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bitia
bitia-cli
Commits
d13dd449
Commit
d13dd449
authored
2 years ago
by
dilawar
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temp:
parent
2632adea
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1 merge request
!2
version 0.2.0
Pipeline
#3705
failed with stages
Stage:
Stage:
in 1 minute and 41 seconds
Changes
3
Pipelines
1
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3 changed files
bitia/__main__.py
+65
-29
65 additions, 29 deletions
bitia/__main__.py
bitia/helper.py
+65
-6
65 additions, 6 deletions
bitia/helper.py
bitia/session.py
+14
-6
14 additions, 6 deletions
bitia/session.py
with
144 additions
and
41 deletions
bitia/__main__.py
+
65
−
29
View file @
d13dd449
"""
BiTIA command line interface to submit job to the BiTIA server.
"""
BiTIA command line interface to submit job to the BiTIA server.
(c) 2022-, Subconscious Compute
https://bitia.link
(c) 2022-, Subconscious Compute, https://subcom.tech
"""
"""
import
typing
as
T
import
functools
import
functools
import
bitia.helper
as
bhelper
import
bitia.helper
as
bhelper
...
@@ -37,6 +40,61 @@ def session(func):
...
@@ -37,6 +40,61 @@ def session(func):
return
wrapper
return
wrapper
@app.command
(
"
create-container
"
)
@session
def
create_remote_container
(
user_input
:
str
,
recreate
:
bool
=
False
,
server
:
str
=
bconfig
.
DEFAULT_SERVER
):
"""
Run a pipeline
"""
pipeline_zip
,
_
=
bhelper
.
user_input_to_pipeline
(
user_input
)
res
=
bhelper
.
post_pipeline_task
(
pipeline_zip
,
server
=
server
,
endpoint
=
"
container/create
"
,
params
=
dict
(
recreate
=
"
true
"
if
recreate
else
"
false
"
),
stream
=
True
,
)
res
.
raise_for_status
()
for
line
in
res
.
iter_lines
():
print
(
line
.
decode
().
rstrip
())
@app.command
(
"
list-container
"
)
@session
def
list_remote_container
(
user_input
:
str
,
server
:
str
=
bconfig
.
DEFAULT_SERVER
)
->
T
.
List
[
str
]:
"""
List the remote server associated with the pipeline.
"""
_
,
pipeline_hash
=
bhelper
.
user_input_to_pipeline
(
user_input
)
logger
.
info
(
f
"
Finding container for
{
user_input
}
, sha256sum=
{
pipeline_hash
}
"
)
res
=
bhelper
.
get
(
endpoint
=
"
container/list
"
,
params
=
dict
(
pipeline_sha256
=
pipeline_hash
),
server
=
server
,
)
res
.
raise_for_status
()
_json
=
res
.
json
()
print
(
_json
)
return
_json
[
"
containers
"
]
@app.command
(
"
logs
"
)
@session
def
stream_log
(
user_input
:
str
,
server
:
str
=
bconfig
.
DEFAULT_SERVER
)
->
T
.
List
[
str
]:
"""
Stream logs for the most recent run of a given pipeline.
"""
_
,
pipeline_hash
=
bhelper
.
user_input_to_pipeline
(
user_input
)
logger
.
info
(
f
"
Finding container for
{
user_input
}
, sha256sum=
{
pipeline_hash
}
"
)
res
=
bhelper
.
get
(
endpoint
=
"
logs
"
,
params
=
dict
(
pipeline_sha256
=
pipeline_hash
),
server
=
server
,
stream
=
True
,
)
res
.
raise_for_status
()
for
line
in
res
.
iter_lines
():
print
(
line
.
decode
().
rstrip
())
@app.command
(
"
submit
"
)
@app.command
(
"
submit
"
)
@session
@session
def
submit_pipeline
(
def
submit_pipeline
(
...
@@ -47,10 +105,8 @@ def submit_pipeline(
...
@@ -47,10 +105,8 @@ def submit_pipeline(
Prepare the user directory to send to the server. User can also provide link
Prepare the user directory to send to the server. User can also provide link
to the pipeline to run.
to the pipeline to run.
