The more I think about step-by-step installation documentation and overall support, the more I realize how many unnecessary dependencies this thing has. Step-by-step installation is a lot easier to document with fewer steps and fewer failure modes.
If you look at builder-sql-guide<https://informatics.gpcnetwork.org/trac/Project/wiki/BuilderSaga#builder-sql-guide>, what this thing is supposed to do is pretty simple: select a subset of rows from your i2b2 star schema. The unit testing support in python is nice, but there comes a time when sql-in-python is inside-out. data_delivery.sql<https://bitbucket.org/gpcnetwork/heron_extract/src/28c69a2c40f4edd3f775925fe3cc4810f0e1e1dd/cdr2edc/data_delivery.sql?at=just_csv_3617> is work toward putting the SQL where we're used to having it: in a .sql file. (It's on a just_csv_3617<https://bitbucket.org/gpcnetwork/heron_extract/branch/just_csv_3617> branch, which comes from some brainstorming on alternatives to sqlite.) Queuing requests in the filesystem brings up all sorts of annoying permissions issues and stuff. Why didn't we queue requests in the database? No good reason. Just momentum from prototyping. Also in the just_csv_3617<https://bitbucket.org/gpcnetwork/heron_extract/branch/just_csv_3617> branch, we're aiming to drop filesystem access. 881. [f0c52f7c7d18/bmi_ops] convert job info from JSON to CSV 883. [b04712d6a797/bmi_ops] SQL script analagous to dfbuilder.py 884. [77ebfd8fd3ca/bmi_ops] idea: separate upload_status stuff from facts 885. [28c69a2c40f4/bmi_ops] idea: reduce exported facts to integers for performance https://bitbucket.org/gpcnetwork/heron_extract/branch/just_csv_3617 Connecting to SQLServer from python is a nightmare. (Installing cx_Oracle is bad enough). We're i2b2 shops - we already had to get Java talking to the database; why not just use that infrastructure? Moving the plugin back-end to jython (in the mod_3006<https://bitbucket.org/gpcnetwork/heron_extract/branch/mod_3006> branch) was a step in that direction, but installing pypi modules such as mechanize is a royal pain. A big part of the "it just works" factor of the Java world is the maven library ecosystem. I've had good luck building single-jar apps using scala. The onejar_g335<https://bitbucket.org/gpcnetwork/heron_extract/branch/onejar_g335> branch is an experiment in that direction; it's only a start, but it looks promising. -- Dan ________________________________ From: French, Tony [[email protected]] Sent: Saturday, July 09, 2016 11:44 AM To: Dan Connolly; [email protected] Subject: RE: DataBuilder installation instructions I was finally successful at implementing Dan’s recommended version of the DataBuilder (ver: 1b8a53f78be0) into the current version of I2B2 (1.7.07c). Besides having to manually apply the patches, I found that the variable declaration was missing for the backend variable in DFBuilder/tool_widgets.js (line 175). var backend = pop(params, 'backend') == 'builder' ? this.builder : this.rgate; I will say that while it is certainly nice to be able to have a quick demo of the plugin using the I2B2 Demo VM, the community would probably be better served by a well-documented step-by-step installation procedure. --Tony Tony French | Software Development Manager Tools and Shared Resources Center for Biomedical Informatics [cid:[email protected]] 1101 West Tenth Street Indianapolis, IN, 46202 Tel 317-274-9087 | Fax: 317-274-9305 Twitter: @Regenstrief | Facebook.com/regenstriefinstitute<redir.aspx?REF=jlOorRWZUdRQ0AZ9DKgZ0tW3QbraEddRDfI70UmDzKfHCQuLyqnTCAFodHRwOi8vZmFjZWJvb2suY29tL3JlZ2Vuc3RyaWVmaW5zdGl0dXRl> www.regenstrief.org<redir.aspx?REF=dFdYxAirKpESLjIv_UEWQOw_QFkpUgo5EnET5F-TzF7HCQuLyqnTCAFodHRwOi8vd3d3LnJlZ2Vuc3RyaWVmLm9yZy8.