as per @julie-sullivan in "[Fwd: Re: publicly declaring our friendship]"

http://intermine.readthedocs.org/en/1.3/embedding/list-widgets/#embedding-mine-widgets-on-a-custom-page

I was going to suggest to someone that they could base their contributing guidelines on ours, but I've noticed there is no licence in this repo. Would it be ok to add one?

Ideally a flexible non-viral licence like MIT.

• Add link to the intermine.org
• Check if the contect is ok

On this page
http://intermine.readthedocs.org/en/latest/web-services/#api-and-client-libraries

In this section:
Look at some example code

I took out this sentence:
If you would like to see more sample code, please visit /web-services/cookbook.

Can you re-add that sentence back in with the correct link to the cookbook?

Near the end of the getting started tutorial in the section "Building a Mine", the user is asked to run the project_build script to demonstrate how the manual steps performed earlier can be done automatically.

However, if the user has no database password set for their PostgreSQL user then project_build asks for a password several times. Hitting return (naively for the blank password) generates an error each time but this isn't fatal for the tutorial if the user has already carried out the manual steps.

Normally, one would expect a database password to be set but some lazy people (like me!) might have it unset. The tutorial implies earlier on in the "Properties file" section that this is okay - "If you don’t have a password for your postgres account you can leave password blank.". Doing the steps manually works fine without a password set.

Digging in to the project_build script, I believe that it ends up asking for a password because it specifies the -h localhost option to the psql at various points. This triggers a network connection rather than a Unix domain socket connection and on Ubuntu 14.10, at least, this makes authentication occur via the password method rather than the peer method. It appears that on PostgreSQL password authentication can't be done with unset passwords. This happens even if the user executing the script is the database superuser. Having a 'blank' password set in the generated ~/.pgpass doesn't help.

Would it be worth changing the tutorial to ask people to always set a database password rather than leave it blank? The alternative of changing build_script to leave out the -h localhost switch if no password is found in ~/.intermine/malariamine.properties looks fiddly. One might also be able to specify /var/run/postgresql as the host so that psql connects over the domain socket. But both these look complicated and still leave other permissions issues to be resolved.

It would be nice to have a copy button beside code examples in our docs.
https://sphinx-copybutton.readthedocs.io/en/latest/

I can't for the life of me seem to get the XML snippets to format in "fenced blocks" correctly. I updated docs/webapp/keyword-search/index.rst with the instructions on configuring Solr for partial string matches. Argh!

On the top right, under the 5.0.0 drop down, remove Next and rename previus versions into Legacy Documentation

https://intermine.readthedocs.io/en/latest/get-started/tutorial/

For installation of SOLR, the last command misses an 'x' at the end
~/git/biotestmine $ ./gradlew postprocess -Pprocess=create-autocomplete-inde .

@kkarra wants a search box that searches the docs at read-the-docs.

This would be different from the search box we hope to add that queries the intermines themselves.

Those are some of the multiple links linking to the same page.

This should be a section under /web-services/how-tos

Move the Path Query API after Database (and remove the intermine API desription)
Move Support and About Us after InterMine Video Tutorial
Rename Style into Documentation Style Guide (Style Guide will be removed foowing #69 )

http://www.crossmodel.org

On the home page I added a paragraph on web services.

I think it would be really great if I could add a link to a tutorial on how to query data specifically for the intermod project. e.g. create a pathways query then run it on all mines.

There are a few wrong links on:
Database index (below an example)

and on GetStarted

If I didn't know IM I'd be completely confused by the mixture of v1 and v2 instructions, referencing malariamine and biotestmine, in the tutorial. Please delete/retype or go over with fine-toothed comb. It's currently utterly confusing to a newbie.

I still had tomcat running while I tried to rebuild the database with
ant clean build-db
The target just hung and did not report any error.

Preferred UI: Report an message stating that the database is still in use and cannot be re-built.

If I search for web service I have 3 suggestions returned. The first is related to next, the second to 4.0.0 and only the last to the current directory.
Is it possible to only show the links related to the version I'm. So if I'm reading 5.0.0, I want the result pointing to the 5.0.0, If i'am reading the 4.0.0 the result point to the 4.0.0

The readthedocs pages don't contain a link back to the intermine.org home page.

in #35, we added a copy/paste button to the code examples throughout the docs - this is awesome, and now every code example is a click away from being copied.

The only problem - we often have $ in front of code examples, with the intent of indicating to the reader that this is a command prompt. When copy/pasting manually they would have had to manually remove the $ each time, which was perhaps a bit annoying - but with the copy/paste button we now have, the $ really needs to go.

Also, some of the code examples have filepaths. These should be deleted too. Example:

docs page: https://intermine.readthedocs.io/en/latest/get-started/tutorial/
code: https://github.com/intermine/im-docs/blob/master/docs/get-started/tutorial/index.rst

$ mkdir git
$ cd git
~/git $ git clone https://github.com/intermine/biotestmine

should become...

mkdir git
cd git
git clone https://github.com/intermine/biotestmine

if you want to pick up this task

0. Take a look at the InterMine contributing guidelines
1. Comment on this issue stating that you intend to work on the task
2. When you're ready, add your work to the repo and create a pull request.

What to do if you need help

Mention @yochannah, tweet @yoyehudi, pop by to say hi on chat or if needed email [email protected]. Don't forget we're usually only available during uk office hours and will not be able to respond at other times :)

In the index on the left there are items duplicated.

Just a few examples:
Systems Requirements> System Requirements
Get Started -> Get Started
It would be great to display the index (now shown on clicking Systems Requirements> System Requirements) on the first level ( Systems Requirements).
Apply it to all the index items duplicated, including the first item Introduction -> Intermine Documentation that should only have Introduction

Replace the green color with the InterMine green color #C0D848