"""
"""
pipeline_zip
=
bhelper
.
user_input_to_pipeline
(
user_input
)
create_remote_container
(
user_input
,
recreate
=
rerun
)
containers
=
bhelper
.
post_pipeline_task
(
containers
=
list_remote_container
(
user_input
)
pipeline_zip
,
rerun
=
rerun
,
server
=
server
,
endpoint
=
f
"
submit/?rerun=
{
rerun
}
"
)
logger
.
info
(
f
"
Got containers
{
containers
}
"
)
logger
.
info
(
f
"
Got containers
{
containers
}
"
)
return
containers
return
containers
...
@@ -58,32 +114,12 @@ def submit_pipeline(
...
@@ -58,32 +114,12 @@ def submit_pipeline(
@app.command
(
"
run
"
)
@app.command
(
"
run
"
)
@session
@session
def
run_pipeline
(
def
run_pipeline
(
user_input
:
str
,
rerun
:
bool
=
False
,
server
:
str
=
bconfig
.
DEFAULT_SERVER
user_input
:
str
,
*
,
rerun
:
bool
=
False
,
server
:
str
=
bconfig
.
DEFAULT_SERVER
):
"""
Run a pipeline
"""
pipeline_zip
=
bhelper
.
user_input_to_pipeline
(
user_input
)
res
=
bhelper
.
post_pipeline_task
(
pipeline_zip
,
endpoint
=
f
"
submit?rerun=
{
rerun
}
"
,
server
=
server
)
return
bhelper
.
log_container
(
res
[
"
container
"
],
server
=
server
)
@app.command
(
"
create
"
)
@session
def
create_remote_infra
(
user_input
:
str
,
recreate
:
bool
=
False
,
server
:
str
=
bconfig
.
DEFAULT_SERVER
):
):
"""
Run a pipeline
"""
"""
Run a pipeline
"""
pipeline_zip
=
bhelper
.
user_input_to_pipeline
(
user_input
)
create_remote_container
(
user_input
,
recreate
=
rerun
,
server
=
server
)
res
=
bhelper
.
post_pipeline_task
(
containers
=
list_remote_container
(
user_input
,
server
=
server
)
pipeline_zip
,
return
[
bhelper
.
log_container
(
container
,
server
=
server
)
for
container
in
containers
]
server
=
server
,
endpoint
=
f
"
container/create?recreate=
{
recreate
}
"
,
stream
=
True
,
)
res
.
raise_for_status
()
for
line
in
res
.
iter_lines
():
print
(
line
.
decode
().
rstrip
())
@app.command
()
@app.command
()
...
...
This diff is collapsed.
Click to expand it.
bitia/helper.py
+
65
−
6
View file @
d13dd449
...
@@ -3,11 +3,13 @@
...
@@ -3,11 +3,13 @@
__author__
=
"
Dilawar Singh
"
__author__
=
"
Dilawar Singh
"
__email__
=
"
dilawar@subcom.tech
"
__email__
=
"
dilawar@subcom.tech
"
import
hashlib
import
sys
import
sys
import
zipfile
import
zipfile
import
shutil
import
shutil
from
pathlib
import
Path
from
pathlib
import
Path
import
tempfile
import
tempfile
import
typing
as
T
import
validators
import
validators
import
requests
import
requests
...
@@ -22,7 +24,6 @@ def log_container(container: str, server: str):
...
@@ -22,7 +24,6 @@ def log_container(container: str, server: str):
assert
(
assert
(
container
container
),
"
Failed to determine the container that is runnning the pipeline. There is probably a bug in server end.
"
),
"
Failed to determine the container that is runnning the pipeline. There is probably a bug in server end.
"
logger
.
info
(
f
"
Fetching logs from
{
container
}
"
)
for
line
in
bsession
.
fetch_logs
(
container
,
server
=
server
):
for
line
in
bsession
.
fetch_logs
(
container
,
server
=
server
):
print
(
line
.
decode
().
rstrip
())
print
(
line
.
decode
().
rstrip
())
...
@@ -98,7 +99,14 @@ def create_pipeline_from_command(cmd: str) -> Path:
...
@@ -98,7 +99,14 @@ def create_pipeline_from_command(cmd: str) -> Path:
return
prepare_archive
(
pipeline_dir
)
return
prepare_archive
(
pipeline_dir
)
def
post_pipeline_task
(
pipeline_zip
:
Path
,
*
,
endpoint
:
str
,
server
:
str
,
**
kwargs
):
def
post_pipeline_task
(
pipeline_zip
:
Path
,
*
,
endpoint
:
str
,
server
:
str
,
params
:
T
.
