-2)\n\n return (x for x in paps if x[1:4] in inner)\n\n return ()\n\n\ndef del_person_not_manually_claimed_papers(pid):\n '''\n Deletes papers from a person which have not been manually claimed.\n '''\n run_sql(\"delete from aidPERSONIDPAPERS \"\n \"where and (flag <> '-2' and flag <> '2') and personid=%s\", (pid,))\n\ndef get_personid_from_uid(uid):\n '''\n Returns the personID associated with the provided ui.\n If the personID is already associated with the person the secon parameter is True, false otherwise.\n @param uid: userID\n @type uid: ((int,),)\n '''\n pid = run_sql(\"select personid from aidPERSONIDDATA where tag=%s and data=%s\", ('uid', str(uid[0][0])))\n if len(pid) == 1:\n return (pid[0], True)\n else:\n return ([-1], False)\n\ndef get_uid_from_personid(pid):\n uid = run_sql(\"select data from aidPERSONIDDATA where tag='uid' and personid = %s\", (pid,))\n if uid:\n return uid[0][0]\n else:\n return None\n\n\ndef get_new_personid():\n pids = (run_sql(\"select max(personid) from aidPERSONIDDATA\")[0][0],\n run_sql(\"select max(personid) from aidPERSONIDPAPERS\")[0][0])\n\n pids = tuple(int(p) for p in pids if p != None)\n\n if len(pids) == 2:\n return max(*pids) + 1\n elif len(pids) == 1:\n return pids[0] + 1\n else:\n return 0\n\n\ndef get_existing_personids():\n try:\n pids_data = set(zip(*run_sql(\"select distinct personid from aidPERSONIDDATA\"))[0])\n except IndexError:\n pids_data = set()\n\n try:\n pids_pap = set(zip(*run_sql(\"select distinct personid from aidPERSONIDPAPERS\"))[0])\n except IndexError:\n pids_pap = set()\n\n return pids_data | pids_pap\n\n\ndef get_existing_result_clusters():\n return run_sql(\"select distinct personid from aidRESULTS\")\n\n\ndef create_new_person(uid= -1, uid_is_owner=False):\n '''\n Create a new person. Set the uid as owner if requested.\n '''\n pid = get_new_personid()\n if uid_is_owner:\n set_personid_row(pid, 'uid', str(uid))\n else:\n set_personid_row(pid, 'user-created', str(uid))\n return pid\n\ndef create_new_person_from_uid(uid):\n return create_new_person(uid, uid_is_owner=True)\n\ndef new_person_from_signature(sig, name=None):\n '''\n Creates a new person from a signature.\n '''\n pid = get_new_personid()\n add_signature(sig, name, pid)\n return pid\n\n\ndef add_signature(sig, name, pid):\n '''\n Inserts a signature in personid.\n '''\n if not name:\n name = get_name_by_bibrecref(sig)\n name = create_normalized_name(split_name_parts(name))\n\n run_sql(\"INSERT INTO aidPERSONIDPAPERS \"\n \"(personid, bibref_table, bibref_value, bibrec, name) \"\n \"VALUES (%s, %s, %s, %s, %s)\"\n , (pid, str(sig[0]), sig[1], sig[2], name))\n\ndef move_signature(sig, pid):\n '''\n Inserts a signature in personid.\n '''\n run_sql(\"update aidPERSONIDPAPERS set personid=%s \"\n \"where bibref_table=%s and bibref_value=%s \"\n \"and bibrec=%s and flag <> 2 and flag <> -2\",\n (pid,) + sig)\n\ndef find_conflicts(sig, pid):\n \"\"\"\n \"\"\"\n return run_sql(\"select bibref_table, bibref_value, bibrec, flag \"\n \"from aidPERSONIDPAPERS where \"\n \"personid = %s and \"\n \"bibrec = %s and \"\n \"flag <> -2\"\n , (pid, sig[2]))\n\ndef update_request_ticket(person_id, tag_data_tuple, ticket_id=None):\n '''\n Creates / updates a request ticket for a personID\n @param: personid int\n @param: tag_data_tuples 'image' of the ticket: (('paper', '700:316,10'), ('owner', 'admin'), ('external_id', 'ticket_18'))\n @return: ticketid\n '''\n #tags: rt_owner (the owner of the ticket, associating the rt_number to the transaction)\n # rt_external_id\n # rt_paper_cornfirm, rt_paper_reject, rt_paper_forget, rt_name, rt_email, rt_whatever\n #flag: rt_number\n if not ticket_id:\n last_id = run_sql(\"select max(opt1) from aidPERSONIDDATA where personid=%s and tag like %s\", (str(person_id), 'rt_%'))[0][0]\n\n if last_id:\n ticket_id = last_id + 1\n else:\n ticket_id = 1\n else:\n delete_request_ticket(person_id, ticket_id)\n\n for d in tag_data_tuple:\n run_sql(\"insert into aidPERSONIDDATA (personid, tag, data, opt1) \"\n \"values (%s,%s,%s,%s)\",\n (str(person_id), 'rt_' + str(d[0]), str(d[1]), str(ticket_id)))\n\n return ticket_id\n\n\ndef delete_request_ticket(person_id, ticket_id=None):\n '''\n Removes a ticket from a person_id.\n If ticket_id is not provider removes all the tickets pending on a person.\n '''\n if ticket_id:\n run_sql(\"delete from aidPERSONIDDATA where personid=%s and tag like %s and opt1 =%s\", (str(person_id), 'rt_%', str(ticket_id)))\n else:\n run_sql(\"delete from aidPERSONIDDATA where personid=%s and tag like %s\", (str(person_id), 'rt_%'))\n\n\ndef get_all_personids_by_name(regexpr):\n return run_sql(\"select personid, name \"\n \"from aidPERSONIDPAPERS \"\n \"where name like %s\",\n (regexpr,))\n\ndef get_personids_by_canonical_name(target):\n pid = run_sql(\"select personid from aidPERSONIDDATA where \"\n \"tag='canonical_name' and data like %s\", (target,))\n if pid:\n return run_sql(\"select personid, name from aidPERSONIDPAPERS \"\n \"where personid=%s\", (pid[0][0],))\n else:\n return []\n\ndef get_bibref_modification_status(bibref):\n '''\n Determines if a record attached to a person has been touched by a human\n by checking the flag.\n\n @param pid: The Person ID of the person to check the assignment from\n @type pid: int\n @param bibref: The paper identifier to be checked (e.g. \"100:12,144\")\n @type bibref: string\n\n returns [bool:human_modified, int:lcul]\n '''\n if not bibref:\n raise ValueError(\"A bibref is expected!\")\n\n head, rec = bibref.split(',')\n table, ref = head.split(':')\n flags = run_sql(\"SELECT flag, lcul FROM aidPERSONIDPAPERS WHERE \"\n \"bibref_table = %s and bibref_value = %s and bibrec = %s\"\n , (table, ref, rec))\n if flags:\n return flags[0]\n else:\n return (False, 0)\n\n\ndef get_canonical_id_from_personid(pid):\n '''\n Finds the person id canonical name (e.g. Ellis_J_R_1)\n\n @param pid\n @type int\n\n @return: sql result of the request\n @rtype: tuple of tuple\n '''\n return run_sql(\"SELECT data FROM aidPERSONIDDATA WHERE \"\n \"tag = %s AND personid = %s\", ('canonical_name', str(pid)))\n\n\ndef get_papers_status(paper):\n '''\n Gets the personID and flag assiciated to papers\n @param papers: list of papers\n @type papers: '100:7531,9024'\n @return: (('data','personID','flag',),)\n @rtype: tuple of tuples\n '''\n head, bibrec = paper.split(',')\n _table, bibref = head.split(':')\n\n rets = run_sql(\"select PersonID, flag \"\n \"from aidPERSONIDPAPERS \"\n \"where bibref_table = %s \"\n \"and bibref_value = %s \"\n \"and bibrec = %s\"\n % (head, bibrec, bibref))\n return [[paper] + list(x) for x in rets]\n\n\ndef get_persons_from_recids(recids, return_alt_names=False,\n return_all_person_papers=False):\n rec_2_pid = dict()\n pid_2_data = dict()\n all_pids = set()\n\n def get_canonical_name(pid):\n return run_sql(\"SELECT data \"\n \"FROM aidPERSONIDDATA \"\n \"WHERE tag = %s \"\n \"AND personid = %s\",\n ('canonical_name', pid))\n\n for rec in recids:\n pids = run_sql(\"SELECT personid \"\n \"FROM aidPERSONIDPAPERS \"\n \"WHERE bibrec = %s \"\n \" and flag > -2 \",\n (rec,))\n\n # for some reason python's set is faster than a mysql distinct\n pids = set(p[0] for p in pids)\n all_pids |= pids\n rec_2_pid[rec] = list(pids)\n\n for pid in all_pids:\n pid_data = {}\n\n canonical = get_canonical_name(pid)\n #We can supposed that this person didn't have a chance to get a canonical name yet\n #because it was not fully processed by it's creator. Anyway it's safe to try to create one\n #before failing miserably\n if not canonical:\n update_personID_canonical_names([pid])\n canonical = get_canonical_name(pid)\n\n #assert len(canonical) == 1\n #This condition cannot hold in case claims or update daemons are run in parallel\n #with this, as it can happen that a person with papers exists for wich a canonical name\n #has not been computed yet. Hence, it will be indexed next time, so it learns.\n #Each person should have at most one canonical name, so:\n assert len(canonical) <= 1\n\n if len(canonical) == 1:\n pid_data = {'canonical_id' : canonical[0][0]}\n\n if return_alt_names:\n names = run_sql(\"SELECT name \"\n \"FROM aidPERSONIDPAPERS \"\n \"WHERE personid = %s \"\n \" and flag > -2 \",\n (pid,))\n names = set(n[0] for n in names)\n\n pid_data['alternatative_names'] = list(names)\n\n if return_all_person_papers:\n recs = run_sql(\"SELECT bibrec \"\n \"FROM aidPERSONIDPAPERS \"\n \"WHERE personid = %s \"\n \" and flag > -2 \",\n (pid,))\n recs = set(r[0] for r in recs)\n\n pid_data['person_records'] = list(recs)\n\n pid_2_data[pid] = pid_data\n\n return (rec_2_pid, pid_2_data)\n\n\ndef get_person_db_names_count(pid, sort_by_count=True):\n '''\n Returns the set of name strings and count associated to a person id.\n The name strings are as found in the database.\n @param pid: ID of the person\n @type pid: ('2',)\n '''\n\n id_2_count = run_sql(\"select bibref_table, bibref_value \"\n \"from aidPERSONIDPAPERS \"\n \"where personid = %s \"\n \"and flag > -2\", (pid,))\n\n ref100 = [refid[1] for refid in id_2_count if refid[0] == '100']\n ref700 = [refid[1] for refid in id_2_count if refid[0] == '700']\n\n ref100_count = dict((key, len(list(data))) for key, data in groupby(sorted(ref100)))\n ref700_count = dict((key, len(list(data))) for key, data in groupby(sorted(ref700)))\n\n if ref100:\n ref100_s = list_2_SQL_str(ref100, str)\n id100_2_str = run_sql(\"select id, value \"\n \"from bib10x \"\n \"where id in %s\"\n % ref100_s)\n else:\n id100_2_str = tuple()\n\n if ref700:\n ref700_s = list_2_SQL_str(ref700, str)\n id700_2_str = run_sql(\"select id, value \"\n \"from bib70x \"\n \"where id in %s\"\n % ref700_s)\n else:\n id700_2_str = tuple()\n\n ret100 = [(name, ref100_count[refid]) for refid, name in id100_2_str]\n ret700 = [(name, ref700_count[refid]) for refid, name in id700_2_str]\n\n ret = ret100 + ret700\n if sort_by_count:\n ret = sorted(ret, key=itemgetter(1), reverse=True)\n return ret\n\n\ndef get_person_id_from_canonical_id(canonical_id):\n '''\n Finds the person id from a canonical name (e.g. Ellis_J_R_1)\n\n @param canonical_id: the canonical ID\n @type canonical_id: string\n\n @return: sql result of the request\n @rtype: tuple of tuple\n '''\n return run_sql(\"SELECT personid FROM aidPERSONIDDATA WHERE \"\n \"tag='canonical_name' AND data = %s\", (canonical_id,))\n\n\ndef get_person_names_count(pid):\n '''\n Returns the set of name strings and count associated to a person id\n @param pid: ID of the person\n @type pid: ('2',)\n @param value: value to be written for the tag\n @type value: string\n '''\n return run_sql(\"select name, count(name) from aidPERSONIDPAPERS where \"\n \"personid=%s and flag > -2 group by name\", (pid,))\n\n\ndef get_person_db_names_set(pid):\n '''\n Returns the set of db_name strings associated to a person id\n @param pid: ID of the person\n @type pid: 2\n '''\n\n names = get_person_db_names_count(pid)\n if names:\n return zip(set(zip(*names)[0]))\n else:\n return []\n\ndef get_personids_from_bibrec(bibrec):\n '''\n Returns all the personids associated to a bibrec.