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The download link in brainspell.org/download provides an xml file with all articles and tags. What would be the best way of organising that data to make it reusable and interoperable? a json file? a csv file? what data to include? Would it be possible to have a script to automatise a monthly creation of this file?

As we discussed, the SQL data was added to the variable "Test" in the Brainspell.php document using the Str_replace function. All of the code is within lines 1543 and 1610. The dictionaries in the variable can be used, but the location data itself is still nested as a string and needs to be parsed.

Here's my branch with I believe the most updated code
https://github.com/Sharabesh/brainspell/tree/Sharabesh_updated

Here's where I set the HTML Variable to an array containing the Database to be parsed in the Javascript
https://github.com/BIDS-collaborative/brainspell/compare/BIDS-collaborative...Sharabesh:Sharabesh_updated#diff-256f7777bc064f9f85c8ecb005d3c8abR1596

And here is the variable declaration in Search.html;

https://github.com/BIDS-collaborative/brainspell/compare/BIDS-collaborative...Sharabesh:Sharabesh_updated#diff-4bc774c1cdab1ae9d323d6c298e20ed6R93

https://blog.andyet.com/2016/01/25/easy-docker-on-osx/

This could be done in the database with PHP, or alternatively by a script that modifies files in docker/postgres/data/*.txt.

From today's morning meeting with JB, I wrote down some notes. Here they are:

From brainspell-search.js:
configureTemplateImage() //change the size of the window to fit the size of the brain
drawTemplateImage: There are various channels for colors in viewing the brain.
tmpl_px.data[ i ] =val; //red
tmpl_px.data[ i+1 ]=val; //green
tmpl_px.data[ i+2 ]=val; // blue channel
tmpl_px.data[ i+3 ]=255; //alpha channel (transparancy)

loadLocations() : load the locations. Since we don't want to load all of them, when 3 are loaded we just display them.

$(".paper-stuff [href]").each(function(){var arr=$(this).attr('href').split("/");refs.push(arr[arr.length-1])});
//.paper-stuff is where papers/articles are stored.

The loop in brainspell.php:
$str='

';
foreach($hits as $hit):
$str.="
• <div class="paper-stuff">\n";
  $str.="

  <a href="".$rootdir."article/".$hit->PMID."">";
  $str.=$hit->Title."

  \n";
  $str.="<p class="info">".$hit->Reference." (".sprintf("%.0f",$hit->score*100)."%)
  \n";
  $str.="
\n";
endforeach;
$str=$str."

Notes

• Variable vs. Comment: Clarified the code regarding to the <!-- Bla Bla Bla --> symbol, more detail explanations in the Documentation.md file.
• Text Search: To find the filename with certain text using command line: grep -lr "any text" *

Next Steps

• Modify all the code to follow the Variable vs. Comment convention.
• Continue to implement the article title snapshot with the button feature indicated in issue #12 .
• Attend the code structure meeting on Tuesday Nov. 3rd at 5pm in the BIDS

P.S. Please feel free to add more notes @anokhikastia. To avoid redundant work, please comment below if you complete any of them. @anokhikastia @SydneyHuang

There are some big files got checked in there... probably don't need them, may be candidates for a filter-branch.

@r03ert0 you mentioned anyone could download this information, but it is not obvious. Can you provide a pointer? Once you've done that, you can un-assign yourself (potentially assigning to another member of the team).

Implemented the upload button on the webpage, now it could browse files and read CSV file.

How can we use these titles read from CSV to reproduce graphs/outputs on the page? @r03ert0 @jbpoline @davclark

While configuring apache, when we type in the 1st command, we get:
ln: failed to create symbol link ' ./headers.load' : Read only file system

How do we fix this?

I tried to modify the /etc/php5/apache2/php.ini file, and couldn’t save the changes — there was a pop-up window requires the super user password, where can I get that password? @jbpoline @davclark @r03ert0

This will involve (relatively) simple jQuery to grab info from the DOM and put into a table.

A first step is to get the titles with jQuery:

$('.paper-stuff a')

Iterate through that and turn it into one string with a title on each line.

Use the jQuery docs.

