multiqc / megaqc

Web application to collect and visualise data across multiple MultiQC runs.

A web application to collect and visualise data from multiple MultiQC reports.

Current Status: “Pretty unstable”

As of mid-October 2017, MegaQC has all basic functionality. We’ve made the repository public, but please bear in mind that it is still under heavy development and changes are being made on a daily basis. It’s safe to assume that the database structure is still at risk and that you shouldn’t yet trust it to be stable. However, we’d love your help in testing, bug finding and development!

---

MegaQC is a web application that you can install and run on your own network. It collects and visualises data parsed by MultiQC across multiple runs. The MegaQC home page looks something like this:

Screenshot of the MegaQC home page.

If you are not sure what MultiQC is yet, check out the main MultiQC website and GitHub repository first. Once MegaQC is installed and running, simply configure MultiQC to automatically save data to the website every time it runs. Users of your group or facility can then replicate MultiQC plots and explore different data fields. Data distributions, timelines and comparisons can all be explored.

Please read the MegaQC Documentation to learn how to install, deploy and use MegaQC.

megaqc's Issues

Make tutorial screencasts

The short YouTube videos on the MultiQC website have been really popular. Should do the same for MegaQC:

• 30 second introduction to the project
• User setup walkthrough (registration, MultiQC config)
• Installation walkthroughs (basic, production)

Edit filters - delete broken

The delete button on Edit Filters doesn't delete the filter. I don't think it does anything actually, but it does get a mouseover cursor change so not 100% on that.

Dashboards

Once plot favourites (#24) are implemented, we can have a new interface to build plot dashboards.

• Select from list of favourite plots
  • Also give an option to add custom HTML blocks as well as plots
• Drag and drop into a grid layout
  • This looks good! http://gridstackjs.com/
• Save with permalinks and meta (eg. title).

Things to make:

• Page to build new dashboard
• Page to list user dashboards, option to edit and delete
• Admin ability to build dashboards visible by all users

Add ability to reset forgotten passwords

We could do with functionality to reset forgotten passwords

Import error

Phil,

trying to find ways to better debug this. Uploading a MultiQC report (either directly with megaqc upload or through an existing file list) results in:

Error on request:
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/werkzeug/serving.py", line 209, in run_wsgi
    execute(self.server.app)
  File "/usr/local/lib/python2.7/site-packages/werkzeug/serving.py", line 197, in execute
    application_iter = app(environ, start_response)
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1994, in __call__
    return self.wsgi_app(environ, start_response)
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1985, in wsgi_app
    response = self.handle_exception(e)
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1540, in handle_exception
    reraise(exc_type, exc_value, tb)
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1982, in wsgi_app
    response = self.full_dispatch_request()
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1614, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1517, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/usr/local/lib/python2.7/site-packages/flask/app.py", line 1612, in full_dispatch_request
    rv = self.dispatch_request()
  File "/usr/local/lib/python2.7/site-packages/flask_debugtoolbar/__init__.py", line 125, in dispatch_request
    return view_func(**req.view_args)
  File "/usr/local/lib/python2.7/site-packages/megaqc/public/views.py", line 32, in home
    num_samples = get_samples(count=True),
  File "/usr/local/lib/python2.7/site-packages/megaqc/api/utils.py", line 517, in get_samples
    return sample_query.one()[0]
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2749, in one
    ret = self.one_or_none()
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2719, in one_or_none
    ret = list(self)
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2790, in __iter__
    return self._execute_and_instances(context)
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2813, in _execute_and_instances
    result = conn.execute(querycontext.statement, self._params)
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 945, in execute
    return meth(self, multiparams, params)
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 263, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1053, in _execute_clauseelement
    compiled_sql, distilled_params
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1189, in _execute_context
    context)
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1393, in _handle_dbapi_exception
    exc_info
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=cause)
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1182, in _execute_context
    context)
  File "/usr/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 470, in do_execute
    cursor.execute(statement, parameters)
OperationalError: (sqlite3.OperationalError) no such table: sample [SQL: u'SELECT count(DISTINCT sample.sample_name) AS count_1 \nFROM sample']

What information can I provide you with to reproduce this? Just the JSON?

