GSOC15 adventuring

Researching WebLogo hosting

Alongside reviewing the API documentation, I've started researching github as a possible host for the WebLogo project. My previous experiments with Heroku didn't work, and it may be possible to use the github pages features. The quickstart makes it seem easy, but running .cgi files makes the process more complicated. I still need to make an appointment with AWS to review that possibility of moving the WebLogo service from Rackspace.

Reviewing API

I started reading the WebLogo API docs and noting questions that I have for the main author regarding updates to it.

Blog Post Workaround: Working IRL

My computer had a hard drive failure that kept me offline for a little bit. It took longer than expected for me to get it back because my working computer is an older model that uses a rare/ obsolete connection for the drive. I had an SSD drive but the shop told me I needed to replace it with a PATA/IDE SSD drive. The Locating and delivery of the part was driving me crazy impatient. I did do offline work with the main author which was good. On one day, he reviewed my code, and he played "devil's advocate" regarding the front-end refactoring. He quizzed me on the decision I made with regards to the frontend. He asked me if I've designed the frontend to "fail gracefully". I hadn't.

Saving logo images

I'm debugging the dropbox save function. I have the logo appearing on the DOM, but I don't have the jquery function that would save the image to dropbox working. I'm studying how the download logo feature works, and then learn how to apply that solution to download to dropbox instead. I'm also still wrestling with pixels on how the weblogo image controls appear on the create page. I'm surprised about how misalignment by a pixel or 2 really sticks in my side.

GSOC presentation & file alerts

Yesterday I gave a presentation on my experience thus far with Google Summer of Code and Portland State University at Hackbright Academy, a programming bootcamp aimed toward women. I was happy to share my experience with GSOC15 and with the PSU GSOC community. I've found the entire process valuable, empowering and affirming. As far as coding, I'm reviewing an issue registered when we made the Github migration. One user submitted that they used the wrong file in WebLogo, and while s/he caught the error, they would have appreciated a warning that the wrong file was being uploaded. I'm looking through the python code on where a warning alert would be effective, or if the front-end should handle that kind of alert.

next steps check-in

I had a meeting with the main author on what the next steps. Part of the project is to make advanced options available on the command line interface to web users. Since I'm working on the page that creates the sequence logo, I needed clarification on which options are to be included. However, the main author wanted to keep the main create page easy and clean to use, and he doesn't want more options added to main page. So he proposed making a new web page that offers command line access. There are a couple of security issues that need to be addressed and thought through. I've never seen such a thing on a web page yet, so I'll have start researching a possible solution. Also, I cleaned up all the references to the new code repository in the new html code, but he wants the current live code to have the new references as well. I finally have commit privileges on the Github account and might be able to push code more quickly.

Serving WebLogo community with Github port

The export to github revealed previously unknown issues that were reported. Apparently the issues tracker in google code wasn't sending notifications. Now 5 open issues appeared that were previously unknown. The WebLogo community is already being served better by the code export because issue tracking seems to be more robust and transparent in Github. I studied the open issue list to try to see if there is anything I can help with. However, it seems that improved documentation, which is the next major part of my project scope, would go far in reducing issue reporting.

Cleaning up Github export

Now that main body of code has been exported successfully, many documentation pieces and links have to be updated. I learned Markdown re-write the README file for the landing page. I wrote and edited the new README file and uploaded the file to WebLogo's github as my first official merged contribution to the WebLogo code base. I also worked on adding the dropbox "saver" button to the create.html page. Adding the saver button was easier than adding the "chooser" button to the front-end, but I anticipate kinks on getting it to work. I think if I write a jquery function that listens for a "checkbox" function, i can trigger the dropbox save javascript function. I'll be scheduling a meeting with the main author regarding porting WebLogo to a new server, and to figure out the what needs to be done with documenting the API, and for him to let me know which command line functions that he wants added to the web application.

Porting WebLogo complete

WebLogo's code is settling in its new home on Github. You can transfer repositories to another owner via the settings button. The history of releases, commits, transfers and branches was successfully ported from Google Code to CrooksEnsemble's github. The last thing to do is set the forwarding link on Google Code. Also, I solved the dropbox file upload issue. The Dropbox link needed some javascript massaging to appear in the html. Also, I had to write a javascript/jquery function that enables the browser to open the text files and to dump contexts into the text box for processing by WebLogo. I'm happy to report that I'm more than halfway through the scope proposal for WebLogo, woohooo! Tomorrow is part of a holiday weekend in the United States, and I'll be offline until Monday.

Github export

We have landed in "The best laid schemes of Mice and Men oft go awry" territory with the Github export situation. I had a meeting with WebLogo's main author,and he finally gave me updating rights on Google Code and the CrooksEnsemble Github repository. I got the go ahead to run the github exporter, after updating the main author about the Github information. I got the go ahead to run the exporter. However, we expected that the exporter would be able to direct the export to the CrooksEnsemble as an organization that I belong to. Alas not. The exporter created the WebLogo repository on my personal github. Now we're in the situation of getting the WebLogo to the right repo, and how to get WebLogo off my repo. To keep the checkout and push/merging record keeping standardized, I should be checking code out/in from the main repo. I've reached out to Github support for guidance again. And the main author is glad that i've spared him the trouble of troubleshooting this.

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