Cytoscape App Store

Alexander Pico edited this page Jun 11, 2018 · 14 revisions

Site Administration

"Contact Us" emails

When a user fills out the form on the "Contact Us" page, the site sends an email to the site administrator's email address (defined in conf.emails.CONTACT_EMAIL). This email is sent out by the automated email account defined in conf.emails.EMAIL_HOST_USER. Thus, when the administrator receives the email, it will be from the automated email account, not from the user who filled out the "Contact Us" form. The first line in the email contains the user's email address.

When responding to "Contact Us" emails, remember to change the reply address to the user's email address.

2.x plugin submissions

2.x plugins are managed by UCSD's chianti server. When a developer submits a 2.x plugin, it goes to chianti, not to the App Store. When a plugin submission is approved, plugins.xml is updated, and an automatic email is sent by Barry.

To update the app page to reflect the update to plugins.xml:

  1. Go to the App Store and make sure you're signed in a staff account.
  2. In the user menu, click "2.x Plugin Management".
  3. In the plugin name field, enter the name of the 2.x plugin whose page you want to update.
  4. The page will present details about the plugin it obtained from plugins.xml. Check these details.
  5. If the details are correct, click on the blue button on the bottom right.

3.0 app submissions

When a jar is submitted to the App Store, the site sends an automated email to the administrator's email address (defined in conf.emails.CONTACT_EMAIL). Even if the app is not approved in the final step by the author, the administrator receives an email. This is done so that the administrator can monitor all submissions.

If an app page already exists for the 3.0 jar submission, the new release becomes immediately available. The administrator will receive an automated email about the submission.

If the app is new, the jar submission requires approval by staff. Sign in as staff, then go to the App Store site. In the user menu on the top right of the page, choose "Pending Apps". At this page, staff can approve an app. Approving an app sends an automatic email to the author and doesn't require any additional work. If the jar is not satisfactory, it can be rejected. No automatic email is sent to the author if the jar is rejected. This is because rejections happen when a jar is malformed and require an individualized email to the author.

App Store Code Structure

Terminology

  • Django app: Django organizes websites into separate modules called apps. Each app has its own directory at the top level typically containing files like __init__.py, model.py, and views.py.
  • templates: HTML files with placeholders, which Django processes by filling in Python code.
  • static files: general website files (images, Java Script, CSS) that are served as is without any processing from Django.
  • media files: general website files referenced by the database; they are served as is without any processing from Django.
  • mod_wsgi: Apache module that interfaces with Python.

Explanation of important files

Configuration Files

  • settings.py: Django settings file for configuring things like the database, location of templates, static files, and so on.
  • urls.py: the general URL layout of the entire site. Each URL entry in this file delegates URL paths to each Django app.
  • django.wsgi: the configuration file used when the App Store is deployed to an Apache server using mod_wsgi.

Django Apps

  • apps: navigation of Cytoscape apps and app pages
  • users: user login/logout
  • search: free text searching
  • backend: JSON representation of 3.0 apps; used by the App Manager in Cytoscape 3.0+
  • help: about, contact us, getting started pages
  • submit_app: Cytoscape 3.0 app submission pages and jar verification
  • download: for downloading releases and tracks download stats for apps

Other Directories

  • templates: Templates used throughout the App Store.
  • static: Each subdirectory has static files for a Django app. The common subdirectory has static files that belong to the entire site. When deploying the site to Apache, Apache should directly serve these files instead of through Django.
  • util: small utility functions used throughout the site's code
  • dbmigration: scripts that directly update SQL tables after changes had been made to database models; only needed when needing to migrate old versions of SQL database backups
  • conf: individual configuration files

Backup System

  • jeff@pinscher.ucsf.edu: Current account and server hosting the App Store.
  • /home/jeff/backup_cyappstore: Dir containing backup script and latest backup SQL and TGZ.
  • backupdb.sh: Backup script run by cron job, daily at 12:03am. The script performs a sqldump of the "cyappstore" database, then tar cfz, then scp both files to jeff@pointer.ucsf.edu:/home/jeff/backup_cyappstore/, where the last 2 weeks' worth of SQL and TGZ files are maintained by the prune_cyappstore script.

