def update_db_from_rss():
existing_recordsets = {}
recordsets = {}
with PostgresDB() as db:
for r in db.fetchall("SELECT * FROM recordsets"):
for recordid in r["recordids"]:
existing_recordsets[recordid] = r["id"]
recordsets[r["id"]] = r
#logger.debug("***existing_recordsets DUMP ***\n")
#logger.debug("{0}".format(existing_recordsets))
pub_recs = db.fetchall("SELECT * FROM publishers")
logger.debug("Checking %d publishers", len(pub_recs))
for r in pub_recs:
uuid, rss_url = r['uuid'], r['rss_url']
logger.info("Starting Publisher Feed: %s %s", uuid, rss_url)
rsscontents = get_feed(rss_url)
if rsscontents:
try:
_do_rss(rsscontents, r, db, recordsets,
existing_recordsets)
db.commit()
except Exception:
logger.exception("Error with %s %s", uuid, rss_url)
db.rollback()
except:
db.rollback()
raise
logger.info("Finished processing add publisher RSS feeds")
def upload_to_storage(self, store, attempt=1):
if not self.ok:
return self
try:
mo = self.media_object
k = mo.get_key(store)
if k.exists() and k.read() and k.etag == '"{0}"'.format(mo.etag):
logger.debug("NoUpload %s etag %s, already present", self.url,
mo.etag)
else:
try:
mo.upload(store, StringIO(self.content), force=True)
logger.debug("Uploaded %s etag %s", self.url, mo.etag)
except (BotoServerError, BotoClientError) as e:
logger.exception("Failed uploading to storage: %s",
self.url)
self.reason = str(e)
self.status_code = Status.STORAGE_ERROR
return self
with PostgresDB() as idbmodel:
# Don't need to ensure_media, we're processing
# through media entries
mo.ensure_object(idbmodel)
mo.ensure_media_object(idbmodel)
idbmodel.commit()
except Exception:
logger.exception("DbSaveErr %s", self.url)
self.status_code = Status.STORAGE_ERROR
return self
def create_tables():
"""
This function is out-of-sync with actual database, unmaintained.
Commenting out all action in this function, it will do nothing until modified again.
"""
db = PostgresDB()
logger.error('create_tables called but has no valid code to run.')
# db.execute("""CREATE TABLE IF NOT EXISTS publishers (
# id BIGSERIAL NOT NULL PRIMARY KEY,
# uuid uuid UNIQUE,
# name text NOT NULL,
# recordids text[] NOT NULL DEFAULT '{}',
# pub_type varchar(20) NOT NULL DEFAULT 'rss',
# portal_url text,
# rss_url text NOT NULL,
# auto_publish boolean NOT NULL DEFAULT false,
# first_seen timestamp NOT NULL DEFAULT now(),
# last_seen timestamp NOT NULL DEFAULT now(),
# pub_date timestamp
# )""")
# #pubid, rsid Ingest, rs_record_id, eml_link, file_link, First Seen Date, Last Seen Date, Feed Date, Harvest Date, Harvest Etag
# db.execute("""CREATE TABLE IF NOT EXISTS recordsets (
# id BIGSERIAL NOT NULL PRIMARY KEY,
# uuid uuid UNIQUE,
# publisher_uuid uuid REFERENCES publishers(uuid),
# name text NOT NULL,
# recordids text[] NOT NULL DEFAULT '{}',
# eml_link text,
# file_link text NOT NULL,
# ingest boolean NOT NULL DEFAULT false,
# first_seen timestamp NOT NULL DEFAULT now(),
# last_seen timestamp NOT NULL DEFAULT now(),
# pub_date timestamp,
# harvest_date timestamp,
# harvest_etag varchar(41)
# )""")
# db.commit()
db.close()
def get_db_dicts(rsid):
id_uuid = {}
uuid_etag = {}
for t in ["record", "mediarecord"]:
id_uuid[t + "s"] = {}
uuid_etag[t + "s"] = {}
for c in PostgresDB().get_children_list_for_ingest(
rsid, t, cursor_factory=NamedTupleCursor):
u = c.uuid
e = c.etag
uuid_etag[t + "s"][u] = e
for i in c.recordids:
id_uuid[t + "s"][i] = u
return (uuid_etag, id_uuid)
def main():
import argparse
from idb.config import config
parser = argparse.ArgumentParser(
description='Generate a report of newly discovered recordsets.')