\n '''\n\n pids = run_sql(\"select distinct personid from aidPERSONIDPAPERS where bibrec=%s and flag > -2\", (bibrec,))\n\n if pids:\n return zip(*pids)[0]\n else:\n return []\n\ndef get_personids_and_papers_from_bibrecs(bibrecs, limit_by_name=None):\n '''\n '''\n if not bibrecs:\n return []\n else:\n bibrecs = list_2_SQL_str(bibrecs)\n if limit_by_name:\n try:\n surname = split_name_parts(limit_by_name)[0]\n except IndexError:\n surname = None\n else:\n surname = None\n if not surname:\n data = run_sql(\"select personid,bibrec from aidPERSONIDPAPERS where bibrec in %s\" % (bibrecs,))\n else:\n surname = split_name_parts(limit_by_name)[0]\n data = run_sql((\"select personid,bibrec from aidPERSONIDPAPERS where bibrec in %s \"\n \"and name like \" % bibrecs) + ' %s ', (surname + '%',))\n pidlist = [(k, set([s[1] for s in d]))\n for k, d in groupby(sorted(data, key=lambda x:x[0]), key=lambda x:x[0])]\n pidlist = sorted(pidlist, key=lambda x:len(x[1]), reverse=True)\n return pidlist\n\ndef get_person_bibrecs(pid):\n '''\n Returns bibrecs associated with a personid\n @param pid: integer personid\n @return [bibrec1,...,bibrecN]\n '''\n papers = run_sql(\"select bibrec from aidPERSONIDPAPERS where personid=%s\", (str(pid),))\n\n if papers:\n return list(set(zip(*papers)[0]))\n else:\n return []\n\ndef get_person_papers(pid, flag,\n show_author_name=False,\n show_title=False,\n show_rt_status=False,\n show_affiliations=False,\n show_date=False,\n show_experiment=False):\n query = \"bibref_table, bibref_value, bibrec, flag\"\n if show_author_name:\n query += \", name\"\n\n all_papers = run_sql(\"SELECT \" + query + \" \"\n \"FROM aidPERSONIDPAPERS \"\n \"WHERE personid = %s \"\n \"AND flag >= %s\",\n (pid, flag))\n\n def format_paper(paper):\n bibrefrec = \"%s:%d,%d\" % paper[:3]\n ret = {'data' : bibrefrec,\n 'flag' : paper[3]\n }\n\n if show_author_name:\n ret['authorname'] = paper[4]\n\n if show_title:\n ret['title'] = \"\"\n title = get_title_from_rec(paper[2])\n if title:\n ret['title'] = (title, )\n\n if show_rt_status:\n rt_count = run_sql(\"SELECT count(personid) \"\n \"FROM aidPERSONIDDATA WHERE \"\n \"tag like 'rt_%%' and data = %s\"\n , (bibrefrec,))\n\n ret['rt_status'] = (rt_count[0][0] > 0)\n\n if show_affiliations:\n tag = '%s__u' % paper[0]\n ret['affiliation'] = get_grouped_records(paper[:3], tag)[tag]\n\n if show_date:\n ret['date'] = []\n date_id = run_sql(\"SELECT id_bibxxx \"\n \"FROM bibrec_bib26x \"\n \"WHERE id_bibrec = %s \"\n , (paper[2],))\n\n if date_id:\n date_id_s = list_2_SQL_str(date_id, lambda x: x[0])\n date = run_sql(\"SELECT value \"\n \"FROM bib26x \"\n \"WHERE id in %s \"\n \"AND tag = %s\"\n % (date_id_s, \"'269__c'\"))\n if date:\n ret['date'] = zip(*date)[0]\n\n\n if show_experiment:\n ret['experiment'] = []\n experiment_id = run_sql(\"SELECT id_bibxxx \"\n \"FROM bibrec_bib69x \"\n \"WHERE id_bibrec = %s \"\n , (paper[2],))\n\n if experiment_id:\n experiment_id_s = list_2_SQL_str(experiment_id, lambda x: x[0])\n experiment = run_sql(\"SELECT value \"\n \"FROM bib69x \"\n \"WHERE id in %s \"\n \"AND tag = %s\"\n % (experiment_id_s, \"'693__e'\"))\n if experiment:\n ret['experiment'] = zip(*experiment)[0]\n\n return ret\n\n return [format_paper(paper) for paper in all_papers]\n\n\ndef get_persons_with_open_tickets_list():\n '''\n Finds all the persons with open tickets and returns pids and count of tickets\n @return: [[pid, ticket_count]]\n '''\n return run_sql(\"select personid, count(distinct opt1) from \"\n \"aidPERSONIDDATA where tag like 'rt_%' group by personid\")\n\ndef get_request_ticket(person_id, ticket_id=None):\n '''\n Retrieves one or many requests tickets from a person\n @param: person_id: person id integer\n @param: matching: couple of values to match ('tag', 'value')\n @param: ticket_id: ticket id (flag) value\n @returns: [[[('tag', 'value')], ticket_id]]\n [[[('a', 'va'), ('b', 'vb')], 1L], [[('b', 'daOEIaoe'), ('a', 'caaoOUIe')], 2L]]\n '''\n if ticket_id:\n tstr = \" and opt1='%s' \" % ticket_id\n else:\n tstr = \" \"\n tickets = run_sql(\"select tag,data,opt1 from aidPERSONIDDATA where personid=%s and \"\n \" tag like 'rt_%%' \" + tstr , (person_id,))\n return [[[(s[0][3:], s[1]) for s in d], k] for k, d in groupby(sorted(tickets, key=lambda k: k[2]), key=lambda k: k[2])]\n\n\ndef insert_user_log(userinfo, personid, action, tag, value, comment='', transactionid=0, timestamp=None):\n '''\n Instert log entries in the user log table.\n For example of entres look at the table generation script.\n @param userinfo: username or user identifier\n @type: string\n @param personid: personid involved in the transaction\n @type: longint\n @param action: action type\n @type: string\n @param tag: tag\n @type: string\n @param value: value for the transaction\n @type: string\n @param comment: optional comment for the transaction\n @type: string\n @param transactionid: optional id for the transaction\n @type: longint\n\n @return: the transactionid\n @rtype: longint\n '''\n# if transactionid == 0:\n# transactionid = max(run_sql('SELECT MAX(transactionid) FROM `aidUSERINPUTLOG`')[0][0], -1) + 1\n\n if not timestamp:\n timestamp = run_sql('select now()')[0][0]\n\n# run_sql('insert into aidUSERINPUTLOG (transactionid,timestamp,userinfo,personid,action,tag,value,comment) values '\n# '(%(transactionid)s,%(timestamp)s,%(userinfo)s,%(personid)s,%(action)s,%(tag)s,%(value)s,%(comment)s)',\n# ({'transactionid':str(transactionid),\n# 'timestamp':timestamp.timestamp,\n# 'userinfo':str(userinfo),\n# 'personid':str(personid),\n# 'action':str(action),\n# 'tag':str(tag),\n# 'value':str(value),\n# 'comment':str(comment)}))\n run_sql('insert into aidUSERINPUTLOG '\n '(transactionid,timestamp,userinfo,personid,action,tag,value,comment) values '\n '(%s,%s,%s,%s,%s,%s,%s,%s)',\n (transactionid, timestamp, userinfo, personid,\n action, tag, value, comment))\n\n return transactionid\n\n\ndef person_bibref_is_touched_old(pid, bibref):\n '''\n Determines if a record attached to a person has been touched by a human\n by checking the flag.\n\n @param pid: The Person ID of the person to check the assignment from\n @type pid: int\n @param bibref: The paper identifier to be checked (e.g. \"100:12,144\")\n @type bibref: string\n '''\n bibref, rec = bibref.split(\",\")\n table, ref = bibref.split(\":\")\n\n flag = run_sql(\"SELECT flag \"\n \"FROM aidPERSONIDPAPERS \"\n \"WHERE personid = %s \"\n \"AND bibref_table = %s \"\n \"AND bibref_value = %s \"\n \"AND bibrec = %s\"\n , (pid, table, ref, rec))\n\n try:\n flag = flag[0][0]\n except (IndexError):\n return False\n\n if not flag:\n return False\n elif -2 < flag < 2:\n return False\n else:\n return True\n\n\ndef confirm_papers_to_person(pid, papers, user_level=0):\n '''\n Confirms the relationship between pid and paper, as from user input.\n @param pid: id of the person\n @type pid: ('2',)\n @param papers: list of papers to confirm\n @type papers: (('100:7531,9024',),)\n @param gather_list: list to store the pids to be updated rather than\n calling update_personID_names_string_set\n @typer gather_list: set([('2',), ('3',)])\n '''\n for p in papers:\n bibref, rec = p[0].split(\",\")\n rec = int(rec)\n table, ref = bibref.split(\":\")\n ref = int(ref)\n\n run_sql(\"delete from aidPERSONIDPAPERS where personid=%s and bibrec=%s\", (pid[0], rec))\n run_sql(\"delete from aidPERSONIDPAPERS where bibref_table=%s and \"\n \" bibref_value = %s and bibrec=%s\",\n (table, ref, rec))\n\n add_signature([table, ref, rec], None, pid[0])\n run_sql(\"update aidPERSONIDPAPERS \"\n \"set personid = %s \"\n \", flag = %s \"\n \", lcul = %s \"\n \"where bibref_table = %s \"\n \"and bibref_value = %s \"\n \"and bibrec = %s\"\n , (str(pid[0]), '2', user_level,\n table, ref, rec))\n\n update_personID_canonical_names(pid)\n\n\ndef reject_papers_from_person(pid, papers, user_level=0):\n '''\n Confirms the negative relationship between pid and paper, as from user input.\n @param pid: id of the person\n @type pid: integer\n @param papers: list of papers to confirm\n @type papers: ('100:7531,9024',)\n '''\n\n new_pid = get_new_personid()\n for p in papers:\n brr, rec = p.split(\",\")\n table, ref = brr.split(':')\n\n sig = (table, ref, rec)\n records = personid_name_from_signature(sig)\n assert(records)\n\n fpid, name = records[0]\n assert fpid == pid\n\n run_sql(\"INSERT INTO aidPERSONIDPAPERS \"\n \"(personid, bibref_table, bibref_value, bibrec, name, flag, lcul) \"\n \"VALUES (%s, %s, %s, %s, %s, %s, %s)\"\n , (pid, table, ref, rec, name, -2, user_level))\n\n move_signature(sig, new_pid)\n\n update_personID_canonical_names((pid,))\n\n\ndef reset_papers_flag(pid, papers):\n '''\n Resets the flag associated to the papers to '0'\n @param papers: list of papers to confirm\n @type papers: (('100:7531,9024',),)\n @param gather_list: list to store the pids to be updated rather than\n calling update_personID_names_string_set\n @typer gather_list: set([('2',), ('3',)])\n '''\n for p in papers:\n bibref, rec = p[0].split(\",\")\n table, ref = bibref.split(\":\")\n run_sql(\"update aidPERSONIDPAPERS \"\n \"set flag = %s, lcul = %s \"\n \"where bibref_table = %s \"\n \"and bibref_value = %s \"\n \"and bibrec = %s\" ,\n ('0', '0',\n table, ref, rec))\n\n\ndef user_can_modify_data(uid, pid):\n '''\n Return True if the uid can modify data of this personID, false otherwise.\n @param uid: the user id\n @type: int\n @param pid: the person id\n @type: int\n\n @return: can user mofidfy data?\n @rtype: boolean\n '''\n\n pid_uid = run_sql(\"select data from aidPERSONIDDATA where tag = %s\"\n \" and personid = %s\", ('uid', str(pid)))\n\n if len(pid_uid) >= 1 and str(uid) == str(pid_uid[0][0]):\n rights = bconfig.CLAIMPAPER_CHANGE_OWN_DATA\n else:\n rights = bconfig.CLAIMPAPER_CHANGE_OTHERS_DATA\n\n return acc_authorize_action(uid, rights)[0] == 0\n\n\ndef get_possible_bibrecref(names, bibrec, always_match=False):\n '''\n Returns a list of bibrefs for which the surname is matching\n @param names: list of names strings\n @param bibrec: bibrec number\n @param always_match: match with all the names (full bibrefs list)\n '''\n splitted_names = [split_name_parts(n) for n in names]\n\n bibrec_names_100 = run_sql(\"select o.id, o.value from bib10x o, \"\n \"(select i.id_bibxxx as iid from bibrec_bib10x i \"\n \"where id_bibrec=%s) as dummy \"\n \"where o.tag='100__a' AND o.id = dummy.iid\",\n (str(bibrec),))\n bibrec_names_700 = run_sql(\"select o.id, o.value from bib70x o, \"\n \"(select i.id_bibxxx as iid from bibrec_bib70x i \"\n \"where id_bibrec=%s) as dummy \"\n \"where o.tag='700__a' AND o.id = dummy.iid\",\n (str(bibrec),))\n# bibrec_names_100 = run_sql(\"select id,value from bib10x where tag='100__a' and id in \"\n# \"(select id_bibxxx from bibrec_bib10x where id_bibrec=%s)\",\n# (str(bibrec),))\n# bibrec_names_700 = run_sql(\"select id,value from bib70x where tag='700__a' and id in \"\n# \"(select id_bibxxx from bibrec_bib70x where id_bibrec=%s)\",\n# (str(bibrec),))\n bibreflist = []\n\n for b in bibrec_names_100:\n spb = split_name_parts(b[1])\n for n in splitted_names:\n if (n[0].lower() == spb[0].lower()) or always_match:\n if ['100:' + str(b[0]), b[1]] not in bibreflist:\n bibreflist.append(['100:' + str(b[0]), b[1]])\n\n for b in bibrec_names_700:\n spb = split_name_parts(b[1])\n for n in splitted_names:\n if (n[0].lower() == spb[0].lower()) or always_match:\n if ['700:' + str(b[0]), b[1]] not in bibreflist:\n bibreflist.append(['700:' + str(b[0]), b[1]])\n\n return bibreflist\n\n\ndef user_can_modify_paper(uid, paper):\n '''\n Return True if the uid can modify this paper, false otherwise.