def backfill_flagged_worker(rows):
"""Parallel worker for backfill_flagged_etags()
Expects a list of records to work on and commit as a group
"""
storage = IDigBioStorage()
with apidbpool.connection(autocommit=False) as conn:
cur = conn.cursor()
for row in rows:
try:
table = make_temp_table_name(row['prefix'])
b = storage.get_bucket(
row['ceph_bucket']
) # Two phase here because validate=False in storage class so etag is not populated
row["etag"] = b.get_key(row["ceph_name"]).etag[1:-1]
cur.execute(
"""UPDATE {0}
SET ceph_etag=%(etag)s
WHERE ceph_bucket=%(ceph_bucket)s AND ceph_name=%(ceph_name)s
""".format(table), row)
except:
logger.error(
"Failed to update etag for {0}:{1} in {2} {3}".format(
row["ceph_bucket"], row["ceph_name"], row["prefix"],
traceback.format_exc()))
conn.commit()
return 0
def get_objects_from_ceph():
local_cur.execute("SELECT etag FROM objects")
existing_objects = set()
for r in local_cur:
existing_objects.add(r[0])
print len(existing_objects)
s = IDigBioStorage()
buckets = ["datasets","images"]
count = 0
rowcount = 0
lrc = 0
for b_k in buckets:
b = s.get_bucket("idigbio-" + b_k + "-prod")
for k in b.list():
if k.name not in existing_objects:
try:
ks = k.get_contents_as_string(headers={'Range' : 'bytes=0-100'})
detected_mime = magic.from_buffer(ks, mime=True)
local_cur.execute("INSERT INTO objects (bucket,etag,detected_mime) SELECT %(bucket)s,%(etag)s,%(dm)s WHERE NOT EXISTS (SELECT 1 FROM objects WHERE etag=%(etag)s)", {"bucket": b_k, "etag": k.name, "dm": detected_mime})
existing_objects.add(k.name)
rowcount += local_cur.rowcount
except:
print "Ceph Error", b_k, k.name
count += 1
if rowcount != lrc and rowcount % 10000 == 0:
print count, rowcount
local_pg.commit()
lrc = rowcount
print count, rowcount
local_pg.commit()
def bucket_list_worker(work):
logger.debug("Listing and inserting prefix {0} from bucket {1}".format(
work["prefix"], work["bucket"]))
storage = IDigBioStorage()
# Read through bucket inserting into temp table
with apidbpool.connection(
autocommit=False
) as conn: # use a single connection from the pool to commit groups of statements
cur = conn.cursor()
# inserted = 1
#logger.info("Importing bucket listing for {0}.".format(bucket))
b = storage.get_bucket(work["bucket"])
for f in b.list(prefix=work["prefix"]):
# see backfill_new_etags() for why no etag here
cur.execute(("INSERT INTO {0} "
"(ceph_bucket, ceph_name, ceph_date, ceph_bytes) "
"VALUES (%s, %s, %s, %s)").format(
make_temp_table_name(work["prefix"])),
(work["bucket"], f.name, f.last_modified, f.size))
# inserted += 1
# if (inserted % 10000) == 0:
# logger.info("Committing {0}".format(inserted))
# conn.commit()
conn.commit()
return 1
def get_objects_from_ceph():
local_cur.execute("SELECT etag FROM objects")
existing_objects = set()
for r in local_cur:
existing_objects.add(r[0])
print len(existing_objects)
s = IDigBioStorage()
buckets = ["datasets","images"]
count = 0
rowcount = 0
lrc = 0
for b_k in buckets:
b = s.get_bucket("idigbio-" + b_k + "-prod")
for k in b.list():
if k.name not in existing_objects:
try:
ks = k.get_contents_as_string(headers={'Range' : 'bytes=0-100'})
detected_mime = magic.from_buffer(ks, mime=True)
local_cur.execute("INSERT INTO objects (bucket,etag,detected_mime) SELECT %(bucket)s,%(etag)s,%(dm)s WHERE NOT EXISTS (SELECT 1 FROM objects WHERE etag=%(etag)s)", {"bucket": b_k, "etag": k.name, "dm": detected_mime})
existing_objects.add(k.name)
rowcount += local_cur.rowcount
except:
print "Ceph Error", b_k, k.name
count += 1
if rowcount != lrc and rowcount % 10000 == 0:
print count, rowcount
local_pg.commit()
lrc = rowcount
print count, rowcount
local_pg.commit()
def upload_download_file_to_ceph(filename):
s = IDigBioStorage()
keyname, bucket = os.path.basename(filename), "idigbio-downloads"
fkey = s.upload(s.get_key(keyname, bucket),
filename,
content_type='application/zip',
public=True)
return "http://s.idigbio.org/idigbio-downloads/" + fkey.name
def upload_all(gr):
if not gr:
return
try:
for item in gr.items:
IDigBioStorage.retry_loop(lambda: upload_item(item))
return gr
except (BotoServerError, BotoClientError):
logger.exception("%s failed uploading derivatives", gr.etag)
except Exception:
logger.exception("%s Unexpected error", gr.etag)
def get_key_object(bucket, name):
"""Get a key object from Ceph for the requested object.