App Store Dependencies

The App Store requires a machine with 2GB RAM and enough disk space to accommodate a growing app collection. The software itself takes 2.2GB and as of September 2015 the media directory takes 4.3GB to hold 238 apps (368 releases/jar files), and the MySQL database takes 61MB to hold associated author, release and tag data. So, 6.51GB in total. Grow your estimate as the number of apps grows and also add 2GB for temporary scratch space.

The App Store requires the following software packages. If you're on a Mac, this can be installed with http://mxcl.github.io/homebrew/. If you're on Linux, use your distribution's package manager.

Note that the versions specified here are not mandatory. They only indicate the version with which I've tested the App Store.

  • Python 2.6
  • xapian 1.2.13 (free-text searching)
  • xapian-bindings 1.2.13
  • libjpeg 8d (used by PIL)
  • libpng 1.5.14 (also used by PIL)
  • GeoIP 1.4.8 (converts IP addresses to geographical locations)

The following Python packages are also required. Each can be installed with pip install. If you don't have pip, type: easy_install pip.

  • Django 1.4.5
  • MySQL-Python (aka MySQLdb; can be installed with Debian/Ubuntu's package manager; Django uses this to connect to the MySQL database)
  • PIL 1.1.7 (can be installed with Debian/Ubuntu's package manager; needed to scale icon and screenshot image files)
    • PIL must be built the JPEG support. At the end of PIL's installation, you'll see a printout titled PIL 1.1.7 SETUP SUMMARY. This must list JPEG as supported.
  • django-social-auth 0.7.23 (aka social_auth; allows users to log in with their Google accounts)
  • IPython -- optional (can be installed with Debian/Ubuntu's package manager; very useful for debugging)

Updated Python 3 Steps:

  • Python 3.6.2 (apt-get install python3 and ln -s /usr/bin/python3 /usr/bin/python3.6)
  • xapian-core 1.4.5 and xapian-bindings 1.4.5
cd xapian-core 1.4.5
./configure
make
sudo make install

cd ../xapian-bindings 1.4.5
./configure --with-python3
make
sudo make install
  • libjpeg 8d (used by PIL) (already installed)
  • libpng 1.5.14 (also used by PIL) (already installed)
  • GeoIP 1.4.8 (converts IP addresses to geographical locations)

The following Python packages are also required. Each can be installed with sudo pip3 install...

  • virtualenv
    • virtualenv /var/www/CyAppStore/myvirtualenv -p /usr/local/bin/python3
    • source myvirtualenv/bin/activate
      • pip3 install Django==1.8.19
      • pip3 install mysqlclient (Django uses this to connect to the MySQL database)
        • If mysqlclient has problematic conflicts between versions, consider alternative pip3 install PyMySQL and adding these lines to top of django.wsgi: import pymysql pymysql.install_as_MySQLdb()
      • pip3 install urllib3
      • pip3 install social-auth-app-django
  • Pillow 5.1.0 (can be installed with Debian/Ubuntu's package manager; needed to scale icon and screenshot image files)
    • PIL must be built for JPEG support. At the end of PIL's installation, you'll see a printout titled PIL 1.1.7 SETUP SUMMARY. This must list JPEG as supported.
  • IPython -- optional (can be installed with Debian/Ubuntu's package manager; very useful for debugging)
  • Had to install mod_wsgi from source to provide configure param pointing to virtualenv python:
    • ./configre --with-python=/var/www/CyAppStore/myvirtualenv/bin/python3.6
    • Then updated wsgi.conf to point to correct python as well: sudo vi /etc/apache2/mods-available/wsgi.conf and enabled sudo a2enmod wsgi

Testing App Store Software Dependencies

Run the test_dependencies.py script like so:

python external_scripts/test_dependencies.py

Test the GeoIP library:

python manage.py test_geoip

Note: this script can only be run after the Django project has been configured.

Migration

If you want to move the App Store to another machine, here is what to do:

  1. Install the needed libraries on the new machine by following the instructions in the App Store Dependencies section above.

  2. Check out the App Store GitHub repository to the new machine: http://github.com/cytoscape/appstore

  3. In the conf directory, make a copy of each -template.py file, removing the -template.py portion of the file name (e.g. cp apikeys-template.py apikeys.py). Open each template file and fill in the fields. Copy the old machine's configuration files if necessary. Do the same for maven-app-repo-settings-template.xml in the parent directory, which contains sensitive username and password information.