parser.add_argument(
'-a',
'--age',
help=
'Number of days ago from today to mark beginning of "recent" period.',
default=31,
type=int)
parser.add_argument('-w',
'--write',
action='store_true',
help='Write to a File instead of STDOUT.')
args = parser.parse_args()
db = PostgresDB()
sql = """
select uuid, name, publisher_uuid, file_link, to_json(first_seen),
to_json(pub_date), to_json(file_harvest_date) from recordsets where ingest=false and
first_seen > now()-'%s days'::interval order by first_seen""" % args.age
results_list = db.fetchall(sql)
if args.write:
fh = open("fresh-recordsets-report.tsv", "w")
output_tsv(results_list, fh)
fh.close()
else:
output_tsv(results_list, sys.stdout)
def update_db_from_rss():
# existing_recordsets is a dict that holds mapping of recordids to DB id
existing_recordsets = {}
# file_links is a dict that holds mapping of file_links to DB id
file_links = {}
# recordsets is a dict that holds entire rows based on DB id (not recordid or uuid)
recordsets = {}
with PostgresDB() as db:
logger.debug("Gathering existing recordsets...")
for row in db.fetchall("SELECT * FROM recordsets"):
recordsets[row["id"]] = row
file_links[row["file_link"]] = row["id"]
for recordid in row["recordids"]:
logger.debug(
"id | recordid | file_link : '{0}' | '{1}' | '{2}'".format(
row["id"], recordid, row["file_link"]))
if recordid in existing_recordsets:
logger.error(
"recordid '{0}' already in existing recordsets. This should never happen."
.format(recordid))
else:
existing_recordsets[recordid] = row["id"]
logger.debug("Gathering existing publishers...")
pub_recs = db.fetchall("SELECT * FROM publishers")
logger.debug("Checking %d publishers", len(pub_recs))
for row in pub_recs:
uuid, rss_url = row['uuid'], row['rss_url']
logger.info("Starting Publisher Feed: %s %s", uuid, rss_url)
rsscontents = get_feed(rss_url)
if rsscontents:
try:
_do_rss(rsscontents, row, db, recordsets,
existing_recordsets, file_links)
logger.debug('_do_rss returned, ready to COMMIT...')
db.commit()
except Exception:
logger.exception(
"An exception occurred processing '{0}' in rss '{1}', will try ROLLBACK..."
.format(uuid, rss_url))
db.rollback()
except:
logger.exception(
"Unknown exception occurred in rss '{0}' in rss '{1}', will try ROLLBACK..."
.format(uuid, rss_url))
db.rollback()
raise
logger.info("Finished processing add publisher RSS feeds")
def harvest_all_eml():
sql = """SELECT *
FROM recordsets
WHERE eml_link IS NOT NULL
AND ingest=true
AND pub_date < now()
AND (eml_harvest_date IS NULL OR eml_harvest_date < pub_date)"""
with PostgresDB() as db:
recs = db.fetchall(sql, cursor_factory=DictCursor)
logger.info("Harvesting %d EML files", len(recs))
for r in recs:
try:
harvest_eml(r, db)
db.commit()
except KeyboardInterrupt:
db.rollback()
raise
except:
db.rollback()
logger.exception("failed Harvest EML %s %s", r["id"],
r["name"])
def harvest_all_file():
sql = """SELECT *
FROM recordsets
WHERE file_link IS NOT NULL
AND uuid IS NOT NULL
AND ingest=true
AND pub_date < now()
AND (file_harvest_date IS NULL OR file_harvest_date < pub_date)"""
with PostgresDB() as db:
recs = db.fetchall(sql)
logger.info("Harvesting %d files", len(recs))
for r in recs:
try:
harvest_file(r, db)
db.commit()
except KeyboardInterrupt:
db.rollback()
raise
except:
logger.exception("Error processing id:%s url:%s", r['id'],
r['file_link'])
db.rollback()
def main():
import argparse
from idb.config import config
parser = argparse.ArgumentParser(
description=
'Delete records and recordset by specifying the recordset uuid')
parse_group = parser.add_mutually_exclusive_group(required=True)
parse_group.add_argument('-u',
'--uuid',
dest='uuid_to_delete',
type=str,
default=None)
parse_group.add_argument('--uuid-file',
dest='uuid_file',
type=str,
default=None)
args = parser.parse_args()
db = PostgresDB()
if args.uuid_file:
# read each line in uuid_file as a uuid
logger.info("Reading uuid_file '{0}'".format(args.uuid_file))
