razorlabs / occams_lims Goto Github PK

Background

A common criticism of the LIMS application is the inability to be able to "group" specimen together visually (say for preparing a shipment, etc).

Suggested Fix

A possible remidy to this issue would be to introduce user tags/flags so that they can keep track of specific samples (e.g. "Dr. Doe's samples", "Samples I have to verify today"), . Note that the user would not take ownership of the sample, but just have an easy way to get to them.

Overview

In new installations, the LIMS application will occasionally display some items as marked for printing when they were not in the first place. This is because currently the print queue uses a single list to keep track of IDs, so if there is overlap in IDs between specimen and aliquot, it will incorrectly show them as marked for printing. We need to use a separate queue for specimen and aliquot.

Steps to Reproduce

1. Install OCCAMS LIMS in a brand new machine
2. Create a specimen and then mark it for aliquot
3. Mark the original specimen for print (specifically one were the ID of the specimen is the same as the aliquot)
4. Go to aliquot view, observe that the aliquot with the same ID is also marked for print

Outcomes

Expected

The aliquot should not be reported as marked for print

Actual

The label count for the aliquot appears.

I am using Ubuntu 16.04 LTS and installed repository, Add Docker’s official GPG key, installed Docker Engine, Docker Compose, Docker machine, system requirements but when I am trying to build source code of occams_lims using “docker-compose build” command that time error is occurred such as “Service 'app' failed to build : The command '/bin/sh -c pip install --upgrade -r /tmp/requirements-develop.txt' returned a non-zero code: 1”.

$/opt/occams_lims# docker version
Client:
Version: 18.09.0
API version: 1.39
Go version: go1.10.4
Git commit: 4d60db4
Built: Wed Nov 7 00:48:57 2018
OS/Arch: linux/amd64
Experimental: false

Server: Docker Engine - Community
Engine:
Version: 18.09.0
API version: 1.39 (minimum version 1.12)
Go version: go1.10.4
Git commit: 4d60db4
Built: Wed Nov 7 00:16:44 2018
OS/Arch: linux/amd64
Experimental: false

$/opt/occams_lims# docker-compose build

Step 10/13 : RUN pip install --upgrade -r /tmp/requirements-develop.txt
---> Running in 029e97ce9d03
Invalid requirement: 'gunicorn > 19.5.0'
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/pip/req/req_install.py", line 78, in init
req = Requirement(req)
File "/usr/lib/python2.7/site-packages/pip/_vendor/packaging/requirements.py", line 96, in init
requirement_string[e.loc:e.loc + 8]))
InvalidRequirement: Invalid requirement, parse error at "u'> 19.5.'"

You are using pip version 8.1.2, however version 20.2.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
ERROR: Service 'app' failed to build : The command '/bin/sh -c pip install --upgrade -r /tmp/requirements-develop.txt' returned a non-zero code: 1

Please guide me

In order to help staff be more productive, a suggestion that has been brought up is for an easier way to "bulk-edit" samples.

This can possibly be implemented, by selecting samples, then clicking on a "Bulk-Edit" button which then guides the user through an edit wizard.

Staff requested that we develop functionality to allow the bulk checkin of aliquot instead of needing to do it one by one as is currently the case.

There is a request from staff for functionality to reserve aliquot so that persons cannot check them out without approval first. Info needed to be stored...

1. That the aliquot is reserved (a checkbox)
2. For whom/what purpose

Each tab has a sample state set as a the default search criteria (e.g. Aliquot is "Pending Check-in"; Check-out Queue is "Pending Check out"). Currently this is not displayed when the user first navigates to the page and causes a lot of confusion as to what the current search criteria are.

History

Currently, label sheet settings are hard-coded in occams_lims:labels.py. They were originally Processing/Clinical lab settings in the Plone objects, which were deprecated with the recent Pyramid migration.

Goals

Our labs use Cryo-babies label sheets, but other sites might not. It would be beneficial for sites to be able to configure LIMS with project-specific label sheets so that they can be selected when printing labels for specimen/aliquot.

A method that will search the db for a set of patient/date pairs in specimen, and allow a user to associate those specimen to be associated with a visit.

Overview

The landing page for LIMS displays all enabled locations to the user even they don't have view permissions for them.