\n If the paper is assigned more then one time (from algorithms) consider the most privileged\n assignment.\n @param uid: the user id\n @type: int\n @param paper: the paper bibref,bibrec pair x00:1234,4321\n @type: str\n\n @return: can user mofidfy paper attribution?\n @rtype: boolean\n '''\n bibref, rec = paper.split(\",\")\n table, ref = bibref.split(\":\")\n prow = run_sql(\"select personid, lcul from aidPERSONIDPAPERS \"\n \"where bibref_table = %s and bibref_value = %s and bibrec = %s \"\n \"order by lcul desc limit 0,1\",\n (table, ref, rec))\n\n if len(prow) == 0:\n return ((acc_authorize_action(uid, bconfig.CLAIMPAPER_CLAIM_OWN_PAPERS)[0] == 0) or\n (acc_authorize_action(uid, bconfig.CLAIMPAPER_CLAIM_OTHERS_PAPERS)[0] == 0))\n\n min_req_acc_n = int(prow[0][1])\n req_acc = resolve_paper_access_right(bconfig.CLAIMPAPER_CLAIM_OWN_PAPERS)\n pid_uid = run_sql(\"select data from aidPERSONIDDATA where tag = %s and personid = %s\", ('uid', str(prow[0][0])))\n if len(pid_uid) > 0:\n if (str(pid_uid[0][0]) != str(uid)) and min_req_acc_n > 0:\n req_acc = resolve_paper_access_right(bconfig.CLAIMPAPER_CLAIM_OTHERS_PAPERS)\n\n if min_req_acc_n < req_acc:\n min_req_acc_n = req_acc\n\n min_req_acc = resolve_paper_access_right(min_req_acc_n)\n\n return (acc_authorize_action(uid, min_req_acc)[0] == 0) and (resolve_paper_access_right(min_req_acc) >= min_req_acc_n)\n\n\ndef resolve_paper_access_right(acc):\n '''\n Given a string or an integer, resolves to the corresponding integer or string\n If asked for a wrong/not present parameter falls back to the minimum privilege.\n '''\n access_dict = {bconfig.CLAIMPAPER_VIEW_PID_UNIVERSE: 0,\n bconfig.CLAIMPAPER_CLAIM_OWN_PAPERS: 25,\n bconfig.CLAIMPAPER_CLAIM_OTHERS_PAPERS: 50}\n\n if isinstance(acc, str):\n try:\n return access_dict[acc]\n except:\n return 0\n\n inverse_dict = dict([[v, k] for k, v in access_dict.items()])\n lower_accs = [a for a in inverse_dict.keys() if a <= acc]\n try:\n return inverse_dict[max(lower_accs)]\n except:\n return bconfig.CLAIMPAPER_VIEW_PID_UNIVERSE\n\n\ndef get_recently_modified_record_ids(date):\n '''\n Returns the bibrecs with modification date more recent then date.\n @param date: date\n '''\n return [p[0] for p in run_sql(\n \"select id from bibrec where modification_date > %s\", (date,))]\n\n\ndef filter_modified_record_ids(bibrecs, date):\n '''\n Returns the bibrecs with modification date before the date.\n @param date: date\n '''\n return ifilter(\n lambda x: run_sql(\"select count(*) from bibrec \"\n \"where id = %s and \"\n \"modification_date < %s\"\n , (x[2], date))[0][0]\n , bibrecs)\n\n\ndef get_cached_author_page(pageparam):\n '''\n Return cached authorpage\n @param: pageparam (int personid)\n @return (id, 'authorpage_cache', personid, authorpage_html, date_cached)\n '''\n #TABLE: id, tag, identifier, data, date\n caches = run_sql(\"select id, object_name, object_key, object_value, last_updated \\\n from aidCACHE \\\n where object_name='authorpage_cache' and object_key=%s\",\n (str(pageparam),))\n if len(caches) >= 1:\n return caches[0]\n else:\n return []\n\ndef delete_cached_author_page(personid):\n '''\n Deletes from the author page cache the page concerning one person\n '''\n run_sql(\"delete from aidCACHE where object_name='authorpage_cache' and object_key=%s\", (str(personid),))\n\ndef update_cached_author_page_timestamp(pageparam):\n '''\n Updates cached author page timestamp\n @param pageparam: int personid\n '''\n #TABLE: id, tag, identifier, data, date\n run_sql(\"update aidCACHE set last_updated=now() where object_name='authorpage_cache' and object_key=%s\", (str(pageparam),))\n\n\ndef update_cached_author_page(pageparam, page):\n '''\n Updates cached author page, deleting old caches for same pageparam\n @param pageparam: int personid\n @param page: string html authorpage\n '''\n #TABLE: id, tag, identifier, data, date\n run_sql(\"delete from aidCACHE where object_name='authorpage_cache' and object_key=%s\", (str(pageparam),))\n run_sql(\"insert into aidCACHE values (Null,'authorpage_cache',%s,%s,now())\", (str(pageparam), str(page)))\n\ndef get_user_log(transactionid='', userinfo='', personID='', action='', tag='', value='', comment='', only_most_recent=False):\n '''\n Get user log table entry matching all the given parameters; all of them are optional.\n IF no parameters are given retuns the complete log table\n @param transactionid: id of the transaction\n @param userinfo: user name or identifier\n @param personid: id of the person involved\n @param action: action\n @param tag: tag\n @param value: value\n @param comment: comment\n '''\n sql_query = ('select id,transactionid,timestamp,userinfo,personid,action,tag,value,comment ' +\n 'from aidUSERINPUTLOG where 1 ')\n if transactionid:\n sql_query += ' and transactionid=\\'' + str(transactionid) + '\\''\n if userinfo:\n sql_query += ' and userinfo=\\'' + str(userinfo) + '\\''\n if personID:\n sql_query += ' and personid=\\'' + str(personID) + '\\''\n if action:\n sql_query += ' and action=\\'' + str(action) + '\\''\n if tag:\n sql_query += ' and tag=\\'' + str(tag) + '\\''\n if value:\n sql_query += ' and value=\\'' + str(value) + '\\''\n if comment:\n sql_query += ' and comment=\\'' + str(comment) + '\\''\n if only_most_recent:\n sql_query += ' order by timestamp desc limit 0,1'\n return run_sql(sql_query)\n\n\ndef list_2_SQL_str(items, f=lambda x: x):\n \"\"\"\n Concatenates all items in items to a sql string using f.\n @param items: a set of items\n @param type items: X\n @param f: a function which transforms each item from items to string\n @param type f: X:->str\n @return: \"(x1, x2, x3, ... xn)\" for xi in items\n @return type: string\n \"\"\"\n strs = (str(f(x)) for x in items)\n return \"(%s)\" % \", \".join(strs)\n\n\ndef get_authors_from_paper(paper):\n '''\n selects all author bibrefs by a given papers\n '''\n fullbibrefs100 = run_sql(\"select id_bibxxx from bibrec_bib10x where id_bibrec=%s\", (paper,))\n if len(fullbibrefs100) > 0:\n fullbibrefs100str = list_2_SQL_str(fullbibrefs100, lambda x: str(x[0]))\n return run_sql(\"select id from bib10x where tag='100__a' and id in %s\" % (fullbibrefs100str,))\n return tuple()\n\ndef get_coauthors_from_paper(paper):\n '''\n selects all coauthor bibrefs by a given papers\n '''\n fullbibrefs700 = run_sql(\"select id_bibxxx from bibrec_bib70x where id_bibrec=%s\", (paper,))\n if len(fullbibrefs700) > 0:\n fullbibrefs700str = list_2_SQL_str(fullbibrefs700, lambda x: str(x[0]))\n return run_sql(\"select id from bib70x where tag='700__a' and id in %s\" % (fullbibrefs700str,))\n return tuple()\n\ndef get_bibrefrec_subset(table, papers, refs):\n table = \"bibrec_bib%sx\" % str(table)[:-1]\n contents = run_sql(\"select id_bibrec, id_bibxxx from %s\" % table)\n papers = set(papers)\n refs = set(refs)\n\n # yes, there are duplicates and we must set them\n return set(ifilter(lambda x: x[0] in papers and x[1] in refs, contents))\n\ndef get_deleted_papers():\n return run_sql(\"select o.id_bibrec from bibrec_bib98x o, \"\n \"(select i.id as iid from bib98x i \"\n \"where value = 'DELETED' \"\n \"and tag like '980__a') as dummy \"\n \"where o.id_bibxxx = dummy.iid\")\n\n#bibauthorid_maintenance personid update private methods\ndef update_personID_canonical_names(persons_list=None, overwrite=False, suggested=''):\n '''\n Updates the personID table creating or updating canonical names for persons\n @param: persons_list: persons to consider for the update (('1'),)\n @param: overwrite: if to touch already existing canonical names\n @param: suggested: string to suggest a canonical name for the person\n '''\n if not persons_list:\n persons_list = [x[0] for x in run_sql('select distinct personid from aidPERSONIDPAPERS')]\n\n for idx, pid in enumerate(persons_list):\n update_status(float(idx) / float(len(persons_list)), \"Updating canonical_names...\")\n current_canonical = run_sql(\"select data from aidPERSONIDDATA where \"\n \"personid=%s and tag=%s\", (pid, 'canonical_name'))\n\n if overwrite or len(current_canonical) == 0:\n names = get_person_names_count(pid)\n\n names = sorted(names, key=lambda k: k[1], reverse=True)\n if len(names) < 1 and not suggested:\n continue\n else:\n if suggested:\n canonical_name = suggested\n else:\n canonical_name = create_canonical_name(names[0][0])\n\n run_sql(\"delete from aidPERSONIDDATA where personid=%s and tag=%s\",\n (pid, 'canonical_name'))\n\n existing_cnames = run_sql(\"select data from aidPERSONIDDATA \"\n \"where tag=%s and data like %s\",\n ('canonical_name', str(canonical_name) + '%'))\n\n existing_cnames = set(name[0] for name in existing_cnames)\n for i in count(1):\n cur_try = canonical_name + '.' + str(i)\n if cur_try not in existing_cnames:\n canonical_name = cur_try\n break\n\n run_sql(\"insert into aidPERSONIDDATA (personid, tag, data) values (%s,%s,%s) \",\n (pid, 'canonical_name', canonical_name))\n\n update_status_final(\"Updating canonical_names finished.\")\n\n\ndef personid_get_recids_affected_since(last_timestamp):\n '''\n Returns a list of recids which have been manually changed since timestamp\n @TODO: extend the system to track and signal even automatic updates (unless a full reindex is\n acceptable in case of magic automatic update)\n @param: last_timestamp: last update, datetime.datetime\n '''\n vset = set(int(v[0].split(',')[1]) for v in run_sql(\n \"select distinct value from aidUSERINPUTLOG \"\n \"where timestamp > %s\", (last_timestamp,))\n if ',' in v[0] and ':' in v[0])\n\n pids = set(int(p[0]) for p in run_sql(\n \"select distinct personid from aidUSERINPUTLOG \"\n \"where timestamp > %s\", (last_timestamp,))\n if p[0] > 0)\n\n if pids:\n pids_s = list_2_SQL_str(pids)\n vset |= set(int(b[0]) for b in run_sql(\n \"select bibrec from aidPERSONIDPAPERS \"\n \"where personid in %s\" % pids_s))\n\n return list(vset) # I'm not sure about this cast. It might work without it.\n\n\ndef get_all_paper_records(pid, claimed_only=False):\n if not claimed_only:\n return run_sql(\"SELECT distinct bibrec FROM aidPERSONIDPAPERS WHERE personid = %s\", (str(pid),))\n else:\n return run_sql(\"SELECT distinct bibrec FROM aidPERSONIDPAPERS WHERE \"\n \"personid = %s and flag=2 or flag=-2\", (str(pid),))\n\n\ndef get_all_names_from_personid():\n return ((name[0][0], set(n[1] for n in name), len(name))\n for name in (run_sql(\n \"SELECT personid, name \"\n \"FROM aidPERSONIDPAPERS \"\n \"WHERE personid = %s \"\n \"AND flag > -2\", p)\n for p in run_sql(\n \"SELECT DISTINCT personid \"\n \"FROM aidPERSONIDPAPERS \"\n \"WHERE flag > -2\")\n ))\n\n\ndef get_grouped_records(bibrefrec, *args):\n '''\n By a given bibrefrec: mark:ref,rec this function will scan\n bibmarkx table and extract all records with tag in argc, which\n are grouped togerther with this bibrec.