hca prints --help insted of run

[oskotsky]

hca dss download --bundle-uuid XXXXXXXXXX --replica aws just prints help output. adding --log-level DEBUG is not recognized as a switch

Thank you

[ttung]

What do you get when you run hca --version?

[oskotsky]

$ hca --version
hca 3.4.6 (CPython 3.4.2 Linux-3.10.0-862.el7.x86_64-x86_64-with-redhat-7.5-Maipo)

I am trying to run this on rhel7 remote server, no gui. Would it be a problem? Does hca use port 443 only? I wonder if any additional traffic blocked by our firewall and that is why it breaks.
Thank you

[ttung]

What's the exact command you're running?

[oskotsky]

I was given a script "hca-download-census". Inside the script this seems to fail: "hca dss download --bundle-uuid XXXXXXXXXX --replica aws". I tried on my home system - Ubuntu Desktop and it worked without any issues.

[ttung]

Ohhhh, yeah, I think this might be firewall-related.

What do you get when you run curl https://dss.data.humancellatlas.org/v1/swagger.json | md5?

[oskotsky]

seems like working
$ curl https://dss.data.humancellatlas.org/v1/swagger.json | md5sum
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 100 55820 100 55820 0 0 144k 0 --:--:-- --:--:-- --:--:-- 144k
b6f06dffb65862d3367ca8e502fb1f06 -

[ttung]

That looks good. Can you zip up the contents of ~/.config/hca and post that here?

[oskotsky]

hca_config.zip
here it is

Thank you

[ttung]

Hm... that looks okay. What do you get when you run hca dss download --help?

[oskotsky]

i see this:

$ hca dss download --help
usage: hca dss download [-h] --bundle-uuid BUNDLE_UUID --replica REPLICA
[--version VERSION] [--dest-name DEST_NAME]

Download a bundle and save it to the local filesystem as a directory.

optional arguments:
-h, --help show this help message and exit
--bundle-uuid BUNDLE_UUID
--replica REPLICA
--version VERSION
--dest-name DEST_NAME

[ttung]

So what do you get when you run:

hca dss download --bundle-uuid c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18 --replica aws?

[oskotsky]

this is what is odd:

$ hca dss download --bundle-uuid c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18 --replica aws
usage: hca dss [-h]
{delete-subscription,post-search,get-file,put-subscription,post-bundles-checkout,get-subscriptions,put-bundle,head-file,get-bundles-checkout,delete-bundle,put-file,get-bundle,get-subscription,login,logout,download,upload}
...

positional arguments:
{delete-subscription,post-search,get-file,put-subscription,post-bundles-checkout,get-subscriptions,put-bundle,head-file,get-bundles-checkout,delete-bundle,put-file,get-bundle,get-subscription,login,logout,download,upload}
delete-subscription
Delete an event subscription.
post-search Find bundles by searching their metadata with an
Elasticsearch query
get-file Retrieve a file given a UUID and optionally a version.
put-subscription Create a event subscription.
post-bundles-checkout
Check out a bundle to DSS-managed or user-managed
cloud object storage destination
get-subscriptions Retrieve a user's event subscriptions.
put-bundle Create a bundle
head-file Retrieve a file's metadata given an UUID and
optionally a version.
get-bundles-checkout
Check the status of a checkout request.
delete-bundle Delete a bundle or a specific bundle version
put-file Create a new version of a file
get-bundle Retrieve a bundle given a UUID and optionally a
version.
get-subscription Retrieve an event subscription given a UUID.
login Configure and save hca dss authentication credentials.
logout Clear hca dss authentication credentials previously
configured with hca dss login.
download Download a bundle and save it to the local filesystem
as a directory.
upload Upload a directory of files from the local filesystem
and create a bundle containing the uploaded files.

optional arguments:
-h, --help show this help message and exit

[ttung]

Can you update your Python to a newer version?

[oskotsky]

this is a big system used by many people - it can't be done quickly and easily. :(

[oskotsky]

we have 2.7 and 3.4

[ttung]

Which 2.7 version?

[oskotsky]

Python 2.7.5

works the same way unfortunately:

$ export PATH=/opt/rh/python27/root/usr/bin/:$PATH
$ python --version
Python 2.7.5
$
$ hca dss download --bundle-uuid c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18 --replica aws
usage: hca dss [-h]
{head-file,get-bundle,put-subscription,post-bundles-checkout,get-bundles-checkout,delete-subscription,put-file,get-file,delete-bundle,get-subscription,get-subscriptions,post-search,put-bundle,login,logout,download,upload}
...

positional arguments:
{head-file,get-bundle,put-subscription,post-bundles-checkout,get-bundles-checkout,delete-subscription,put-file,get-file,delete-bundle,get-subscription,get-subscriptions,post-search,put-bundle,login,logout,download,upload}
head-file Retrieve a file's metadata given an UUID and
optionally a version.
get-bundle Retrieve a bundle given a UUID and optionally a
version.
put-subscription Create a event subscription.
post-bundles-checkout
Check out a bundle to DSS-managed or user-managed
cloud object storage destination
get-bundles-checkout
Check the status of a checkout request.
delete-subscription
Delete an event subscription.
put-file Create a new version of a file
get-file Retrieve a file given a UUID and optionally a version.
delete-bundle Delete a bundle or a specific bundle version
get-subscription Retrieve an event subscription given a UUID.
get-subscriptions Retrieve a user's event subscriptions.
post-search Find bundles by searching their metadata with an
Elasticsearch query
put-bundle Create a bundle
login Configure and save hca dss authentication credentials.
logout Clear hca dss authentication credentials previously
configured with hca dss login.
download Download a bundle and save it to the local filesystem
as a directory.
upload Upload a directory of files from the local filesystem
and create a bundle containing the uploaded files.

optional arguments:
-h, --help show this help message and exit
$

[kislyuk]

Hi @oskotsky, I recognize where the bug is coming from and will push out a fix shortly. The issue has been fixed in Python 2.7, but, just putting Python 2.7 into your $PATH is not sufficient to trigger its use - you actually have to use pip2 or a virtualenv to re-install the package.

[oskotsky]

Thank you! Running in virtualenv solved the problem. It should be encouraged anyway, right?

[oskotsky]

@kislyuk pointed the solution - running hca in virtualenv. solves the problem. Thank you so much!

[kozbo]

Closing