with open(args.uuid_file) as f:
for uuid_string in f:
uuid = uuid_string.strip()
if check_uuid(uuid):
delete_recordset(uuid, db)
else:
# operate on a single uuid
if check_uuid(args.uuid_to_delete):
delete_recordset(args.uuid_to_delete, db)
import os
import requests
from requests.auth import HTTPBasicAuth
import traceback
import json
import datetime
import time
s = requests.Session()
adapter = requests.adapters.HTTPAdapter(pool_connections=100, pool_maxsize=100)
s.mount('http://', adapter)
s.mount('https://', adapter)
auth = HTTPBasicAuth(os.environ.get("IDB_UUID"), os.environ.get("IDB_APIKEY"))
db = PostgresDB()
local_pg = db._pg
local_cur = db._cur
def create_schema():
local_cur.execute("BEGIN")
local_cur.execute("""CREATE TABLE IF NOT EXISTS media (
id BIGSERIAL PRIMARY KEY,
url text UNIQUE,
type varchar(20),
mime varchar(255),
last_status integer,
last_check timestamp
)
""")
def file_list_iter(fn):
with open(fn, 'r') as f:
for l in f:
fields = l.split()
if "current" in fields[11]:
fields[0] = fields[0][:-1] # trim ":" from end of server name
fields[11] = fields[11].replace("\\\\", "\\") # de-escape slashes produced by `find -ls` to get the real file name
fields.append(os.path.basename(fields[11])) # only fn for prefix searching
yield fields
if __name__ == '__main__':
fn = sys.argv[1]
with PostgresDB() as db:
q = """INSERT INTO ceph_server_files
(server, line, unk, perms, unk2, owner_name, group_name,
size, month, day, year_time, fullname, filename)
VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s, %s)
ON CONFLICT DO NOTHING
"""
c = 1
for l in file_list_iter(fn):
db.execute(q, l)
c += 1
if (c % 100000) == 0:
db.commit()
c = 1
# break
buff = buff + '''
DATA INGESTION STATUS REPORT
'''
buff = buff + datetime.date.today().strftime("%B %d, %Y") + "\n\n"
buff = buff + hr + "\n"
api = idigbio.json()
record_count = locale.format("%d", api.count_records(), grouping=True)
media_record_count = locale.format("%d", api.count_media(), grouping=True)
recordset_count = locale.format("%d", api.count_recordsets(), grouping=True)
# Paused count is the count of recordsets where ingest is true,
# and paused is also true. Will not count paused recordsets where
# ingest is false.
db = PostgresDB()
sql = """
SELECT count(*) FROM recordsets WHERE ingest = true AND ingest_is_paused = true;
"""
db_r = db.fetchone(sql)
paused_count = db_r["count"]
# Updated recordsets is an approximation based on the number of items
# appearing in the Ingestion summary log, minus 15% to take into account
# that we usually overlap ingest periods for db-check operations by a few weeks.
# Currently the summary is in an expected, hard-coded path:
# /mnt/data/new_ingestion/summary.pretty.txt
summary_path = "/mnt/data/new_ingestion/summary.pretty.txt"
if os.path.exists(summary_path):
linecount = len(open(summary_path).readlines())
updated_recordsets_blurb = (
def process_file(fname,
mime,
rsid,
existing_etags,
existing_ids,
ingest=False,
commit_force=False,
ispaused=False):
rlogger = getrslogger(rsid)
rlogger.info("Processing %s, type: %s", fname, mime)
counts = {}
t = datetime.datetime.now()
filehash = calcFileHash(fname)
db = PostgresDB()
commited = False
try:
if mime == "application/zip":
dwcaobj = Dwca(fname, skipeml=True, logname="idb")
for dwcrf in dwcaobj.extensions:
rlogger.debug("Processing %r", dwcrf.name)
counts[dwcrf.name] = process_subfile(dwcrf,
rsid,
existing_etags,
existing_ids,
ingest=ingest,
db=db)
dwcrf.close()
rlogger.debug("processing core %r", dwcaobj.core.name)
counts[dwcaobj.core.name] = process_subfile(dwcaobj.core,
rsid,
existing_etags,
existing_ids,
ingest=ingest,
db=db)
dwcaobj.core.close()
dwcaobj.close()
elif mime == "text/plain":
commas = False
with open(fname, "rb") as testf:
commas = "," in testf.readline()
if commas:
csvrf = DelimitedFile(fname, logname="idigbio")
counts[fname] = process_subfile(csvrf,
rsid,
existing_etags,
existing_ids,
ingest=ingest,
db=db)
