Question: {Disarmed} Extra Hack To Get Own Database Connection To Work?
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gravatar for Perdacher,Martin
7.6 years ago by
Perdacher,Martin10 wrote:
hello galaxy-community, we stored a lot of peak-information in a database. to import these files into galaxy, i read the DataConnectionProtocol (https://bitbucket.org/galaxy/galaxy-central/wiki/DataSources) and i also took a look at the biomart.xml example (https://bitbucket.org/galaxy/galaxy- dist/src/8729d2e29b02/tools/data_source/biomart.xml). biomart does exactly what i want. here is my full tool configuration xml-file: <tool id="regionDb" name="RegionDb-Import"> <description>Import from regionDb</description> ../data_source/data_source.py $output $__app__.config.output_size_limit <inputs action="http://localhost:8888/index.html" check_values="false" method="get"> <display>Display-Text</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner"/> <param name="tool_id" type="hidden" value="regionDb"/> </inputs> <request_param_translation> <request_param galaxy_name="URL" remote_name="URL" missing=""/> <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get"/> <request_param galaxy_name="name" remote_name="name" missing="Biomart test query"/> </request_param_translation> <outputs> <data name="regionDb File" format="bed" label="regionDb import"/> </outputs> <help> **What it does** import ... </help> </tool> content of http://localhost:8888/index.html:
i also tried a different action="http://galaxy/tool_runner?tool_id=reg ionDb&type=text&name=new%20history%20entry&URL=http://localhost:8888/g etfile.php" with the same error message (shown below). what actually works is, if i try to receive biomart data with this request.
my question is: was there some extra hack to get the biomart tool to run? i found some lines in the lib/galaxy/web/controllers/tool_runner.py which confirm that assumption: #Hack to get biomart to work, ideally, we could pass tool_id to biomart and receive it back @web.expose def biomart(self, trans, tool_id='biomart', **kwd): """Catches the tool id and redirects as needed""" return self.index(trans, tool_id=tool_id, **kwd) Server Error URL: http://galaxy/tool_runner/regionDb?type=text&name=new%20history%2 0entry&URL=http://localhost:8888/getfile.php Module paste.exceptions.errormiddleware:143 in __call__ Module paste.debug.prints:98 in __call__ Module paste.wsgilib:539 in intercept_output Module paste.recursive:80 in __call__ Module galaxy.web.framework.middleware.remoteuser:109 in __call__ Module paste.httpexceptions:632 in __call__ Module galaxy.web.framework.base:145 in __call__ Module galaxy.web.controllers.tool_runner:27 in regionDb Module galaxy.web.controllers.tool_runner:75 in index Module galaxy.tools:933 in handle_input Module galaxy.tools:1225 in execute Module galaxy.tools.actions:291 in execute Module galaxy.tools.actions:154 in wrap_values KeyError: 'GALAXY_URL' extra data CGI Variables CONTENT_LENGTH '-1' CONTENT_TYPE 'application/x-www-form-urlencoded' HTTP_ACCEPT 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET 'ISO-8859-1,utf-8;q=0.7,*;q=0.7' HTTP_ACCEPT_ENCODING 'gzip,deflate' HTTP_ACCEPT_LANGUAGE 'en-us,en;q=0.5' HTTP_CONNECTION 'Keep-Alive' HTTP_COOKIE 'galaxysession=c6ca0ddb55be603af8ffade046cb8ca7fe7a18f 326db29b947c846a3b24831e1362e15c491e90b43' HTTP_HOST 'gen43' HTTP_REFERER 'http://localhost:8888/index2.php?GALAXY_URL=http%3A// gen43/galaxy/tool_runner&tool_id=regionDb' HTTP_REMOTE_USER 'perdacher@genau.at' HTTP_USER_AGENT 'Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.3) Gecko/20100401 Firefox/3.6.3' HTTP_VIA '1.1 gen43.imp.univie.ac.at' PATH_INFO '/tool_runner/regionDb' QUERY_STRING 'type=text&name=new%20history%20entry&URL=http://local host:8888/getfile.php' REMOTE_ADDR '10.42.111.27' REQUEST_METHOD 'POST' SCRIPT_NAME '/galaxy' SERVER_NAME 'gen43.imp.univie.ac.at' SERVER_PORT '9191' SERVER_PROTOCOL 'HTTP/1.1' Configuration __file__ '/projects/solexadst/serverData/galaxy- devel/universe_wsgi.webapp.ini' admin_users 'tamir@genau.at' apache_xsendfile 'False' brand 'GenAu-Epx Development!!!' cookie_path '/galaxy' debug 'TRUE' enable_api 'True' enable_job_running 'False' enable_pages 'True' here '/projects/solexadst/serverData/galaxy-devel' log_level 'DEBUG' new_user_dataset_access_role_default_private 'True' remote_user_logout_href '/logout' remote_user_maildomain 'genau.at' require_login 'True' set_metadata_externally 'True' static_cache_time '360' static_dir '/projects/solexadst/serverData/galaxy-devel/static/' static_enabled 'True' static_favicon_dir '/projects/solexadst/serverData/galaxy- devel/static/favicon.ico' static_images_dir '/projects/solexadst/serverData/galaxy- devel/static/images' static_scripts_dir '/projects/solexadst/serverData/galaxy- devel/static/scripts/' static_style_dir '/projects/solexadst/serverData/galaxy- devel/static/june_2007_style/blue' upstream_gzip 'False' use_interactive 'False' use_remote_user 'True'
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ADD COMMENTlink written 7.6 years ago by Perdacher,Martin10
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