Demo installation

Once we have a website (#33), it would be great to have a sandboxed demo installation, where people can play with a demo instance to see how it works without having to mess around with installations.

• Would need to be automatically overwritten periodically in case people delete all data.
• Should be on its own server partition as it's at a fairly high risk of being hacked.
• Could be cool if it automatically pulled the latest release :)

Clean up MegaQC config

The MegaQC config is a mess at the moment. It's split across several places - the default Flask setup, some stuff that mimics MultiQC config files, all sorts.

Resolve all of this into one system, and document how to change stuff.

Better app logging

Visible logging is currently just access log type info (get, post, 4xx, 5xx, etc.). No errors printed when, e.g., a file sent from multiqc could not be inserted. Makes it difficult to track down where the issues are happening.

Flask.app.logger should be accessible everywhere, but doesn't seem to be writing to console currently. I think this is just a config flag somewhere, or maybe setting a log file location?

Add in missing plot config options

Some of the plot config options are pretty low-priority and high-work, so should be collected here for a later date when we're into polishing / fine-tuning mode.

• yFloor
• yCeiling
• yMinRange

Violin Plots

The Violin Plots dropdown option on the Distributions page doesn't work.

Make a MegaQC website

MegaQC needs its own fancy website.

Interface to select & filter by samples in a plot

Plot.ly has a brilliant interface to select samples in a plot. We can use this to allow users to interactively build sample filters from plots. This allows simple follow-up interrogation of these same samples.

Make psycopg2 an optional dependency

Postgresql is a pain in the *** to install on Mac.

Since it's not a hard dependency, would it not be nice if psycopg2 was an optional dependency since it fails when Postgreql isn't install on your system?

Reference for optional dependencies:
https://setuptools.readthedocs.io/en/latest/setuptools.html#declaring-extras-optional-features-with-their-own-dependencies

Handling of MultiQC timestamps

Following up on our discussion in Stockholm: I'd love to see a slightly different handling of MultiQC timestamps during the import. We'd love to import historical data which is tricky right now as MegaQC associated imported data with the time of when the MultiQC report was generated -- not when the sample was actually run / processed.

This is also problematic for current data. We frequently sequence data, but then do not analyse it for 2-3 months until all samples of a cohort are available. QC data generated and visualized in MegaQC then appear out of sync with when they were created.

Allowing for a 'timestamp' to be submitted during import would allow us to work around this issue and provide a relatively quick fix.

Long term, a better solution would be to associate timestamps with samples (not MultiQC reports) in the backend database, and to allow users to submit sample name : timestamp mappings in the same way that MultiQC allows for samples to be batch re-labelled.

Sorry for taking so long to follow up on this ;-)

Login after registration doesn't work

After registration, the following message is presented:

Thanks for registering! You're now logged in.

Except, it's often not true. But occasionally is. Track down what's going on.

URL linking to plots

Add a button to give a shareable URL for a plot, complete with fields and filters.

Edit filters - intermittent filter creation failure

When creating new filters from the plot view (or /trends, at least), every second filter will fail to save.

Reproduce:

• Create a filter normally
• Try to create another filter
• Creation fails / no-ops
  • no fail message, but no success message either and no entry is added to the DB
• Next attempt will succeed

The flash header doesn't show up, but there's no info written to the logs about a failure. It might be from the redirect after creating the first filter, as navigating away and back will allow the filter to be created without issue. After the filter fails to save, the next filter attempt will work. And the following will fail. Super weird.

Create Dashboard UI needs is_public toggle

Dashboards are able to shared between users, but need a UI to actually toggle the is_public flag so that users can do so without having to update the DB directly.

Rewrite plot.ly tooltips

The default plot.ly tooltips are pretty ugly and don't look anything like HighCharts. They're also pretty difficult to customise.

According to this thread we can essentially rewrite our own by creating a custom <div> on hover. By doing this we should be able to recreate what we're looking for.

Plots don't work with lots of samples

Major issue - most of the plots stop working when there are lots of samples in the database.

