Show information about a case/patient

[Nicklas Nordborg]

The idea is to implement a function that takes a case number or personal number as input and display a lot of information about this case/patient:

• Case and patient information (including checks for missing values)
• Blood sample information
• Specimen information
• DNA/RNA information, quality control values, etc.
• Histology information
• etc...

The details need to be discussed, but it should be simple enough to start with some basic information and then add more when we see a need for it.

[Nicklas Nordborg]

Case overview mockup

[Nicklas Nordborg]

(In [1821]) References #450: Show information about a case/patient

First step has been implemented that show information about the case, patient, blood samples and specimen (or nospecimen). It should handle the various cases with missing information well.

[Nicklas Nordborg]

(In [1824]) References #450: Show information about a case/patient

Implemented two extensions that provide shortcuts to the "Case overview" page.

• A button in the toolbar on single-item pages for samples and extracts with a name that starts with 7 digits.
• A section in the "Item overview" that has a link to the "Case overview" if the current item has a name that starts with 7 digits.

In both cases, the 7 digits in the name are extracted and used as the case name.

Also added a input field for entering a new case name on the overview page so that one doesn't have to go back to the index page all the time.

[Nicklas Nordborg]

(In [1826]) References #450: Show information about a case/patient

Added information about histology, paraffin blocks and stained slides.

[Nicklas Nordborg]

(In [1827]) References #450: Show information about a case/patient

Added a column to the sample and extract list pages that generates a shortcut link to the "Case overview" function in reggie.

[Nicklas Nordborg]

(In [1828]) References #450: Show information about a case/patient

Redesigned the "Case overview" page. It is now styled independently of BASE-defined styles. It should also be better at handling cases that have more than 3 of any item (eg. 3 or more specimen).

[Nicklas Nordborg]

(In [1831]) References #450: Show information about a case/patient

Added information about the lysate.

[Nicklas Nordborg]

(In [1832]) References #450: Show information about a case/patient

Added information about RNA and RNAQC.

Except for maybe some minor details I think this would be more or less production read now.

[Nicklas Nordborg]

(In [1833]) References #450: Show information about a case/patient

Added 'Multiple pieces' field to Lysate section. Fixed an exception that happen if the QC bioplate doesn't have a PDF.

[Nicklas Nordborg]

(In [1834]) References #450: Show information about a case/patient

Hide non-existing RNAQC information when it doesn't exists.

[Nicklas Nordborg]

(In [1836]) References #450: Show information about a case/patient

Reworked the design of the information page. Added a checkbox to show sensitive information (eg. personal number) which is hidden by default. RNAQC date should be taken from the bioplate QC_RUN_DATE annotation since the creation date is the date the aliquot was put on the caliper plate and is not the same as the run date.

[Nicklas Nordborg]

(In [1838]) References #450: Show information about a case/patient

Fixed an issue with formatting numbers. Now uses the javascript builtin formatting function Number.toFixed() instead of the buggy one provided by BASE. Fixed an issue with adding '0' as value to a columns which interpreted it as missing and printed nothing instead.

[Nicklas Nordborg]

(In [1839]) References #450: Show information about a case/patient

Renamed "Case overview" to "Case summary", including file names, java class names, etc.

[Nicklas Nordborg]

(In [1841]) References #450: Show information about a case/patient

Remove menu and apply some other styles to make it possible to print the case summary with good result.

[Nicklas Nordborg]

(In [1844]) References #450: Show information about a case/patient

• Added 'Comment' fields for a lot of items
• Some RNAQC items may be new NanoDrop concentration measurements and should not be included in the RNAQC summary section
• The last RNAQC must be found be checking the QC_RUN_DATE annotation on the associated bioplate instead of using the creation date.
• Columns in the summary could get misaligned when multiple items of the same type exists and only some of them have a value since the column was not added for those that was missing the value
• For the same reason, a complete section/row could be hidden if the last item was missing a value even if some of the previous items had a value.