Dict
[
str
,
str
]
=
{},
**
kwargs
,
):
"""
Submit to the api for a given endpoint and pipeline file
"""
"""
Submit to the api for a given endpoint and pipeline file
"""
numbytes
=
pipeline_zip
.
stat
().
st_size
numbytes
=
pipeline_zip
.
stat
().
st_size
if
(
code
:
=
_check_server_status
(
server
))
!=
200
:
if
(
code
:
=
_check_server_status
(
server
))
!=
200
:
...
@@ -121,12 +129,45 @@ def post_pipeline_task(pipeline_zip: Path, *, endpoint: str, server: str, **kwar
...
@@ -121,12 +129,45 @@ def post_pipeline_task(pipeline_zip: Path, *, endpoint: str, server: str, **kwar
return
bsession
.
post
(
return
bsession
.
post
(
f
"
{
server
}
/
{
endpoint
}
"
,
f
"
{
server
}
/
{
endpoint
}
"
,
files
=
files
,
files
=
files
,
params
=
params
,
data
=
dict
(
filename
=
pipeline_zip
).
update
(
**
kwargs
),
data
=
dict
(
filename
=
pipeline_zip
).
update
(
**
kwargs
),
stream
=
kwargs
.
get
(
"
stream
"
,
False
),
stream
=
kwargs
.
get
(
"
stream
"
,
False
),
)
)
def
submit_job
(
pipeline_zip
:
Path
,
*
,
server
:
str
,
rerun
:
bool
=
False
):
def
post
(
endpoint
:
str
,
*
,
server
:
str
,
stream
:
bool
=
False
,
params
:
T
.
Dict
[
str
,
str
]
=
{},
**
kwargs
,
):
"""
A generic post function.
"""
logger
.
info
(
f
"
Posting with data
{
kwargs
}
"
)
return
bsession
.
post
(
f
"
{
server
}
/
{
endpoint
}
"
,
json
=
kwargs
,
params
=
params
,
stream
=
stream
)
def
get
(
endpoint
:
str
,
*
,
server
:
str
,
stream
:
bool
=
False
,
params
:
T
.
Dict
[
str
,
str
]
=
{},
**
kwargs
,
):
"""
A generic post function.
"""
logger
.
info
(
f
"
Posting with data
{
kwargs
}
"
)
return
bsession
.
get
(
f
"
{
server
}
/
{
endpoint
}
"
,
params
=
params
,
json
=
kwargs
,
stream
=
stream
)
def
submit_job
(
pipeline_zip
:
Path
,
*
,
server
:
str
,
rerun
:
bool
=
False
,
params
:
dict
=
{}
):
"""
Submit job to the API and stream the output.
"""
"""
Submit job to the API and stream the output.
"""
numbytes
=
pipeline_zip
.
stat
().
st_size
numbytes
=
pipeline_zip
.
stat
().
st_size
if
(
code
:
=
_check_server_status
(
server
))
!=
200
:
if
(
code
:
=
_check_server_status
(
server
))
!=
200
:
...
@@ -148,12 +189,30 @@ def submit_job(pipeline_zip: Path, *, server: str, rerun: bool = False):
...
@@ -148,12 +189,30 @@ def submit_job(pipeline_zip: Path, *, server: str, rerun: bool = False):
response
=
bsession
.
post
(
response
=
bsession
.
post
(
f
"
{
server
}
/submit/?rerun=
{
rerun
}
"
,
f
"
{
server
}
/submit/?rerun=
{
rerun
}
"
,
files
=
files
,
files
=
files
,
data
=
dict
(
filename
=
pipeline_zip
,
rerun
=
rerun
),
params
=
params
,
json
=
dict
(
filename
=
pipeline_zip
,
rerun
=
rerun
),
)
)
return
response
.
json
()
return
response
.
json
()
def
user_input_to_pipeline
(
user_input
:
str
)
->
Path
:
def
sha256sum
(
infile
:
Path
)
->
str
:
"""
Compute sha256sum of a file.
