The gnomAD browser open repository is very complex and I'm having trouble figuring out how to start or what steps to follow to do it.
Basically, I have my own data, so I would like to try to create my own type of exome aggregation database, and the idea was to try to replicate gnomAD and take advantage of its open code source, eventually being able to load my data into it.
gnomAD repo: https://github.com/broadinstitute/gnomad-browser
Thanks in advance!
Note: My background is in bioinformatics, but I don't have much knowledge of web development.
I believe I should begin by following the instructions available in the CONTRIBUTING.md file of the gnomAD repository, is that right?
Related
The title says it all. I need to create a form that the user fills in and on submit, I want the data to go to a database and a PDF to a directory on the server.
I don't think AngularJS can do all of these things, can it? I'm very new to programming -- trying to crossover from HTML/CSS/JS to more in-depth projects.
Can anyone please suggest the best course for this? What language for the form, writing to the DB and generating a PDF? I can do the rest of the research and build it out once I have some direction.
How would you go about achieving this?
Thanks!
Ugh. I forgot to mention that PHP is not an option. Is there another way?
All you need is to apply the paradigm Client / Server.
With angular.js you can build the client software for handling the form but this is not necessary...
With a single script php you can generate the page with the form and handling the incoming data.
You can use a standard relational database like mysql for storing it and, about the pdf, take a look here
I have implemented the file upload functionality with reference to this link
http://www.slideshare.net/mongodb/mongo-db-bangalore-2012-15070802
But the file is not stored into the Gridfs.
I had done some research for the same and also with reference to this blog post
http://php-and-symfony.matthiasnoback.nl/2012/10/uploading-files-to-mongodb-gridfs-2/
But again, unfortunately, I stuck with this issue since last from 15 days
please help.
Please take a look at KnpLabs/Gaufrette and the related KnpLabs/KnpGaufretteBundle
The Gaufrette bundle provides a level of abstraction around file systems and, it helped me get file-oriented operations up and running quickly. I found it very useful, and in fact the Symfony CMS package leverages this bundle. It may help you out as well.
I hope someone have already faced an issue to verify that application shows correct data from database. I reviewd how groovy used SQL, but I have no idea where and how I should do that. I'm just starting to use gradle+Spock+Geb for testing application. I have a few files where I described a couple of pages from application, a couple of modules and a file with spock specification. Where and how I need to connect to Oracle DB, use SQL and compare result's data with application's ones?
P.S. I write everything in notepad++ and launch from command line writing 'gradlew firefoxTest'. Does exist any more comfortable way to work with gradle+spock+geb?
Thanks in advance.
Because there are no other answers, I wanted to provide a solution someone at my company thought of. This assumes you already have a project that uses some sort of JDBC. In our case it is JDBI.
The idea is to extend Classloader and then use that to directly access the data access object class via the JVM. That idea should work.
I have not tested it out because it doesn't completely fit our use-case. I'll admit that this does not completely apply to your use case, but technically you could just run the jar of an existing project, which can access the database.
I just want to know about the best way to store simple data in wfp application. I'm using SQL CE, but sometimes I need to store simple data (for instance one string). I don't want to use for it db, and I think it's the right decision.
Could you please give me a guidance on how should I do that in best way or any useful resource?
Is there any particular features data settings storage for pattern MVVM?
Thank You.
Use Settings for exactly this scenario. It's simple, allows per user and system wide scenarios and is build into Visual Studio nicely.
Double clicking on Settings.settings in the Properties folder of your project (in Solution Explorer) brings up the editor and you can access these in code with something simple like Properties.Settings.Default.StringPropertyX.
http://msdn.microsoft.com/en-us/library/aa730869(v=vs.80).aspx
if you're going to be upgrading in the future, I suggest that you create a small abstraction layer that you can upgrade to using any DB or other source, when you need to.
Until you do the upgrade, I would suggest a simple XML file using XDocument and XElement (and the rest of that api).
The reason why I am suggesting this is because you can use Linq on them easily and this enables you to change the provider in the future without any problems.
here is the MSDN on XDocument http://msdn.microsoft.com/en-us/library/system.xml.linq.xdocument.aspx .
I hope this proves to be helpful to you ;-)
Cheers,
Max
p.s. lemme know if this is what you needed or not!
If you publish the application through ClickOnce then you can use IsolatedStorage. It is pretty easy to use, just a few lines of code. You can learn how to use it on WPF isolated storage.
If you don't publish it through ClickOnce then I would suggest you keep it simple and use static class.
you can use file system.. try to create xml file or csv file in the wpf app directory...
you can read and write to same file.. so that you can save what ever you want to that file and read from the same file..
I have used log4C and it is great. However, I would like to get Pantheios working as well and was wondering if it supports a rolling file appender? I mean if I have something logging to file in Production I need it to be a rolling file?
Also, stupid question but let's say I have DEBUG, INFO and ERROR type logs when using Pantheios, how do you limit to only seeing INFO (for example) using some "sort of config file" like with log4C?
Thanks for the help, any advise would be greatly appreciated ;-)
Lynton
I started evaluating Pantheios since yesterday. Therefore my reply may not be perfect.
1) For rolling file, you can customize the back-end to roll the file by yourself (pantheios_be_file_setFilePath), or use log4c as your logging transport in the back-end. :-)
2) Customize the front-end and make pantheios_fe_isSeverityLogged() function return true only for INFO. You can make it configurable by picking up the settings from .ini file.