For example, when trying to get a trend plot with 6526 samples, 53 reports (not even that much compared to what people will try to use this for in the future), I get the following Traceback:

  File "build/bdist.macosx-10.9-x86_64/egg/sqlalchemy/engine/default.py", line 470, in do_execute
    cursor.execute(statement, parameters)
OperationalError: (sqlite3.OperationalError) too many SQL variables [SQL: u'SELECT sample.sample_name AS sample_sample_name \nFROM sample \nWHERE sample.sample_id IN (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, 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That's right folks - that's a SQL query which is 57,580 characters long. SQLite does not like that, or any SQL database I suspect.

Need to rethink how to structure these super long queries.

More documentation inside the application

Allow the docs to be viewed inside the running MegaQC application. This will be more useful when we have more docs for the user..

Python 3(.6) compatibility

A few inconsistencies with Python 3. Example in megaqc/public/views.py

from urllib import unquote_plus
# Should be
try:
    from urllib import unquote_plus
except ImportError:
    from urllib.parse import unquote_plus

I'm sure there's a few others.

Also, I suspect https://github.com/pallets/itsdangerous is not 3.6 compatible

flask db init not working

I was trying to run flask db init and it started up the livereload server and never got to the db initialisation.

I think it has do to with this check:

# Live reload
if get_debug_flag():
    ...

Should I unset the FLASK_DEBUG variable maybe?

(BTW super impressed with your setup if this is your first serious Flask app!!)

Allow customisation of user privileges

MegaQC has three levels of authentication - administrators, users and visitors. Visitors require no authentication. The default permissions for each group should be as follows:

• Visitors
  • View basic website description page
• Users
  • View plots and data on MegaQC website
  • Submit data when running MultiQC
  • Save plot configs and dashboards
  • Delete own data submissions
  • Edit own profile
• Administrators
  • Delete other people's data submissions
  • Create, edit and remove user profiles
  • Enable and disable user registration
  • Limit registration to listed e-mail domains
  • Choose auth types

However, it would be nice to be able to allow admins to change these (eg. allow unauthenticated users to view plots).

User Authentication

• Basic user authentication
• Option to require email confirmation (configurable through config)

Favourite fields for fast selection

The interface for this is half-written and partially functional.

• MultiQC Report: Plot Type favourites
• Field Type favourites (Data Distributions, Data Trends, Compare Data)
• Page to list and delete field type favourites

Edit Filters - sample counts incorrect

Edit Filters now loads after the fix for #18 , but the counts for each filter are incorrect. The filters themselves still work, so some part of the count mechanism isn't work as intended.

New version plotly error

Pip will install version 3.0_rc1 of plotly. This doesn't work (never mind my python 3.6 experimentation):