Credit
------
Thanks https://stackoverflow.com/a/44873382/1805129
"""
h
=
hashlib
.
sha256
()
b
=
bytearray
(
128
*
1024
)
mv
=
memoryview
(
b
)
with
infile
.
open
(
"
rb
"
,
buffering
=
0
)
as
handler
:
while
n
:
=
handler
.
readinto
(
mv
):
h
.
update
(
mv
[:
n
])
return
h
.
hexdigest
()
def
user_input_to_pipeline
(
user_input
:
str
)
->
tuple
[
Path
,
str
]:
"""
Create a pipeline file from user_input
"""
"""
Create a pipeline file from user_input
"""
if
(
path
:
=
Path
(
user_input
)).
exists
():
if
(
path
:
=
Path
(
user_input
)).
exists
():
if
path
.
is_dir
():
if
path
.
is_dir
():
...
@@ -171,4 +230,4 @@ def user_input_to_pipeline(user_input: str) -> Path:
...
@@ -171,4 +230,4 @@ def user_input_to_pipeline(user_input: str) -> Path:
# generate a temporary pipeline and submit.
# generate a temporary pipeline and submit.
pipeline_zip
=
create_pipeline_from_command
(
user_input
)
pipeline_zip
=
create_pipeline_from_command
(
user_input
)
logger
.
info
(
f
"
Created pipeline in
{
pipeline_zip
}
"
)
logger
.
info
(
f
"
Created pipeline in
{
pipeline_zip
}
"
)
return
pipeline_zip
return
pipeline_zip
,
sha256sum
(
pipeline_zip
)
This diff is collapsed.
Click to expand it.
bitia/session.py
+
14
−
6
View file @
d13dd449
...
@@ -5,7 +5,7 @@ import pickle
...
@@ -5,7 +5,7 @@ import pickle
import
bitia.config
as
bconfig
import
bitia.config
as
bconfig
from
bitia.logger
import
logger
from
bitia.logger
import
logger
g_session
=
requests
.
s
ession
()
g_session
=
requests
.
S
ession
()
SESSION_PICKLE_FILE
=
bconfig
.
bitia_dir
()
/
"
.session.pickle
"
SESSION_PICKLE_FILE
=
bconfig
.
bitia_dir
()
/
"
.session.pickle
"
...
@@ -13,8 +13,7 @@ def fetch_logs(container: str, *, server):
...
@@ -13,8 +13,7 @@ def fetch_logs(container: str, *, server):
"""
Fetch logs from a container.
"""
"""
Fetch logs from a container.
"""
logger
.
info
(
f
"
Fetching logs for container `
{
container
}
`
"
)
logger
.
info
(
f
"
Fetching logs for container `
{
container
}
`
"
)
return
g_session
.
post
(
return
g_session
.
post
(
f
"
{
server
}
/logs
"
,
f
"
{
server
}
/logs/?container=
{
container
}
"
,
json
=
dict
(
container
=
container
,
follow
=
True
),
stream
=
True
,
stream
=
True
,
)
)
...
@@ -26,17 +25,26 @@ def save_session():
...
@@ -26,17 +25,26 @@ def save_session():
pickle
.
dump
(
g_session
,
fsession
)
pickle
.
dump
(
g_session
,
fsession
)
def
load_session
():
def
load_session
(
force_new
:
bool
=
False
):
"""
Load the pickled session.
"""
"""
Load the pickled session.
"""
global
g_session
global
g_session
if
force_new
:
g_session
=
requests
.
Session
()
return
if
not
SESSION_PICKLE_FILE
.
is_file
():
if
not
SESSION_PICKLE_FILE
.
is_file
():
return
None
g_session
=
requests
.
Session
()
return
with
SESSION_PICKLE_FILE
.
open
(
"
rb
"
)
as
fsession
:
with
SESSION_PICKLE_FILE
.
open
(
"
rb
"
)
as
fsession
:
try
:
try
:
logger
.
info
(
f
"
Loading session from
{
fsession
.
name
}
"
)
g_session
=
pickle
.
load
(
fsession
)
g_session
=
pickle
.
load
(
fsession
)
except
Exception
:
except
Exception
:
return
None
g_session
=
requests
.
Session
()
def
post
(
*
args
,
**
kwargs
):
def
post
(
*
args
,
**
kwargs
):
return
g_session
.
post
(
*
args
,
**
kwargs
)
return
g_session
.
post
(
*
args
,
**
kwargs
)
def
get
(
*
args
,
**
kwargs
):
return
g_session
.
get
(
*
args
,
**
kwargs
)
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