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Trackhub S3 Integration #13

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Trackhub S3 Integration #13

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00f8a0b
Fixed file parsing issue (.'s weren't allowed)
Aug 21, 2014
c463175
Added basic s3 integration, only works for yeo-lab bucket at the moment.
Aug 21, 2014
a1ad5f3
fixed bug where I couldn't disable s3
Oct 6, 2014
cdbc2f8
fixed bug in uploading tracks to local server instead of s3
Dec 2, 2014
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2 changes: 1 addition & 1 deletion trackhub/track.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@


def _check_name(name):
regex = re.compile('[^a-zA-Z0-9-_]')
regex = re.compile('[^a-zA-Z0-9-_.]')
if regex.search(name):
raise ValueError('Non-alphanumeric character in name "%s"' % name)

Expand Down
37 changes: 29 additions & 8 deletions trackhub/upload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,19 @@
from fabric.api import local, settings, run, abort, cd, env, hide, put
from fabric.contrib.console import confirm
import track
import boto
from boto.s3.key import Key


def upload_s3(local_fn, remote_fn, **kwargs):
s3 = boto.connect_s3()
bucket = s3.get_bucket("sauron-yeo")
k = Key(bucket)
k.key = remote_fn
k.set_contents_from_filename(local_fn)
k.make_public()
return ["done"]


def upload_file(host, user, local_fn, remote_fn, port=22,
rsync_options='-azvr --progress', run_local=False):
Expand Down Expand Up @@ -33,15 +46,18 @@ def upload_file(host, user, local_fn, remote_fn, port=22,


def upload_hub(host, user, hub, port=22, rsync_options='-azvr --progress',
run_local=False):
run_local=False, run_s3=False):
kwargs = dict(host=host, user=user, port=port, rsync_options=rsync_options,
run_local=run_local)
print kwargs
results = []

if run_s3:
cur_upload_file = upload_s3
else:
cur_upload_file = upload_file
# First the hub file:
results.extend(
upload_file(
cur_upload_file(
local_fn=hub.local_fn,
remote_fn=hub.remote_fn,
**kwargs)
Expand All @@ -50,7 +66,7 @@ def upload_hub(host, user, hub, port=22, rsync_options='-azvr --progress',
# Then the genomes file:
print hub.genomes_file.local_fn
results.extend(
upload_file(
cur_upload_file(
local_fn=hub.genomes_file.local_fn,
remote_fn=hub.genomes_file.remote_fn,
**kwargs)
Expand All @@ -59,7 +75,7 @@ def upload_hub(host, user, hub, port=22, rsync_options='-azvr --progress',
# then the trackDB file:
for g in hub.genomes_file.genomes:
results.extend(
upload_file(
cur_upload_file(
local_fn=g.trackdb.local_fn,
remote_fn=g.trackdb.remote_fn,
**kwargs
Expand All @@ -70,7 +86,7 @@ def upload_hub(host, user, hub, port=22, rsync_options='-azvr --progress',
print repr(t)
if t._html:
results.extend(
upload_file(
cur_upload_file(
local_fn=t._html.local_fn,
remote_fn=t._html.remote_fn,
**kwargs)
Expand All @@ -79,11 +95,16 @@ def upload_hub(host, user, hub, port=22, rsync_options='-azvr --progress',


def upload_track(host, user, track, port=22, rsync_options='-azvr --progress',
run_local=False):
run_local=False, run_s3=False):

if run_s3:
cur_upload_file = upload_s3
else:
cur_upload_file = upload_file
kwargs = dict(host=host, user=user, local_fn=track.local_fn,
remote_fn=track.remote_fn, rsync_options=rsync_options,
run_local=run_local)
results = upload_file(**kwargs)
results = cur_upload_file(**kwargs)
if track.tracktype == 'bam':
kwargs['local_fn'] += '.bai'
kwargs['remote_fn'] += '.bai'
Expand Down