Opened 10 years ago

Closed 10 years ago

#372 closed task (fixed)

Generate lab protocol for FFPE

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v2.7
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

This is the second wizard that follows #371. In this wizard the user should select which paraffin blocks that should be processed. The default list should include only those paraffin blocks that hasn't been processed yet (eg. there are no child HEGlass items). It should also be possible to select paraffin blocks manually.

This should be the first wizard. The first step includes selecting a number of Histology items that have not yet been embedded in paraffin blocks. This can be determined by filtering on items without a creation date. To begin with the items should be sorted by bioplate and position, but this will change when the backlog has been processed since then only temporary boxes are used.

UPDATE: To simplify the other wizards the selection made here should be saved in a biomaterial list which should then be used when registering paraffin blocks. Otherwise the risk is that differences in the selection cause information to be registered incorrectly.

The wizards should generate a printable form containing 3 paraffin blocks on each page.

Change History (19)

comment:1 Changed 10 years ago by Nicklas Nordborg

Milestone: Reggie v2.5

comment:2 Changed 10 years ago by Nicklas Nordborg

Status: newassigned

comment:3 Changed 10 years ago by Nicklas Nordborg

(In [1591]) References #372: Generate lab protocol for FFPE

This should now be working. There are two entry points. Just after the 'Move histology' wizard has been completed it is possible to create a protocol for the new PB plates created.

It is also possible to select a specific set of PB plates in a separate wizard. The default list in this wizard currently contain all PB plates but it should only contain PB plates for which no HE glass exists. This remains to be implemented.

comment:4 Changed 10 years ago by Nicklas Nordborg

Milestone: Reggie v2.5Reggie v2.7

comment:5 Changed 10 years ago by Nicklas Nordborg

(In [1612]) References #371, #372, #373. Remove links to Histology wizards since we will wait with this until Reggie 2.7.

comment:6 Changed 10 years ago by Nicklas Nordborg

(In [1666]) References #371, #372, #373. Fix things that was removed/disabled in [1612] and [1621] due to the delay of the Histology wizards.

comment:7 Changed 10 years ago by Nicklas Nordborg

(In [1667]) References #372: Generate lab protocol for FFPE

Cleaning up the code and fixing some minor things in the printout.

comment:8 Changed 10 years ago by Nicklas Nordborg

Description: modified (diff)

comment:9 Changed 10 years ago by Nicklas Nordborg

(In [1669]) References #372: Generate lab protocol for FFPE

This wizard has now been changed to start with selecting Histology items instead of paraffin blocks. The protocol include the current bioplate location if this information is available. Items with a bioplate location are always sorted before items without location (which are sorted by id).

comment:10 Changed 10 years ago by Nicklas Nordborg

Description: modified (diff)

comment:11 Changed 10 years ago by Nicklas Nordborg

(In [1681]) References #372: Generate lab protocol for FFPE

This wizard now creates 'Histology work lists' which can then be used to generate the lab protocol. The paraffin block wizard (#371) should be changed to use the work lists.

comment:12 Changed 10 years ago by Nicklas Nordborg

(In [1682]) References #372: Generate lab protocol for FFPE

Sorting on MySQL places null values first, but on PostgreSQL places them last. Using coalesce() should make it consistent. Eg. Nulls last since we want to process all histology items with a bioplate before those without.

comment:13 Changed 10 years ago by Nicklas Nordborg

(In [1684]) References #371 and #372. Create (empty) paraffin block plates at the same time as the work lists are created otherwise the plate names on the lab tracking protocol may not match plate names that would have been generated by the registration wizard.

The registration wizard can now select a protocol (Histology subtype).

comment:14 Changed 10 years ago by Nicklas Nordborg

(In [1685]) References #371, #372 and #373. Synchonized names with existing items on the production server.

comment:15 Changed 10 years ago by Nicklas Nordborg

(In [1688]) References #372: Generate lab protocol for FFPE

Rename test data files. Do not use a 'Histology storage box' anymore.

comment:16 Changed 10 years ago by Nicklas Nordborg

(In [1690]) References #372: Generate lab protocol for FFPE

Added HE glass name to the protocol and a box that can be used for recording the location and other info about the block and glass slides.

comment:17 Changed 10 years ago by Nicklas Nordborg

(In [1691]) References #372: Generate lab protocol for FFPE

Added function to create a downloadable file with HE glass labels for printing.

comment:18 Changed 10 years ago by Nicklas Nordborg

(In [1699]) References #372: Generate lab protocol for FFPE

Tried to make the boxes for the block and slides depend less on the browser/os that is used to print the protocol. There was an issue with line-wrapping the last box for the slides.

comment:19 Changed 10 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

Closing this so that 2.7 can be released. If changes/fixes are needed, new tickets should be created.

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