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
Aysam Guerler
dfe698a2d4
ToolForm: Parses dynamic options and rerun states to tool model
2014-10-14 17:57:01 -04:00
Aysam Guerler
cdf368931d
Ui/ToolForm: Enable caching of GET requests.
2014-09-30 16:21:17 -04:00
Aysam Guerler
145f9acb91
ToolForm: Scrolling to error, basic validation, success message, style fixes
2014-09-23 14:18:45 -04:00
Aysam Guerler
9ac19b5fb3
Charts: Fix selection grid
2014-09-19 13:11:06 -04:00
Aysam Guerler
c18f13c85c
ToolForm/Ui: Improve and extend option fields, add dataset/collection selector
2014-09-19 12:47:17 -04:00
Nate Coraor
8fadc6392b
Rename universe_wsgi.ini -> galaxy.ini everywhere.
2014-09-15 16:43:51 -04:00
Dannon Baker
3125e5fa09
Charts to_json_string/dumps swap.
2014-09-08 17:11:18 -04:00
Carl Eberhard
7017833f42
Vis registry: add two tests (has_attribute, not_eq); add see also for test types in visualization.dtd; correct applicability tests for trackster and circster using not_eq on datatype.track_type
2014-08-28 09:44:56 -04:00
Aysam Guerler
d995301098
ToolForm: Add data selector, dynamic column selector and checkboxes, extends json content for basic parameters
2014-08-19 15:01:57 -04:00
Aysam Guerler
5a3741ab3c
Use floating instead of float as member id, pack code
2014-08-14 11:21:37 -04:00
Aysam Guerler
1799e4d5ee
Add tool form basics, refactor ui libraries, add alternative tool form template
2014-08-13 13:53:07 -04:00
Aysam Guerler
7d1d530c5e
Charts: Add crossfilter
2014-07-25 11:22:43 -04:00
Aysam Guerler
9c15798dfa
Fix for grids, pack scripts
2014-07-02 16:05:41 -04:00
Aysam Guerler
bc520f0bf8
Charts: Add comments, minor code clean up
2014-07-02 10:56:02 -04:00
Aysam Guerler
c4591d4426
Charts: Fix last change
2014-06-20 03:37:10 -04:00
Aysam Guerler
a71f9a5d51
Charts: Connect data points with template url
2014-06-20 03:28:41 -04:00
Aysam Guerler
f62e25c549
Charts: Allow empty columns
2014-06-20 02:24:24 -04:00
Aysam Guerler
bd97344b7e
Charts: Discrete histogram for jqplot
2014-06-19 14:13:49 -04:00
Aysam Guerler
847c6e8a0e
Charts: Reduce wrapper overhead
2014-06-19 13:43:13 -04:00
Aysam Guerler
ca720a709f
Charts: Fix canvas id parsing
2014-06-19 11:08:26 -04:00
Aysam Guerler
e1c441b54b
Charts: Fix options hiding
2014-06-19 07:58:50 -04:00
Aysam Guerler
19e643e12c
Charts: Simplify canvas id parsing
2014-06-19 07:56:03 -04:00
Aysam Guerler
0c19d260fe
Charts: Use other icons for processing chart types
2014-06-19 03:57:57 -04:00
Aysam Guerler
01ac0e7aee
Charts: Re-add pdf export
2014-06-18 09:48:57 -04:00
Aysam Guerler
c2da932c01
Charts: Pad y axis
2014-06-18 06:53:16 -04:00
Eric Rasche