Opened 4 years ago

Closed 4 years ago

#910 closed defect (fixed)

The Mark extracts for retraction wizard doesn't find all items in some cases

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.7
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

If case has multiple child specimen items with different SCAN-B ID, only the items with the same SCAN-B ID as the case are listed in the wizard. The generated protocols for destruction of items in the freezer are also missing the items.

Change History (18)

comment:1 Changed 4 years ago by Nicklas Nordborg

For example, try the cases lined to 'PAT000056' in the test database.

Version 0, edited 4 years ago by Nicklas Nordborg (next)

comment:2 Changed 4 years ago by Nicklas Nordborg

Status: newassigned

comment:3 Changed 4 years ago by Nicklas Nordborg

(In [4102]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Cleaned up some code:

  • Site information is loaded per case
  • List with case names is generated from the list with case items instead of having special JSON properties just for this (which only worked for 2 cases).

comment:4 Changed 4 years ago by Nicklas Nordborg

(In [4103]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

More cleanup:

  • Display error immediately if no patient is found, since the registration will not work otherwise
  • Simplified loading of cases and blood now that we are sure to have a patient
  • Found another list with case names (patient.allCases). Use this list instead of re-creating a new one for displaying the "All cases" value.

comment:5 Changed 4 years ago by Nicklas Nordborg

(In [4104]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Load all child items by following links (uses the existing functionality for doing so). Case and Blood items in the returned JSON data is now populated from this information. Other information is still using the old way to load child items.

comment:6 Changed 4 years ago by Nicklas Nordborg

(In [4105]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Specimen and NoSpecimen item information updated to use the new child loading.

comment:7 Changed 4 years ago by Nicklas Nordborg

(In [4106]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Same change for Lysate, RNA, DNA and FlowThrough.

comment:8 Changed 4 years ago by Nicklas Nordborg

(In [4107]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Same change for RNAQC. Needed some changes in the javascript as well since the RNAQC items are now top-level in the JSON data instead of a separate array below each RNA item.

comment:9 Changed 4 years ago by Nicklas Nordborg

(In [4108]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Same change for Blood DNA, mRNA and cDNA.

comment:10 Changed 4 years ago by Nicklas Nordborg

(In [4109]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Same change for Histology and Stained items.

comment:11 Changed 4 years ago by Nicklas Nordborg

(In [4110]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Same change for Library items.

comment:12 Changed 4 years ago by Nicklas Nordborg

(In [4111]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Removed some of the unused code.

comment:13 Changed 4 years ago by Nicklas Nordborg

(In [4112]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Pooled libraries and sequencing runs are now loaded from the actual libraries instead of matching against case name. All items displayed in the table should now be those that descend from the top-level patient record.

comment:14 Changed 4 years ago by Nicklas Nordborg

(In [4113]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Removing the "Preview" and "Download" buttons and all code that is associated with this functionality.

comment:15 Changed 4 years ago by Nicklas Nordborg

(In [4114]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

The "Cases" field in the lab protocol now uses the correct list with cases names. Storage box coordinate is displayed in a separate column instead of mixed with the freezer location.

comment:16 Changed 4 years ago by Nicklas Nordborg

(In [4115]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Turned out that pooled libraries are loaded as child items so there is no need for special handling.

comment:17 Changed 4 years ago by Nicklas Nordborg

(In [4116]) References #910: The Mark extracts for retraction wizard doesn't find all items in some cases

Fixed the display of "No case information has been registered" (and other similar messages) so that they use the whole table width.

Removed some unused style declarations.

comment:18 Changed 4 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
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