Note that most of the metadata with the key won't be populated
until after it has been fetched.
"""
global STORAGE_HOST
storage = IDigBioStorage(host=STORAGE_HOST)
logger.debug("Retreiving key for {0}:{1}".format(bucket, name))
key = storage.get_key(name, bucket)
return key
def set_deriv_from_ceph():
s = IDigBioStorage()
b = s.get_bucket("idigbio-images-prod-thumbnail")
count = 0
for k in b.list():
local_cur.execute("UPDATE objects SET derivatives=true WHERE etag=%s", (k.name.split(".")[0],))
count += 1
if count % 10000 == 0:
print count
local_pg.commit()
print count
local_pg.commit()
def set_deriv_from_ceph():
s = IDigBioStorage()
b = s.get_bucket("idigbio-images-prod-thumbnail")
count = 0
for k in b.list():
local_cur.execute("UPDATE objects SET derivatives=true WHERE etag=%s", (k.name.split(".")[0],))
count += 1
if count % 10000 == 0:
print count
local_pg.commit()
print count
local_pg.commit()
def get_objects_from_ceph():
import magic
existing_objects = set(r[0] for r in apidbpool.fetchiter(
"SELECT etag FROM objects", cursor_factory=cursor))
logger.info("Found %d objects", len(existing_objects))
s = IDigBioStorage()
buckets = ["datasets", "images"]
count = 0
rowcount = 0
lrc = 0
with apidbpool.connection() as conn:
with apidbpool.cursor() as cur:
for b_k in buckets:
b = s.get_bucket("idigbio-" + b_k + "-prod")
for k in b.list():
if k.name not in existing_objects:
try:
ks = k.get_contents_as_string(
headers={'Range': 'bytes=0-100'})
detected_mime = magic.from_buffer(ks, mime=True)
cur.execute(
"""INSERT INTO objects (bucket,etag,detected_mime)
SELECT %(bucket)s,%(etag)s,%(dm)s
WHERE NOT EXISTS(
SELECT 1 FROM objects WHERE etag=%(etag)s)""",
{
"bucket": b_k,
"etag": k.name,
"dm": detected_mime
})
existing_objects.add(k.name)
rowcount += cur.rowcount
except:
logger.exception(
"Ceph Error; bucket:%s keyname:%s", b_k,
k.name)
count += 1
if rowcount != lrc and rowcount % 10000 == 0:
logger.info("Count: %8d, rowcount: %8d", count,
rowcount)
conn.commit()
lrc = rowcount
conn.commit()
logger.info("Count: %8d, rowcount: %8d (Finished %s)", count,
rowcount, b_k)
def fetch_media(key):
try:
return IDigBioStorage.get_contents_to_mem(key, md5=key.name)
except BotoServerError as e:
logger.error("%r failed downloading with %r %s %s", key, e.status,
e.reason, key.name)
raise
except S3DataError as e:
logger.error("%r failed downloading on md5 mismatch", key)
raise
except BotoClientError as e:
logger.exception("%r failed downloading because...")
