLS:
colname = colinfo[0]
# NB: each val already contains no quotes because of sanitize()
......@@ -385,7 +423,7 @@ def save_scholar(uid, date, safe_recs, reg_db, uactive=True, update_flag=False):
reg_db_c = reg_db.cursor()
if not update_flag:
if not update_luid:
# expected colnames "(doors_uid, last_modified_date, email, ...)"
db_tgtcols_str = ','.join(db_tgtcols)
......@@ -404,63 +442,82 @@ def save_scholar(uid, date, safe_recs, reg_db, uactive=True, update_flag=False):
set_full_str = ','.join([db_tgtcols[i] + '=' + db_qstrvals[i] for i in range(len(db_tgtcols))])
# UPDATE: full_statement with formated values
full_statmt = 'UPDATE scholars SET %s WHERE doors_uid = "%s"' % (
full_statmt = 'UPDATE scholars SET %s WHERE luid = "%s"' % (
set_full_str,
uid
update_luid
)
mlog("DEBUG", "UPDATE" if update_flag else "INSERT", "SQL statement:", full_statmt)
mlog("DEBUG", "UPDATE" if update_luid else "INSERT", "SQL statement:", full_statmt)
reg_db_c.execute(full_statmt)
if not update_luid:
luid = reg_db_c.lastrowid
else:
luid = update_luid
reg_db.commit()
return luid
def save_pairs_sch_kw(pairings_list, comex_db):
def save_pairs_sch_tok(pairings_list, comex_db, map_table='sch_kw'):
"""
Simply save all pairings (uid, kwid) in the list
Simply save all pairings (luid, kwid) or (luid, htid) in the list
"""
db_cursor = comex_db.cursor()
for id_pair in pairings_list:
db_cursor.execute('INSERT INTO sch_kw VALUES %s' % str(id_pair))
db_cursor.execute('INSERT INTO %s VALUES %s' % (map_table, str(id_pair)))
comex_db.commit()
mlog("DEBUG", "Keywords: saved %s pair" % str(id_pair))
mlog("DEBUG", "%s: saved %s pair" % (map_table, str(id_pair)))
def delete_pairs_sch_kw(uid, comex_db):
def delete_pairs_sch_tok(uid, comex_db, map_table='sch_kw'):
"""
Simply deletes all pairings (uid, *) in the table
Simply deletes all pairings (luid, *) in the table
"""
if map_table not in ['sch_kw', 'sch_ht']:
raise TypeError('ERROR: Unknown map_table')
db_cursor = comex_db.cursor()
n = db_cursor.execute('DELETE FROM sch_kw WHERE uid = "%s"' % uid)
n = db_cursor.execute('DELETE FROM %s WHERE uid = "%s"' % (map_table, uid))
comex_db.commit()
mlog("DEBUG", "Keywords: DELETED %i pairings for %s" % (n, str(uid)))
mlog("DEBUG", "%s: DELETED %i pairings for %s" % (map_table, n, str(uid)))
def get_or_create_keywords(kw_list, comex_db):
def get_or_create_tokitems(tok_list, comex_db, tok_table='keywords'):
"""
kw_str -> lookup/add to *keywords* table -> kw_id
ht_str -> lookup/add to *hashtags* table -> ht_id
-------------------------------------------------
kw_list is an array of strings
tok_list is an array of strings
NB keywords are mandatory: each registration should provide at least MIN_KW
hashtags aren't
for loop
1) query to *keywords* table (exact match)
1) query to *keywords* or *hashtags* table (exact match)
2) return id
=> if a keyword matches return kwid
=> if no keyword matches create new and return kwid
=> if a keyword/tag matches return kwid/htid
=> if no keyword/tag matches create new and return kwid/htid
"""
# sql names
fill = {'tb': tok_table}
if tok_table == 'keywords':
fill['idc'] = 'kwid'
fill['strc']= 'kwstr'
elif tok_table == 'hashtags':
fill['idc'] = 'htid'
fill['strc']= 'htstr'
db_cursor = comex_db.cursor()
found_ids = []
for kw_str in kw_list:
for tok_str in tok_list:
# TODO better string normalization here or in read_record
kw_str = kw_str.lower()
tok_str = tok_str.lower()
fill['q'] = tok_str
