Pilot report wizard

[Nicklas Nordborg]

A new report wizard for the clinical pilot project is needed. It is basically the same as the "Gene report" but with a different R script, input/output parameters and pdf template.

The wizard should work manually and with auto-confirmation using the same rules as the "Gene report" wizard.

Details about the R script, parameters and pdf template are not yet complete. To begin with everything can be implemented as a copy of the "Gene report". One thing that is already known is that the script needs the cufflinks fpkm data file, so we can prepare for this by copying the file to the temporary working directory.

[Nicklas Nordborg]

(In [3492]) References #812: Pilot report wizard

Added a pilot wizard stub. The report is more more or less a copy of the current gene report but without the validation cohort reference. The GUI and servlet is using the same code as the gene report. The plug-in is currently an independent class, but I think it is possible to refactor this code as well to make a common "Report" plug-in with multiple configurations.

[Nicklas Nordborg]

(In [3499]) References #812: Pilot report wizard

Refactored the gene report plug-in so that it can create both the gene report and pilot report (or any other upcoming report that is similar). The pilot report plug-in has now been replaced with a configuration item.

Programmatically it is also possible to let a single job create more than one report. This is used by the auto-confirm feature so that both reports are created by a single job.

[Nicklas Nordborg]

(In [3500]) References #812: Pilot report wizard

The combine reports plug-in now uses configurations to decide which report to combine.

[Nicklas Nordborg]

(In [3506]) References #812: Pilot report wizard

Refactored the reporting plug-ins. Classes for running the R scripts are now separated from the classes that does the PDF generation. There is now only one class for working with a single PDF report. That class is responsible for both creating the first version and adding personal information when combining reports.

[Nicklas Nordborg]

(In [3508]) References #812: Pilot report wizard

The auto-confirmation service should now be able to handle cases were the pilot report fails and set the 'ReProcess' flag on the raw bioassay.

[Nicklas Nordborg]

(In [3513]) References #812: Pilot report wizard

Fixes title on the "Gene/Pilot report" wizard. This requried some changes to the code that puts the Reggie version in the top right corner on the page and the print stylesheet.

[Nicklas Nordborg]

(In [3525]) References #812: Pilot report wizard

The pilot report is updated to the new template pdf. Information about the patient, case, etc. is loaded and written to the header section.

Images are still the output from the GeneReport script and.

Other values are still left blank.

[Nicklas Nordborg]

(In [3528]) References #812: Pilot report wizard

Print out molecular subtype scores and other values. The values are currently randomly generated.

[Nicklas Nordborg]

(In [3531]) References #812: Pilot report wizard

Prepared the script for sending the FPKM file as input to the pilot report R script.

[Nicklas Nordborg]

(In [3533]) References #812: Pilot report wizard

The pilot report now uses the pilot report R script. The molecular subtype values are parsed from the PAM50.txt file. The plots generated from the script are used. The text values on the left side are still based on random numbers.

[Nicklas Nordborg]

(In [3534]) References #812: Pilot report wizard

Adding link to the pilot report in the case summary page.

[Nicklas Nordborg]

(In [3535]) References #812: Pilot report wizard

Parse the *.txt files containing the score for each plot. The score is converted to text (Låg/Hög, Negativ/Positiv) depending on if the score is lower or higher than 0. If no txt file is available N/A is written instead.

[Nicklas Nordborg]

(In [3541]) References #812: Pilot report wizard

Setting R source encoding to UTF-8 to make sure that scripts containing non-ansi characters are parsed correctly. For example: LÃ¥g --> Låg

[Nicklas Nordborg]

(In [3542]) References #812: Pilot report wizard

Importing the *_validationClass.pdf/.txt files with plot and group information.

[Nicklas Nordborg]

(In [3543]) References #812: Pilot report wizard

Minor adjusments to text positions.

A new version of the R script has "class" name in the pam50.txt file that doesn't match any of the headers, so we need to check which score that is the highest to be able to print it in bold.

[Nicklas Nordborg]

(In [3548]) References #812: Pilot report wizard

Adjusting text and plot positions to the new template.

[Nicklas Nordborg]

(In [3556]) References #812: Pilot report wizard

Adjusting text and plot positions to a new version of the template.

[Nicklas Nordborg]

(In [3557]) References #812: Pilot report wizard

Adding "Pilot report" thumbnail column to the raw bioassays list page.