\n\n Returns a dictionary with { tag : [extracted_values] }\n if the values is not found.\n\n @type bibrefrec: (mark(int), ref(int), rec(int))\n '''\n table, ref, rec = bibrefrec\n\n target_table = \"bib%sx\" % (str(table)[:-1])\n mapping_table = \"bibrec_%s\" % target_table\n\n group_id = run_sql(\"SELECT field_number \"\n \"FROM %s \"\n \"WHERE id_bibrec = %d \"\n \"AND id_bibxxx = %d\" %\n (mapping_table, rec, ref))\n\n if len(group_id) == 0:\n # unfortunately the mapping is not found, so\n # we cannot find anything\n return dict((arg, []) for arg in args)\n elif len(group_id) == 1:\n # All is fine\n field_number = group_id[0][0]\n else:\n # sounds bad, but ignore the error\n field_number = group_id[0][0]\n\n grouped = run_sql(\"SELECT id_bibxxx \"\n \"FROM %s \"\n \"WHERE id_bibrec = %d \"\n \"AND field_number = %d\" %\n (mapping_table, rec, int(field_number)))\n assert len(grouped) > 0\n grouped_s = list_2_SQL_str(grouped, lambda x: str(x[0]))\n\n ret = {}\n for arg in args:\n qry = run_sql(\"SELECT value \"\n \"FROM %s \"\n \"WHERE tag LIKE '%s' \"\n \"AND id IN %s\" %\n (target_table, arg, grouped_s))\n ret[arg] = [q[0] for q in qry]\n\n return ret\n\ndef get_name_by_bibrecref(bib):\n '''\n @param bib: bibrefrec or bibref\n @type bib: (mark, bibref, bibrec) OR (mark, bibref)\n '''\n table = \"bib%sx\" % (str(bib[0])[:-1])\n refid = bib[1]\n tag = \"%s__a\" % bib[0]\n ret = run_sql(\"select value from %s where id = '%s' and tag = '%s'\" % (table, refid, tag))\n\n # if zero - check if the garbage collector has run\n assert len(ret) == 1\n return ret[0][0]\n\n\ndef get_collaboration(bibrec):\n bibxxx = run_sql(\"select id_bibxxx from bibrec_bib71x where id_bibrec = %s\", (str(bibrec),))\n\n if len(bibxxx) == 0:\n return ()\n\n bibxxx = list_2_SQL_str(bibxxx, lambda x: str(x[0]))\n\n ret = run_sql(\"select value from bib71x where id in %s and tag like '%s'\" % (bibxxx, \"710__g\"))\n return [r[0] for r in ret]\n\n\ndef get_key_words(bibrec):\n if bconfig.CFG_ADS_SITE:\n bibxxx = run_sql(\"select id_bibxxx from bibrec_bib65x where id_bibrec = %s\", (str(bibrec),))\n else:\n bibxxx = run_sql(\"select id_bibxxx from bibrec_bib69x where id_bibrec = %s\", (str(bibrec),))\n\n if len(bibxxx) == 0:\n return ()\n\n bibxxx = list_2_SQL_str(bibxxx, lambda x: str(x[0]))\n\n if bconfig.CFG_ADS_SITE:\n ret = run_sql(\"select value from bib69x where id in %s and tag like '%s'\" % (bibxxx, \"6531_a\"))\n else:\n ret = run_sql(\"select value from bib69x where id in %s and tag like '%s'\" % (bibxxx, \"695__a\"))\n\n return [r[0] for r in ret]\n\n\ndef get_all_authors(bibrec):\n bibxxx_1 = run_sql(\"select id_bibxxx from bibrec_bib10x where id_bibrec = %s\", (str(bibrec),))\n bibxxx_7 = run_sql(\"select id_bibxxx from bibrec_bib70x where id_bibrec = %s\", (str(bibrec),))\n\n if bibxxx_1:\n bibxxxs_1 = list_2_SQL_str(bibxxx_1, lambda x: str(x[0]))\n authors_1 = run_sql(\"select value from bib10x where tag = '%s' and id in %s\" % ('100__a', bibxxxs_1,))\n else:\n authors_1 = []\n\n if bibxxx_7:\n bibxxxs_7 = list_2_SQL_str(bibxxx_7, lambda x: str(x[0]))\n authors_7 = run_sql(\"select value from bib70x where tag = '%s' and id in %s\" % ('700__a', bibxxxs_7,))\n else:\n authors_7 = []\n\n return [a[0] for a in authors_1] + [a[0] for a in authors_7]\n\n\ndef get_title_from_rec(rec):\n \"\"\"\n Returns the name of the paper like str if found.\n Otherwise returns None.\n \"\"\"\n title_id = run_sql(\"SELECT id_bibxxx \"\n \"FROM bibrec_bib24x \"\n \"WHERE id_bibrec = %s\",\n (rec,))\n\n if title_id:\n title_id_s = list_2_SQL_str(title_id, lambda x: x[0])\n title = run_sql(\"SELECT value \"\n \"FROM bib24x \"\n \"WHERE id in %s \"\n \"AND tag = '245__a'\"\n % title_id_s)\n\n if title:\n return title[0][0]\n\ndef get_bib10x():\n return run_sql(\"select id, value from bib10x where tag like %s\", (\"100__a\",))\n\n\ndef get_bib70x():\n return run_sql(\"select id, value from bib70x where tag like %s\", (\"700__a\",))\n\n\nclass bib_matrix:\n '''\n This small class contains the sparse matrix\n and encapsulates it.\n '''\n # please increment this value every time you\n # change the output of the comparison functions\n current_comparison_version = 9\n\n special_items = ((None, -3., 'N'), ('+', -2., '+'), ('-', -1., '-'))\n special_symbols = dict((x[0], (x[1], x[2])) for x in special_items)\n special_numbers = dict((x[1], (x[0], x[2])) for x in special_items)\n special_strings = dict((x[2], (x[0], x[1])) for x in special_items)\n\n def __init__(self, cluster_set=None):\n if cluster_set:\n bibs = chain(*(cl.bibs for cl in cluster_set.clusters))\n self._bibmap = dict((b[1], b[0]) for b in enumerate(bibs))\n width = len(self._bibmap)\n size = ((width - 1) * width) / 2\n self._matrix = bib_matrix.create_empty_matrix(size)\n else:\n self._bibmap = dict()\n\n @staticmethod\n def create_empty_matrix(lenght):\n ret = numpy.ndarray(shape=(lenght, 2), dtype=float, order='C')\n ret.fill(bib_matrix.special_symbols[None][0])\n return ret\n\n def _resolve_entry(self, bibs):\n entry = sorted(self._bibmap[bib] for bib in bibs)\n assert entry[0] < entry[1]\n return entry[0] + ((entry[1] - 1) * entry[1]) / 2\n\n def __setitem__(self, bibs, val):\n entry = self._resolve_entry(bibs)\n\n if val in self.special_symbols:\n num = self.special_symbols[val][0]\n val = (num, num)\n\n self._matrix[entry] = val\n\n def __getitem__(self, bibs):\n entry = self._resolve_entry(bibs)\n ret = self._matrix[entry]\n if ret[0] in self.special_numbers:\n return self.special_numbers[ret[0]][0]\n return ret[0], ret[1]\n\n def __contains__(self, bib):\n return bib in self._bibmap\n\n def get_keys(self):\n return self._bibmap.keys()\n\n @staticmethod\n def __pickle_tuple(tupy):\n '''\n tupy can be a very special iterable. It may contain:\n * (float, float)\n * None\n * '+', '-' or '?'\n '''\n def to_str(elem):\n if elem[0] in bib_matrix.special_numbers:\n return \"%s\" % bib_matrix.special_numbers[elem[0]][1]\n return \"%.2f:%.2f\" % (elem[0], elem[1])\n\n return \"|\".join(imap(to_str, tupy))\n\n @staticmethod\n def __unpickle_tuple(tupy):\n '''\n tupy must be an object created by pickle_tuple.\n '''\n def from_str(elem):\n if elem in bib_matrix.special_strings:\n nummy = bib_matrix.special_strings[elem][1]\n return (nummy, nummy)\n fls = elem.split(\":\")\n assert len(fls) == 2\n return (float(fls[0]), float(fls[1]))\n\n strs = tupy.split(\"|\")\n if strs == ['']:\n strs = []\n ret = bib_matrix.create_empty_matrix(len(strs))\n for i, stri in enumerate(strs):\n if i % 100000 == 0:\n update_status(float(i) / len(strs), \"Loading the cache...\")\n ret[i][0], ret[i][1] = from_str(stri)\n update_status_final(\"Probability matrix loaded.\")\n return ret\n\n def load(self, name):\n '''\n This method will load the matrix from the\n database.\n '''\n row = run_sql(\"select bibmap, matrix \"\n \"from aidPROBCACHE \"\n \"where cluster like %s\",\n (name,))\n if len(row) == 0:\n self._bibmap = dict()\n return False\n elif len(row) == 1:\n bibmap_vs = zlib.decompress(row[0][0])\n bibmap_v = cPickle.loads(bibmap_vs)\n rec_v, self.creation_time, self._bibmap = bibmap_v\n if (rec_v != bib_matrix.current_comparison_version or\n bib_matrix.current_comparison_version < 0): # you can use negative\n # version to recalculate\n self._bibmap = dict()\n return False\n\n matrix_s = zlib.decompress(row[0][1])\n self._matrix = bib_matrix.__unpickle_tuple(matrix_s)\n if self._bibmap and self._matrix != None:\n if len(self._bibmap) * (len(self._bibmap) - 1) / 2 != len(self._matrix):\n print >> sys.stderr, (\"Error: aidPROBCACHE is corrupted! \"\n \"Cluster %s has bibmap with %d bibs, \"\n \"but matrix with %d entries.\"\n % (name, len(self._bibmap), len(self._matrix)))\n print >> sys.stderr, \"Try to increase max_packet_size.\"\n assert False, \"Bibmap: %d, Matrix %d\" % (len(self._bibmap), len(self._matrix))\n return False\n return True\n else:\n self._bibmap = dict()\n return False\n else:\n assert False, \"aidPROBCACHE is corrupted\"\n self._bibmap = dict()\n return False\n\n def store(self, name, creation_time):\n bibmap_v = (bib_matrix.current_comparison_version, creation_time, self._bibmap)\n bibmap_vs = cPickle.dumps(bibmap_v)\n bibmap_vsc = zlib.compress(bibmap_vs)\n\n matrix_s = bib_matrix.__pickle_tuple(self._matrix)\n matrix_sc = zlib.compress(matrix_s)\n\n run_sql(\"delete from aidPROBCACHE where cluster like %s\", (name,))\n run_sql(\"insert low_priority \"\n \"into aidPROBCACHE \"\n \"set cluster = %s, \"\n \"bibmap = %s, \"\n \"matrix = %s\",\n (name, bibmap_vsc, matrix_sc))\n\n\ndef delete_paper_from_personid(rec):\n '''\n Deletes all information in PERSONID about a given paper\n '''\n run_sql(\"delete from aidPERSONIDPAPERS where bibrec = %s\", (rec,))\n\n\ndef get_signatures_from_rec(bibrec):\n '''\n Retrieves all information in PERSONID\n about a given bibrec.\n '''\n return run_sql(\"select personid, bibref_table, bibref_value, bibrec, name \"\n \"from aidPERSONIDPAPERS where bibrec = %s\"\n , (bibrec,))\n\n\ndef modify_signature(oldref, oldrec, newref, newname):\n '''\n Modifies a signature in aidPERSONIDpapers.\n '''\n return run_sql(\"UPDATE aidPERSONIDPAPERS \"\n \"SET bibref_table = %s, bibref_value = %s, name = %s \"\n \"WHERE bibref_table = %s AND bibref_value = %s AND bibrec = %s\"\n , (str(newref[0]), newref[1], newname,\n str(oldref[0]), oldref[1], oldrec))\n\n\ndef find_pids_by_name(name):\n '''\n Finds names and personids by a prefix name.\n '''\n return set(run_sql(\"SELECT personid, name \"\n \"FROM aidPERSONIDPAPERS \"\n \"WHERE name like %s\"\n , (name + ',%',)))\n\ndef find_pids_by_exact_name(name):\n \"\"\"\n Finds names and personids by a name.\n \"\"\"\n return set(run_sql(\"SELECT personid \"\n \"FROM aidPERSONIDPAPERS \"\n \"WHERE name = %s\"\n , (name,)))\n\ndef remove_sigs(signatures):\n '''\n Removes records from aidPERSONIDPAPERS\n '''\n for sig in signatures:\n run_sql(\"DELETE FROM aidPERSONIDPAPERS \"\n \"WHERE bibref_table like %s AND bibref_value = %s AND bibrec = %s\"\n , (str(sig[0]), sig[1], sig[2]))\n\n\ndef remove_personid_papers(pids):\n '''\n Removes all signatures from aidPERSONIDPAPERS with pid in pids\n '''\n if pids:\n run_sql(\"delete from aidPERSONIDPAPERS where personid in %s\"\n % list_2_SQL_str(pids))\n\n\ndef get_full_personid_papers(table_name=\"`aidPERSONIDPAPERS`\"):\n '''\n Get all columns and rows from aidPERSONIDPAPERS\n or any other table with the same structure.\n '''\n return run_sql(\"select personid, bibref_table, \"\n \"bibref_value, bibrec, name, flag, \"\n \"lcul from %s\" % table_name)\n\n\ndef get_full_results():\n '''\n Depricated. Should be removed soon.\n '''\n return run_sql(\"select personid, bibref_table, bibref_value, bibrec \"\n \"from aidRESULTS\")\n\n\ndef get_lastname_results(last_name):\n '''\n Returns rows from aidRESULTS which share a common last name.\n '''\n return run_sql(\"select personid, bibref_table, bibref_value, bibrec \"\n \"from aidRESULTS \"\n \"where personid like '\" + last_name + \".