n_matched = db_cursor.execute('SELECT kwid FROM keywords WHERE kwstr = "%s"' % kw_str)
# ex: SELECT kwid FROM keywords WHERE kwstr = "complexity"
n_matched = db_cursor.execute('SELECT %(idc)s FROM %(tb)s WHERE %(strc)s = "%(q)s"' % fill)
# ok existing keyword => row id
if n_matched == 1:
......@@ -468,15 +525,17 @@ def get_or_create_keywords(kw_list, comex_db):
# no matching keyword => add => row id
elif n_matched == 0:
db_cursor.execute('INSERT INTO keywords(kwstr) VALUES ("%s")' % kw_str)
# ex: INSERT INTO keywords(kwstr) VALUES ("complexity")
db_cursor.execute('INSERT INTO %(tb)s(%(strc)s) VALUES ("%(q)s")' % fill)
comex_db.commit()
mlog("INFO", "Added keyword '%s'" % kw_str)
mlog("INFO", "Added '%s' to %s table" % (tok_str, tok_table))
found_ids.append(db_cursor.lastrowid)
else:
raise Exception("ERROR: non-unique keyword '%s'" % kw_str)
raise Exception("ERROR: non-unique token '%s'" % tok_str)
return found_ids
......@@ -489,9 +548,11 @@ def get_or_create_affiliation(org_info, comex_db):
1) query to *affiliations* table
2) return id
=> TODO if institution almost matches send suggestion
=> TODO unicity constraint on institution + lab
=> unicity constraint on institution + lab + org_type
=> if an institution matches return affid
=> if no institution matches create new and return affid
TODO test more
"""
the_aff_id = None
......@@ -512,11 +573,9 @@ def get_or_create_affiliation(org_info, comex_db):
db_qstrvals.append(quotedstrval)
# for select
if colname != 'org_type':
db_constraints.append("%s = %s" % (colname, quotedstrval))
db_constraints.append("%s = %s" % (colname, quotedstrval))
else:
if colname != 'org_type':
db_constraints.append("%s IS NULL" % colname)
db_constraints.append("%s IS NULL" % colname)
db_cursor = comex_db.cursor()
......
services/main.py
View file @ b79f438f
......@@ -43,7 +43,7 @@ if __package__ == 'services':
from services.user import User, login_manager, doors_login, UCACHE
from services.text import keywords
from services.tools import restparse, mlog, re_hash, REALCONFIG
from services.db import connect_db, get_or_create_keywords, save_pairs_sch_kw, delete_pairs_sch_kw, get_or_create_affiliation, save_scholar, get_field_aggs
from services.db import connect_db, get_or_create_tokitems, save_pairs_sch_tok, delete_pairs_sch_tok, get_or_create_affiliation, save_scholar, get_field_aggs
from services.db_to_tina_api.extractDataCustom import MyExtractor as MySQL
else:
# when this script is run directly
......@@ -51,7 +51,7 @@ else:
from user import User, login_manager, doors_login, UCACHE
from text import keywords
from tools import restparse, mlog, re_hash, REALCONFIG
from db import connect_db, get_or_create_keywords, save_pairs_sch_kw, delete_pairs_sch_kw, get_or_create_affiliation, save_scholar, get_field_aggs
from db import connect_db, get_or_create_tokitems, save_pairs_sch_tok, delete_pairs_sch_tok, get_or_create_affiliation, save_scholar, get_field_aggs
from db_to_tina_api.extractDataCustom import MyExtractor as MySQL
# ============= app creation ============
......@@ -61,7 +61,7 @@ app = Flask("services",
static_folder=path.join(config['HOME'],"static"),
template_folder=path.join(config['HOME'],"templates"))
app.config['DEBUG'] = (config['LOG_LEVEL'] == "DEBUG")
app.config['DEBUG'] = (config['LOG_LEVEL'] in ["DEBUG","DEBUGSQL"])
app.config['SECRET_KEY'] = 'TODO fill secret key for sessions for login'
# for SSL
......@@ -82,6 +82,7 @@ login_manager.init_app(app)
