• Remove paired field if found to be necessary
• Remove all references to format field

All of the y-axis hash marks are labelled with 0-values.

Occurs when a user without virus modification permissions views a virus with a non-empty isolate.

This message should only be shown when the virus is empty. For a privileged user, a button for adding a sequence would be shown.

Only a list of virus sequences should be shown, when the virus is not empty.

So far, this only seems to happen on Safari.

A simple solution may be to clear the IndexedDB and rebuild it when the client version number changes. Look into making use of the IndexedDB database versioning capability.

The status labels for importing and analysing are not working properly. This needs to be reworked.

The "added" flag was renamed "ready" in v1.8.0 to conform with other document types in the database. Databases made before v1.8.0 use the "added" keyword.

The organize.py module needs to be updated to update the host documents on start.

Eliminate simplejson as a dependency by using the json module from the standard library.

Large amounts of SAM output use too much memory. Find a way to deal with these rare situations.

One idea is to flush the data to a file when the memory usage reaches a set threshold.

Right now, the method only takes a single argument that is passed to the collection method. Use args and
kwargs to pass the actual method arguments to the method.

The virtool process consume 10+ GB of memory in short order.

This may be due to file upload buffers not being cleared after the upload completes.

When cancelled, Rebuild jobs leave the bowtie2-build subprocess running. Fix this to make the process terminate on job cancellation.

Hosts are imported from FASTA files in the file manager since v1.8.0. The host data tree was changed from:

data_path/reference/hosts
data_path/reference/hosts/fasta
data_path/reference/hosts/index

to

data_path/reference/hosts

Only indexes are retained in this directory, not FASTA files.

Hosts imported before v1.8.0 will have to have their host file tree changed appropriately.

Change client transactions to use function chaining or promises:

eg. collection.request('test.test', {}).onSuccess().onFailure()

Alternatively, we could look into moving Redux, which may resolve this issue.

A list of the external dependencies required by Virtool, their versions, and statuses.

Ideas:

• functions for querying the dependency binaries that are required in PATH
• functions for automatically installing these programs specifically for Virtool (installation sub-directory)
• button for refreshing information
• publication references
• view licenses
• descriptions
• path returned by which

Allow configuration of drawing regular virus database updates from the web.

Improve and simplify the jobs view in the client by:

• removing archiving function
• switching to a ListGroup instead of DynamicTable
• allowing easy removal of completed, erroneous, or cancelled jobs
• improving sorting

Move to ECMAScript 6.

Not much feedback and progress information is shown to the user while importing a virus reference. Upgrade this functionality to show:

• errors
• progress bar
• stats on imported viruses
• better formatting

FASTA files currently have to be manually placed in the data/references/hosts/fasta path. A new interface for uploading hosts FASTAs or downloading from external URLs must be implemented.

Assess and fix a bug that is causing read files that no longer exist in watch on the server to remain in the client read listing.

There are some things the file manager currently does not do that it needs to:

• remove untracked files from the files data path
• remove database documents for files that have been manually removed from the files data path
• remove tracked files that have expired

Implement unit testing for:

• Python code
• Javascript code

The top emboldened lines of text in the General and Server setting are not at the same height.

It is jarring.

Traceback has exception being raised at line 264 in files.py. This is probably due to the file still being checked for changes even though it no longer exists.

May be fixed by dealing with #26.

This exception is raised during the software update.

Exception in callback functools.partial(<function wrap.<locals>.null_wrapper at 0x7fdc147e6158>, <tornado.concurrent.Future object at 0x7fdc34074438>)
Traceback (most recent call last):
  File "site-packages/tornado/ioloop.py", line 604, in _run_callback
  File "site-packages/tornado/stack_context.py", line 275, in null_wrapper
  File "site-packages/tornado/ioloop.py", line 619, in <lambda>
  File "site-packages/tornado/concurrent.py", line 237, in result
  File "<string>", line 3, in raise_exc_info
  File "site-packages/tornado/gen.py", line 1021, in run
  File "virtool/updates.py", line 180, in install_update
  File "site-packages/tornado/gen.py", line 1015, in run
  File "site-packages/tornado/concurrent.py", line 237, in result
  File "<string>", line 3, in raise_exc_info
  File "site-packages/tornado/gen.py", line 270, in wrapper
  File "/home/igboyes/.virtualenvs/virtool/lib/python3.5/types.py", line 243, in wrapped
  File "virtool/web.py", line 265, in _reload
  File "virtool/web.py", line 89, in initialize
  File "virtool/dispatcher.py", line 54, in add_interface
ValueError: Dispatcher already has interface with name 'settings'

Software update install needs more testing overall!