%'\")\n\n\n\ndef get_full_personid_data(table_name=\"`aidPERSONIDDATA`\"):\n '''\n Get all columns and rows from aidPERSONIDDATA\n or any other table with the same structure.\n '''\n return run_sql(\"select personid, tag, data, \"\n \"opt1, opt2, opt3 from %s\" % table_name)\n\n\ndef get_wrong_names():\n '''\n Returns a generator with all wrong names in aidPERSONIDPAPERS.\n Every element is (table, ref, correct_name).\n '''\n\n bib100 = dict(((x[0], create_normalized_name(split_name_parts(x[1]))) for x in get_bib10x()))\n bib700 = dict(((x[0], create_normalized_name(split_name_parts(x[1]))) for x in get_bib70x()))\n\n pidnames100 = run_sql(\"select distinct bibref_value, name from aidPERSONIDPAPERS \"\n \" where bibref_table='100'\")\n pidnames700 = run_sql(\"select distinct bibref_value, name from aidPERSONIDPAPERS \"\n \" where bibref_table='700'\")\n\n wrong100 = set(('100', x[0], bib100.get(x[0], None)) for x in pidnames100 if x[1] != bib100.get(x[0], None))\n wrong700 = set(('700', x[0], bib700.get(x[0], None)) for x in pidnames700 if x[1] != bib700.get(x[0], None))\n\n total = len(wrong100) + len(wrong700)\n\n return chain(wrong100, wrong700), total\n\n\ndef check_personid_papers(output_file=None):\n '''\n Checks all invariants of personid.\n Writes in stdout if output_file if False.\n '''\n\n if output_file:\n fp = open(output_file, \"w\")\n printer = lambda x: fp.write(x + '\\n')\n else:\n printer = bibauthor_print\n\n checkers = (check_duplicated_papers,\n check_duplicated_signatures,\n check_wrong_names,\n check_canonical_names,\n check_empty_personids,\n check_wrong_rejection,\n# check_claim_ispireid_contradiction,\n )\n\n # Avoid writing f(a) or g(a), because one of the calls\n # might be optimized.\n return all([check(printer) for check in checkers])\n\n\ndef check_duplicated_papers(printer):\n ret = True\n pids = run_sql(\"select distinct personid from aidPERSONIDPAPERS\")\n for pid in pids:\n pid = pid[0]\n recs = run_sql(\"select bibrec from aidPERSONIDPAPERS where personid = %s and flag <> %s\", (pid, -2))\n recs = [rec[0] for rec in recs]\n for rec in set(recs):\n recs.remove(rec)\n\n if recs:\n ret = False\n printer(\"Person %d has duplicated papers: %s\" % (pid, str(tuple(set(recs)))))\n\n return ret\n\n\ndef check_duplicated_signatures(printer):\n ret = True\n recs = run_sql(\"select distinct bibrec from aidPERSONIDPAPERS\")\n for rec in recs:\n rec = rec[0]\n refs = list(run_sql(\"select bibref_table, bibref_value from aidPERSONIDPAPERS where bibrec = %s and flag > %s\", (rec, \"-2\")))\n\n for ref in set(refs):\n refs.remove(ref)\n\n if refs:\n ret = False\n refs = sorted(refs)\n refs = groupby(refs)\n refs = [\"Found %s:%s %d times.\" % (key[0], key[1], len(list(data)) + 1) for key, data in refs]\n printer(\"Paper %d has duplicated signatures:\" % rec)\n for ref in refs:\n printer(\"\\t%s\" % ref)\n\n return ret\n\n\ndef check_wrong_names(printer):\n ret = True\n wrong_names, number = get_wrong_names()\n\n if number > 0:\n ret = False\n printer(\"%d corrupted names in aidPERSONIDPAPERS.\" % number)\n for wrong_name in wrong_names:\n if wrong_name[2]:\n printer(\"Outdated name, '%s'(%s:%d).\" % (wrong_name[2], wrong_name[0], wrong_name[1]))\n else:\n printer(\"Invalid id(%s:%d).\" % (wrong_name[0], wrong_name[1]))\n\n return ret\n\n\ndef check_canonical_names(printer):\n ret = True\n\n pid_cn = run_sql(\"select personid, data from aidPERSONIDDATA where tag = %s\", ('canonical_name',))\n pid_2_cn = dict((k, len(list(d))) for k, d in groupby(sorted(pid_cn, key=itemgetter(0)), key=itemgetter(0)))\n\n for pid in get_existing_personids():\n canon = pid_2_cn.get(pid, 0)\n\n if canon != 1:\n if canon == 0:\n papers = run_sql(\"select count(*) from aidPERSONIDPAPERS where personid = %s\", (pid,))[0][0]\n if papers != 0:\n printer(\"Personid %d does not have a canonical name, but have %d papers.\" % (pid, papers))\n ret = False\n else:\n printer(\"Personid %d has %d canonical names.\", (pid, canon))\n ret = False\n\n return ret\n\n\ndef check_empty_personids(printer):\n ret = True\n\n paper_pids = set(p[0] for p in run_sql(\"select personid from aidPERSONIDPAPERS\"))\n data_pids = set(p[0] for p in run_sql(\"select personid from aidPERSONIDDATA\"))\n\n for p in data_pids - paper_pids:\n fields = run_sql(\"select count(*) from aidPERSONIDDATA where personid = %s and tag <> %s\", (p, \"canonical_name\",))[0][0]\n\n if fields == 0:\n printer(\"Personid %d has no papers and nothing else than canonical_name.\" % p)\n ret = False\n\n return ret\n\ndef check_wrong_rejection(printer):\n ret = True\n\n all_rejections = run_sql(\"select personid, bibref_table, bibref_value, bibrec \"\n \"from aidPERSONIDPAPERS \"\n \"where flag = %s\",\n ('-2',))\n\n for rej in all_rejections:\n sigs = run_sql(\"select personid from aidPERSONIDPAPERS \"\n \"where bibref_table = %s \"\n \"and bibref_value = %s \"\n \"and bibrec = %s \"\n \"and flag <> '-2'\", rej[1:])\n\n # To avoid duplication of error messages don't complain\n # if the papers is assigned to more than one personids.\n if not sigs:\n printer(\"The paper (%s:%s,%s) was rejected from person %d, but never assigned or claimed.\" % (rej[1:] + rej[:1]))\n ret = False\n\n elif rej[1] in sigs:\n printer(\"Personid %d has both assigned and rejected paper (%s:%s,%s).\" % rej)\n ret = False\n\n return ret\n\n\ndef check_merger():\n '''\n This function presumes that copy_personid was\n called before the merger.\n '''\n is_ok = True\n\n old_claims = set(run_sql(\"select personid, bibref_table, bibref_value, bibrec, flag \"\n \"from aidPERSONIDPAPERS_copy \"\n \"where flag = -2 or flag = 2\"))\n\n cur_claims = set(run_sql(\"select personid, bibref_table, bibref_value, bibrec, flag \"\n \"from aidPERSONIDPAPERS \"\n \"where flag = -2 or flag = 2\"))\n\n errors = ((old_claims - cur_claims, \"Some claims were lost during the merge.\"),\n (cur_claims - old_claims, \"Some new claims appeared after the merge.\"))\n act = { -2 : 'Rejection', 2 : 'Claim' }\n\n for err_set, err_msg in errors:\n if err_set:\n is_ok = False\n bibauthor_print(err_msg)\n bibauthor_print(\"\".join(\" %s: personid %d %d:%d,%d\\n\" %\n (act[cl[6]], cl[0], int(cl[1]), cl[2], cl[3]) for cl in err_set))\n\n old_assigned = set(run_sql(\"select bibref_table, bibref_value, bibrec \"\n \"from aidPERSONIDPAPERS_copy\"))\n #\"where flag <> -2 and flag <> 2\"))\n\n cur_assigned = set(run_sql(\"select bibref_table, bibref_value, bibrec \"\n \"from aidPERSONIDPAPERS\"))\n #\"where flag <> -2 and flag <> 2\"))\n\n errors = ((old_assigned - cur_assigned, \"Some signatures were lost during the merge.\"),\n (cur_assigned - old_assigned, \"Some new signatures appeared after the merge.\"))\n\n for err_sig, err_msg in errors:\n if err_sig:\n is_ok = False\n bibauthor_print(err_msg)\n bibauthor_print(\"\".join(\" %s:%d,%d\\n\" % sig for sig in err_sig))\n\n return is_ok\n\ndef check_results():\n is_ok = True\n\n all_result_rows = run_sql(\"select * from aidRESULTS\")\n\n keyfunc = lambda x: x[1:]\n duplicated = (d for d in (list(d) for k, d in groupby(sorted(all_result_rows, key=keyfunc), key=keyfunc)) if len(d) > 1)\n\n for dd in duplicated:\n is_ok = False\n for d in dd:\n print \"%s %s %s %s\" % d\n print\n\n\n clusters = {}\n for rr in all_result_rows:\n clusters[rr[0]] = clusters.get(rr[0], []) + [rr[3]]\n\n faulty_clusters = dict((cid, len(recs) - len(set(recs)))\n for cid, recs in clusters.items()\n if not len(recs) == len(set(recs)))\n\n if faulty_clusters:\n is_ok = False\n print \"Recids NOT unique in clusters!\"\n print (\"A total of %s clusters hold an average of %.2f duplicates\" %\n (len(faulty_clusters), (sum(faulty_clusters.values()) / float(len(faulty_clusters)))))\n\n for c in faulty_clusters:\n print \"Name: %-20s Size: %4d Faulty: %2d\" % (c, len(clusters[c]), faulty_clusters[c])\n\n return is_ok\n\ndef check_claim_inspireid_contradiction():\n iids10x = run_sql(\"select id from bib10x where tag = '100__i'\")\n iids70x = run_sql(\"select id from bib70x where tag = '700__i'\")\n\n refs10x = set(x[0] for x in run_sql(\"select id from bib10x where tag = '100__a'\"))\n refs70x = set(x[0] for x in run_sql(\"select id from bib70x where tag = '700__a'\"))\n\n if iids10x:\n iids10x = list_2_SQL_str(iids10x, lambda x: str(x[0]))\n\n iids10x = run_sql(\"select id_bibxxx, id_bibrec, field_number \"\n \"from bibrec_bib10x \"\n \"where id_bibxxx in %s\"\n % iids10x)\n\n iids10x = ((row[0], [(ref, rec) for ref, rec in run_sql(\n \"select id_bibxxx, id_bibrec \"\n \"from bibrec_bib10x \"\n \"where id_bibrec = '%s' \"\n \"and field_number = '%s'\"\n % row[1:])\n if ref in refs10x])\n for row in iids10x)\n else:\n iids10x = ()\n\n if iids70x:\n iids70x = list_2_SQL_str(iids70x, lambda x: str(x[0]))\n\n iids70x = run_sql(\"select id_bibxxx, id_bibrec, field_number \"\n \"from bibrec_bib70x \"\n \"where id_bibxxx in %s\"\n % iids70x)\n\n iids70x = ((row[0], [(ref, rec) for ref, rec in run_sql(\n \"select id_bibxxx, id_bibrec \"\n \"from bibrec_bib70x \"\n \"where id_bibrec = '%s' \"\n \"and field_number = '%s'\"\n % (row[1:]))\n if ref in refs70x])\n for row in iids70x)\n else:\n iids70x = ()\n\n # [(iids, [bibs])]\n inspired = list(chain(((iid, list(set(('100', ) + bib for bib in bibs))) for iid, bibs in iids10x),\n ((iid, list(set(('700', ) + bib for bib in bibs))) for iid, bibs in iids70x)))\n\n assert all(len(x[1]) == 1 for x in inspired)\n\n inspired = ((k, map(itemgetter(0), map(itemgetter(1), d)))\n for k, d in groupby(sorted(inspired, key=itemgetter(0)), key=itemgetter(0)))\n\n # [(inspireid, [bibs])]\n inspired = [([(run_sql(\"select personid \"\n \"from aidPERSONIDPAPERS \"\n \"where bibref_table = %s \"\n \"and bibref_value = %s \"\n \"and bibrec = %s \"\n \"and flag = '2'\"\n , bib), bib)\n for bib in cluster[1]], cluster[0])\n for cluster in inspired]\n\n # [([([pid], bibs)], inspireid)]\n for cluster, iid in inspired:\n pids = set(chain.from_iterable(imap(itemgetter(0), cluster)))\n\n if len(pids) > 1:\n print \"InspireID: %s links the following papers:\" % iid\n print map(itemgetter(1), cluster)\n print \"More than one personid claimed them:\"\n print list(pids)\n print\n continue\n\n if len(pids) == 0:\n # not even one paper with this inspireid has been\n # claimed, screw it\n continue\n\n pid = list(pids)[0][0]\n\n # The last step is to check all non-claimed papers for being\n # claimed by the person on some different signature.\n problem = (run_sql(\"select bibref_table, bibref_value, bibrec \"\n \"from aidPERSONIDPAPERS \"\n \"where bibrec = %s \"\n \"and personid = %s \"\n \"and flag = %s\"\n , (bib[2], pid, 2))\n for bib in (bib for lpid, bib in cluster if not lpid))\n problem = list(chain.from_iterable(problem))\n\n if problem:\n print \"A personid has claimed a paper from an inspireid cluster and a contradictory paper.\"\n print \"Personid %d\" % pid\n print \"Inspireid cluster %s\" % str(map(itemgetter(1), cluster))\n print \"Contradicting claims: %s\" % str(problem)\n print\n\n\ndef repair_personid():\n '''\n This should make check_personid_papers() to return true.