SCAN-B report

[Nicklas Nordborg]

A new report, the "SCAN-B report" should be implemented. It will probably use information produced by the Single Sample Predictor (#1186). Details are still not available. The report should be produced from StringTie data in a manner that is similar to how the pilot and gene reports are currently produced for Cufflinks data.

[Nicklas Nordborg]

In 5647:

References #1190: SCAN-B report

Added first version of a SCAN-B report. It is a simple copy of the pilot report but without plots and other things calculated/generated by the pilot report R script.

Instead all installed SSP models are executed and the result is printed on top.

The "Report plugin" has been updated with a "SCANB_REPORT" option. There is an issue with it only accepting Cufflinks rawbioassays the needs to be solved in a better way.

[Nicklas Nordborg]

In 5650:

References #1190: SCAN-B report

Linked a report template to a specified raw data type and updated the report plug-in to use that raw data type for checking if the selected raw bioassay can be used for the specific report. Eg. the pilot and gene reports are linked to Cufflinks and the SCAN-B report is linked to StringTie.

[Nicklas Nordborg]

In 5664:

References #1190: SCAN-B report

Added "SCANB_REPORT" as an option to the ReportTemplate annotation to make it possible to select/register a software item when running the report plug-in for generating a SCAN-B report.

[Nicklas Nordborg]

In 5665:

References #1190: SCAN-B report

Added a counter for rawbioassays without a SCAN-B report and a link on the front page for entering the report wizard in SCAN-B report mode. One problem is that the wizard has a hard-coded filter for the Legacy pipeline and Cufflinks rawbioassays.

[Nicklas Nordborg]

In 5666:

References #1190: SCAN-B report

Added a pipeline setting to the PdfReportTemplate which means that the report wizard now can find the correct raw bioassays to use for a report.

The manual selection can still bypass this, but a check in the wizard has been implemented to verify that only raw bioassays from the correct pipeline are selected (this is the same check that is already implemented in, for example, the alignment wizard).

[Nicklas Nordborg]

In 5669:

References #1190: SCAN-B report

Implemented support for updating SSP annotations when the SCAN-B report is generated.

[Nicklas Nordborg]

In 5670:

References #1190: SCAN-B report

Implemented support for auto-confirmation to create the SCAN-B report after StringTie has been completed. It is currently disabled (in the code) since a proper report has not yet been designed.

[Nicklas Nordborg]

In 5671:

References #1190: SCAN-B report

Renamed the "Accept" column/action in the StringTie confirmation wizard to "SCAN-B report".

[Nicklas Nordborg]

In 5672:

References #1190: SCAN-B report

Added an activity log definition for SCAN-B reports.

[Nicklas Nordborg]

In 5673:

References #1190: SCAN-B report

The report combiner plug-in now supports the SCAN-B report. One issue with the combiner is that it always generate file names based on the raw bioassay name (with internal id). This may need to change in the future depending on if the reports include internal or external id values.

[Nicklas Nordborg]

In 5674:

References #1190: SCAN-B report

Just added a note to remember to check the filename also in the report plug-in. The raw bioassay name is used as the name of the pdf when running this plug-in in "immediate download" mode.

[Nicklas Nordborg]

In 5682:

References #1190: SCAN-B report

Added plug-in configurations for the SCAN-B report.

[Nicklas Nordborg]

In 5694:

References #1190 (and #1199). Implemented a simple check for some known ESR1 mutations and include the result as an output on the report. It should be considered as proof-of-concept only and the implementation need major changes in a final setting.

[Nicklas Nordborg]

In 5737:

References #1186 and #1190. Disabling code related to the SSP plug-in and SCAN-B report. They will be postponed to a later release.

[Nicklas Nordborg]

In 6024:

References #1190: SCAN-B report

Re-enabled the SCAN-B report wizard.

[Nicklas Nordborg]

In 6026:

References #1190: SCAN-B report

Added support for extracting FPKM values from StringTie gene.tsv files.

[Nicklas Nordborg]

In 6027:

References #1190: SCAN-B report

Re-worked the SCAN-B report implementation so that it loads and prints a lot of information that has been up for discussion. The template is a very early draft and need some "cleaning" before actual information can be added. The same plots as are on the Gene report are added to the report, but they will be replaced with new versions that are based on StringTie data.

[Nicklas Nordborg]

In 6028:

References #1190: SCAN-B report

Implemented a "debug mode" option that can be controlled via a parameter.

[Nicklas Nordborg]

In 6029:

References #1190: SCAN-B report

Implemented support for translating some values before they are printed to the report.

