Re: [galaxy-dev] Bug: Galaxy Tool Shed dependency communication via HTTP GET method
Folks, After checking a little closer last night, I have one clarification. The Tool Shed does use POSTs as well as GETs, but even when it's POSTing, the encoded dictionaries (encoded_repo_info_dicts) are part of the query string. The encoded_repo_info_dicts should probably become part of the POSTed data. -rico On Sep 12, 2013, at 3:55 PM, Richard Burhans wrote: When installing Galaxy Tool Shed repositories into a local Galaxy instance, tool shed dependecies are exchanged as an encoded python dictionary via the HTTP GET method. If a tool shed repository contains enough dependencies, the length of this encoded dictionary can become extremely long. In my case, it became long enough for my Apache server to choke on it: [Wed Sep 11 15:34:53 2013] [error] [client XXX.XXX.XXX.XXX] request failed: URI too long (longer than 8190) The HTTP standard does not place a limit on the length of a URI, but the de facto limit is 2000 characters. See the following stackoverflow answer: http://stackoverflow.com/a/417184 I would recommend either: 1) communicating toolshed dependencies via an HTTP POST 2) redesigning tool shed - instance communications As a stopgap measure, I've modified lib/tool_shed/util/ encoding_util.py to use a more compact encoding scheme. I'm attaching a copy in case someone else runs into the same problem. -ricoencoding_util.py ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Conditional and validator: refresh_on_change without validation
You're not missing anything; using validators is the right way for checking parameter values. However, the page refreshes + validation errors is certainly less than ideal for usability. We're in the process of transitioning tool forms to a JavaScript-based framework so that full page refreshes (and associated validation checks) are no longer necessary. J. On Sep 11, 2013, at 4:26 AM, Kahlke Tim wrote: Hi I'm using the validator tag for simple sanity checks of a tool input. But I realized that any conditional in the form will automatically call refresh_on_change which also validates all fields and prints errror messages. So questioin: is there a more galaxy-like way of checking input parameters? I am aware of the possibility to do sanity checks through custom code (http://wiki.galaxyproject.org/Admin/Tools/Custom%20Code) but the page states it should only be done if there is no other way. Regards, Tim ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Geek question re HTTP POST and Galaxy
Take a look at the histories controller (histories.py) for an example + documentation on how Galaxy realizes a RESTful interface. In short, you'll want to implement different methods for create, read, update, and delete. Kwds are miscellaneous parameters included in a request that are not explicitly specified in a method signature. Good luck, J. On Sep 13, 2013, at 7:52 PM, Ted Goldstein, Ph.D. wrote: I've been knocking my head over this all afternoon and I was hoping to buy a vowel, use a lifeline, whatever. I'm trying to use the Ember JS framework (which is very nice) for some extensions. It relies heavily on a REST model using the same method with all of the HTTP forms including ActionHTTP Verb URL Find GET /people/123 Find All GET /people UpdatePUT /people/123 (with the HTTP payload packed with the JSON content) CreatePOST/people DeleteDELETE /people/123 How can I make an API function that responds to all five forms and what should be in buildapp.py? All of the code in Galaxy currently uses the kwd (keyword) parameter. But there are no keywords here. Confused, Ted ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Geek question re HTTP POST and Galaxy
Sweet! Thanks Ted On Sep 14, 2013, at 11:04 AM, Jeremy Goecks jeremy.goe...@emory.edu wrote: Take a look at the histories controller (histories.py) for an example + documentation on how Galaxy realizes a RESTful interface. In short, you'll want to implement different methods for create, read, update, and delete. Kwds are miscellaneous parameters included in a request that are not explicitly specified in a method signature. Good luck, J. On Sep 13, 2013, at 7:52 PM, Ted Goldstein, Ph.D. wrote: I've been knocking my head over this all afternoon and I was hoping to buy a vowel, use a lifeline, whatever. I'm trying to use the Ember JS framework (which is very nice) for some extensions. It relies heavily on a REST model using the same method with all of the HTTP forms including Action HTTP Verb URL Find GET /people/123 Find All GET /people Update PUT /people/123 (with the HTTP payload packed with the JSON content) Create POST/people Delete DELETE /people/123 How can I make an API function that responds to all five forms and what should be in buildapp.py? All of the code in Galaxy currently uses the kwd (keyword) parameter. But there are no keywords here. Confused, Ted ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
