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stan-core's Introduction

Stan (Core)

CI

TODO

  • Finish README

    Database setup:

  • Install MySQL via home-brew

  • Create a schema in your local mysql db called stan

  • Create users and passwords in your local mysql matching the details in application-dev.properties

  • Create appropriate permissions on the user

  • In your run configuration for StanApplication, override the parameter spring.profiles.active giving it the value dev.

    For setting users

      $ mysql -u root
  > create user 'stan'@'%' identified by 'stanpassword';
  > grant delete, insert, execute, select, update on `stan%`.* to 'stan'@'%';
  > create user 'stan_admin'@'%' identified by 'stanadminpassword';
  > grant all on `stan%`.* to 'stan_admin'@'%';

    Use the schema and static data patches in the stan-sql repo to set up your schema

    > Create a db schema using file stan-sql/schema/create_schema.sql
> Run script ./cat_sequence.py schema static view which will output SQL to set up database (There is a file called sequence.txt in stan-sql/sequence.txt that list all the patches applied
> Create an empty schema called `stantest` for the tests to run in. Liquibase is responsible for setting up tables and data for unit tests.

Notes:-

  • For your unit test schema, liquibase should update it automatically when you run unit tests. If it doesn't, run liquibase.dropAll in the tab of IntelliJ
  • For your schema that you use to run core locally, all the required changes are defined in the stan-sql repo and listed in sequence.txt. The cat_sequence.py script in that repo will concatenate patches together in a particular range for you to run into your database, and it will add records to the db_history table of your schema so you can check which patches you have already applied.

Stan Application:

  • Install IntelliJ
  • Load stan-core application in IntelliJ
  • Update stan.mail.alert.recipents field in application-dev.properties so it won’t send email in case of an error in your local setup.
  • Run the package job in the maven tab of IntelliJ
  • To run the application, find and run the StanApplication class

stan-core's People

Contributors

khelwood avatar sabrine33 avatar seenanair avatar bentopping avatar snyk-bot avatar dependabot[bot] avatar dasunpubudumal avatar

Watchers

James Cloos avatar Andrew Sparkes avatar avatar avatar avatar

Forkers

khelwood jbeast

stan-core's Issues

x942 CytAssist_view

User Story
As TS (katy) I would like a new view for the cytassist operation in x883 to allow for accurate billing and tracking, view called CytAssist_view

Acceptance
Columns needed:
*Worknumber,
*Operation ID,
*source barcode,
*source slot.
*Cytassist slide type,
*Cytassist slide barcode (destination barcode),
*Cytassist slot.,
*date stamp,
*slide costing - Faculty or SGP

x943 Transfer_view

User story
As TS (katy) I would like a new view for the enhancement in x932 to allow for accurate billing and tracking, view to be called Transfer_view

Acceptance
Columns needed:
Worknumber,
Operation ID,
source barcode,
source slot,
source state,
detination barcode,
destination slot,
destination state,
date stamp,

row is per section/slot

x928 Update the spatial locations and add a new tissue type

User story:
As a TS (Katy) I would like to update the spatial locations for the rest of the samples not aligned and add a new tissue type

Acceptance:
"New Tissue type:

  • Tissue type: Tumour, Code: TUM, spatial code: 0 – no spatial information

Delete spatial codes:

  • Terminal ileum spatial location 1 and 2 - so only 0 exists
  • Gonad spatial location 1 and 2 - so only 0 exists"

x962—As an end user (Ceci), I want to search for multiple blocks at the same time

if you want to search for multiple blocks from the same donor, e.g. A16-UTR-0-FO-1, A16-UTR-0-FO-2, and A16-UTR-0-FO-3, you have to search one by one. It would be better if we could just type “A16-UTR-0-FO-“ and it would bring them all up. Or if there are multiple donors for the same organ but also we want to specify by block type, we’d type “ADR FFPE” and it would bring up AC5-ADR-0-FFPE-3 and A13-ADR-0-FFPE-1 and A13-ADR-3-FFPE-6.

x896 - Release file perm times

User story
As ARA (ilaria) I would the release file to display any perm. time operations performed

Who are the primary contacts for this story
Ilaria

Acceptance criteria
To be considered successful the solution must allow:

  • If an LP/TO slide is released, then it is from that barcode.
  • If it's a 96 well plate, then the operation will have occurred on the source barcode

x883—As TS (Katy), I want to record a new operation called CytAssist

Select worknumber
Scan in one or two source barcodes (slides).
Scan in one (external) destination barcode, and specify labware type (see x884 and x885).
Select which section goes to which slot on the new cytassist slide.
Transfer section from the sources to the destination slide. Source section/slides become Used (not discarded) so it can be stored/released/destroyed
State change of transferred: Probes

x989 As a PO (Minal) I would like to specify the locations of sections inside a slot on an Visium slide to support lots of small sections for HTA purposes

Visium Slides - TO, LP,

new category of comments to describe section location in the sectioning confirmation page.
Only select one comment.
Only select when there are multiple sections in a slot
'Slot Region' field is mandatory for slots with multiple sections

Comments:
Top Left:
Top Right:
Bottom Left:
Bottom right:
Middle
Top
Bottom
Left
Right"

Notes:
need to look at this and its impact on Cytassist

XXL

x917 - Stan core rejecting certain URL chars

User story
Filtering by status in the work management page produces an invalid URL on UAT

Who are the primary contacts for this story
David

Acceptance criteria
To be considered successful the solution must allow:

  • Stan-core needs to allow urls containing [] characters for client pages.

x1028 AS TS (Katy) I would like to update the information on the SGP management page to allow for data flow to be better

"visible and editable by enduser and normal accounts

Add new dropdown list called - "DNAP study ID and description"
*to be not compulsory for all worktypes, needed for visium workflows only
*drop down list to be editable on the config page
*to appear in the SGP management search table and dropdown list to be update-able (similar to the omero project field)

Change the title for project dropdown on the SGP management page to "Project (cost code description)"

Note:
to be created so dropdownlist for DNAP study ID and description and omero project would be pulled from with central list - would get a lot of data that might not come our way

x1027—As TS (Katy) I want replicate numbers to be any mix of up to 7 digits and letters, to match the faculty convention, for futureproofing

Needed on section registration and block registration. Will affect sectioning and lab processing pages.

Current rules for replicates:
Block processing:

  • cannot specify the same replicate from the same source block multiple times in the request
  • cannot specify the same replicate as a previously created replicate with the same donor and spatial location

Katy will look into the effect on labels.

x957 As SRA (Katy) I would like to add Visium Reagent LOT number to visium QC slide processing operation, to allow for linking and tracking of issues between LOT numbers

Visium QC slide processing page to have a scannable area to scan in one Reagent LOT number for all the visium reagents in this operation (multiple slides might have the same LOT numbers)
Reagent LOT number to be associated with all slides in operation
To appear on the history page

add to visium qc slide processing view

LOT numbers are 6-7 digits.

x972 As TS (Katy) I would like a new feature to record issues in the SPRI clean-up step on visium, on the Visium QC called "SPRI clean-up", to allow for issues in protocol to be records

Select work number
Select QC type = ""SPRI clean up""
Scan in Lab barcode
for each slot in the labware assign a comment per slot or apply all

Comments:
• Difficult/very slow to separate
• Bead loss during clean up
• Carryover beads in final eluate transferred to new tube
• Beads cracked during drying step
• Difficult to resuspend beads/grainy appearance
• Reduced volume in final eluate transferred to new tube

Not manditory for every slot

Comments to be editable on config page. And appear in alphabetical order

Comments to appear on history page"

x696 Adding OMERO project name to SGP management page when creating requests to track imaging projects

"Enter Omero Project name on SGP management page, searchable dropdown list, editable via config. page

not manditory at the moment, but will make it mandatory later

column to appear on Main dashboard and SGP manangement page search tables

appear on the work_view

List of projects so far:
KR_SMAN
SGP_R&D
VK_SKM
KK_HEA
KM_FLNG
KM_LNG
NA_RMS

"Add new field to work number that specifies an omero project name. Fixed set of values specified in config page (deactivatable).
Selected from dropdown and shown in SGP management page.
Not compulsory.
Show in work_view."

x808 file uploader

User Story
As a TS (Katy) I would like to upload a file and associate it with a worknumber, to reflect and record the work performed out of STAN and to allow customers easier access to them.

Acceptance
Select worknumber from dropdown list

Upload file(s)
*to rewrite over file with the same name (warning appear you are doing this)

be able to retrieve/roll back database

How much space does this need? roughly ~5mb month = 56.18mb per year round up to 60-75mb per year

x705—As a PO (Minal), I want the slide printer to print directly from STAN to reduce errors and save money and time

Printing software links a template set up on computer, that STAN creates a CSV type file to send the information to to print

Need to know what information is needed on the template: STAN barcode, Donor ID, tissue type - short code (starting with stage), Spatial location number, replicate

Computer slide printer is connected to is 115848 - but could put them both on the same computer

Used for slide and 4-slot slide (when slide has 3 or fewer samples on)

Need to be able to print either labels or slides from these labware types.

x956 As SRA (Katy) I would like to be able to to add slide lot number and slide costings (Faculty/SGP) feature to visium slides on the sectioning page, to allow for linking and tracking of issues between lot number and billing purposes

Section planning page to have scannable areas to scan in LOT numbers for the visium slides (multiple slides might have the same LOT numbers)
Visium LP, Visium TO and Visium ADH slides
LOT number to be associated with a (destination) slide (which is being used in an operation)
To appear on the history page

Add Slide costings and Slide LOT number to sectioning view
Both fields (lot number and costing) are compulsory in the specified contexts

Slide LOT numbers are 6-7 digits

x909 - Review dependency updates

Describe the Housekeeping
As a developer I would like the dependencies to be updated in STAN Core.

  • Review library dependencies that have updated version available.
  • If simple attempt upgrade, else if complicated we may need to discuss and plan what can be done.

x979—As TS (Katy), I want to transfer stored labware from one storage area to another, because we need to be able to transfer labware from one lab to another

"transfer whole boxes/trays from one place to another
can't move into storage which has labware already in
box to box, or tray to tray"

Transfer contents (labware) from one named (barcoded) box to another existing box. Not transferring parent locations; only using boxes that directly contain labware to other existing empty boxes with the same dimensions.

x940 Add Faculty/SGP flag for Visium QC - Slide Processing

User Story:
As TS (Katy) I would like to enhance the "Visium QC - Slide processing" to have a flag/dropdown list for if visium slide is coming from Faculty or SGP, this will allow us to calculate the number of Visium slides coming from faculty or from SGP for accurate and flexible billing purposes.

Acceptance:
"use flag as per x883
we need to flag whether the slide is coming from Faculty - 'Slide costing'

Slide_processing_view: can column be added to show this

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