def extract_logs_mongo2gs(course_id, start="2012-09-01", end="2014-09-24", verbose=False,
dbname=DBNAME,
collection = 'tracking_log',
tracking_logs_directory="TRACKING_LOGS",
):
print "extracting logs for course %s" % course_id
# list of dates to dump
dates = daterange(d2dt(start), d2dt(end))
if verbose:
print "Dates to dump:", [x['dstr'] for x in dates]
# what files already on gs?
gspath = "%s/DAILY" % gs_path_from_course_id(course_id)
gsfiles = get_gs_file_list(gspath)
DIR = tracking_logs_directory
if not os.path.exists(DIR):
os.mkdir(DIR)
DIR += '/' + path_from_course_id(course_id)
if not os.path.exists(DIR):
os.mkdir(DIR)
filebuf = []
for k in range(len(dates)-1):
d = dates[k]
ofn = '%s/tracklog-%s.json.gz' % (DIR, d['dstr'])
start = d['start']
end = d['end']
ofnb = os.path.basename(ofn)
if ofnb in gsfiles:
print "Already have %s, skipping" % ofnb
sys.stdout.flush()
continue
# dump tracking log of certain date using mongoexport, if needed
if not os.path.exists(ofn):
# db.tracking_log.find({'course_id': "HarvardX/ER22x/2013_Spring",
# 'time': { '$gte': "2013-08-01T00:00:00.000000", '$lt': "2013-08-02T00:00:00.000000" }}).count()
query = '{"course_id": "%s", "time": {"$gte": "%s", "$lt": "%s" }}' % (course_id, start, end)
cmd = "mongoexport -d %s -c %s -q '%s'| edx2bigquery rephrase_logs | gzip -9 > %s" % (dbname, collection, query, ofn)
# print cmd
os.system(cmd)
upload_file_to_gs(ofn, gspath + '/' + ofnb)
filebuf.append(ofn)
if len(filebuf)>20:
ffn = filebuf.pop(0)
os.unlink(ffn)
print "...Deleted %s" % ffn
sys.stdout.flush()
def process_dir(course_id,
gspath='gs://x-data',
logs_directory="TRACKING_LOGS",
verbose=True):
cdir = path(logs_directory) / gsutil.path_from_course_id(course_id)
print "=" * 77
print "Transferring tracking logs for %s from directory %s (start %s)" % (
course_id, cdir, datetime.datetime.now())
print "=" * 77
if not os.path.exists(cdir):
print "Oops! non-existent course tracking logs directory %s" % cdir
return
sys.stdout.flush()
cdir = path(cdir)
gp = path(gspath + "/" + cdir.basename()) / 'DAILY'
filelist = gsutil.get_gs_file_list(gp)
# print filelist
local_files = glob.glob(cdir / 'tracklog*.gz')
local_files.sort()
for fn in local_files:
fnp = path(fn)
fnb = fnp.basename()
statbuf = os.stat(fn)
mt = datetime.datetime.fromtimestamp(statbuf.st_mtime)
# do some date checking to upload log files which have changed, and are newer than that on google cloud storage
local = pytz.timezone("America/New_York")
# naive = datetime.datetime.strptime ("2001-2-3 10:11:12", "%Y-%m-%d %H:%M:%S")
local_dt = local.localize(mt, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
if fnb in filelist and filelist[fnb]['date'] > utc_dt:
if verbose:
print "%s already exists, skipping" % fn
continue
elif fnb in filelist:
print "%s already exists, but has date=%s and mtime=%s, re-uploading" % (
fn, filelist[fnb]['date'], mt)
cmd = 'gsutil cp %s %s' % (fn, gp + '/')
print cmd
sys.stdout.flush()
os.system(cmd)
print "done with %s (%s)" % (cdir, datetime.datetime.now())
print "-" * 77
def process_dir(course_id, gspath='gs://x-data', logs_directory="TRACKING_LOGS", verbose=True):
cdir = path(logs_directory) / gsutil.path_from_course_id(course_id)
print "="*77
print "Transferring tracking logs for %s from directory %s (start %s)" % (course_id, cdir, datetime.datetime.now())
print "="*77
if not os.path.exists(cdir):
print "Oops! non-existent course tracking logs directory %s" % cdir
return
sys.stdout.flush()
cdir = path(cdir)
gp = path(gspath + "/" + cdir.basename()) / 'DAILY'
filelist = gsutil.get_gs_file_list(gp)
# print filelist
local_files = glob.glob(cdir / 'tracklog*.gz')
local_files.sort()
for fn in local_files:
fnp = path(fn)
fnb = fnp.basename()
statbuf = os.stat(fn)
mt = datetime.datetime.fromtimestamp(statbuf.st_mtime)
# do some date checking to upload log files which have changed, and are newer than that on google cloud storage
local = pytz.timezone ("America/New_York")
# naive = datetime.datetime.strptime ("2001-2-3 10:11:12", "%Y-%m-%d %H:%M:%S")
local_dt = local.localize(mt, is_dst=None)