raise
def get_file(rsid):
fname = rsid
if not os.path.exists(fname):
try:
RecordSet.fetch_file(rsid,
fname,
media_store=IDigBioStorage(),
logger=logger.getChild(rsid))
except (S3ResponseError, S3DataError):
getrslogger(rsid).exception("failed fetching archive")
raise
mime = magic.from_file(fname, mime=True)
return (fname, mime)
def upload_recordset(rsid, fname, idbmodel):
filereference = "http://api.idigbio.org/v1/recordsets/" + rsid
logger.debug("Starting Upload of %r", rsid)
stor = IDigBioStorage()
with open(fname, 'rb') as fobj:
mo = MediaObject.fromobj(fobj,
url=filereference,
type='datasets',
owner=config.IDB_UUID)
k = mo.get_key(stor)
if k.exists():
logger.debug("ETAG %s already present in Storage.", mo.etag)
else:
mo.upload(stor, fobj)
logger.debug("ETAG %s uploading from %r", mo.etag, fname)
mo.ensure_media(idbmodel)
mo.ensure_object(idbmodel)
mo.ensure_media_object(idbmodel)
logger.debug("Finished Upload of %r, etag = %s", rsid, mo.etag)
return mo.etag
def process_list(fetchitems, forprefix=''):
"""Process a list of FetchItems.
This is intended to be the toplevel entry point of a subprocess
working on a list of one domain's urls
"""
try:
store = IDigBioStorage()
fetchrpool = gevent.pool.Pool(get_fetcher_count(forprefix))
uploadpool = gevent.pool.Pool(8)
items = fetchrpool.imap_unordered(lambda fi: fi.get_media(),
fetchitems,
maxsize=10)
items = uploadpool.imap_unordered(
lambda fi: fi.upload_to_storage(store), items, maxsize=10)
items = itertools.imap(FetchItem.cleanup, items)
items = update_db_status(items)
items = count_result_types(items, forprefix=forprefix)
return ilen(items) # consume the generator
except StandardError:
logger.exception("Unhandled error forprefix:%s", forprefix)
raise
def verify_object(row_obj, key_obj):
"""Download an object and check it against the expected metadata.
Return is a string status of result of checking the file:
verified - Object downloads and all available data matches
stashed - Object is verified and a copy has been kept in stash directory
timeout - Download times out, probably due to file being truncated
nosuchkey - Object does not exist, 404 error when downloading
invalid - Some of the metadata does not match
failed - No longer used, when this function was boolean this was False
"""
storage = IDigBioStorage(host=STORAGE_HOST)
try:
if not os.path.exists(TMP_DIR):
os.makedirs(TMP_DIR)
fn = os.path.join(TMP_DIR, key_obj.name)
logger.debug("Fetching file {0}:{1}".format(key_obj.bucket.name,
key_obj.name))
storage.get_contents_to_filename(key_obj, fn)
md5 = calc_md5(fn)
size = os.stat(fn).st_size
except (S3ResponseError) as ex:
if "NoSuchKey" in str(ex):
logger.error("No such key when getting {0}:{1}".format(
key_obj.bucket.name, key_obj.name))
return "nosuchkey"
else:
logger.error(
"Exception while attempting to get file {0}:{1} {2}".format(
key_obj.bucket.name, key_obj.name, traceback.format_exc()))
# raise
return "S3ResponseError"
except (HTTPException, socket_error) as ex:
# Timeout can be controlled by /etc/boto.cfg - see http://boto.cloudhackers.com/en/latest/boto_config_tut.html
logger.error(
"Socket timeout when getting {0}:{1}, file is probably corrupt in ceph"
.format(key_obj.bucket.name, key_obj.name))
if os.path.exists(fn):
os.unlink(fn)
return "timeout"
except Exception as ex:
if "503 Service Unavailable" in str(ex):
logger.error("Service unavailable getting {0}:{1}".format(
key_obj.bucket.name, key_obj.name))
return "503Error"
else:
logger.error(
"Exception while attempting to get file {0}:{1} {2}".format(
key_obj.bucket.name, key_obj.name, traceback.format_exc()))