megaqc initdb
This is MegaQC v0.1.dev0

Traceback (most recent call last):
  File "/Users/remi-andreolsen/miniconda3/bin/megaqc", line 6, in <module>
    exec(compile(open(__file__).read(), __file__, 'exec'))
  File "/Users/remi-andreolsen/code/MegaQC/scripts/megaqc", line 31, in <module>
    cli()
  File "/Users/remi-andreolsen/miniconda3/lib/python3.6/site-packages/click-6.7-py3.6.egg/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/Users/remi-andreolsen/miniconda3/lib/python3.6/site-packages/Flask-0.12-py3.6.egg/flask/cli.py", line 374, in main
    return AppGroup.main(self, *args, **kwargs)
  File "/Users/remi-andreolsen/miniconda3/lib/python3.6/site-packages/click-6.7-py3.6.egg/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/Users/remi-andreolsen/miniconda3/lib/python3.6/site-packages/click-6.7-py3.6.egg/click/core.py", line 1061, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
  File "/Users/remi-andreolsen/miniconda3/lib/python3.6/site-packages/click-6.7-py3.6.egg/click/core.py", line 1100, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
  File "/Users/remi-andreolsen/miniconda3/lib/python3.6/site-packages/Flask-0.12-py3.6.egg/flask/cli.py", line 345, in get_command
    rv = info.load_app().cli.get_command(ctx, name)
  File "/Users/remi-andreolsen/miniconda3/lib/python3.6/site-packages/Flask-0.12-py3.6.egg/flask/cli.py", line 223, in load_app
    rv = self.create_app(self)
  File "/Users/remi-andreolsen/code/MegaQC/scripts/megaqc", line 11, in create_megaqc_app
    from megaqc.app import create_app
  File "/Users/remi-andreolsen/code/MegaQC/megaqc/app.py", line 7, in <module>
    from megaqc.scheduler import init_scheduler
  File "/Users/remi-andreolsen/code/MegaQC/megaqc/scheduler.py", line 6, in <module>
    from megaqc.api.utils import handle_report_data
  File "/Users/remi-andreolsen/code/MegaQC/megaqc/api/__init__.py", line 3, in <module>
    from . import views  # noqa
  File "/Users/remi-andreolsen/code/MegaQC/megaqc/api/views.py", line 8, in <module>
    from megaqc.api.utils import handle_report_data, generate_report_plot, generate_distribution_plot, \
  File "/Users/remi-andreolsen/code/MegaQC/megaqc/api/utils.py", line 16, in <module>
    import plotly.offline as py
  File "/Users/remi-andreolsen/miniconda3/lib/python3.6/site-packages/plotly-3.0.0rc1-py3.6.egg/plotly/__init__.py", line 31, in <module>
    from plotly import (plotly, dashboard_objs, graph_objs, grid_objs, tools,
  File "/Users/remi-andreolsen/miniconda3/lib/python3.6/site-packages/plotly-3.0.0rc1-py3.6.egg/plotly/graph_objs/__init__.py", line 14, in <module>
    from plotly.graph_objs.graph_objs import *  # this is protected with __all__
  File "/Users/remi-andreolsen/miniconda3/lib/python3.6/site-packages/plotly-3.0.0rc1-py3.6.egg/plotly/graph_objs/graph_objs.py", line 802, in <module>
    from plotly.datatypes import FigureWidget
ModuleNotFoundError: No module named 'plotly.datatypes'

Config option to make MultiQC paths unique

Have an option (off by default) to overwrite previous report uploads if they share the same MultiQC run directory as a new report.

aborted transactions on upload import

I've gotten this one intermittently a few times now, mostly when the import has taken a few minutes. I don't have a lot of visibility into the postgres logs, but it looks like the connection is getting timed out while waiting for the data to be processed. The loading of data appears to complete without issue, but it's failing on the step to update the upload record.

Job "job1 (trigger: interval[0:00:30], next run at: 2018-05-30 13:13:08 CEST)" raised an exception
Traceback (most recent call last):
  File "megaqc/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context
    context)
  File "megaqc/lib/python3.5/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute
    cursor.execute(statement, parameters)
psycopg2.InternalError: current transaction is aborted, commands ignored until end of transaction block


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "megaqc/lib/python3.5/site-packages/apscheduler/executors/base.py", line 125, in run_job
    retval = job.func(*job.args, **job.kwargs)
  File "megaqc/lib/python3.5/site-packages/megaqc-0.1.dev0-py3.5.egg/megaqc/scheduler.py", line 61, in upload_reports_job
    db.session.commit()

 ...

  File "megaqc/lib/python3.5/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.InternalError: (psycopg2.InternalError) current transaction is aborted, commands ignored until end of transaction block
 [SQL: 'SELECT uploads.upload_id AS uploads_upload_id, uploads.path AS uploads_path, uploads.created_at AS uploads_created_at, uploads.user_id AS uploads_user_id \nFROM uploads \nWHERE uploads.upload_id = %(param_1)s'] [parameters: {'param_1': 1}] (Background on this error at: http://sqlalche.me/e/2j85)

I don't think this is necessarily a code issue, but we might want to look at some of the options for handling pool disconnects. All else fails, could just Try ... Except the commit step.

Favourite plots

• Add database table back end
• Page to list saved plots
  • List plots
  • Plot saved plots
  • Delete plots
• Add functionality to save favourite plots
  • Report plots
  • Distribution plots
  • Trend plots
  • Comparison plots

Populate megaqc_url with front-end javascript

Something we talked about during the hackathon that I just remembered.

When viewing users/multiqc_config, the hostname and port are the local values. These won't match up if MegaQC is running in Docker or if there's apache/nginx running in front of gunicorn, etc. The easiest fix we came up with was to have the browser javascript pull the info and display it that way.