utc_dt = local_dt.astimezone (pytz.utc)
if fnb in filelist and filelist[fnb]['date'] > utc_dt:
if verbose:
print "%s already exists, skipping" % fn
continue
elif fnb in filelist:
print "%s already exists, but has date=%s and mtime=%s, re-uploading" % (fn, filelist[fnb]['date'], mt)
cmd = 'gsutil cp %s %s' % (fn, gp + '/')
print cmd
sys.stdout.flush()
os.system(cmd)
print "done with %s (%s)" % (cdir, datetime.datetime.now())
print "-"*77
def do_combine(
course_id_set,
project_id,
outdir="DATA",
nskip=0,
output_project_id=None,
output_dataset_id=None,
output_bucket=None,
use_dataset_latest=False,
):
print "=" * 77
print "Concatenating person course datasets from the following courses:"
print course_id_set
print "-" * 77
outdir = path(outdir)
if not outdir.exists():
os.mkdir(outdir)
ofnset = []
cnt = 0
for course_id in course_id_set:
gb = gsutil.gs_path_from_course_id(
course_id, use_dataset_latest=use_dataset_latest)
ofn = outdir / ('person_course_%s.csv.gz' %
(course_id.replace('/', '__')))
ofnset.append(ofn)
if (nskip > 0) and ofn.exists():
print "%s already exists, not downloading" % ofn
sys.stdout.flush()
continue
if ofn.exists():
fnset = gsutil.get_gs_file_list(gb)
local_dt = gsutil.get_local_file_mtime_in_utc(ofn)
fnb = 'person_course.csv.gz'
if not fnb in fnset:
print "%s/%s missing! skipping %s" % (gb, fnb, course_id)
continue
if (fnb in fnset) and (local_dt >= fnset[fnb]['date']):
print "%s already exists with date %s (gs file date %s), not re-downloading" % (
ofn, local_dt, fnset[fnb]['date'])
sys.stdout.flush()
continue
else:
print "%s already exists but has date %s (gs file date %s), so re-downloading" % (
ofn, local_dt, fnset[fnb]['date'])
sys.stdout.flush()
cmd = 'gsutil cp %s/person_course.csv.gz %s' % (gb, ofn)
print "Retrieving %s via %s" % (course_id, cmd)
sys.stdout.flush()
os.system(cmd)
cnt += 1
#if cnt>2:
# break
org = course_id_set[0].split('/', 1)[0]
ofn = "person_course_%s_%s.csv" % (
org, datetime.datetime.now().strftime('%Y-%m-%d-%H%M%S'))
print "=" * 77
print "Combining CSV files to produce %s" % ofn
sys.stdout.flush()
if (nskip > 1) and os.path.exists(ofn):
print "%s already exists, not downloading" % ofn
else:
first = 1
for zfn in ofnset:
if first:
cmd = "zcat %s > %s" % (zfn, ofn)
else:
cmd = "zcat %s | tail -n +2 >> %s" % (
zfn, ofn
) # first row is header; don't keep when concatenating
print cmd
first = 0
os.system(cmd)
gb = gsutil.gs_path_from_course_id('course_report_%s' % org,
gsbucket=output_bucket)
print "=" * 77
print "Uploading combined CSV file to google cloud storage in bucket: %s" % gb
sys.stdout.flush()
cmd = "TMPDIR=/var/tmp gsutil cp -z csv %s %s/" % (ofn, gb)
print cmd
os.system(cmd)
gsfn = gb + '/' + ofn
print "Combined person_course dataset CSV download link: %s" % gsutil.gs_download_link(
gsfn)
# import into BigQuery
crname = ('course_report_%s' % org)
if use_dataset_latest:
crname = 'course_report_latest'
dataset = output_dataset_id or crname
table = ofn[:-4].replace('-', '_')
print "Importing into BigQuery as %s:%s.%s" % (project_id, dataset, table)
sys.stdout.flush()
mypath = os.path.dirname(os.path.realpath(__file__))
SCHEMA_FILE = '%s/schemas/schema_person_course.json' % mypath
the_schema = json.loads(open(SCHEMA_FILE).read())['person_course']
bqutil.load_data_to_table(dataset,
table,
gsfn,
the_schema,
format='csv',
skiprows=1,
project_id=output_project_id)
msg = ''
msg += "Combined person-course dataset, with data from:\n"
msg += str(course_id_set)
msg += "\n\n"
msg += "=" * 100 + "\n"
msg += "CSV download link: %s" % gsutil.gs_download_link(gsfn)
bqutil.add_description_to_table(dataset,
table,
msg,
append=True,
project_id=output_project_id)
print "Done"
sys.stdout.flush()
def extract_logs_mongo2gs(
course_id,
start="2012-09-01",
end="2014-09-24",
verbose=False,
dbname=DBNAME,
collection='tracking_log',
tracking_logs_directory="TRACKING_LOGS",
):
print "extracting logs for course %s" % course_id
# list of dates to dump
dates = daterange(d2dt(start), d2dt(end))
if verbose:
print "Dates to dump:", [x['dstr'] for x in dates]