  4. In the download/geolite directory, type make. This will download the needed !GeoLite data files. (!GeoLite maps IP addresses to geographical locations.)

  5. Create the following daily cron jobs on the new machine:

    • Database backups described above in the subsection Backup System.
    • Free text search reindexing: the crob job should run make index in the App Store directory.
  6. Take a snapshot of the database using mysqldump then load it to the new machine's database:

Run this on the old machine

mysqldump -u USER_NAME DB_NAME > CyAppStoreDbDump.sql

Transfer CyAppStoreDbDump.sql from the old to new machine

Run this on the new machine

mysql -u USER_NAME DB_NAME < CyAppStoreDbDump.sql```

  1. Create an entry in Apache's sites-enabled directory for the App Store. Use the old machine's entry if necessary.

  2. Restart Apache and run the test protocol that's described below.

SSL for HTTPS

We are using letsencrypt for our SSL certificate. It should automatically renew every 3 months. Here are its components:

  • /etc/apache2/sites-available/appstore.conf = VirtualHost information for port 443 access.
  • /etc/letsencrypt/live/apps.cytoscape.org/ = certificate, etc.
  • sudo crontab -e = auto renew cronjob.

To manually renew the certificate:

  • sudo /usr/local/bin/certbot-auto renew --quiet --post-hook "/usr/sbin/service apache2 reload"

Other resources

In addition to getting the !CyAppStore code up and running along with its dependencies, there are other systems required for a full migration:

How requests are handled

         ||             |                               |                    |                    |            ||
Request=>|| ==Apache==> | == sites-enabled/appstore ==> | == django.wsgi ==> | == settings.py ==> | == urls.py ||
         ||             |                               |                    |                    |            ||
  1. An HTTP request is made to the Apache server.
  2. Apache looks in /etc/apache2/sites-enabled to see how to handle the request. The appstore configuration file is set to handle requests made to http://apps.cytoscape.org.
  3. appstore tells Apache to use mod_wsgi. mod_wsgi runs a Python interpreter within Apache. appstore tells mod_wsgi to start Python with /var/www/CyAppStore/django.wsgi.
  4. django.wsgi starts the Django library. It also tells Django the location of settings.py, which Django needs to start the site.
  5. settings.py contains the location of urls.py (defined in the ROOT_URLCONF variable), which is a list of URLs (in the form of regular expressions) and the Python functions that handle them.
  6. urls.py in the top directory of the App Store merely imports additional URLs from each Django app. It dispatches the request to the appropriate function that is designated to handle requests for a given URL. Functions are defined in the views.py file in each Django app.
  7. The handler function returns with a processed HTML page.

Debugging

  1. /etc/apache2/sites-enabled/appstore This file tells Apache and mod_wsgi where to find the site. The most important line is this:
WSGIScriptAlias / /var/www/CyAppStore/django.wsgi

This tells Apache and mod_wsgi where to locate the site code. Make sure the path to django.wsgi is correct.

  1. /var/www/CyAppStore/django.wsgi This file invokes Django's WSGI handler. It needs to correctly reference settings.py to start the site. Make sure these two lines are correct:
SITE_PARENT_DIR '/var/www'
SITE_DIR filejoin(SITE_PARENT_DIR, 'CyAppStore')

To check if these variables are being defined correctly, you can launch a separate Python interpreter and enter these lines (with = added for syntax):

from os.path import join as filejoin
SITE_PARENT_DIR='/var/www'
SITE_DIR=filejoin(SITE_PARENT_DIR, 'CyAppStore')

Then check if the variables SITE_PARENT_DIR and SITE_DIR are correct.