Update libraries

Need to update bootstrap, plotly, jquery etc and check that everything still works.

More profile personalisation

More fields for the user profile:

• Avatar
• Description
• Homepage
• Twitter / GitHub / LinkedIn etc..?

Google OAuth

It would be nice to have the option for using other authentication systems, to avoid people having to remember yet another password.

My preference for this would be Google OAuth, as we're already using this across several of our systems.

This should be disabled by default (I think it'll need an API key anyway).

Make first-run more user friendly

Streamline the experience for the first time user. Ideas:

Back end:

• Automatically init a database if not already created (or at least throw an error with the command)
• Log main parameters (eg. database type and location) on launch

Front end:

• Homepage warning if no registered users
• Registration page warning if first user, explaining that user will be an admin

single-user mode

It would be nice to be able to run MegaQC without any authentication. This would be useful when doing quick local runs, no need to go through the hassle of the usual setup.

• One admin user only which all users are automatically logged into
• Command line flag: --noauth?
• Remove a bunch of pages in this mode (profile, password, admin etc)
• Uploads should work without an API key

Global histogram binning size

The Data Distributions Histogram plot uses a fixed number of bins per-field, each with its own data range. This means that the resulting bars are of varying widths across fields.

Needs to use a plot-global data range instead.

Edit Filters page is broken

The edit_filters/ page triggers an error:

127.0.0.1 - - [12/May/2018 07:52:19] "GET /edit_filters/ HTTP/1.1" 500 -
Error on request:
Traceback (most recent call last):
  File "/Users/ewels/miniconda2/envs/work/lib/python2.7/site-packages/Werkzeug-0.12.2-py2.7.egg/werkzeug/serving.py", line 209, in run_wsgi
    execute(self.server.app)
  File "/Users/ewels/miniconda2/envs/work/lib/python2.7/site-packages/Werkzeug-0.12.2-py2.7.egg/werkzeug/serving.py", line 197, in execute
    application_iter = app(environ, start_response)
  File "/Users/ewels/miniconda2/envs/work/lib/python2.7/site-packages/Flask-0.12-py2.7.egg/flask/app.py", line 1994, in __call__
    return self.wsgi_app(environ, start_response)
  File "/Users/ewels/miniconda2/envs/work/lib/python2.7/site-packages/Flask-0.12-py2.7.egg/flask/app.py", line 1985, in wsgi_app
    response = self.handle_exception(e)
  File "/Users/ewels/miniconda2/envs/work/lib/python2.7/site-packages/Flask-0.12-py2.7.egg/flask/app.py", line 1540, in handle_exception
    reraise(exc_type, exc_value, tb)
  File "/Users/ewels/miniconda2/envs/work/lib/python2.7/site-packages/Flask-0.12-py2.7.egg/flask/app.py", line 1982, in wsgi_app
    response = self.full_dispatch_request()
  File "/Users/ewels/miniconda2/envs/work/lib/python2.7/site-packages/Flask-0.12-py2.7.egg/flask/app.py", line 1614, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/Users/ewels/miniconda2/envs/work/lib/python2.7/site-packages/Flask-0.12-py2.7.egg/flask/app.py", line 1517, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/Users/ewels/miniconda2/envs/work/lib/python2.7/site-packages/Flask-0.12-py2.7.egg/flask/app.py", line 1612, in full_dispatch_request
    rv = self.dispatch_request()
  File "/Users/ewels/miniconda2/envs/work/lib/python2.7/site-packages/Flask_DebugToolbar-0.10.1-py2.7.egg/flask_debugtoolbar/__init__.py", line 125, in dispatch_request
    return view_func(**req.view_args)
  File "/Users/ewels/miniconda2/envs/work/lib/python2.7/site-packages/Flask_Login-0.4.0-py2.7.egg/flask_login/utils.py", line 228, in decorated_view
    return func(*args, **kwargs)
  File "/Users/ewels/GitHub/MegaQC/megaqc/public/views.py", line 132, in edit_filters
    sample_filter_counts[sf['id']] = get_samples(filters=sf['id'], count=True)
  File "/Users/ewels/GitHub/MegaQC/megaqc/api/utils.py", line 520, in get_samples
    sample_query = build_filter(sample_query, filters, Sample)
  File "/Users/ewels/GitHub/MegaQC/megaqc/api/utils.py", line 621, in build_filter
    for filter_group in filters:
TypeError: 'int' object is not iterable

Improve documentation.