# what files already on gs?
gspath = "%s/DAILY" % gs_path_from_course_id(course_id)
gsfiles = get_gs_file_list(gspath)
DIR = tracking_logs_directory
if not os.path.exists(DIR):
os.mkdir(DIR)
DIR += '/' + path_from_course_id(course_id)
if not os.path.exists(DIR):
os.mkdir(DIR)
filebuf = []
for k in range(len(dates) - 1):
d = dates[k]
ofn = '%s/tracklog-%s.json.gz' % (DIR, d['dstr'])
start = d['start']
end = d['end']
ofnb = os.path.basename(ofn)
if ofnb in gsfiles:
print "Already have %s, skipping" % ofnb
sys.stdout.flush()
continue
# dump tracking log of certain date using mongoexport, if needed
if not os.path.exists(ofn):
# db.tracking_log.find({'course_id': "HarvardX/ER22x/2013_Spring",
# 'time': { '$gte': "2013-08-01T00:00:00.000000", '$lt': "2013-08-02T00:00:00.000000" }}).count()
query = '{"course_id": "%s", "time": {"$gte": "%s", "$lt": "%s" }}' % (
course_id, start, end)
cmd = "mongoexport -d %s -c %s -q '%s'| edx2bigquery rephrase_logs | gzip -9 > %s" % (
dbname, collection, query, ofn)
# print cmd
os.system(cmd)
upload_file_to_gs(ofn, gspath + '/' + ofnb)
filebuf.append(ofn)
if len(filebuf) > 20:
ffn = filebuf.pop(0)
os.unlink(ffn)
print "...Deleted %s" % ffn
sys.stdout.flush()
def do_combine(
course_id_set,
project_id,
outdir="DATA",
nskip=0,
output_project_id=None,
output_dataset_id=None,
output_bucket=None,
use_dataset_latest=False,
extract_subset_tables=True,
):
'''
Combine individual person_course tables (from the set of specified course_id's) to create one single large
person_course table. Do this by downloading each file, checking to make sure they all have the same
fields, concatenating, and uploading back to bigquery. This is cheaper than doing a select *, and also
uncovers person_course files which have the wrong schema (and it works around BQ's limitation on large
result sizes). The result is stored in the course_report_latest dataset (if use_dataset_latest), else
in course_report_ORG, where ORG is the configured organization name.
If extract_subset_tables is True, then the subset of those who viewed (ie "participants"), and the subset
of those who enrolled for IDV, are extracted and saved as person_course_viewed, and person_course_idv.
(those are created using a select *, for efficiency, despite the cost).
'''
print "=" * 77
print "Concatenating person course datasets from the following courses:"
print course_id_set
print "-" * 77
outdir = path(outdir)
if not outdir.exists():
os.mkdir(outdir)
ofnset = []
cnt = 0
for course_id in course_id_set:
gb = gsutil.gs_path_from_course_id(
course_id, use_dataset_latest=use_dataset_latest)
ofn = outdir / ('person_course_%s.csv.gz' %
(course_id.replace('/', '__')))
ofnset.append(ofn)
if (nskip > 0) and ofn.exists():
print "%s already exists, not downloading" % ofn
sys.stdout.flush()
continue
if ofn.exists():
fnset = gsutil.get_gs_file_list(gb)
local_dt = gsutil.get_local_file_mtime_in_utc(ofn)
fnb = 'person_course.csv.gz'
if not fnb in fnset:
print "%s/%s missing! skipping %s" % (gb, fnb, course_id)
continue
if (fnb in fnset) and (local_dt >= fnset[fnb]['date']):
print "%s already exists with date %s (gs file date %s), not re-downloading" % (
ofn, local_dt, fnset[fnb]['date'])
sys.stdout.flush()
continue
else:
print "%s already exists but has date %s (gs file date %s), so re-downloading" % (
ofn, local_dt, fnset[fnb]['date'])
sys.stdout.flush()
cmd = 'gsutil cp %s/person_course.csv.gz %s' % (gb, ofn)
print "Retrieving %s via %s" % (course_id, cmd)
sys.stdout.flush()
os.system(cmd)
cnt += 1
#if cnt>2:
# break
org = course_id_set[0].split('/', 1)[0]
ofn = "person_course_%s_%s.csv" % (
org, datetime.datetime.now().strftime('%Y-%m-%d-%H%M%S'))
print "=" * 77
print "Combining CSV files to produce %s" % ofn
sys.stdout.flush()
if (nskip > 1) and os.path.exists(ofn):
print "%s already exists, not downloading" % ofn
else:
first = 1
header = None
for zfn in ofnset:
if first:
cmd = "zcat %s > %s" % (zfn, ofn)
header = os.popen("zcat %s | head -1" % zfn).read().strip()
firstfn = zfn
else:
cmd = "zcat %s | tail -n +2 >> %s" % (
zfn, ofn
) # first row is header; don't keep when concatenating
print cmd
first = 0
new_header = os.popen("zcat %s | head -1" % zfn).read().strip()
if not header == new_header:
print "==> Warning! header mismatch for %s vs %s" % (zfn,
firstfn)
print " %s has: %s" % (firstfn, header)
print " but %s has: %s" % (zfn, new_header)
sys.stdout.flush()
os.system(cmd)
gb = gsutil.gs_path_from_course_id('course_report_%s' % org,
gsbucket=output_bucket)
print "=" * 77
print "Uploading combined CSV file to google cloud storage in bucket: %s" % gb
sys.stdout.flush()
cmd = "TMPDIR=/var/tmp gsutil cp -z csv %s %s/" % (ofn, gb)
print cmd
os.system(cmd)
gsfn = gb + '/' + ofn
print "Combined person_course dataset CSV download link: %s" % gsutil.gs_download_link(
gsfn)
# import into BigQuery
crname = ('course_report_%s' % org)
if use_dataset_latest:
crname = 'course_report_latest'
dataset = output_dataset_id or crname
table = ofn[:-4].replace('-', '_')
print "Importing into BigQuery as %s:%s.%s" % (project_id, dataset, table)
sys.stdout.flush()
mypath = os.path.dirname(os.path.realpath(__file__))
SCHEMA_FILE = '%s/schemas/schema_person_course.json' % mypath
the_schema = json.loads(open(SCHEMA_FILE).read())['person_course']
bqutil.load_data_to_table(dataset,
table,
gsfn,
the_schema,
format='csv',
skiprows=1,
project_id=output_project_id)
msg = ''
msg += "Combined person-course dataset, with data from:\n"
msg += str(course_id_set)
msg += "\n\n"
msg += "=" * 100 + "\n"
msg += "CSV download link: %s" % gsutil.gs_download_link(gsfn)
bqutil.add_description_to_table(dataset,
table,
msg,
append=True,
project_id=output_project_id)
# copy the new table (which has a specific date in its name) to a generically named "person_course_latest"
# so that future SQL queries can simply use this as the latest person course table
print "-> Copying %s to %s.person_course_latest" % (table, dataset)
bqutil.copy_bq_table(dataset, table, "person_course_latest")
if extract_subset_tables:
do_extract_subset_person_course_tables(dataset, table)
print "Done"
sys.stdout.flush()
def load_sql_for_course(course_id,
gsbucket="gs://x-data",
basedir="X-Year-2-data-sql",
datedir="2014-09-21",
do_gs_copy=False,
use_dataset_latest=False):
'''
Load SQL files into google cloud storage then import into BigQuery.