@r03ert0 (and possibly @jbpoline) can you let me know if there's a better way to access the database than via the CSV dump? If it's a hassle, don't worry - it shouldn't be TOO much trouble to parse the CDATA blocks, just a minor nuisance.

List of SQL query locations in brainspell.php. Please put your name next to a function if you're updating it. Maybe we should also prioritize the functions that are part of the "core" functionality - querying and constructing maps:

• user_register
• user_login
• ... add remaining functions here!

I cannot upload the file into myphpadmin because it says that the file is too large. How do I go about fixing this? Thanks! @jbpoline @davclark

Notes

• Display all existing branches:

git branch -vaa

If you want to checkout any remote branch:

git checkout remotes/origin/SomeBranch

• Training Wheels:

After you pull, you should see there is a new branch called remotes/origin/training-wheels

git checkout training-wheels

Link the configurations:

cd /etc/apache2/
sudo ln -s ~/brainspell/conf/apache-site-training.conf sites-enabled/
sudo ln -s ~/brainspell/conf/base-apache-training.conf conf-enabled/

Then the sites should be linked, to check:

ls -l sites-enabled/
ls -l conf-enabled/

All the *.conf file should be in blue.

Then, restart the apache by running:

sudo service apache2 reload

Then if you open localhost:8000 on the Firefox, you should be able to see the simplified version of brainspell. By clicking on the button, you should see the alert "Yo!"

Next Steps:

• Modify the templates/base.html file to make the button works for download.

P.S. More details in Issue #12, and more notes in Issue #15

I successfully imported the brainspell_sanitized.sql file into the database, but the brainspell.dev still doesn't work. It only displays the Apache 2 Ubuntu Default Page.
Any suggestion on how to fix this? @jbpoline @r03ert0 @davclark

Notes:

Need to add the article ID (and other info) into the download csv file as another column

Next Steps:

• Add article ID
• Prepare for the Presentation

Presentation: 12/08 from 4pm - 6pm. Present around 10 mins.

1. Give a demo of the website
2. How & why implemented the download feature
3. Future perspectives

@anokhikastia @SydneyHuang

When trying to click on Blog, I get the following error:
Warning: file_get_contents(): php_network_getaddresses: getaddrinfo failed: Temporary failure in name resolution in /home/oski/brainspell/site/php/brainspell.php on line 330
Warning: file_get_contents(http://brainspell.org/php/blog.php): failed to open stream: php_network_getaddresses: getaddrinfo failed: Temporary failure in name resolution in /home/oski/brainspell/site/php/brainspell.php on line 330

Line 330:
$blog=file_get_contents("http://brainspell.org/php/blog.php");

I haven't modified anything. When I switch to someone else's branch, I still get that error. Is something wrong with just my computer or there is an actual error in accessing this file?

They don't need to be correct yet! Just come up with a mechanism.

cc @kevinyu927

I'm trusting @stefanv can keep things straight, so putting this here prior to settling on the final development location... I'll keep notes below.

Create a downloadable file (csv/json/other formats) at the bottom of the searching result page that store articles' info with given searching query.
More discussion at #11

For my search by location function (which seems to work on keyword inputs as well), I am not sure how to format the String I get into polished HTML that we see on the page. The code is between lines 1590 and 1610 in Brainspell.php

Right now outputs look something like this:

I know that Search_lucene uses a similar method to yield outputs given a query, but I am not seeing quite where that happens.

It's available here (you may need to log in).

An initial goal is to start including statistical scores in the computation of aggregate results/maps.

@jbpoline is likely in the lead on this as of "right now," though I've talked about making a simple ansible script, given the lack of provisioning scripts at the moment.

As it stands, we think we have reasonable instructions in the Wiki for getting apache configured. MySql still needs to be set up, and the stock Ubuntu instructions don't seem to work for setting the root password, which is a pre-req for other things working (like phpmyadmin).

I very much prefers to use ansible in situations like this. I expect there to be a lot of errors that take time to track down as beginners go about setting up the project.

@r03ert0 gave a demo of this, but I don't see how to access it. Is it a "private" feature?