The docs need a major overhaul before the first release.

• Collect some example MultiQC JSON files for easy testing.
• Check that existing installation docs are still valid
• Write the setup and administration docs
• Write a FAQ docs

List & delete report uploads

The edit_reports/ page is partially written, needs a few additions to make it work fully:

• Basic page with list and delete functionality
• List only the user's reports by default, unless an admin (may already be the case?)
• Only allow the user to delete own report (back end), unless an admin
• Option to show more columns of report-level info about each upload (eg. MultiQC run path)
• Options for bulk-deleting reports with check boxes (+ check all with filters)
• Better filters. eg. Time ranges, more variables.

Feature: see report info from plot view

Currently you can mouseover a point on a plot / trend and see some overall info about the report grouping. It would be really useful to be able to click on it and have it either take the user to a separate page with detailed info on that report, or pop up a sidebar with some additional information and a link to the more detailed report view. Maybe have an option to include a path to the MultiQC report with the MegaQC upload? I guess there are a few new features here. Thoughts?

Tests????

Flask comes with a pretty nice framework for linting and testing. Of course, we haven't used it at all yet. Would be nice to get this up and running!

Profile upload statistics

Generate the report and sample count stats on the user profile page.

Fix "Fields to Plot" text filter

The text filter for the MultiQC plot page works fine, but the others does nothing.

Also, comment out button for Favourites if it's not doing anything currently.

Automated alerts

If we're tracking data over time, we should be able to set manual limits and send automated alerts when a report is submitted with samples that exceed these.

For example: % aligned must be > 80%. If a sample is uploaded with 45% aligned, trigger an alert.

Would be good to have alerts in browser (eg. notifications) and also via email.

Edit filters - edit broken

When clicking on the Edit button of an existing filter, it brings up the new filter modal. Is there an edit modal that it should be pointed to instead, or was the plan to populate the new filter modal with existing values and an update instead of create button?

Single MultiQC report mode

Once we have --noauth (#38), we can have a command line flag to run MegaQC with a single MultiQC JSON file. This would be useful when people generate huuuuge MultiQC runs (eg. single cell) which are not very usable. Here, they could quickly install MegaQC and then interactively look into the data.

Workflow:

pip install multiqc megaqc
multiqc huge_project/data
megaqc run --multiqc-json multiqc_data/multiqc_data.json

MegaQC could ignore usual installation (if any is present) and create a SQLite db file in /tmp. Everything will be lost when exited, so a warning should probably be added to the header.

API to access data

We now have a tonne of data sat in a database. It would be great to write an API to expose this for downstream applications.

This shouldn't be too huge a leap - much of the website already runs using API calls. Just need to separate this into a different namespace and figure out what the spec should be.

Unable to upload Stats.json - KeyError: 'config_creation_date'

Hi there,
Installed the latest version of MegaQC without problems (commit bcdef4f), but was unable to upload my files. megaqc upload *.json completes successfully, but the 'pending uploads' section of the application displays the following traceback for each file:

Traceback (most recent call last):
  File "/home/nana/Documents/megaqc/py2env/local/lib/python2.7/site-packages/megaqc-0.1.dev0-py2.7.egg/megaqc/scheduler.py", line 49, in upload_reports_job
    ret = handle_report_data(user, data)
  File "/home/nana/Documents/megaqc/py2env/local/lib/python2.7/site-packages/megaqc-0.1.dev0-py2.7.egg/megaqc/api/utils.py", line 72, in handle_report_data
    report_hash = generate_hash(report_data)
  File "/home/nana/Documents/megaqc/py2env/local/lib/python2.7/site-packages/megaqc-0.1.dev0-py2.7.egg/megaqc/api/utils.py", line 39, in generate_hash
    data.pop("config_creation_date")
KeyError: 'config_creation_date'

Would it have anything to do with the empty field in megaqc/utils/config_defaults.yaml? Appreciate any assistance,
-Nana