hitz / python-flask-es-test Goto Github PK

in scripts/worm.py, in load_go method, a line in the code read:

print("Fetching go data from WormBase txt file...")

It should read:
print("Fetching go data from WormBase tsv file...")

These two separate issues where group into one out of convenience.

The make file refers to Python as "python". This can lead to problems with machines where "python" refers to Python 3 rather than 2. So, Python 2 needs to explicitly be mentioned.

The .gitigore file should ignore "prototype" generated for virtual environments and package.json.lock. This will prevent accidentally merging them into a repo.

A personal habit I have is to add "gotcha" to help people debug issues. Here are some things I would add:

• make sure you are running elastic search version 2.4.6 rather than the lastest version
• ensure elastic search is running before running the make file
• In the make file, you may need to change the word "python" to "python2"; depending on how your machine runs python2.7

in scripts/worm.py, line 70, the code is: go_data_csv_filename = "data/WormGOGeneMapping.tsv"
However, the file name is "WormGoGeneMapping.tsv". In the tsv file, the second 'o' is upper case, while the exact file name has it as lower case. This can lead to an error when running the code in linux

In master branch, Worm disease and OMIM files are loaded but there is some error with search or mapping that doesn't seem to work right - if you type in a mapped disease word like "polycystic" you don't get Diseases although genes with the term in the description do show up.

It is good practice to provide links to where do download dependencies. It cannot be assumed all readers know where to get them from or realize they can search online for them.

When I followed the installation instructions in the README, I got an error from this step as follows:

brew cask install homebrew/cask-versions/java8 
Error: Cask 'java8' is unavailable: '/usr/local/Homebrew/Library/Taps/homebrew/homebrew-cask-versions/Casks/java8.rb' does not exist.

A quick troubleshooting process yielded this alternative command from StackOverflow that seems to have done the trick. It turns out that Java8 as listed is no longer offered through Homebrew. I thought I would let you know in case you want to update the instructions in your tutorial.

brew cask install homebrew/cask-versions/adoptopenjdk8

Cheers,
Dana