\n '''\n pids = run_sql(\"select distinct personid from aidPERSONIDPAPERS\")\n lpids = len(pids)\n for i, pid in enumerate((p[0] for p in pids)):\n update_status(float(i) / lpids, \"Checking per-pid...\")\n rows = run_sql(\"select bibrec, bibref_table, bibref_value, flag \"\n \"from aidPERSONIDPAPERS where personid = %s\", (pid,))\n\n rows = ((k, list(d))\n for k, d in groupby(sorted(rows, key=itemgetter(0)), itemgetter(0)))\n\n for rec, sigs in rows:\n if len(sigs) > 1:\n claimed = [sig for sig in sigs if sig[3] > 1]\n rejected = [sig for sig in sigs if sig[3] < -1]\n\n if len(claimed) == 1:\n sigs.remove(claimed[0])\n elif len(claimed) == 0 and len(rejected) == 1:\n sigs.remove(rejected[0])\n\n for sig in set(sigs):\n run_sql(\"delete from aidPERSONIDPAPERS \"\n \"where personid = %s \"\n \"and bibrec = %s \"\n \"and bibref_table = %s \"\n \"and bibref_value = %s \"\n \"and flag = %s\"\n , (pid, sig[0], sig[1], sig[2], sig[3]))\n update_status_final(\"Done with per-pid fixing.\")\n\n recs = run_sql(\"select distinct bibrec from aidPERSONIDPAPERS\")\n lrecs = len(recs)\n for i, rec in enumerate((r[0] for r in recs)):\n update_status(float(i) / lrecs, \"Checking per-rec...\")\n rows = run_sql(\"select bibref_table, bibref_value, flag from aidPERSONIDPAPERS \"\n \"where bibrec = %s\", (rec,))\n kfuc = itemgetter(slice(0, 2))\n rows = ((k, map(itemgetter(2), d)) for k, d in groupby(sorted(rows), kfuc))\n\n for bibref, flags in rows:\n if len(flags) > 1:\n claimed = sum(1 for f in flags if f > 1)\n rejected = sum(1 for f in flags if f < -1)\n\n if claimed == 1:\n run_sql(\"delete from aidPERSONIDPAPERS \"\n \"where bibrec = %s \"\n \"and bibref_table = %s \"\n \"and bibref_value = %s \"\n \"and flag <> %s\"\n , (rec, bibref[0], bibref[1], 2))\n elif claimed == 0 and rejected == 1:\n run_sql(\"delete from aidPERSONIDPAPERS \"\n \"where bibrec = %s \"\n \"and bibref_table = %s \"\n \"and bibref_value = %s \"\n \"and flag <> %s\"\n , (rec, bibref[0], bibref[1], -2))\n else:\n run_sql(\"delete from aidPERSONIDPAPERS \"\n \"where bibrec = %s \"\n \"and bibref_table = %s \"\n \"and bibref_value = %s\"\n , (rec, bibref[0], bibref[1]))\n update_status_final(\"Done with per-rec fixing.\")\n\n update_status(0 / 1, \"Fixing wrong names...\")\n wrong_names, number = get_wrong_names()\n for i, w in enumerate(wrong_names):\n update_status(i / number, \"Fixing wrong names...\")\n if w[2]:\n run_sql(\"update aidPERSONIDPAPERS set name=%s where bibref_table=%s and bibref_value=%s\",\n (w[2], w[0], w[1]))\n else:\n run_sql(\"delete from aidPERSONIDPAPERS where bibref_table=%s and bibref_value=%s\",\n (w[0], w[1]))\n\n no_rejs = frozenset(run_sql(\"select bibref_table, bibref_value, bibrec from aidPERSONIDPAPERS where flag <> -2\"))\n rejs = frozenset(run_sql(\"select bibref_table, bibref_value, bibrec from aidPERSONIDPAPERS where flag = -2\"))\n floating_rejs = rejs - no_rejs\n\n update_personID_canonical_names(map(new_person_from_signature, floating_rejs))\n\n update_status_final(\"Fixed all wrong names.\")\n\n update_status(0, \"Checking missing canonical names...\")\n paper_pids = run_sql(\"select distinct personid from aidPERSONIDPAPERS\")\n cname_pids = run_sql(\"select distinct personid from aidPERSONIDDATA where tag='canonical_name'\")\n missing_cnames = list(set(p[0] for p in paper_pids) - set(p[0] for p in cname_pids))\n npids = len(missing_cnames)\n for pid in missing_cnames:\n update_status(missing_cnames.index(pid) / float(npids), \"Creating missing canonical names...\")\n update_personID_canonical_names([pid])\n update_status_final(\"Done restoring canonical names.\")\n\n\ndef get_all_bibrecs():\n return [x[0] for x in run_sql(\"select distinct bibrec from aidPERSONIDPAPERS\")]\n\n\ndef remove_all_bibrecs(bibrecs):\n bibrecs_s = list_2_SQL_str(bibrecs)\n run_sql(\"delete from aidPERSONIDPAPERS where bibrec in %s\" % bibrecs_s)\n\n\ndef empty_results_table():\n run_sql(\"TRUNCATE aidRESULTS\")\n\n\ndef save_cluster(named_cluster):\n name, cluster = named_cluster\n for bib in cluster.bibs:\n run_sql(\"INSERT INTO aidRESULTS \"\n \"(personid, bibref_table, bibref_value, bibrec) \"\n \"VALUES (%s, %s, %s, %s) \"\n , (name, str(bib[0]), bib[1], bib[2]))\n\n\ndef remove_result_cluster(name):\n run_sql(\"DELETE FROM aidRESULTS \"\n \"WHERE personid like '%s%%'\"\n % name)\n\n\ndef personid_name_from_signature(sig):\n ret = run_sql(\"select personid, name \"\n \"from aidPERSONIDPAPERS \"\n \"where bibref_table = %s and bibref_value = %s and bibrec = %s \"\n \"and flag > '-2'\"\n , sig)\n assert len(ret) < 2, ret\n return ret\n\ndef personid_from_signature(sig):\n ret = run_sql(\"select personid, flag \"\n \"from aidPERSONIDPAPERS \"\n \"where bibref_table = %s and bibref_value = %s and bibrec = %s \"\n \"and flag > '-2'\"\n , sig)\n assert len(ret) < 2, ret\n return ret\n\ndef in_results(name):\n return run_sql(\"select count(*) \"\n \"from aidRESULTS \"\n \"where personid like %s\"\n , (name + '.0',))[0][0] > 0\n\ndef get_signature_info(sig):\n ret = run_sql(\"select personid, flag \"\n \"from aidPERSONIDPAPERS \"\n \"where bibref_table = %s and bibref_value = %s and bibrec = %s \"\n \"order by flag\"\n , sig)\n return ret\n\ndef get_claimed_papers(pid):\n return run_sql(\"select bibref_table, bibref_value, bibrec \"\n \"from aidPERSONIDPAPERS \"\n \"where personid = %s \"\n \"and flag > %s\",\n (pid, 1))\n\n\ndef copy_personids():\n run_sql(\"DROP TABLE IF EXISTS `aidPERSONIDDATA_copy`\")\n run_sql(\"CREATE TABLE `aidPERSONIDDATA_copy` ( \"\n \"`personid` BIGINT( 16 ) UNSIGNED NOT NULL , \"\n \"`tag` VARCHAR( 64 ) NOT NULL , \"\n \"`data` VARCHAR( 256 ) NOT NULL , \"\n \"`opt1` MEDIUMINT( 8 ) DEFAULT NULL , \"\n \"`opt2` MEDIUMINT( 8 ) DEFAULT NULL , \"\n \"`opt3` VARCHAR( 256 ) DEFAULT NULL , \"\n \"KEY `personid-b` ( `personid` ) , \"\n \"KEY `tag-b` ( `tag` ) , \"\n \"KEY `data-b` ( `data` ) , \"\n \"KEY `opt1` ( `opt1` ) \"\n \") ENGINE = MYISAM DEFAULT CHARSET = utf8\")\n run_sql(\"INSERT INTO `aidPERSONIDDATA_copy` \"\n \"SELECT * \"\n \"FROM `aidPERSONIDDATA`\")\n\n run_sql(\"DROP TABLE IF EXISTS `aidPERSONIDPAPERS_copy`\")\n run_sql(\"CREATE TABLE `aidPERSONIDPAPERS_copy` ( \"\n \"`personid` bigint( 16 ) unsigned NOT NULL , \"\n \"`bibref_table` enum( '100', '700' ) NOT NULL , \"\n \"`bibref_value` mediumint( 8 ) unsigned NOT NULL , \"\n \"`bibrec` mediumint( 8 ) unsigned NOT NULL , \"\n \"`name` varchar( 256 ) NOT NULL , \"\n \"`flag` smallint( 2 ) NOT NULL DEFAULT '0', \"\n \"`lcul` smallint( 2 ) NOT NULL DEFAULT '0', \"\n \"`last_updated` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP , \"\n \"KEY `personid-b` ( `personid` ) , \"\n \"KEY `reftable-b` ( `bibref_table` ) , \"\n \"KEY `refvalue-b` ( `bibref_value` ) , \"\n \"KEY `rec-b` ( `bibrec` ) , \"\n \"KEY `name-b` ( `name` ) , \"\n \"KEY `timestamp-b` ( `last_updated` ) , \"\n \"KEY `ptvrf-b` ( `personid` , `bibref_table` , `bibref_value` , `bibrec` , `flag` ) \"\n \") ENGINE = MyISAM DEFAULT CHARSET = utf8\")\n run_sql(\"INSERT INTO `aidPERSONIDPAPERS_copy` \"\n \"SELECT * \"\n \"FROM `aidPERSONIDPAPERS\")\n\n\ndef delete_empty_persons():\n pp = run_sql(\"select personid from aidPERSONIDPAPERS\")\n pp = set(p[0] for p in pp)\n pd = run_sql(\"select personid from aidPERSONIDDATA\")\n pd = set(p[0] for p in pd)\n fpd = run_sql(\"select personid from aidPERSONIDDATA where tag <> 'canonical_name'\")\n fpd = set(p[0] for p in fpd)\n to_delete = pd - (pp | fpd)\n if to_delete:\n run_sql(\"delete from aidPERSONIDDATA where personid in %s\" % list_2_SQL_str(to_delete))\n\ndef restore_personids():\n run_sql(\"TRUNCATE `aidPERSONIDDATA`\")\n run_sql(\"INSERT INTO `aidPERSONIDDATA` \"\n \"SELECT * \"\n \"FROM `aidPERSONIDDATA_copy`\")\n\n run_sql(\"TRUNCATE `aidPERSONIDPAPERS`\")\n run_sql(\"INSERT INTO `aidPERSONIDPAPERS` \"\n \"SELECT * \"\n \"FROM `aidPERSONIDPAPERS_copy\")\n\n\ndef get_possible_personids_from_paperlist_old(bibrecreflist):\n '''\n @param bibrecreflist: list of bibrecref couples, (('100:123,123',),) or bibrecs (('123',),)\n returns a list of pids and connected bibrefs in order of number of bibrefs per pid\n [ [['1'],['123:123.123','123:123.123']] , [['2'],['123:123.123']] ]\n '''\n\n pid_bibrecref_dict = {}\n for b in bibrecreflist:\n pids = []\n\n try:\n pids = run_sql(\"select personid from aidPERSONID \"\n \"use index (`tdf-b`) where tag=%s and data=%s\", ('paper', str(b[0])))\n except (OperationalError, ProgrammingError):\n pids = run_sql(\"select personid from aidPERSONID \"\n \"where tag=%s and data=%s\", ('paper', str(b[0])))\n\n for pid in pids:\n if pid[0] in pid_bibrecref_dict:\n pid_bibrecref_dict[pid[0]].append(str(b[0]))\n else:\n pid_bibrecref_dict[pid[0]] = [str(b[0])]\n\n pid_list = [[i, pid_bibrecref_dict[i]] for i in pid_bibrecref_dict]\n\n return sorted(pid_list, key=lambda k: len(k[2]), reverse=True)\n\n\ndef resolve_affiliation(ambiguous_aff_string):\n \"\"\"\n This is a method available in the context of author disambiguation in ADS\n only. No other platform provides the db table used by this function.\n @warning: to be used in an ADS context only.\n @param ambiguous_aff_string: Ambiguous affiliation string\n @type ambiguous_aff_string: str\n @return: The normalized version of the name string as presented in the database\n @rtype: str\n \"\"\"\n if not ambiguous_aff_string or not bconfig.CFG_ADS_SITE:\n return \"None\"\n\n aff_id = run_sql(\"select aff_id from ads_affiliations where affstring=%s\", (ambiguous_aff_string,))\n\n if aff_id:\n return aff_id[0][0]\n else:\n return \"None\"\n"},"domain":{"kind":"string","value":"codeparrot/github-code-clean"}}}],"truncated":false,"partial":false},"paginationData":{"pageIndex":2282,"numItemsPerPage":100,"numTotalItems":228459,"offset":228200,"length":100}},"jwt":"eyJhbGciOiJFZERTQSIsImtpZCI6IjVHZDBvd0g5MTM2eDZjc1FvbE1zcktNWUZoRVFoUm5PVVVybEpjOUhaUEEifQ.eyJyZWFkIjp0cnVlLCJwZXJtaXNzaW9ucyI6eyJyZXBvLmNvbnRlbnQucmVhZCI6dHJ1ZX0sImlhdCI6MTc4Njg5ODQ4OCwianRpIjoiOWUxNjNhOTItY2VjMS00ZTg3LWE3MzYtNjEzMTQ0YTQ4ZGFhIiwic3ViIjoiL2RhdGFzZXRzL0phY2tCaW5hcnkvTWl4ZWRUZXh0LTIiLCJleHAiOjE3ODY5MDIwODgsImlzcyI6Imh0dHBzOi8vaHVnZ2luZ2ZhY2UuY28ifQ.GOhlkr0IBswFDpp2p6B2AyHr8LU_PW1IYnniFXpSReC9cQ0qn21Z84CtatdbZk1U0qJMyYP9TTzMD5AlthUnDQ","displayUrls":true,"splitSizeSummaries":[{"config":"default","split":"train","numRows":228459,"numBytesParquet":7695109915}]},"discussionsStats":{"closed":0,"open":1,"total":1},"fullWidth":true,"hasGatedAccess":true,"hasFullAccess":true,"isEmbedded":false,"savedQueries":{"community":[],"user":[]}}">
text stringlengths 5.09k 178k | domain stringclasses 106
values |
|---|---|
from datetime import (
date,
datetime,
timedelta,
)
from itertools import product
import numpy as np
import pytest
import pandas as pd
from pandas import (
Categorical,
DataFrame,
Grouper,
Index,
MultiIndex,
Series,
concat,
date_range,
)
import pandas._testing as tm
from pa... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
'''
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a fre... | codeparrot/github-code-clean |
#!/usr/bin/python
# -*- coding: utf8 -*-
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3, or (at your option) any later