# all inputs as they are declared in form, as a couple
SOURCE_FIELDS = [
# NAME, SANITIZE?
("luid", False ),
("doors_uid", False ),
("last_modified_date", False ), # ex 2016-11-16T17:47:07.308Z
("email", True ),
......@@ -95,8 +96,7 @@ SOURCE_FIELDS = [
("position", True ),
("hon_title", True ),
("interests_text", True ),
("community_hashtags", True ),
("gender", True ), # M|F
("gender", False ), # M|F
("job_looking_date", True ), # def null: not looking for a job
("home_url", True ), # scholar's homepage
("pic_url", True ),
......@@ -110,8 +110,11 @@ SOURCE_FIELDS = [
("org_city", True ),
# => for *affiliations* table
("keywords", True )
("keywords", True ),
# => for *keywords* table (after split str)
("community_hashtags", True )
# => for *hashtags* table (after split str)
]
# NB password values have already been sent by ajax to Doors
......@@ -442,10 +445,11 @@ def save_form(request_form, request_files, update_flag=False):
"""
# only safe values
clean_records = {}
kw_array = []
# 1) handles all the inputs from form, no matter what target table
(duuid, rdate, kw_array, clean_records) = read_record(request_form)
clean_records = read_record(request_form)
mlog("DEBUG", "===== clean_records =====", clean_records)
# 2) handles the pic_file if present
if 'pic_file' in request_files:
......@@ -461,28 +465,42 @@ def save_form(request_form, request_files, update_flag=False):
# B) read/fill the affiliation table to get associated id
clean_records['affiliation_id'] = get_or_create_affiliation(clean_records, reg_db)
# C) create record into the primary user table
# ---------------------------------------------
# C) create/update record into the primary user table
# ----------------------------------------------------
# TODO class User method !!
save_scholar(duuid, rdate, clean_records, reg_db, update_flag=update_flag)
luid = None
if update_flag:
luid = clean_records['luid']
save_scholar(clean_records, reg_db, update_luid=luid)
else:
luid = save_scholar(clean_records, reg_db)
# D) read/fill each keyword and save the (uid <=> kwid) pairings
kwids = get_or_create_keywords(kw_array, reg_db)
# read/fill each hashtag and save the (uid <=> htid) pairings
for intables in [['keywords', 'keywords', 'sch_kw'],
['community_hashtags', 'hashtags', 'sch_ht']]:
tok_field = intables[0]
if tok_field in clean_records:
tok_table = intables[1]
map_table = intables[2]
# TODO class User method !!
# POSS selective delete ?
if update_flag:
delete_pairs_sch_kw(duuid, reg_db)
tokids = get_or_create_tokitems(clean_records[tok_field], reg_db, tok_table)
save_pairs_sch_kw([(duuid, kwid) for kwid in kwids], reg_db)
# TODO class User method !!
# POSS selective delete ?
if update_flag:
delete_pairs_sch_tok(luid, reg_db, map_table)
# clear cache concerning this scholar
# TODO class User method !!
if duuid in UCACHE: UCACHE.pop(duuid)
save_pairs_sch_tok([(luid, tokid) for tokid in tokids], reg_db, map_table)
# E) end connection
# F) end connection
reg_db.close()
# clear cache concerning this scholar
# TODO class User method !!
if luid in UCACHE: UCACHE.pop(luid)
return clean_records
......@@ -492,14 +510,9 @@ def read_record(incoming_data):
- custom made for regcomex/templates/base_form
- uses SOURCE_FIELDS
"""
# init var
clean_records = {}
# read in + sanitize values
duuid = None
rdate = None
# we should have all the mandatory fields (checked in client-side js)
# TODO recheck b/c if post comes from elsewhere
for field_info in SOURCE_FIELDS:
......@@ -513,31 +526,29 @@ def read_record(incoming_data):
else:
# mysql will want None instead of ''
val = None
# these 2 fields already validated and useful separately
elif field == 'doors_uid':
duuid = incoming_data[field]
elif field == 'last_modified_date':
rdate = incoming_data[field]
# any other fields that don't need sanitization (ex: menu options)
else:
clean_records[field] = incoming_data[field]
# special treatment for "other" subquestions
if 'org_type' in clean_records:
if clean_records['org_type'] == 'other' and 'other_org_type' in clean_records:
clean_records['org_type'] = clean_records['other_org_type']
# split for kw_array
kw_array = []
if 'keywords' in clean_records:
for kw in clean_records['keywords'].split(','):
kw = sanitize(kw)
if kw != '':
kw_array.append(kw)
# splits for kw_array and ht_array
for tok_field in ['keywords', 'community_hashtags']:
if tok_field in clean_records:
print(tok_field, "in clean_records")
temp_array = []
for tok in clean_records[tok_field].split(','):
tok = sanitize(tok)
if tok != '':
temp_array.append(tok)
# replace str by array
clean_records[tok_field] = temp_array
return (duuid, rdate, kw_array, clean_records)
return clean_records
# TODO move to text submodules
......
setup/dockers/comex2_mysql_server/init_comex_shared.sql
View file @ b79f438f
......@@ -11,7 +11,7 @@ CREATE TABLE scholars (
-- local uid necessary for users who still have no doors_uid
luid int(15) not null auto_increment unique primary key,
-- doors uid common to all lab's services
doors_uid char(36) not null unique,
doors_uid char(36) unique,
last_modified_date char(24) not null,
email varchar(255) not null unique,
country varchar(60) not null,
......
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