else:
tsvrf = DelimitedFile(fname,
delimiter="\t",
fieldenc=None,
logname="idigbio")
counts[fname] = process_subfile(tsvrf,
rsid,
existing_etags,
existing_ids,
ingest=ingest,
db=db)
if ingest:
commit_ok = commit_force
type_commits = []
for k in counts:
if k not in ingestion_types:
continue
if (counts[k]["create"] /
float(counts[k]["processed_line_count"]) >= 0.5
and counts[k]["delete"] /
float(counts[k]["processed_line_count"]) >= 0.5):
type_commits.append(True)
else:
type_commits.append(False)
commit_ok = all(type_commits)
if commit_ok:
rlogger.info("Ready to Commit")
db.commit()
commited = True
else:
rlogger.error("Rollback")
db.rollback()
else:
db.rollback()
db.close()
except Exception:
logger.exception(
"Unhandled Exception when processing {0}".format(fname))
db.rollback()
db.close()
# Clear after processing an archive
unconsumed_extensions.clear()
core_siblings.clear()
return {
"name": fname,
"filemd5": filehash,
"recordset_id": rsid,
"counts": counts,
"processing_start_datetime": t.isoformat(),
"total_processing_time": (datetime.datetime.now() - t).total_seconds(),
"commited": commited,
"paused": ispaused
}
def upload_recordset_from_file(rsid, fname):
"""
Given a recordset uuid and a local dataset filename, upload the local
dataset file as the "current" file for that uuid.
Parameters
----------
rsid : uuid
An iDigBio recordset uuid
fname : string
Filename (full path or current directory only)
Returns
-------
bool
True if successful, False otherwise
"""
# convert rsid uuid to string here because of either:
# psycopg2.ProgrammingError: can't adapt type 'UUID'
# or
# TypeError: 'UUID' object does not support indexing
rsuuid = str(rsid)
logger.info("Manual upload of '{0}' from file '{1}' requested.".format(
rsuuid, fname))
# do some checks here
try:
f = open(fname)
f.close()
except:
logger.error(
"Cannot access file: '{0}'. Aborting upload.".format(fname))
raise
db = PostgresDB()
sql = ("""SELECT id FROM recordsets WHERE uuid=%s""", (rsuuid, ))
idcount = db.execute(*sql)
if idcount < 1:
logger.error(
"Cannot find uuid '{0}' in db. Aborting upload.".format(rsuuid))
db.rollback()
return False
# output the "before" state
results = db.fetchall(
"""SELECT id,file_harvest_date,file_harvest_etag FROM recordsets WHERE uuid=%s""",
(rsuuid, ))
for each in results:
logger.debug("{0}".format(each))
try:
etag = upload_recordset(rsuuid, fname, db)
assert etag
sql = ("""UPDATE recordsets
SET file_harvest_etag=%s, file_harvest_date=%s
WHERE uuid=%s""", (etag, datetime.datetime.now(), rsuuid))
update_count = db.execute(*sql)
db.commit()
logger.info("UPDATED {0} rows.".format(update_count))
logger.info(
"Finished manual upload of file '{0}', result etag = '{1}', saved to db."
.format(fname, etag))
except:
logger.error(
"An exception occurred during upload of file or db update for '{0}'"
.format(fname))
raise
# output the "after" state
results = db.fetchall(
"""SELECT id,file_harvest_date,file_harvest_etag FROM recordsets WHERE uuid=%s""",
(rsuuid, ))
for each in results:
logger.debug("{0}".format(each))
return True
def get_idb():
return PostgresDB(pool=current_app.config['DB'])
def main2():
for r in PostgresDB().get_type_list("recordset", limit=None):
try:
print r["uuid"]
except:
traceback.print_exc()
import uuid
import hashlib
import string
import random
from idb.postgres_backend.db import PostgresDB
from idb.helpers.encryption import _encrypt
from idb import config
db = PostgresDB()
def getCode(length=100, char=None):
if char is None:
char = string.ascii_letters + string.digits
return ''.join(random.choice(char) for x in range(length))
user_uuid = str(uuid.uuid4())
m = hashlib.md5()
m.update(getCode())
api_key = m.hexdigest()
api_key_e = _encrypt(api_key, config.IDB_CRYPT_KEY)
feeder_parent_id = "520dcbb3-f35a-424c-8778-6df11afc9f95"
rs_rid = "http://feeder.idigbio.org/datasets/{0}".format(user_uuid)
db.execute("INSERT INTO idb_api_keys (user_uuid,apikey) VALUES (%s,%s)",