Improve the jobs view with the following changes:

• remove the archived section as it is not necessary
• add a button for clearing all completed, successful, or failed jobs
• add a dashboard showing real resource usage on the host machine
• add a component showing Virtool job resource reservations

An alert is visible in the host management view when no hosts have been successfully added. When a new host is added, the alert does not disappear without a page refresh.

All versions more recent than the installed version are labelled as latest.

Implement report printing. Features:

• options for automatic formatting and letterheads
• print a summary for multiple samples
• print a report for a single analysis
• print a report for all analyses attached to a single sample

The install script needs a number of improvements:

• render new lines cleanly when requesting input from the user
• handle updates (in addition to installs)

• Any files placed in the watch folder will be uploaded by the Virtool file manager
• Allow administrators to configure whether uploaded files are removed from the watch folder on upload

Make analyses individually retrievable by the client. Sample detail will not have to retrieved every time an analysis is added or removed for the sample.

Job sorting does not work.

Add options for automatically dumping the Virtool database to a local or remote file system location. Possible features:

• backup interval setting
• use SSH or SFTP

Problem is in web.py.

This module contains functions that clean up the Virtool database on start. None of these functions are currently called.

They should be called as one of the first steps of starting the server.

• Allow BLASTing of contigs on NCBI, saving the result
• Show the families for each contig
• Show the highest e-value for each contig

These lists are basically useless to the user at this point. Make more informative lists or consider getting rid of lists and having info blurbs.

For example, here is a current argument list:

• algorithm: pathoscope_bowtie
• username: igboyes
• sample_id: fktma5
• index_id: 9e94a2fc
• name:
• analysis_id: 0199cb5b

Modifications could include:

• replacing database ids with human readable links to samples, analyses, etc
• formatting algorithm names
• giving index versions instead of ids

Getting this exceptions during some analyses:

Traceback (most recent call last):
File "virtool/job.py", line 116, in run
File "virtool/analysis.py", line 217, in pathoscope
TypeError: 'NoneType' object is not subscriptable

This occurs during the Pathoscope stage of PathoscopeBowtie. Not if it occurs during PathoscopeSNAP. Is this due to having no high-quality mappings for that sample (ie. it is clean).

One CPH sample that causes this error is 16TFP146.

The Settings object is the cause of this bug. Make sure it is reinitialized properly during reload.

Implement a framework that will allow users to attach diagnostic decisions to analysis and sample records. Features will include:

• marking of decisive diagnostic hits in the Pathoscope viewer
• marking of 'needs more work' hits in the Pathoscope viewer
• searching samples by viruses as described by diagnostic decisions
• text box or drop-down for hit decision rationale

The D3 library has recently moved to a more modular structure.

This modularity is not currently being utilised by Virtool (the whole library is imported). Refactor all usage of
D3 to import only the bits needed.

The code for verifying virus collections and their associated data in the data path does not work. Fix this for use during setup and normal repair of the database.

Add a view for managing the HMM files and annotations included in Virtool for NuVs. Annotations should have:

• editable names or nicknames
• name of the user that assigned the nickname
• date of nickname
• read-only information from the annotation text files

HMM files should be described with:

• file names and sizes
• stats generated by hmmstat

Right now, sample FASTQ files have to be manually places in the watch path. Implement an upload system for these files.

In both the server and client code, these variable names need to be improved. For example:

_id changes to virus_id

Biopython is a large library and only a very small part of it is used in Virtool. It drags Numpy and Scipy into the application. It should be replaced with a slimmer custom module.

Problems

• Virtool is slow to start
• pip install is slow
• builds are slow
• ugly font-list warnings in terminal

Candidate replacements

• in-browser using d3
• bokeh

This is no longer working after v1.8.0.

Self-explanatory