Datasets are typically named by course_id, with "__" replacing "/", and "_" replacing "."
If use_dataset_latest then "_latest" is appended to the dataset name.
Thus, the latest SQL dataset can always be put in a consistently named dataset.
'''
print "Loading SQL for course %s into BigQuery (start: %s)" % (
course_id, datetime.datetime.now())
sys.stdout.flush()
lfp = find_course_sql_dir(course_id,
basedir,
datedir,
use_dataset_latest=use_dataset_latest)
print "Using this directory for local files: ", lfp
sys.stdout.flush()
# convert studentmodule if necessary
fn_sm = lfp / 'studentmodule.csv.gz'
if not fn_sm.exists():
fn_sm = lfp / 'studentmodule.csv'
if not fn_sm.exists():
fn_sm = lfp / 'studentmodule.sql.gz'
if not fn_sm.exists():
fn_sm = lfp / 'studentmodule.sql'
if not fn_sm.exists():
print "Error! Missing studentmodule.[sql,csv][.gz]"
if fn_sm.exists(): # have .sql or .sql.gz version: convert to .csv
newfn = lfp / 'studentmodule.csv.gz'
print "--> Converting %s to %s" % (fn_sm, newfn)
tsv2csv(fn_sm, newfn)
fn_sm = newfn
if fn_sm.exists():
# rephrase studentmodule if it's using opaque keys
fline = ''
smfp = openfile(fn_sm)
fline = smfp.readline() # skip first line - it's a header
fline = smfp.readline()
if 'block-v1:' in fline or 'course-v1' in fline:
rephrase_studentmodule_opaque_keys(fn_sm)
def convert_sql(fnroot):
if os.path.exists(fnroot + ".csv") or os.path.exists(fnroot +
".csv.gz"):
return
if os.path.exists(fnroot + ".sql") or os.path.exists(fnroot +
".sql.gz"):
infn = fnroot + '.sql'
outfn = fnroot + '.csv.gz'
print "--> Converting %s to %s" % (infn, outfn)
tsv2csv(infn, outfn)
# convert sql files if necesssary
fnset = [
'users', 'certificates', 'enrollment', "profiles", 'user_id_map',
'rolecourse', 'roleforum'
]
for fn in fnset:
convert_sql(lfp / fn)
local_files = glob.glob(lfp / '*')
# if using latest date directory, also look for course_image.jpg one level up
if use_dataset_latest:
print lfp.dirname()
ci_files = glob.glob(lfp.dirname() / 'course_image.jpg')
if ci_files:
local_files += list(ci_files)
print "--> local course_image file: %s" % ci_files
gsdir = gsutil.gs_path_from_course_id(
course_id, gsbucket=gsbucket, use_dataset_latest=use_dataset_latest)
local = pytz.timezone("America/New_York")
if do_gs_copy:
try:
fnset = get_gs_file_list(gsdir)
except Exception as err:
fnset = []
def copy_if_newer(fn, fnset, options='-z csv,json'):
statbuf = os.stat(fn)
mt = datetime.datetime.fromtimestamp(statbuf.st_mtime)
# do some date checking to upload files which have changed, and are newer than that on google cloud storage
local_dt = local.localize(mt, is_dst=None)
utc_dt = local_dt.astimezone(pytz.utc)
fnb = os.path.basename(fn)
if fnb in fnset and fnset[fnb]['date'] > utc_dt:
print "...%s already copied, skipping" % fn
sys.stdout.flush()
return
elif fnb in fnset:
print "...%s already exists, but has date=%s and mtime=%s, re-uploading" % (
fn, fnset[fnb]['date'], mt)
gsutil.upload_file_to_gs(fn,
gsdir / fnb,
options=options,
verbose=True)
for fn in local_files:
fnb = os.path.basename(fn)
if fnb == 'course_image.jpg':
copy_if_newer(fn, fnset, options='-a public-read')
if not (fnb.endswith('.csv') or fnb.endswith('.json')
or fnb.endswith('.csv.gz') or fnb.endswith('.json.gz')
or fnb.endswith('.mongo.gz')):
print "...unknown file type %s, skipping" % fn
sys.stdout.flush()
continue
copy_if_newer(fn, fnset)
# load into bigquery
dataset = bqutil.course_id2dataset(course_id,
use_dataset_latest=use_dataset_latest)
bqutil.create_dataset_if_nonexistent(dataset)
mypath = os.path.dirname(os.path.realpath(__file__))
# load user_info_combo
uicfn = lfp / 'user_info_combo.json.gz'
if uicfn.exists():
uic_schema = json.loads(
open('%s/schemas/schema_user_info_combo.json' %
mypath).read())['user_info_combo']
bqutil.load_data_to_table(dataset,
'user_info_combo',
gsdir / "user_info_combo.json.gz",
uic_schema,
wait=False)
else:
print "--> File %s does not exist, not loading user_info_combo into BigQuery" % uicfn
# load studentmodule
if fn_sm.exists():
schemas = json.loads(open('%s/schemas/schemas.json' % mypath).read())
cwsm_schema = schemas['courseware_studentmodule']
bqutil.load_data_to_table(dataset,
'studentmodule',
gsdir / fn_sm.basename(),
cwsm_schema,
format='csv',
wait=False,
skiprows=1)
else:
print "--> Not loading studentmodule: file %s not found" % fn_sm
def load_sql_for_course(course_id, gsbucket="gs://x-data", basedir="X-Year-2-data-sql", datedir="2014-09-21",
do_gs_copy=False,
use_dataset_latest=False):
'''
Load SQL files into google cloud storage then import into BigQuery.