IMPORTANT Even though the user can see a lab's existence they will not be able to actually access the data. This ticket only addresses the fact that the user can inadvertently click on a site they do not have access too and receive a 403 error (which might intimidate them)

Steps to Reproduce

1. Give member access to a user to a specific location
2. Go to /lims

Outcomes

Expected:
User should only see a listing of locations they have access to

Actual:
They see all the locations and if they click on one they do not have membership they receive "insufficient privildeges" error.

This field has never been utilized and only takes up visual real estate.

Requirements

• Remove in the UI
• Write alembic migration to remove from the database

Overview

When a user creates a visit, they have the option to also request specimens from their site's lab location. Currently, all existing installations have been grand-fathered with this information, but new studies such as AEGiS need to be configured. There needs to be a configuration option in LIMS to allow an administrator to assign lab locations to sites.

A current work-around is to just link these manually in the database.

Background Knowledge

The structure for this already exists in the LIMS tableset, but is regrettably configured a a many-to-many relationship, assume one-to-many from site to lab locations.

Steps to Reproduce

1. Create a patient
2. Assign enrollment
3. Click on "Add visit" button in the visits panel
4. In the modal window, ensure "Request specimen" checkbox is selected
5. Save visit

Outcomes

Expected

The LIMS app should be updated with requested specimen

Actual

Nothing happens

Overview

When logging into LIMS, if no lab is created the attached image error is generated.

Background Knowledge

Current permissions are handled through ldap group management which can be found on the local server in /opt/occams/etc/production.ini

Each lab location has different procedures for how they store their samples:

• box/position
• freezer/rack/box

It would be helpful to have a section in LIMS to allow administrators configure the lab location's storage parameters in order to keep the UI consistent with the lab's storage protocols.

When I tried to install occams_lims following the steps that you supplied. But I get the following errors at the step 4.

Pulling postgres (postgres:9.5)...
9.5: Pulling from library/postgres
8ad8b3f87b37: Pull complete
c5f4a4b21ab6: Pull complete
ba05db8b0a52: Pull complete
47b491cd21ab: Pull complete
d70407e3e64d: Pull complete
295c246dd69f: Pull complete
89bc4bb8bcfd: Pull complete
106ff44c5f06: Pull complete
867cd91e76bb: Pull complete
a227948d6d8c: Pull complete
fc2ec20bdaf0: Pull complete
Digest: sha256:1115f095242a490cb79561124a79125e25b0595d5ae47d44fab5b4c1cd10735f
Status: Downloaded newer image for postgres:9.5
Creating occamslims_postgres_1
Creating occamslims_redis_1
Creating occamslims_app_1

ERROR: for app Cannot start service app: oci runtime error: rootfs_linux.go:53: mounting "/mnt/sda1/var/lib/docker/aufs/mnt/8bef63d5f956506bfb8af68697180681c5af9386ae59ec31bfb537bf6bd55748/app/develop.ini" to rootfs "/mnt/sda1/var/lib/docker/aufs/mnt/8bef63d5f956506bfb8af68697180681c5af9386ae59ec31bfb537bf6bd55748" caused "not a directory"
ERROR: Encountered errors while bringing up the project.

Please help me to install it, Thanks!

Overview

This is similar to #14 in that specimen types need to be linked to a study cycle so that they can automatically be created on visit add. The UI for this does not exist in the LIMS configuration view.

Background Knowledge

The table to populate is specimentype_cycle

Steps to Reproduce

1. Create a patient
2. Assign enrollment
3. Click on "Add visit" button in the visits panel
4. In the modal window, ensure "Request specimen" checkbox is selected
5. Save visit

Outcomes

Expected

The LIMS app should be updated with requested specimen

Actual

Nothing happens

Reported by staff:

In order to identify and pull a specific specimen aliquot - one must page down though many individual lines and count the aliquots/date manually to determine how many are present. Would be much more functional to have the number of aliquots per date collapsed/counted per date so that one could quickly determine the number of samples per date per patient (i.e., 5 plasma on date 1, 20 plasma on date 2, 15 plasma on date 3, etc). Then, date 2 selected since this date has the most samples, select this date - drop down to select the individual sample(s) to pull.