[Nicklas Nordborg]

In 6030:

References #1190: SCAN-B report

Added a <scanb-report> section to reggie-config.xml. The template system has been extended to allow for multiple pages in the report. A second page has been added which simple copy a static page from the template pdf.

[Nicklas Nordborg]

In 6031:

References #1190: SCAN-B report

The SCAN-B report should use external id in the auto-generated file name.

[Nicklas Nordborg]

In 6032:

References #1190: SCAN-B report

The debug mode (added in [6020]) didn't work well in list context since we can only execute the list query once and then we need to use the raw bioassays as they are stored.

[Nicklas Nordborg]

In 6033:

References #1190: SCAN-B report

Updated the report combiner plug-in to use external id in file names when adding reports to zip files. The changes made in [6031] are also affected and we now use the same approach in both places.

[Nicklas Nordborg]

In 6034:

References #1190: SCAN-B report

The report combiner plug-in now supports combining to a PDF when the source PDF files have multiple pages.

[Nicklas Nordborg]

In 6035:

References #1190: SCAN-B report

Renaming the net.sf.basedb.reggie.r package to net.sf.basedb.reggie.script since the generic functionality of starting an external script-like process is needed for other types of scripts.

[Nicklas Nordborg]

In 6036:

References #1190: SCAN-B report

Added ScriptDefinition and moved some generic stuff from RScriptDefinition to it.

Renamed the RResult class to ScriptResult since there is nothing that is special to R in it.

[Nicklas Nordborg]

In 6037:

References #1190: SCAN-B report

Made a copy of the GeneReport to ScanBReport. The new class will be used to run the updated scripts when they become available.

[Nicklas Nordborg]

In 6039:

References #1190: SCAN-B report

Adding helper methods to the PdfUtil class for drawing colored and underlined text.

[Nicklas Nordborg]

In 6041:

References #1190: SCAN-B report

Added extension for adding a "SCAN-B report" column to the raw bioassays list page that display a thumbnail of the PDF.

Added extension for displaying a thumbnail of the "SCAN-B report" on the raw bioassay single-item page.

[Nicklas Nordborg]

In 6056:

References #1190: SCAN-B report

Updated the report generation to use the latest template.

[Nicklas Nordborg]

In 6057:

References #1190: SCAN-B report

Added colored circles to ROR section.

[Nicklas Nordborg]

In 6059:

References #1190: SCAN-B report

The changes in [6026] broke the Rawbioassay.getFpkmSumFromFile() implementation for Cufflinks data (the column header for "Gene name" was never set to gene_short_name).

[Nicklas Nordborg]

In 6065:

References #1190: SCAN-B report

Changed the "warning" and "ok" icons for CC15 to svg icons.

[Nicklas Nordborg]

In 6066:

References #1190: SCAN-B report

Changed the "yellow-label" icon to svg.

[Nicklas Nordborg]

In 6067:

References #1190: SCAN-B report

Changed HER2 status to use one of the ER-related HER2 classifications if ER-status is available.

[Nicklas Nordborg]

In 6068:

References #1190: SCAN-B report

Fixed some issues that causes report to fail if information is missing.

• Missing RIN/RQS caused an exception
• A specimen without an external id caused an exception

[Nicklas Nordborg]

In 6075:

References #1190: SCAN-B report

The new showcase report script is now used instead of the genereport to produce the plots for the report.

Matched ROR colors to the colors used in the plot.

[Nicklas Nordborg]

In 6076:

References #1190: SCAN-B report

Added more translations for BiopsyType, Subtype and Library protocol.

Fixed some issues that would have caused exceptions if some information is missing.

[Nicklas Nordborg]

In 6078:

References #1190: SCAN-B report

Implemented functionality for fitting text into a specified width. The strategy is to decrease the font size in steps down to ~75% of the original and if that is not enough, characters are removed from the end of the text until it fits (replaced with ...).

Read string values could be duplicated if they had the same number of "T" but different "B" or "S".

[Nicklas Nordborg]

In 6080:

References #1190: SCAN-B report

Changed the orange color for ROR to a bit darker.

[Nicklas Nordborg]

In 6081:

References #1190: SCAN-B report

Re-designed the configuration settings for the template files. It is now possible to list an arbitrary number of templates to include in the report. The first file must be the template for the report. Other files are included as is without any modification.

[Nicklas Nordborg]

In 6082:

References #1190: SCAN-B report

The "Reads total" value should be from the PF_READS annotation.

[Nicklas Nordborg]

In 6086:

References #1190: SCAN-B report

Removed debug code.

[Nicklas Nordborg]

In 6087:

References #1190: SCAN-B report

The installation wizard was missing checks for plug-in configurations related to the SCAN-B report and the configuration for the Report combiner plug-in was missing.