Datasets are typically named by course_id, with "__" replacing "/", and "_" replacing "."
If use_dataset_latest then "_latest" is appended to the dataset name.
Thus, the latest SQL dataset can always be put in a consistently named dataset.
'''
print "Loading SQL for course %s into BigQuery (start: %s)" % (course_id, datetime.datetime.now())
sys.stdout.flush()
lfp = find_course_sql_dir(course_id, basedir, datedir, use_dataset_latest=use_dataset_latest)
print "Using this directory for local files: ", lfp
sys.stdout.flush()
# convert studentmodule if necessary
fn_sm = lfp / 'studentmodule.csv.gz'
if not fn_sm.exists():
fn_sm = lfp / 'studentmodule.csv'
if not fn_sm.exists():
fn_sm = lfp / 'studentmodule.sql.gz'
if not fn_sm.exists():
fn_sm = lfp / 'studentmodule.sql'
if not fn_sm.exists():
print "Error! Missing studentmodule.[sql,csv][.gz]"
if fn_sm.exists(): # have .sql or .sql.gz version: convert to .csv
newfn = lfp / 'studentmodule.csv.gz'
print "--> Converting %s to %s" % (fn_sm, newfn)
tsv2csv(fn_sm, newfn)
fn_sm = newfn
if fn_sm.exists():
# rephrase studentmodule if it's using opaque keys
fline = ''
smfp = openfile(fn_sm)
fline = smfp.readline() # skip first line - it's a header
fline = smfp.readline()
if 'block-v1:' in fline or 'course-v1' in fline:
rephrase_studentmodule_opaque_keys(fn_sm)
def convert_sql(fnroot):
if os.path.exists(fnroot + ".csv") or os.path.exists(fnroot + ".csv.gz"):
return
if os.path.exists(fnroot + ".sql") or os.path.exists(fnroot + ".sql.gz"):
infn = fnroot + '.sql'
outfn = fnroot + '.csv.gz'
print "--> Converting %s to %s" % (infn, outfn)
tsv2csv(infn, outfn)
# convert sql files if necesssary
fnset = ['users', 'certificates', 'enrollment', "profiles", 'user_id_map', 'rolecourse', 'roleforum']
for fn in fnset:
convert_sql(lfp / fn)
local_files = glob.glob(lfp / '*')
# if using latest date directory, also look for course_image.jpg one level up
if use_dataset_latest:
print lfp.dirname()
ci_files = glob.glob(lfp.dirname() / 'course_image.jpg')
if ci_files:
local_files += list(ci_files)
print "--> local course_image file: %s" % ci_files
gsdir = gsutil.gs_path_from_course_id(course_id, gsbucket=gsbucket, use_dataset_latest=use_dataset_latest)
local = pytz.timezone ("America/New_York")
if do_gs_copy:
try:
fnset = get_gs_file_list(gsdir)
except Exception as err:
fnset = []
def copy_if_newer(fn, fnset, options='-z csv,json'):
statbuf = os.stat(fn)
mt = datetime.datetime.fromtimestamp(statbuf.st_mtime)
# do some date checking to upload files which have changed, and are newer than that on google cloud storage
local_dt = local.localize(mt, is_dst=None)
utc_dt = local_dt.astimezone (pytz.utc)
fnb = os.path.basename(fn)
if fnb in fnset and fnset[fnb]['date'] > utc_dt:
print "...%s already copied, skipping" % fn
sys.stdout.flush()
return
elif fnb in fnset:
print "...%s already exists, but has date=%s and mtime=%s, re-uploading" % (fn, fnset[fnb]['date'], mt)
gsutil.upload_file_to_gs(fn, gsdir / fnb, options=options, verbose=True)
for fn in local_files:
fnb = os.path.basename(fn)
if fnb=='course_image.jpg':
copy_if_newer(fn, fnset, options='-a public-read')
if not (fnb.endswith('.csv') or fnb.endswith('.json') or fnb.endswith('.csv.gz')
or fnb.endswith('.json.gz') or fnb.endswith('.mongo.gz')):
print "...unknown file type %s, skipping" % fn
sys.stdout.flush()
continue
copy_if_newer(fn, fnset)
# load into bigquery
dataset = bqutil.course_id2dataset(course_id, use_dataset_latest=use_dataset_latest)
bqutil.create_dataset_if_nonexistent(dataset)
mypath = os.path.dirname(os.path.realpath(__file__))
# load user_info_combo
uicfn = lfp / 'user_info_combo.json.gz'
if uicfn.exists():
uic_schema = json.loads(open('%s/schemas/schema_user_info_combo.json' % mypath).read())['user_info_combo']
bqutil.load_data_to_table(dataset, 'user_info_combo', gsdir / "user_info_combo.json.gz", uic_schema, wait=False)
else:
print "--> File %s does not exist, not loading user_info_combo into BigQuery" % uicfn
# load studentmodule
if fn_sm.exists():
schemas = json.loads(open('%s/schemas/schemas.json' % mypath).read())
cwsm_schema = schemas['courseware_studentmodule']
bqutil.load_data_to_table(dataset, 'studentmodule', gsdir / fn_sm.basename(), cwsm_schema, format='csv', wait=False, skiprows=1)
else:
print "--> Not loading studentmodule: file %s not found" % fn_sm
def do_combine(course_id_set, project_id, outdir="DATA", nskip=0,
output_project_id=None, output_dataset_id=None, output_bucket=None,
use_dataset_latest=False,
extract_subset_tables=True,
):
'''
Combine individual person_course tables (from the set of specified course_id's) to create one single large
person_course table. Do this by downloading each file, checking to make sure they all have the same