# version.
#
# This program is distributed in the hope th... | codeparrot/github-code-clean |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-2010 Tiny SPRL (<http://tiny.be>).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU... | codeparrot/github-code-clean |
## @file
# Routines for generating AutoGen.h and AutoGen.c
#
# Copyright (c) 2007 - 2012, Intel Corporation. All rights reserved.<BR>
# This program and the accompanying materials
# are licensed and made available under the terms and conditions of the BSD License
# which accompanies this distribution. The full text of... | codeparrot/github-code-clean |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""code generator for GL/GLES extension wrangler."""
import optparse
import os
import collections
import re
import sys
GL_FUNCTIO... | codeparrot/github-code-clean |
import unittest
from unittest import mock
from test import support
import subprocess
import sys
import signal
import io
import os
import errno
import tempfile
import time
import selectors
import sysconfig
import select
import shutil
import gc
import textwrap
try:
import threading
except ImportError:
threading ... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Inventory
#
import wx
import wx.grid as gridlib
import sys,re
import faulthandler
import json
import time
import numpy
import xml.etree.cElementTree as ET
import wx.lib.masked as masked
import datetime
import pout
import handy_utils as HUD
from button_stuff import Butt... | codeparrot/github-code-clean |
# coding=utf-8
# --------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# Code generated by Microsoft (R) AutoRest Code Generator.
# Changes may ... | codeparrot/github-code-clean |
#####################################################################
# #
# Refinement Script with SHELX and CCP4/REFMAC5 #
# #
# Copyright: Molecular Images 2005 ... | codeparrot/github-code-clean |
# This file is part of HamsiManager.
#
# Copyright (c) 2010 - 2015 Murat Demir <mopened@gmail.com>
#
# Hamsi Manager is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at yo... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
################################
######## Red - Discord bot #####
################################
# made by Twentysix
#
#
import discord
import logging
import time
import datetime
import requests
import aiohttp
import traceback
import re
import youtube_dl
import os
import... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'VCMBirthRecord.SettlementCode'
db.delete_column(u'sourc... | codeparrot/github-code-clean |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | codeparrot/github-code-clean |
# Copyright 2010 United States Government as represented by the
# Administrator of the National Aeronautics and Space Administration.
# Copyright 2011 Piston Cloud Computing, Inc.
# All Rights Reserved.
# Copyright 2013 Red Hat, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# no... | codeparrot/github-code-clean |
# Copyright (c) 2014 Dell Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | codeparrot/github-code-clean |
#! /usr/bin/env python
#####################################################################################################################
# CUICUILCO: A general purpose framework that allows the construction and evaluation of #
# hierarchical networks for supervised learning ... | codeparrot/github-code-clean |
"""Tools for spectral analysis.
"""
from __future__ import division, print_function, absolute_import
import numpy as np
from scipy import fftpack
from . import signaltools
from .windows import get_window
from ._spectral import _lombscargle
from ._arraytools import const_ext, even_ext, odd_ext, zero_ext
import warning... | codeparrot/github-code-clean |
from sqlalchemy.testing import eq_, assert_raises, assert_raises_message
import operator
from sqlalchemy import *
from sqlalchemy import exc as sa_exc, util
from sqlalchemy.sql import compiler, table, column
from sqlalchemy.engine import default
from sqlalchemy.orm import *
from sqlalchemy.orm import attributes
from s... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
from sympy.matrices import Matrix
from sympy.core import Add, diff, Symbol
from sympy.simplify import simplify
from tensor_analysis.arraypy import Arraypy, TensorArray, matrix2arraypy, \
matrix2tensor, list2arraypy, list2tensor
from tensor_analysis.tensor_methods import is_symmetric
from te... | codeparrot/github-code-clean |
from pybindgen import Module, FileCodeSink, param, retval, cppclass, typehandlers
import pybindgen.settings
import warnings
class ErrorHandler(pybindgen.settings.ErrorHandler):
def handle_error(self, wrapper, exception, traceback_):
warnings.warn("exception %r in wrapper %s" % (exception, wrapper))
... | codeparrot/github-code-clean |
# encoding=UTF8
# Copyright 2010 United States Government as represented by the
# Administrator of the National Aeronautics and Space Administration.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You m... | codeparrot/github-code-clean |
""" Classes for interpolating values.
"""
from __future__ import division, print_function, absolute_import
__all__ = ['interp1d', 'interp2d', 'spline', 'spleval', 'splmake', 'spltopp',
'ppform', 'lagrange', 'PPoly', 'BPoly', 'NdPPoly',
'RegularGridInterpolator', 'interpn']
import itertools
imp... | codeparrot/github-code-clean |
# Copyright (c) 2012 - 2015 EMC Corporation.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unle... | codeparrot/github-code-clean |
# pylint: disable=function-redefined
import codecs
import string
from enum import Enum
from itertools import accumulate
from typing import Callable, Iterable, List, Optional, Tuple, TypeVar, Union, cast
from prompt_toolkit.application.current import get_app
from prompt_toolkit.buffer import Buffer, indent, reshape_tex... | codeparrot/github-code-clean |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""
This module contains classes that help to emulate xcodebuild behavior on top of
other build systems, such as make and ninja.
"""
from __future__ import print_... | codeparrot/github-code-clean |
# pylint: disable=E1101,E1103,W0232
import datetime
import warnings
from functools import partial
from sys import getsizeof
import numpy as np
from pandas._libs import index as libindex, lib, Timestamp
from pandas.compat import range, zip, lrange, lzip, map
from pandas.compat.numpy import function as nv
from pandas ... | codeparrot/github-code-clean |
"""
libguestfs tools test utility functions.
"""
import logging
import signal
import os
import re
import aexpect
from avocado.utils import path
from avocado.utils import process
from . import propcan
class LibguestfsCmdError(Exception):
"""
Error of libguestfs-tool command.
"""
def __init__(self,... | codeparrot/github-code-clean |
'''
Copyright 2015 Google Inc. All Rights Reserved.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in ... | codeparrot/github-code-clean |
import collections
import typing
from . import _inspect, _iterate, _update
from . import duration as _duration
from . import enums as _enums
from . import format as _format
from . import indicators as _indicators
from . import iterate as iterate_
from . import markups as _markups
from . import parentage as _parentage
... | codeparrot/github-code-clean |
"""
Module contains tools for processing files into DataFrames or other objects
"""
from __future__ import print_function
from pandas.compat import range, lrange, StringIO, lzip, zip, string_types, map
from pandas import compat
import re
import csv
import numpy as np
from pandas.core.index import Index, MultiIndex
fr... | codeparrot/github-code-clean |
# $HeadURL$
__RCSID__ = "$Id$"
import datetime, time
import types
import threading
import random
from DIRAC.Core.Base.DB import DB
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.FrameworkSystem.Client.MonitoringClient import gMonitor
from DIRAC.Core.Utilities import List, ThreadSafe, Time, DEncode
from DIRAC.Acco... | codeparrot/github-code-clean |
# The level editor GUI.
# The following workflow is expected:
# 1) User load a level
# 2) main windows display the scene layout
# right-side-top-dock display:
# - level scene tree
# - level tree (a list in fact)
# - level resources tree (a list in fact)
# 3) user select an element in one of the tree, related p... | codeparrot/github-code-clean |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | codeparrot/github-code-clean |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | codeparrot/github-code-clean |
#
# Cython/Python language types
#
from __future__ import absolute_import
import copy
import re
try:
reduce
except NameError:
from functools import reduce
from .Code import UtilityCode, LazyUtilityCode, TempitaUtilityCode
from . import StringEncoding
from . import Naming
from .Errors import error
class... | codeparrot/github-code-clean |
from cStringIO import StringIO
from datetime import date, datetime, timedelta
import json
import time
from xml.sax.saxutils import escape
import mock
from nose.tools import eq_, ok_
from nose.plugins.attrib import attr
from django.conf import settings
from django.core.exceptions import ValidationError
from django.tes... | codeparrot/github-code-clean |
from typing import Any, Dict
EMOJI_NAME_MAPS: Dict[str, Dict[str, Any]] = {
# seems like best emoji for happy
"1f600": {"canonical_name": "grinning", "aliases": ["happy"]},
"1f603": {"canonical_name": "smiley", "aliases": []},
# the Google emoji for this is not great, so made People/9 'smile' and
#... | codeparrot/github-code-clean |
import fractions
import operator
import os
import random
import sys
import struct
import time
import unittest
from test import support
from test.test_grammar import (VALID_UNDERSCORE_LITERALS,
INVALID_UNDERSCORE_LITERALS)
from math import isinf, isnan, copysign, ldexp
INF = float("inf")... | codeparrot/github-code-clean |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | codeparrot/github-code-clean |
from pybindgen import Module, FileCodeSink, param, retval, cppclass, typehandlers
import pybindgen.settings
import warnings
class ErrorHandler(pybindgen.settings.ErrorHandler):
def handle_error(self, wrapper, exception, traceback_):
warnings.warn("exception %r in wrapper %s" % (exception, wrapper))
... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
# PLEASE DO NOT EDIT THIS FILE, IT IS GENERATED AND WILL BE OVERWRITTEN:
# https://github.com/ccxt/ccxt/blob/master/CONTRIBUTING.md#how-to-contribute-code
from ccxt.base.exchange import Exchange
import json
from ccxt.base.errors import ExchangeError
from ccxt.base.errors import AuthenticationE... | codeparrot/github-code-clean |
"""
KVM test utility functions.
@copyright: 2008-2009 Red Hat Inc.