raise
# The db may have partial information so we need to support it being
# empty, but if it exists, it should match. Use logging to say what's
# wrong with file, maintain a return value if anything fails.
retval = False
if not retval and (not size == key_obj.size):
logger.error(
"File size {0} does not match ceph size {1} for {2}:{3}".format(
size, key_obj.size, key_obj.bucket.name, key_obj.name))
retval = "invalid"
if not retval and (row_obj["ceph_bytes"] and
(not size == row_obj["ceph_bytes"])):
logger.error(
"File size {0} does not match db size {1} for {2}:{3}".format(
size, row_obj["ceph_bytes"], key_obj.bucket.name,
key_obj.name))
retval = "invalid"
if not retval and (not md5 == key_obj.etag[1:-1]): # etag is wraped in ""
logger.error(
"File md5 {0} does not match ceph etag {1} for {2}:{3}".format(
md5, key_obj.etag[1:-1], key_obj.bucket.name, key_obj.name))
retval = "invalid"
# db etag has extra '-' chars
if not retval and (row_obj["ceph_etag"] and
(not md5 == row_obj["ceph_etag"].replace('-', ''))):
logger.error(
"File md5 {0} does not match db etag {1} for {2}:{3}".format(
md5, row_obj["ceph_etag"], key_obj.bucket.name, key_obj.name))
retval = "invalid"
if not retval:
logger.debug("Object {0}:{1} verified".format(key_obj.bucket.name,
key_obj.name))
#global args
if STASH and stash_file(fn, key_obj):
retval = "stashed"
if DELETE and not TEST:
logger.debug("Deleting {0}:{1} from ceph.".format(
key_obj.bucket.name, key_obj.name))
try:
key_obj.delete()
DELETED.append(key_obj.name)
except:
logger.error(
"Unable to delete object {0}:{1} in ceph.".format(
key_obj.bucket.name, key_obj.name))
else:
retval = "verified"
else:
logger.warn("Object {0}:{1} failed verification".format(
key_obj.bucket.name, key_obj.name))
try:
os.unlink(fn)
except:
pass
return retval
from idb.helpers.storage import IDigBioStorage
from idb.helpers import gipcpool
from idigbio_ingestion.lib.dwca import Dwca
from idigbio_ingestion.lib.delimited import DelimitedFile
bad_chars = u"\ufeff"
bad_char_re = re.compile("[%s]" % re.escape(bad_chars))
logger = idblogger.getChild("db-check")
uuid_re = re.compile(
"([a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12})"
)
s = IDigBioStorage()
class RecordException(Exception):
pass
def getrslogger(rsid):
return logger.getChild(rsid)
def mungeid(s):
return bad_char_re.sub('', s).strip()
identifier_fields = {
from __future__ import division, absolute_import, print_function
from idb.helpers.logging import getLogger, configure_app_log
from idb.helpers.storage import IDigBioStorage
from idb.helpers.media_validation import sniff_mime
from idb.helpers.memoize import filecached
import hashlib
logger = getLogger("restore")
store = IDigBioStorage()
def get_object_from_backup(etag):
"need to return a buffer that is the contents of the object that should be in `idigbio-images-prod/$etag`"
obj = open('reestores/' + etag, 'rb').read()
md5 = hashlib.md5()
md5.update(obj)
assert etag == md5.hexdigest()
return obj
@filecached("/tmp/restore-from-backup.picklecache")
def get_fouled():
"""Return the original list, cached in a file that is written back as
we make progress. This way as we make progrss and kill/rerun- the
file it only tries new ones
"""
return {(u'images', u'06fbc3c99d7d9f06e1487adbbe171f82', u'image/jpeg'),
(u'images', u'0f4ceba6d970ad48e43e740a794b288a', u'image/jpeg'),
(u'images', u'1155e9e1d4af33ebf3ab841523bb9a4c', None),
def main():
index_file_name = "index.txt"
query = {
"size": 0,
"aggs": {
"rs": {
"terms": {
"field": "recordset",