fields, concatenating, and uploading back to bigquery. This is cheaper than doing a select *, and also
uncovers person_course files which have the wrong schema (and it works around BQ's limitation on large
result sizes). The result is stored in the course_report_latest dataset (if use_dataset_latest), else
in course_report_ORG, where ORG is the configured organization name.
If extract_subset_tables is True, then the subset of those who viewed (ie "participants"), and the subset
of those who enrolled for IDV, are extracted and saved as person_course_viewed, and person_course_idv.
(those are created using a select *, for efficiency, despite the cost).
'''
print "="*77
print "Concatenating person course datasets from the following courses:"
print course_id_set
print "-"*77
outdir = path(outdir)
if not outdir.exists():
os.mkdir(outdir)
ofnset = []
cnt = 0
for course_id in course_id_set:
gb = gsutil.gs_path_from_course_id(course_id, use_dataset_latest=use_dataset_latest)
ofn = outdir / ('person_course_%s.csv.gz' % (course_id.replace('/', '__')))
ofnset.append(ofn)
if (nskip>0) and ofn.exists():
print "%s already exists, not downloading" % ofn
sys.stdout.flush()
continue
if ofn.exists():
fnset = gsutil.get_gs_file_list(gb)
local_dt = gsutil.get_local_file_mtime_in_utc(ofn)
fnb = 'person_course.csv.gz'
if not fnb in fnset:
print "%s/%s missing! skipping %s" % (gb, fnb, course_id)
continue
if (fnb in fnset) and (local_dt >= fnset[fnb]['date']):
print "%s already exists with date %s (gs file date %s), not re-downloading" % (ofn, local_dt, fnset[fnb]['date'])
sys.stdout.flush()
continue
else:
print "%s already exists but has date %s (gs file date %s), so re-downloading" % (ofn, local_dt, fnset[fnb]['date'])
sys.stdout.flush()
cmd = 'gsutil cp %s/person_course.csv.gz %s' % (gb, ofn)
print "Retrieving %s via %s" % (course_id, cmd)
sys.stdout.flush()
os.system(cmd)
cnt += 1
#if cnt>2:
# break
org = course_id_set[0].split('/',1)[0]
ofn = "person_course_%s_%s.csv" % (org, datetime.datetime.now().strftime('%Y-%m-%d-%H%M%S'))
print "="*77
print "Combining CSV files to produce %s" % ofn
sys.stdout.flush()
if (nskip>1) and os.path.exists(ofn):
print "%s already exists, not downloading" % ofn
else:
first = 1
header = None
for zfn in ofnset:
if first:
cmd = "zcat %s > %s" % (zfn, ofn)
header = os.popen("zcat %s | head -1" % zfn).read().strip()
firstfn = zfn
else:
cmd = "zcat %s | tail -n +2 >> %s" % (zfn, ofn) # first row is header; don't keep when concatenating
print cmd
first = 0
new_header = os.popen("zcat %s | head -1" % zfn).read().strip()
if not header == new_header:
print "==> Warning! header mismatch for %s vs %s" % (zfn, firstfn)
print " %s has: %s" % (firstfn, header)
print " but %s has: %s" % (zfn, new_header)
sys.stdout.flush()
os.system(cmd)
gb = gsutil.gs_path_from_course_id('course_report_%s' % org, gsbucket=output_bucket)
print "="*77
print "Uploading combined CSV file to google cloud storage in bucket: %s" % gb
sys.stdout.flush()
cmd = "TMPDIR=/var/tmp gsutil cp -z csv %s %s/" % (ofn, gb)
print cmd
os.system(cmd)
gsfn = gb + '/' + ofn
print "Combined person_course dataset CSV download link: %s" % gsutil.gs_download_link(gsfn)
# import into BigQuery
crname = ('course_report_%s' % org)
if use_dataset_latest:
crname = 'course_report_latest'
dataset = output_dataset_id or crname
table = ofn[:-4].replace('-','_')
print "Importing into BigQuery as %s:%s.%s" % (project_id, dataset, table)
sys.stdout.flush()
mypath = os.path.dirname(os.path.realpath(__file__))
SCHEMA_FILE = '%s/schemas/schema_person_course.json' % mypath
the_schema = json.loads(open(SCHEMA_FILE).read())['person_course']
bqutil.load_data_to_table(dataset, table, gsfn, the_schema, format='csv', skiprows=1, project_id=output_project_id)
msg = ''
msg += "Combined person-course dataset, with data from:\n"
msg += str(course_id_set)
msg += "\n\n"
msg += "="*100 + "\n"
msg += "CSV download link: %s" % gsutil.gs_download_link(gsfn)
bqutil.add_description_to_table(dataset, table, msg, append=True, project_id=output_project_id)
# copy the new table (which has a specific date in its name) to a generically named "person_course_latest"
# so that future SQL queries can simply use this as the latest person course table
print "-> Copying %s to %s.person_course_latest" % (table, dataset)
bqutil.copy_bq_table(dataset, table, "person_course_latest")
if extract_subset_tables:
do_extract_subset_person_course_tables(dataset, table)
print "Done"
sys.stdout.flush()
def load_all_daily_logs_for_course(course_id, gsbucket="gs://x-data", verbose=True, wait=False,
check_dates=True):
'''
Load daily tracking logs for course from google storage into BigQuery.