  1. /var/www/CyAppStore/settings.py This file is pretty complicated. But if you've checked everything at this point, here's some ways to pinpoint problems in settings.py.

a. If you're getting an HTTP 500 error, you can get the stack trace by turning on debug mode then reloading the page. Note that debug mode exposes sensitive information about the site to the public. Make sure to keep debug mode off as much as possible. Change to following line to True:DEBUG False

b. You can poke at the code by running a Python shell. Enter this command at the shell prompt in the same directory as settings.py:python manage.py shell You can check to see if the site's code is working correctly without having debug mode on. For example, to see if the list of all apps is working, enter this into the Python interpreter:

from apps.models import App
App.objects.all()

c. The SQL database settings are specified by the DATABASES variable:

DATABASES {
        'default': deploy_database
}

Make sure that 'default' is pointing to the correct dictionary:

deploy_database {
        'ENGINE':   'django.db.backends.mysql',
        'NAME':     ...
        'USER':     ...,
        'PASSWORD': ...
}

d. If you're getting database errors, enter this command at the shell prompt in the same directory as settings.py:python manage.py dbshell If you're able to get a SQL prompt, that means Django can connect to the SQL database.

e. If you make changes to a Python file but you're not seeing the changes taking effect, you may have to delete all the .pyc files. To do so, type this:make nopyc

Known ERROR notifications

  1. MultipleObjectsReturned: get() returned more than one AppDownloadsByGeoLoc -- it returned 2!

a. log into mysql: mysql -u root --password=PASSWORD cyappstore

b. list any duplicate country entries per app

   select app_id, geoloc_id, count(*) as c 
   from download_appdownloadsbygeoloc 
   where app_id is not null 
   group by app_id,geoloc_id having c > 1;

c. arbitrarily select the MAX record id from these duplicate cases and delete those records. Note: this potentially deletes valid download records and must be repeated if duplicate count is > 2

   delete from download_appdownloadsbygeoloc where id in 
   (select max from (select MAX(id) as max, app_id, geoloc_id, count(*) as c 
   from download_appdownloadsbygeoloc 
   where app_id is not null 
   group by app_id,geoloc_id having c > 1) 
   as T);
  1. MultipleObjectsReturned: get() returned more than one ReleaseDownloadsByDate -- it returned 2!

a. log into mysql: mysql -u root --password=PASSWORD cyappstore

b. list any duplicate country entries per app

   select release_id, download_releasedownloadsbydate.when, count(*) as c 
   from download_releasedownloadsbydate 
   where release_id is not null 
   group by release_id,download_releasedownloadsbydate.when having c > 1;

c. arbitrarily select the MAX record id from these duplicate cases and delete those records. Note: this potentially deletes valid download records and must be repeated if duplicate count is > 2

   delete from download_releasedownloadsbydate where id in 
   (select max from (select MAX(id) as max, release_id, download_releasedownloadsbydate.when, count(*) as c 
   from download_releasedownloadsbydate 
   where release_id is not null 
   group by release_id,download_releasedownloadsbydate.when having c > 1) 
   as T);

Tips

  • You can reindex the text search engine with this command:
make index
  • If you edit any Python files and need it to be refreshed by Apache, you will need to remove all pyc files:
make nopyc

App Store Test Protocol

  1. Does the front page load?
  2. Does "All Apps" load? a. Does sorting work as expected?
  3. Does a category load?
  4. Does a 2.x plugin page load? (e.g. /apps/psicquicuniversalclient) a. Does plugin downloading work? b. Does "Search for posts" work? c. Does ratings work?
  5. Does a 3.x app page load? (e.g. /apps/cluego) a. Do release downloads work? b. When a release is downloaded, is it reflected in the stats page?
  6. Does app page editing work? a. Icon? b. Any link field? c. Details editing? d. Deleting a 3.0 release? i. Does the release still show in the download stats? ii. Does the release no longer show in the app page? iii. Does the release no longer show in the backend? iv. Does depending on the deleted release fail? v. Does submitting a jar with the same name and version succeed?
  7. Does search work?
  8. Do app author pages work? (e.g. /apps/with_author/John%20"Scooter"%20Morris)
  9. Does the "About" page load?
  10. Does the "Contact Us" page load and work?
  11. Does the /backend/all_apps page work? a. Does it refer accurately to icon and release URLs?
  12. Do the admin pages load?

App Submission Test Protocol

App submissions will principally test the manifest file. The following snippets are for jars created with the manifest files listed below.

To create an empty jar with just a given manifest, first make sure to have an empty file in the current directory. This is because jar requires at least one input file (besides the manifest) to create a jar. Run this command to create the jar:

jar cmf manifest jar-name.jar empty```

### Empty manifest test

This should fail: no `Cytoscape-App-Name` in the manifest.

### Simple app test: no version

This should fail: no `Cytoscape-App-Version` in the manifest.