"size": 1000
},
"aggs": {
"ic":{
"terms": {
"field": "institutioncode",
"size": 1000,
},
"aggs": {
"cc": {
"terms":{
"field": "collectioncode",
"size": 1000,
}
}
}
}
}
}
}
}
r = requests.post("http://search.idigbio.org/idigbio/records/_search",
data=json.dumps(query),
headers={"Content-Type": "application/json"})
r.raise_for_status()
ro = r.json()
recordsets = {}
for rs_b in ro["aggregations"]["rs"]["buckets"]:
rsid = rs_b["key"]
ic = ""
cc = ""
if len(rs_b["ic"]["buckets"]) == 0:
ic = ""
cc = ""
elif len(rs_b["ic"]["buckets"]) == 1 or (
float(rs_b["ic"]["buckets"][0]["doc_count"]) / float(rs_b["doc_count"]) > 0.9
):
ic_b = rs_b["ic"]["buckets"][0]
ic = get_true_ic(ic_b["key"])
if len(ic_b["cc"]["buckets"]) == 0:
cc = ""
elif len(ic_b["cc"]["buckets"]) == 1:
cc = ic_b["cc"]["buckets"][0]["key"]
else:
cc = "MULTIPLE"
else:
# print(rs_b)
ic = "MULTIPLE"
cc = "MULTIPLE"
recordsets[rsid] = {
"institutioncode": ic,
"collectioncode": cc
}
s = IDigBioStorage()
b = s.get_bucket("idigbio-static-downloads")
headers = ["zipfile","emlfile","etag","modified","recordset_id", "institutioncode", "collectioncode"]
files = {}
for k in b.list():
# Skip the index itself
if k == index_file_name:
continue
# Skip files older than 8 days
lm_d = dateutil.parser.parse(k.last_modified).date()
if lm_d < (datetime.datetime.now() - datetime.timedelta(7)).date():
continue
fkey = k.name.split(".")[0]
if fkey not in files:
files[fkey] = {k:"" for k in headers}
if k.name.endswith(".eml"):
files[fkey]["emlfile"] = k.name
elif k.name.endswith(".zip"):
files[fkey]["zipfile"] = k.name
files[fkey]["modified"] = k.last_modified
files[fkey]["etag"] = k.etag
if is_uuid(fkey):
files[fkey]["recordset_id"] = fkey
if fkey in recordsets:
files[fkey]["institutioncode"] = recordsets[fkey]["institutioncode"]
files[fkey]["collectioncode"] = recordsets[fkey]["collectioncode"]
else:
files[fkey]["institutioncode"] = ""
files[fkey]["collectioncode"] = ""
fil = StringIO()
cw = csv.writer(fil,delimiter="\t")
cw.writerow(headers)
for k in files:
if files[k]["zipfile"] != "":
cw.writerow([files[k][h].replace("\"","") for h in headers])
fil.seek(0)
ik = b.get_key(index_file_name,validate=False)
ik.content_type = 'text/tsv'
ik.set_contents_from_file(fil)
ik.make_public()
def thumb_key(img_etag):
from idb.helpers.storage import IDigBioStorage
return IDigBioStorage().get_key(img_etag + '.jpg',
'idigbio-images-prod-thumbnail')
def img_key(img_etag):
from idb.helpers.storage import IDigBioStorage
return IDigBioStorage().get_key(img_etag, 'idigbio-images-prod')
def sounds_key(sounds_etag):
from idb.helpers.storage import IDigBioStorage
return IDigBioStorage().get_key(sounds_etag, 'idigbio-sounds-prod')
def upload():
vals = {}
j = request.get_json()
if j is not None:
vals.update(j)
for k, v in request.values.iteritems():
vals[k] = v
filereference = vals.get("filereference")
if not filereference:
logger.warning("No filereference specified")
return json_error(400, "Missing filereference")
obj = request.files.get('file')
etag = vals.get('etag')
media_type = vals.get("media_type")
mime = vals.get("mime")
try:
mime, media_type = validate_mime_for_type(mime, media_type)
except MediaValidationError as mve:
logger.warning("Bad mime/media_type combo: %r/%r", mime, media_type)
return json_error(400, str(mve))
r = MediaObject.fromurl(filereference, idbmodel=idbmodel)
if r:
logger.warning("Found existing object for %r", r.url)
if r.owner != request.authorization.username:
return json_error(403)
if obj:
# if either type or mime are null it will be ignored, if
# present they change the behavior of fromobj
try:
mo = MediaObject.fromobj(obj, type=media_type, mime=mime, url=filereference, etag=etag)
except MediaValidationError as mve:
logger.warning("Validation failure, %r", mve)
return json_error(400, str(mve))
mo.upload(IDigBioStorage(), obj)
mo.insert_object(idbmodel)
elif etag:
mo = MediaObject.frometag(etag, idbmodel)
if not mo or not mo.get_key(IDigBioStorage()).exists():
return json_error(404, "Unknown etag {0!r}".format(etag))
mo.last_status = 200
mo.last_check = datetime.now()
mo.mime = mime or mo.detected_mime
mo.type = media_type or mo.bucket
else:
mo = r or MediaObject()
mo.last_status = None
mo.last_check = None
try:
mo.mime, mo.type = validate_mime_for_type(mo.mime or mime, mo.type or media_type)
if not (mo.mime and mo.type):
logger.warning("Missing either mime(%r) or type(%r)", mo.mime, mo.type)
return json_error(400, "Incomplete request")
except MediaValidationError as mve:
logger.warning("Validation Failure, %r", mve)
return json_error(400, str(mve))
mo.url = filereference
mo.owner = request.authorization.username
if r:
mo.update_media(idbmodel)
else:
mo.insert_media(idbmodel)
if mo.etag:
mo.ensure_media_object(idbmodel)
idbmodel.commit()
return respond_to_record(mo, format='json')
c['erred'] += 1
elif len(result.items) > 0:
c['generated'] += 1
else:
c['existed'] += 1
if count % update_freq == 0:
output()
yield result
except KeyboardInterrupt:
output()
raise
output()
get_store = memoized()(lambda: IDigBioStorage())
def get_keys(obj):
etag, bucket = obj.etag, obj.bucket
etag = unicode(etag)
s = get_store()
bucketbase = u"idigbio-{0}-{1}".format(bucket, config.ENV)
mediakey = s.get_key(etag, bucketbase)
keys = [
s.get_key(etag + ".jpg", bucketbase + '-' + dtype) for dtype in DTYPES
]
return CheckItem(etag, bucket, mediakey, keys)
def generate_all(item):
def main():
s = IDigBioStorage()
# static_queries = [
# ({},"idigbio"),
# ({"hasImage": True},"idigbio-images"),
# ({"geopoint":{"type":"exists"},"taxonid":{"type":"exists"}},"idigbio-geotaxon")
# ]
# rsquery = {
# "query": {
# "match_all": {}
# },
# "size": 0,
# "aggs": {
# "recordset_counts": {
# "terms": {
# "field": "recordset",
# "size": 10000
# }
# }
# }
# }
# ro = runQuery(rsquery)
# if ro is not None:
# print(len(ro["aggregations"]["recordset_counts"]["buckets"]))
# for b in ro["aggregations"]["recordset_counts"]["buckets"]:
# #print(b["key"], b["doc_count"], b["doc_count"] * 7 / 10000)
# static_queries.append(({
# "recordset": b["key"]
# },b["key"]))
# print(len(static_queries))
# count = 0
# for q in reversed(static_queries):
# print(count, q)
# file_name = generate_files(record_query=queryFromShim(q[0])["query"],form="dwca-csv",filename=q[1])
# print(q[1], file_name)
# u = upload_download_file_to_ceph(s,file_name)
# # # rseml = eml_from_recordset(q[1],env="prod")
# # # e = upload_eml_file_to_ceph(s,q[1],rseml)
# print(q[1], u)
# count += 1
file_name = generate_files(record_query=queryFromShim({
"geopoint": {
"type": "exists"
},
"taxonomicstatus": "accepted",
"taxonid": {
"type": "exists"
},
"flags": "gbif_taxon_corrected",
"kingdom": "plantae",
"geopoint": {
"type": "geo_bounding_box",
"top_left": {
"lat": 89,
"lon": -179
},
"bottom_right": {
"lat": -89,
"lon": -33
}
}
})["query"],
form="dwca-csv",
filename="idigbio-plantae-w")
u = upload_download_file_to_ceph(s, file_name)
def store(request):
from idb.helpers.storage import IDigBioStorage
store = IDigBioStorage()
return store