If wait=True then waits for loading jobs to be completed. It's desirable to wait
if subsequent jobs which need these tables (like person_day) are to be run
immediately afterwards.
'''
print "Loading daily tracking logs for course %s into BigQuery (start: %s)" % (course_id, datetime.datetime.now())
sys.stdout.flush()
gsroot = gsutil.path_from_course_id(course_id)
mypath = os.path.dirname(os.path.realpath(__file__))
SCHEMA = json.loads(open('%s/schemas/schema_tracking_log.json' % mypath).read())['tracking_log']
gsdir = '%s/%s/DAILY/' % (gsbucket, gsroot)
fnset = gsutil.get_gs_file_list(gsdir)
dataset = bqutil.course_id2dataset(gsroot, dtype="logs")
# create this dataset if necessary
bqutil.create_dataset_if_nonexistent(dataset)
tables = bqutil.get_list_of_table_ids(dataset)
tables = [x for x in tables if x.startswith('track')]
if verbose:
print "-"*77
print "current tables loaded:", json.dumps(tables, indent=4)
print "files to load: ", json.dumps(fnset.keys(), indent=4)
print "-"*77
sys.stdout.flush()
for fn, fninfo in fnset.iteritems():
if int(fninfo['size'])<=45:
print "Zero size file %s, skipping" % fn
continue
m = re.search('(\d\d\d\d-\d\d-\d\d)', fn)
if not m:
continue
date = m.group(1)
tablename = "tracklog_%s" % date.replace('-','') # YYYYMMDD for compatibility with table wildcards
# file_date = gsutil.get_local_file_mtime_in_utc(fn, make_tz_unaware=True)
file_date = fninfo['date'].replace(tzinfo=None)
if tablename in tables:
skip = True
if check_dates:
table_date = bqutil.get_bq_table_last_modified_datetime(dataset, tablename)
if not (table_date > file_date):
print "Already have table %s, but %s file_date=%s, table_date=%s; re-loading from gs" % (tablename, fn, file_date, table_date)
skip = False
if skip:
if verbose:
print "Already have table %s, skipping file %s" % (tablename, fn)
sys.stdout.flush()
continue
#if date < '2014-07-27':
# continue
print "Loading %s into table %s " % (fn, tablename)
if verbose:
print "start [%s]" % datetime.datetime.now()
sys.stdout.flush()
gsfn = fninfo['name']
ret = bqutil.load_data_to_table(dataset, tablename, gsfn, SCHEMA, wait=wait, maxbad=1000)
if verbose:
print "-" * 77
print "done with %s [%s]" % (course_id, datetime.datetime.now())
print "=" * 77
sys.stdout.flush()
def do_combine(course_id_set, project_id, outdir="DATA", nskip=0,
output_project_id=None, output_dataset_id=None, output_bucket=None,
use_dataset_latest=False,
):
print "="*77
print "Concatenating person course datasets from the following courses:"
print course_id_set
print "-"*77
outdir = path(outdir)
if not outdir.exists():
os.mkdir(outdir)
ofnset = []
cnt = 0
for course_id in course_id_set:
gb = gsutil.gs_path_from_course_id(course_id, use_dataset_latest=use_dataset_latest)
ofn = outdir / ('person_course_%s.csv.gz' % (course_id.replace('/', '__')))
ofnset.append(ofn)
if (nskip>0) and ofn.exists():
print "%s already exists, not downloading" % ofn
sys.stdout.flush()
continue
if ofn.exists():
fnset = gsutil.get_gs_file_list(gb)
local_dt = gsutil.get_local_file_mtime_in_utc(ofn)
fnb = 'person_course.csv.gz'
if not fnb in fnset:
print "%s/%s missing! skipping %s" % (gb, fnb, course_id)
continue
if (fnb in fnset) and (local_dt >= fnset[fnb]['date']):
print "%s already exists with date %s (gs file date %s), not re-downloading" % (ofn, local_dt, fnset[fnb]['date'])
sys.stdout.flush()
continue
else:
print "%s already exists but has date %s (gs file date %s), so re-downloading" % (ofn, local_dt, fnset[fnb]['date'])
sys.stdout.flush()
cmd = 'gsutil cp %s/person_course.csv.gz %s' % (gb, ofn)
print "Retrieving %s via %s" % (course_id, cmd)
sys.stdout.flush()
os.system(cmd)
cnt += 1
#if cnt>2:
# break
org = course_id_set[0].split('/',1)[0]
ofn = "person_course_%s_%s.csv" % (org, datetime.datetime.now().strftime('%Y-%m-%d-%H%M%S'))
print "="*77
print "Combining CSV files to produce %s" % ofn
sys.stdout.flush()
if (nskip>1) and os.path.exists(ofn):
print "%s already exists, not downloading" % ofn
