Commit Graph
25 Commits
Author SHA1 Message Date
Eric Rasche bab456fd01 Redirect lsof's stderr to ignored device 2014-10-18 18:38:03 -04:00
Eric Rasche d9a29812cc Found port properly 2014-10-18 18:38:03 -04:00
Eric Rasche 01c0633fd8 Added code to obtain port information from galaxy 2014-10-18 18:38:03 -04:00
Eric Rasche e8c619d01b Changed flow style for easier grepping
See the [PyYAML](http://pyyaml.org/wiki/PyYAMLDocumentation) docs for more information as to flow
style. Essentially it should make sure the `conf.yaml` file is greppable, which may be necessary for
IP address whitelisting.
2014-10-18 18:38:03 -04:00
Eric Rasche 4b64a70906 Added remote_host variable to docker conf
In order to whitelist IPs allowed to connect to notebooks, we need to know who the remote target
connecting is. We can blacklist on IP address only, as we have no way of authenticating them. While
we do have access to other information like cookies, we have no SSL nor way to know what
authentication method the galaxy server will be using.
2014-10-18 18:38:03 -04:00
Eric Rasche 7ae8deb202 Rewrote netstat commands as Popen piped commands
The original version actually failed for me. I am led to believe that all the pipes were being
passed to netstat as it said "I don't understand the option ':'" which came from the cut command.
At the cost of simplicity, this should do what we want properly. Alternatively we could move the
awk/cut/sort into python.
2014-10-18 18:38:03 -04:00
Eric Rasche 93ed4fe859 Working load from existing notebooks in history 2014-10-18 18:38:03 -04:00
Bjoern Gruening 7c02e8ce53 Style fixes 2014-10-18 18:38:03 -04:00
Bjoern Gruening 7ebbb74fc7 Remove copying of datatsets from Galaxy to docker. From now on, docker can fetch data from galaxy on demand. 2014-10-18 18:38:03 -04:00
Bjoern Gruening adfee3ba65 add random port assignment for different docker containers, for multiple users 2014-10-18 18:38:03 -04:00
Bjoern Gruening 73d728d1e2 update readme file 2014-10-18 18:38:03 -04:00
Bjoern Gruening 7048f38915 restructure repository layout 2014-10-18 18:38:02 -04:00
Eric Rasche c6559b4d70 Exchanged localhost for proper hostname
`request` provides a `host_url` like "fqdn:port" from which we can extract the FQDN that this server
was accessed at. This is important so that we are accessing the IPyNB on the correct host.
2014-10-18 18:38:02 -04:00
Eric Rasche 93c3695b10 Located full application URL
This should now work properly for galaxy instances hosted on different ports, on different
proxy-prefixes, on different fqdns, etc.
2014-10-18 18:38:01 -04:00
Eric Rasche 6f7e7805a1 Found the API key 2014-10-18 18:38:01 -04:00
Eric Rasche 6950aa2906 Typo, wrong destination and all datasets overwrote one another. This fixes that issue 2014-10-18 18:38:01 -04:00
Eric Rasche 5aa1cc13df Import all datasets by default
Need to provide a method to allow selecting a subset of datasets to copy, however for now they are
all copied over.
2014-10-18 18:38:01 -04:00
Eric Rasche 1a1b22874e Found the history ID 2014-10-18 18:38:01 -04:00
Eric Rasche 23b4ddc947 Notebook signatures must be unique
Rather than assigning a static notebook signature, this has been replaced with a randomly,
deterministically generated notebook signature. This is currently done off of the dataset's id,
encoded through trans (so it's the unique hash, and not just the number), however this will need to
be exchanged for history_id whenever we have access to that.
2014-10-18 18:38:01 -04:00
Eric Rasche 12ae652284 Added conf file generation 2014-10-18 18:38:00 -04:00
Bjoern Gruening 1a894a6e39 Fix for delay in displaying IPython NB
Fixes https://github.com/bgruening/galaxy-ipython/issues/1
2014-10-18 18:38:00 -04:00
Bjoern Gruening 5ecaa970eb use the new autokill container 2014-10-18 18:38:00 -04:00
Bjoern Gruening 7b8f457586 update readme file 2014-10-18 18:38:00 -04:00
Bjoern Gruening 3f4be5ece0 add the initial IPython Integration 2014-10-18 18:37:57 -04:00
Bjoern Gruening 4d210bbb8f Initial commit 2014-10-18 18:37:57 -04:00