> Confidentiality Notice: The contents of this message and any files transmitted with it may contain confidential and/or privileged information and are intended solely for the use of the named addressee(s). Additionally, the information contained herein may have been disclosed to you from medical records with confidentiality protected by federal and state laws. Federal regulations and State laws prohibit you from making further disclosure of such information without the specific written consent of the person to whom the information pertains or as otherwise permitted by such regulations. A general authorization for the release of medical or other information is not sufficient for this purpose. If you have received this message in error, please notify the sender by return e-mail and delete the original message. Any retention, disclosure, copying, distribution or use of this information by anyone other than the intended recipient is strictly prohibited. From: Dan Connolly [mailto:[email protected]] Sent: Thursday, July 07, 2016 12:11 PM To: French, Tony; [email protected] Subject: RE: DataBuilder installation instructions That's pretty much the main installation documentation, still. And that it is out of date is a known problem: * #335: problem: DataBuilder VM deployment outdated by migration of middle tier to jboss <redir.aspx?REF=y8vc-F24zCACCWDiAk0ZThOL1TPyI8-KWfajTPVJv_nHCQuLyqnTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC90aWNrZXQvMzM1> I suggest you report details of the errors you're getting; perhaps there are easy fixes to the documentation that will get you going. Be sure to include the exact revision hash of the code you're trying to use; if you checked out the current code from the heron_extract<UrlBlockedError.aspx> repository, you might have better luck with an older version (such as rev 1b8a53f78be0 from Nov 2014, available in heron_extract.zip<redir.aspx?REF=meECLHjUndC_gy9XF-y7BM9iKmWm3ymkLZKr3EhUdqbHCQuLyqnTCAFodHRwczovL2luZm9ybWF0aWNzLmdwY25ldHdvcmsub3JnL3RyYWMvUHJvamVjdC9hdHRhY2htZW50L3dpa2kvQnVpbGRlclNhZ2EvaGVyb25fZXh0cmFjdC56aXA.>). -- Dan ________________________________ From: [email protected]<redir.aspx?REF=w2VUj1erqrm_nEfwpz12ouEbhuchZlI4APAXqdkLUDzHCQuLyqnTCAFtYWlsdG86Z3BjLWRldi1ib3VuY2VzQGxpc3RzZXJ2Lmt1bWMuZWR1> [[email protected]] on behalf of French, Tony [[email protected]] Sent: Thursday, July 07, 2016 10:56 AM To: [email protected]<redir.aspx?REF=EDQUzamTnOEBcFqLIwN2pzFKjYXU8YtpJu9GevkMHfTHCQuLyqnTCAFtYWlsdG86R1BDLURFVkBMSVNUU0VSVi5LVU1DLkVEVQ..> Subject: DataBuilder installation instructions We are working on getting DataBuilder installed in our environment. I found the BuilderSaga<UrlBlockedError.aspx> article for installing it into an i2b2 demo VM. Is that the best guide to reference for installing it into an actual working environment or are there step by step manual instructions available anywhere? I have tried following the screencast to install using the latest i2b2 demo VM but have already ran into several errors. Does anyone have a historical link to i2b2vmware-1703a.zip ? Thanks, Tony Tony French | Software Development Manager Tools and Shared Resources Center for Biomedical Informatics [cid:[email protected]] 1101 West Tenth Street Indianapolis, IN, 46202 Tel 317-274-9087 | Fax: 317-274-9305 Twitter: @Regenstrief | Facebook.com/regenstriefinstitute<UrlBlockedError.aspx> www.regenstrief.org<UrlBlockedError.aspx> Confidentiality Notice: The contents of this message and any files transmitted with it may contain confidential and/or privileged information and are intended solely for the use of the named addressee(s). Additionally, the information contained herein may have been disclosed to you from medical records with confidentiality protected by federal and state laws. Federal regulations and State laws prohibit you from making further disclosure of such information without the specific written consent of the person to whom the information pertains or as otherwise permitted by such regulations. A general authorization for the release of medical or other information is not sufficient for this purpose. If you have received this message in error, please notify the sender by return e-mail and delete the original message. Any retention, disclosure, copying, distribution or use of this information by anyone other than the intended recipient is strictly prohibited.
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