else:
first = 1
for zfn in ofnset:
if first:
cmd = "zcat %s > %s" % (zfn, ofn)
else:
cmd = "zcat %s | tail -n +2 >> %s" % (zfn, ofn) # first row is header; don't keep when concatenating
print cmd
first = 0
os.system(cmd)
gb = gsutil.gs_path_from_course_id('course_report_%s' % org, gsbucket=output_bucket)
print "="*77
print "Uploading combined CSV file to google cloud storage in bucket: %s" % gb
sys.stdout.flush()
cmd = "TMPDIR=/var/tmp gsutil cp -z csv %s %s/" % (ofn, gb)
print cmd
os.system(cmd)
gsfn = gb + '/' + ofn
print "Combined person_course dataset CSV download link: %s" % gsutil.gs_download_link(gsfn)
# import into BigQuery
crname = ('course_report_%s' % org)
if use_dataset_latest:
crname = 'course_report_latest'
dataset = output_dataset_id or crname
table = ofn[:-4].replace('-','_')
print "Importing into BigQuery as %s:%s.%s" % (project_id, dataset, table)
sys.stdout.flush()
mypath = os.path.dirname(os.path.realpath(__file__))
SCHEMA_FILE = '%s/schemas/schema_person_course.json' % mypath
the_schema = json.loads(open(SCHEMA_FILE).read())['person_course']
bqutil.load_data_to_table(dataset, table, gsfn, the_schema, format='csv', skiprows=1, project_id=output_project_id)
msg = ''
msg += "Combined person-course dataset, with data from:\n"
msg += str(course_id_set)
msg += "\n\n"
msg += "="*100 + "\n"
msg += "CSV download link: %s" % gsutil.gs_download_link(gsfn)
bqutil.add_description_to_table(dataset, table, msg, append=True, project_id=output_project_id)
print "Done"
sys.stdout.flush()
def load_all_daily_logs_for_course(course_id,
gsbucket="gs://x-data",
verbose=True,
wait=False,
check_dates=True):
'''
Load daily tracking logs for course from google storage into BigQuery.
If wait=True then waits for loading jobs to be completed. It's desirable to wait
if subsequent jobs which need these tables (like person_day) are to be run
immediately afterwards.
'''
print "Loading daily tracking logs for course %s into BigQuery (start: %s)" % (
course_id, datetime.datetime.now())
sys.stdout.flush()
gsroot = gsutil.path_from_course_id(course_id)
mypath = os.path.dirname(os.path.realpath(__file__))
SCHEMA = json.loads(
open('%s/schemas/schema_tracking_log.json' %
mypath).read())['tracking_log']
gsdir = '%s/%s/DAILY/' % (gsbucket, gsroot)
fnset = gsutil.get_gs_file_list(gsdir)
dataset = bqutil.course_id2dataset(gsroot, dtype="logs")
# create this dataset if necessary
bqutil.create_dataset_if_nonexistent(dataset)
tables = bqutil.get_list_of_table_ids(dataset)
tables = [x for x in tables if x.startswith('track')]
if verbose:
print "-" * 77
print "current tables loaded:", json.dumps(tables, indent=4)
print "files to load: ", json.dumps(fnset.keys(), indent=4)
print "-" * 77
sys.stdout.flush()
for fn, fninfo in fnset.iteritems():
if int(fninfo['size']) <= 45:
print "Zero size file %s, skipping" % fn
continue
m = re.search('(\d\d\d\d-\d\d-\d\d)', fn)
if not m:
continue
date = m.group(1)
tablename = "tracklog_%s" % date.replace(
'-', '') # YYYYMMDD for compatibility with table wildcards
# file_date = gsutil.get_local_file_mtime_in_utc(fn, make_tz_unaware=True)
file_date = fninfo['date'].replace(tzinfo=None)
if tablename in tables:
skip = True
if check_dates:
table_date = bqutil.get_bq_table_last_modified_datetime(
dataset, tablename)
if not (table_date > file_date):
print "Already have table %s, but %s file_date=%s, table_date=%s; re-loading from gs" % (
tablename, fn, file_date, table_date)
skip = False
if skip:
if verbose:
print "Already have table %s, skipping file %s" % (
tablename, fn)
sys.stdout.flush()
continue
#if date < '2014-07-27':
# continue
print "Loading %s into table %s " % (fn, tablename)
if verbose:
print "start [%s]" % datetime.datetime.now()
sys.stdout.flush()
gsfn = fninfo['name']
ret = bqutil.load_data_to_table(dataset,
tablename,
gsfn,
SCHEMA,
wait=wait,
maxbad=1000)
if verbose:
print "-" * 77
print "done with %s [%s]" % (course_id, datetime.datetime.now())
print "=" * 77
sys.stdout.flush()