Manifest:

Cytoscape-App-Name: blah


### Simple app test: no API compatibility

This should fail: no `Cytoscape-API-Compatibility` in the manifest.

Manifest:

Cytoscape-App-Name: blah Cytoscape-App-Version: 1.0


### Simple app test: new app

 * This should succeed and require adding a new app page.
 * After submission, the admin should receive an email about the submission. It should be listed in the Pending Apps page.
 * Go back to the "Confirmation" page, then click "No, cancel it". It should no longer be listed in Pending Apps.
 * Resubmit the app, and accept it. It should successfully create an app page.
 * An email from the account in `conf/emails.py/EMAIL_ADDR` should have been sent to the app author confirming the app.
 * The new app page must have the submitter's email address listed as an editor.

Manifest:

Cytoscape-App-Name: blah Cytoscape-App-Version: 1.0 Cytoscape-API-Compatibility: 3.0


### Simple app test: new release

This should succeed and not require admin approval. It should still send an email to the admin about the submission.

Manifest:

Cytoscape-App-Name: blah Cytoscape-App-Version: 2.0 Cytoscape-API-Compatibility: 3.0



### Simple app test: no authorization

Submit the jar with the same manifest as above but under a different, non-admin account. Submission should be rejected.

### OSGi bundle: no name

This should fail: no `Bundle-Name`.

Manifest:

Bundle-SymbolicName: blah


### OSGi bundle: no version

This should fail: no `Bundle-Version`.

Manifest:

Bundle-SymbolicName: blah Bundle-Name: blah


### OSGi bundle: no Cytoscape imports

This should fail: no Cytoscape packages in `Import-Package`.

Manifest:

Bundle-SymbolicName: blah Bundle-Name: blah Bundle-Version: 3.0 Import-Package: xyz,abc


### OSGi bundle: no Cytoscape version in imports

This should fail: no Cytoscape packages in `Import-Package`.

Manifest:

Bundle-SymbolicName: blah Bundle-Name: blah Bundle-Version: 3.0 Import-Package: org.cytoscape.a, org.cytoscape.b


### OSGi bundle: new release

This should succeed.

 - The minimum Cytoscape version _must_ be `3.5`.

Manifest:

Bundle-SymbolicName: blah Bundle-Name: blah Bundle-Version: 3.0 Import-Package: org.cytoscape.a;version="(3.0,4]", org.cytoscape.b;version="(3.5,4]"


### OSGi bundle: export package

This should succeed and ask for a pom and Javadocs.

Manifest:

Bundle-SymbolicName: blah Bundle-Name: blah Bundle-Version: 4.0 Import-Package: org.cytoscape.a;version="(3.0,4]", org.cytoscape.b;version="(3.5,4]" Export-Package: blah


### OSGi bundle: deleted dependency

Delete an existing release. Then try to submit an app that depends on it. This should fail.

Manifest:

Bundle-SymbolicName: blah Bundle-Name: blah Bundle-Version: 3.0 Import-Package: org.cytoscape.a;version="(3.0,4]", org.cytoscape.b;version="(3.5,4]" Cytoscape-App-Dependencies: GeneMANIA;3.0.0.beta1


### OSGi bundle: multiple dependencies

Submission should succeed. After submission, GeneMANIA and ClueGO must list blah as a dependency.

Manifest:

Bundle-SymbolicName: blah Bundle-Name: blah Bundle-Version: 5.0 Import-Package: org.cytoscape.a;version="(3.0,4]", org.cytoscape.b;version="(3.5,4]" Cytoscape-App-Dependencies: GeneMANIA;3.0.0.beta2, ClueGO;2.0.0


### Extract list of authors for recently updated/submitted apps
Use case: producing a contact list for F1000Research channel authors

 1. log into server: `root@apps.cytoscape.org`
 1. log into docker (if a docker instance): docker exec -it appstore_mysql_1 /bin/bash
 1. log into mysql: mysql -u root --password=PASSWORD cyappstore
 1. `select distinct first_name,last_name,email,release_file from apps_app_editors left join apps_release on apps_app_editors.app_id=apps_release.app_id left join auth_user on apps_app_editors.user_id=auth_user.id where apps_release.created>"2015-03-01 01:01:01"; `
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