"""
import time, string, random, socket, os, signal, re, logging, commands, cPickle
import fcntl, shelve, ConfigParser, threading, sys, UserDict, inspect, tarfile
import struct, shutil, glob
from autotest_lib.client.bin import utils, os_dep
from autot... | codeparrot/github-code-clean |
"""This file contains code for use with "Think Stats" and
"Think Bayes", both by Allen B. Downey, available from greenteapress.com
Copyright 2014 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
from __future__ import print_function, division
"""This file contains class definitions for:
H... | codeparrot/github-code-clean |
from header_common import *
from header_presentations import *
from header_mission_templates import *
from header_operations import *
from header_triggers import *
from header_items import *
from module_constants import *
import header_debug as dbg
import header_lazy_evaluation as lazy
################################... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
# Resource object code
#
# Created by: The Resource Compiler for PyQt4 (Qt v4.8.7)
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore
qt_resource_data = "\
\x00\x00\x00\xd0\
\x51\
\x4c\x61\x62\x65\x6c\x7b\x0d\x0a\x20\x20\x20\x20\x62\x61\x63\x6b\
\x67\x72\x6f\x75... | codeparrot/github-code-clean |
"""
handhRL
Hulks and Horrors: The Roguelike
Copyright 2014 by John S. Berry III
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later versio... | codeparrot/github-code-clean |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2009-2014:
# Gabes Jean, naparuba@gmail.com
# Gerhard Lausser, Gerhard.Lausser@consol.de
# Gregory Starck, g.starck@gmail.com
# Hartmut Goebel, h.goebel@goebel-consult.de
#
# This file is part of Shinken.
#
# Shinken is free software: you c... | codeparrot/github-code-clean |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | codeparrot/github-code-clean |
"""Tests for UIAWrapper"""
from __future__ import print_function
from __future__ import unicode_literals
import time
import os
import sys
import collections
import unittest
import mock
import six
sys.path.append(".")
from pywinauto.windows.application import Application # noqa: E402
from pywinauto.base_application i... | codeparrot/github-code-clean |
from __future__ import division, absolute_import, print_function
import copy
import pickle
import sys
import platform
import gc
import copy
import warnings
import tempfile
from os import path
from io import BytesIO
import numpy as np
from numpy.testing import (
run_module_suite, TestCase, assert_, assert_equa... | codeparrot/github-code-clean |
"""Metrics to assess performance on classification task given classe prediction
Functions named as ``*_score`` return a scalar value to maximize: the higher
the better
Function named as ``*_error`` or ``*_loss`` return a scalar value to minimize:
the lower the better
"""
# Authors: Alexandre Gramfort <alexandre.gram... | codeparrot/github-code-clean |
# -*- encoding: utf-8 -*-
import re
import string
from unicodedata import normalize
from lxml import etree
from lxml.etree import ElementTree, Element, SubElement
from datetime import datetime
import time
import netsvc
from osv import fields, osv
import decimal_precision as dp
from tools.translate import _
class ac... | codeparrot/github-code-clean |
#!/bin/env python
"""
This file defines a set of system_info classes for getting
information about various resources (libraries, library directories,
include directories, etc.) in the system. Currently, the following
classes are available:
atlas_info
atlas_threads_info
atlas_blas_info
atlas_blas_threads_info
... | codeparrot/github-code-clean |
from pybindgen import Module, FileCodeSink, param, retval, cppclass, typehandlers
import pybindgen.settings
import warnings
class ErrorHandler(pybindgen.settings.ErrorHandler):
def handle_error(self, wrapper, exception, traceback_):
warnings.warn("exception %r in wrapper %s" % (exception, wrapper))
... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-2010 Tiny SPRL (<http://tiny.be>).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU... | codeparrot/github-code-clean |
import datetime
import pickle
from io import StringIO
from operator import attrgetter
from django.contrib.auth.models import User
from django.contrib.contenttypes.models import ContentType
from django.core import management
from django.db import DEFAULT_DB_ALIAS, connections, router, transaction
from django.db.models ... | codeparrot/github-code-clean |
# region Description
"""
test_network.py: Unit tests for Raw-packet network classes
Author: Vladimir Ivanov
License: MIT
Copyright 2020, Raw-packet Project
"""
# endregion
# region Import
from sys import path
from os.path import dirname, abspath
import unittest
# endregion
# region Authorship information
__author__ =... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2009-2021 Tom Keffer <tkeffer@gmail.com>
#
# See the file LICENSE.txt for your full rights.
#
"""Classes and functions for interfacing with a Davis VantagePro, VantagePro2,
or VantageVue weather station"""
from __future__ import absolute_import
from __future__ import di... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
# Copyright (C) 2006-2012 Søren Roug, European Environment Agency
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at you... | codeparrot/github-code-clean |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
# Copyright 2010 Joanmarie Diggs
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your op... | codeparrot/github-code-clean |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2010 United States Government as represented by the
# Administrator of the National Aeronautics and Space Administration.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compli... | codeparrot/github-code-clean |
# Copyright 2011 OpenStack Foundation # All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | codeparrot/github-code-clean |
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | codeparrot/github-code-clean |
""" Cisco_IOS_XR_ipv4_acl_oper
This module contains a collection of YANG definitions
for Cisco IOS\-XR ipv4\-acl package operational data.
This module contains definitions
for the following management objects\:
ipv4\-acl\-and\-prefix\-list\: Root class of IPv4 Oper schema tree
Copyright (c) 2013\-2015 by Cisco Sy... | codeparrot/github-code-clean |
input = """
1 2 0 0
1 3 0 0
1 4 0 0
1 5 0 0
1 6 0 0
1 7 0 0
1 8 0 0
1 9 0 0
1 10 0 0
1 11 0 0
1 12 0 0
1 13 0 0
1 14 0 0
1 15 0 0
1 16 0 0
1 17 0 0
1 18 0 0
1 19 0 0
1 20 0 0
1 21 0 0
1 22 0 0
1 23 0 0
1 24 0 0
1 25 0 0
1 26 0 0
1 27 0 0
1 28 0 0
1 29 0 0
1 30 0 0
1 31 0 0
1 32 0 0
1 33 0 0
1 34 0 0
1 35 0 0
1 36 0 0
1... | codeparrot/github-code-clean |
"""
@package mi.instrument.seabird.sbe26plus_v2.driver
@file mi/instrument/seabird/sbe16plus_v2/driver.py
@author David Everett
@brief Driver base class for sbe16plus V2 CTD instrument.
"""
__author__ = 'David Everett'
__license__ = 'Apache 2.0'
import time
import re
from mi.core.log import get_logger, get_loggin... | codeparrot/github-code-clean |
# Author: Travis Oliphant
# 1999 -- 2002
from __future__ import division, print_function, absolute_import
import operator
import math
import sys
import timeit
from scipy.spatial import cKDTree
from . import sigtools, dlti
from ._upfirdn import upfirdn, _output_len, _upfirdn_modes
from scipy import linalg, fft as sp_f... | codeparrot/github-code-clean |
from pybindgen import Module, FileCodeSink, param, retval, cppclass, typehandlers
import pybindgen.settings
import warnings
class ErrorHandler(pybindgen.settings.ErrorHandler):
def handle_error(self, wrapper, exception, traceback_):
warnings.warn("exception %r in wrapper %s" % (exception, wrapper))
... | codeparrot/github-code-clean |
# Copyright 2010-2011 OpenStack Foundation
# Copyright 2011 Piston Cloud Computing, Inc.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www... | codeparrot/github-code-clean |
"""
There are three types of functions implemented in SymPy:
1) defined functions (in the sense that they can be evaluated) like
exp or sin; they have a name and a body:
f = exp
2) undefined function which have a name but no body. Undefined
functions can be defined using a Function cla... | codeparrot/github-code-clean |
"""
Logistic Regression
"""
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Fabian Pedregosa <f@bianp.net>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Manoj Kumar <manojkumarsivaraj334@gmail.com>
# Lars Buitinck
# Simon Wu <s8wu@uwaterloo.ca>
# ... | codeparrot/github-code-clean |
# orm/relationships.py
# Copyright (C) 2005-2015 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Heuristics related to join conditions as used in
:func:`.relationship`.
Pro... | codeparrot/github-code-clean |
#!/usr/bin/env python
# File created on 05 Jun 2011
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso", "Jose Antonio Navas Molina", "Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Greg Capor... | codeparrot/github-code-clean |
# coding=utf-8
# --------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# Code generated by Microsoft (R) AutoRest Code Generator.
# Changes may ... | codeparrot/github-code-clean |
# Use of this source code is governed by the MIT license.
__license__ = "MIT"
try:
from collections.abc import Callable # Python 3.6
except ImportError as e:
from collections import Callable
import re
import sys
import warnings
try:
import thlib.side.soupsieve as soupsieve
except ImportError as e:
soup... | codeparrot/github-code-clean |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2011 Michiel D. Nauta
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any la... | codeparrot/github-code-clean |
import math
import unittest
from datetime import datetime, time, timedelta, tzinfo
from asynctest.mock import patch
from tests.unittest.base_custom import TestCustomField
# Needs to be imported last
from lib.data import timezones
from lib.data.timedelta import format
from ..custom import countdown
class TimeZone(... | codeparrot/github-code-clean |
from distutils.command.clean import clean
import logging
import os
from crispy_forms.bootstrap import Alert, InlineRadios
from crispy_forms.layout import (HTML, Button, Field, Fieldset,
Layout, Row, Div)
from django import forms
from django.conf import settings
from django.contrib.con... | codeparrot/github-code-clean |
""" Integral Transforms """
from __future__ import print_function, division
from sympy.core import S
from sympy.core.compatibility import reduce
from sympy.core.function import Function
from sympy.core.numbers import oo
from sympy.core.symbol import Dummy
from sympy.integrals import integrate, Integral
from sympy.int... | codeparrot/github-code-clean |
# -*- encoding: utf-8 -*-
"""
Factory object creation for all CLI methods
"""
import datetime
import json
import logging
import os
import random
import time
from fauxfactory import (
gen_alphanumeric,
gen_choice,
gen_integer,
gen_ipaddr,
gen_mac,
gen_netmask,
gen_string,
)
from os import c... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 02 11:54:33 2012
@author: a1185872
"""
import os
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.pylab as pylab
from matplotlib.ticker import MultipleLocator, FormatStrFormatter
from matplotlib.patches import Ellipse, Rectangle, Arrow
from matplotli... | codeparrot/github-code-clean |
from __future__ import unicode_literals
import calendar
import json
import logging
import os
import pycountry
import pytz
import random
import regex
import stripe
import traceback
from datetime import datetime, timedelta
from dateutil.relativedelta import relativedelta
from decimal import Decimal
from django.core.fil... | codeparrot/github-code-clean |
# Copyright (c) 2015 Mirantis inc.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... | codeparrot/github-code-clean |
#!/usr/bin/env python
# Copyright 2016 Daniel Nunes
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | codeparrot/github-code-clean |
import re
import collections
from enum import Enum
from ydk._core._dm_meta_info import _MetaInfoClassMember, _MetaInfoClass, _MetaInfoEnum
from ydk.types import Empty, YList, YLeafList, DELETE, Decimal64, FixedBitsDict
from ydk._core._dm_meta_info import ATTRIBUTE, REFERENCE_CLASS, REFERENCE_LIST, REFERENCE_LEAFLI... | codeparrot/github-code-clean |
import bz2
from collections import Counter
from contextlib import contextmanager
from datetime import datetime
from functools import wraps
import gzip
import http.client
import os
import re
from shutil import rmtree
import string
import tempfile
import traceback
from typing import Union, cast
import warnings
import zip... | codeparrot/github-code-clean |
# encoding: latin2
"""Algorithm utilities
G{packagetree core}
"""
__author__ = "Juan C. Duque"
__credits__ = "Copyright (c) 2009-11 Juan C. Duque"
__license__ = "GPL"
__version__ = "1.0.0"
__maintainer__ = "RiSE Group"
__email__ = "contacto@rise-group.org"
import copy
import numpy
import dist2Regions
imp... | codeparrot/github-code-clean |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
import datetime
import hashlib
import itertools
import json
import os
import re
import time
import urlparse
import uuid
from django.conf import settings
from django.core.cache import cache
from django.core.exceptions import ObjectDoesNotExist
from django.core.files.storage import default_storag... | codeparrot/github-code-clean |
"""Tests for base_events.py"""
import errno
import logging
import math
import os
import socket
import sys
import threading
import time
import unittest
from unittest import mock
import asyncio
from asyncio import base_events
from asyncio import constants
from asyncio import events
from test.test_asyncio import utils a... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
# Resource object code
#
# Created: Thu May 2 15:49:03 2013
# by: The Resource Compiler for PyQt (Qt v5.0.2)
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore
qt_resource_data = b"\
\x00\x00\x36\xe2\
\x89\
\x50\x4e\x47\x0d\x0a\x1a\x0a\x00\x00\x00\x0d\x49\x... | codeparrot/github-code-clean |
from __future__ import print_function
__author__ = "John Kirkham <kirkhamj@janelia.hhmi.org>"
__date__ = "$Jul 30, 2014 19:35:11 EDT$"
import imp
import nose
import nose.plugins
import nose.plugins.attrib
import numpy
import scipy
import scipy.spatial
import scipy.spatial.distance
import scipy.stats
import nan... | codeparrot/github-code-clean |
"""Tests for events.py."""
import functools
import gc
import io
import os
import platform
import re
import signal
import socket
try:
import ssl
except ImportError:
ssl = None
import subprocess
import sys
import threading
import time
import errno
import unittest
from unittest import mock
import weakref
import... | codeparrot/github-code-clean |
#!/usr/bin/env python
#
# Copyright 2009 Facebook
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | codeparrot/github-code-clean |
"""Tests for http/cookiejar.py."""
import os
import re
import test.support
import time
import unittest
import urllib.request
from http.cookiejar import (time2isoz, http2time, iso2time, time2netscape,
parse_ns_headers, join_header_words, split_header_words, Cookie,
CookieJar, DefaultCookiePolicy, LWPCookieJa... | codeparrot/github-code-clean |
from numpy.testing import assert_array_equal, assert_equal, assert_raises
import numpy as np
from skimage._shared.testing import test_parallel
from skimage.draw import (set_color, line, line_aa, polygon, polygon_perimeter,
circle, circle_perimeter, circle_perimeter_aa,
... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding unique constraint on 'Cfda', fields ['program_number']
db.create_unique('data_cfda', ['program_numb... | codeparrot/github-code-clean |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2011, 2012 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your opt... | codeparrot/github-code-clean |
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