For samples belonging to the same panel but different sites, allow an option in the process request wizard for creating multiple jobs simultaneously split by site. Maybe the best place for this is in the first step of the PR wizard, where if samples from multiple sites are shown, the user is presented with a check box to automatically split the jobs by site. If this is selected, the PR label should be appended with the site name.

Currently, new ReFlow users must be added using the Django admin interface. Add functionality to create new users in the ReFlow admin view. Should also allow modifying them (make them inactive, change their password, etc.) as well as deleting them.

An alternative to "-" as delimiter would make it simpler to extract the marker, antibody and data type. For example, IFN-IL2-PE-A is hard to parse correctly because "-" is used both as a delimiter and to join the names of the multiplexed cytokines. An alternative delimiter that is less susceptible to such delimiter collisions would be preferable

When a session times out, the URL displays a "next" URL parameter, but after re-login the parameter is ignored and the user is taken to the main dashboard. This occurred during the AngularJS view conversion.

It would be nice to get back project, site and visit objects given the pk from the restclient interface by adding a pk argument, in the same way that is done for get_samples.

Allow the user to specify the random seed & sub-sample count when submitting both stage 1 & 2 process requests. Currently, the random seed is available in the stage 1 PR wizard.

Add download of CSV results to PR detail view. Use comma-delimited quoted values to handle comma separated labels (one-to-many). Include columns:

• stage
• parent
• Sample (filename & PK)
• Cluster index
• Cluster labels
• Event %
• Parent cluster event %

Create a mechanism for ReFlow admins to disable (and re-enable) workers from the ReFlow server. This would be useful for testing a specific worker. Since a worker is just a sub-classed User, perhaps this could be easily achieved by simply setting the user's active status?

When files are added to the categorization queue the user should not be allowed to select the check box unless all the required fields on the left are chosen. Currently, if no cytometer is chosen this is allowed.

Also, the select all check box interferes with the sample annotation modal. If the user toggles the select all on & off, then subsequent toggling of a single FCS file will not initiate the sample annotation modal.

This was mostly addressed in c47c4e2 however if a view doesn't make a REST API it will seem as if everything is ok and the user is still logged in until they happen to hit a view that tries to retrieve something. Perhaps every state change should "check-in" with the server in some way, ideally using minimal bandwidth. Another idea is to have some periodic check-in that could re-direct on session expiration.

When saving an edit to an existing sample, server returns 500 error. Traceback shows an error in line 1425 of models.py:

exceptions:AttributeError: 'Sample' object has no attribute 'sample_metadata_dict'

This is due to the fact that the metadata dictionary is only created for new Sample instances.

The clusters are currently identified by an rather arbitrary "cluster index" that does not provide any biological meaning. A useful feature would be to allow users to apply more meaningful labels to the clusters.

After selecting the FCS samples to analyze, the use selects which channels to include in the analysis among the channels common across all the selected files. By default, all the parameters are selected. However, it is unlikely that the user will ever want to analyze the Time & Null channels. These should be de-selected by default.

Once an FCS sample has been uploaded and associated with a panel, then edits to that PanelTemplate would require existing SitePanels to be re-validated and what would happen if the validation fails? This would be quite a mess. We should disable editing PanelTemplates once there are associated SitePanels. If the user needs them to be changed, they can delete the PanelTemplate and re-upload the files.

Seems that Firefox truncates file names for downloaded files if there is a space in the name and possibly truncates the file extensions. Verified on Windows, and may occur in Firefox on other platforms.

Currently, the default value is 0.003 and is hard-coded in the ReFlowWorker Sample class method "apply_asinh_tranform". If user-configurable, perhaps this should go in an advanced settings area?

There's no mechanism to view the metadata for uploaded FCS files. The upload page allows viewing the metadata, but this is prior to upload. This could be implemented as another "action" button on the the SampleList view and the metadata could be shown in a modal dialog window.

Also, when a user changes his/her password, create a new token for that user for TokenAuthentication. Should we have another mechanism to just generate a new token without changing the password?

Allow a description for the Panel model. This is especially useful in cases were the panel parameters may look incorrect because an FCS file has incorrect PnN text, i.e. if 2 parameters were reversed. The Panel would look incorrect, but is actually correcting a mistake in the file. A description field would be useful to explain this.

Implement downloading of FCS files with ReFlow channel annotations. This allows a project user to export all the files with a common set of channel names. Also, create a file name convention for the "clean" files that is consistent and contains useful metadata about the file such as the site code, subject code, etc.

Perhaps a multi-select combo box for the cell subsets in the stage 2 modal as opposed to a set of check-boxes (which would potentially use a lot of screen real estate)

Panel variants are intended to be used for Full Stain, FMO, ISO, etc. Within the PR wizard, there is no way to distinguish samples belonging to the same panel family other than the user knowing which file name belongs to a particular panel variant.

Recently changed the behavior of Null and duplicate channels, and the rules were already complex. All the documentation needs to be re-visited, but documenting the panel template is the first priority.

At the end of the wizard to create a new process request, it would be helpful to display the list of choices made during the various steps. This is useful for creating PR labels.

Some FCS files may have already been compensated and/or transformed, and therefore should not be compensated or transformed. There needs to be an option to turn these steps off in the PR request wizard. However, this will require possibly major changes the way the PR creation controllers work, as well as changes to the ReFlowWorker code.

List the samples in the SampleCollection chosen for a specific process request on that PR's detail page.

Not sure if it is possible, but it would be nice to be able to hit the enter key to submit forms in the modal dialogs. Perhaps keybinding for opening the modal to create a new record as well?

Once an FCS file has been categorized, there is no mechanism to make ReFlow "forget" that specific annotation set. If the user incorrectly labelled one or more channels this becomes a problem, and the only way to fix it is to use the Django admin interface or accessing the DB directly. We need to re-expose the SitePanel list, but perhaps come up with a more intuitive name for it – something like "Sample Annotations" or "Stored Panel Parameters". It should be possible to re-use the SitePanel modal from the sample upload code to allow editing the saved annotations, as well as allowing their deletion. Deleting a SitePanel should also delete the related Samples, which would be easier than deleting the Samples individually.

Update project dependencies including Django, Django REST Framework, AngularJS, Bootstrap, d3, and jQuery.

Current versions -> target versions:
Django 1.7.7 -> 1.8.2
DRF 2.3.13 -> 3.1.3
AngularJS 1.2.18 -> 1.4.1
Bootstrap 3.1.1 -> 3.3.5
d3 3.4.13 -> 3.5.5
jQuery 1.9.2 -> 2.1.4

For ReFlow admins, create a worker dashboard for monitoring worker status, showing if a worker is busy, and if so, the project for the worker's current assignment. Currently, it is difficult to determine if any worker is active without checking each project's PR list.

If the original file has a $SPILL value in the metadata, copy it to the clean FCS file. This is especially helpful when using the exported files in FlowJo as it is cumbersome to re-add the compensation.