Support for Excel files as an alternative to tab-separated files

[Nicklas Nordborg]

There are indications that software and hardware that we are interacting with via tab-separated file will have support for Excel files in the future. In some cases they may even lack support for tab-separated files.

It would be a good time to start testing if we can work with Excel files. In the first stage:

• Sample names for the Qubit step in the library preparation. There is both an export step and an import step.
• Label files for the printer software

As for an API to use, the Apache POI project seems to be doing what we need: ​https://poi.apache.org/

[Nicklas Nordborg]

In 5296:

References #1110: Support for Excel files as an alternative to tab-separated files

Added JAR files from the Apache POI project. The commons-compress-1.18.jar and xmlbeans-3.0.1.jar are dependencies that we have found so far while trying to generate a simple HelloWorld-like spreadsheet.

[Nicklas Nordborg]

In 5297:

References #1110: Support for Excel files as an alternative to tab-separated files

Implemented an xlsx version of the Qubit sample name export. A simple helper class XlsxTableWriter was implemented that acts as a wrapper for the TableWriter (from BASE) that is used to create CSV files. With this helper class it is possible to let the same code export either a CSV file or XLSX file as long as the TableWriter.tablePrintData() method is used.

The helper class is currently limited to string values, but it should not be difficult to support also other values types if required.

[Nicklas Nordborg]

In 5298:

References #1110: Support for Excel files as an alternative to tab-separated files

Added file format option to the regular plug-in api dialogs for the QubitSampleNameExporter.

Added styling to comments and the header line in the generated xlsx file.

[Nicklas Nordborg]

In 5299:

References #1110: Support for Excel files as an alternative to tab-separated files

The partition wizard can now create the label file in Excel format.

[Nicklas Nordborg]

In 5300:

References #1110: Support for Excel files as an alternative to tab-separated files

Prepared the Library registration wizard with support for Excel files. We may have to rename the QUBIT_CSV subtype to something else. I tried defining a new subtype (QUBIT_XLSX), but when there is more than one to select from BASE will not automatically assign a subtype to uploaded files. This causes the filter to not display the file after upload which is very annoying. Unless this can be solved at the BASE level, we need to use a single subtype for both CSV and XLSX files.

[Nicklas Nordborg]

In 5301:

References #1110: Support for Excel files as an alternative to tab-separated files

The Library registration wizard should now support Qubit files in Excel format. In order to not complicate the importer code, the XlsxToCxsUtil class was implemented. It can read an Excel file and generate CSV as output (per worksheet), which is then fed to the already existing importer code.

[Nicklas Nordborg]

In 5303:

References #1110: Support for Excel files as an alternative to tab-separated files

Make sure that opened stream while reading Qubit and Caliper files closed.

[Nicklas Nordborg]

In 5304:

References #1110: Support for Excel files as an alternative to tab-separated files

The "Lab tracking protocol for Allprep isolation" wizard and the "DNA/RNA/FlowThrough registration" can now also generate label files in Excel format.

[Nicklas Nordborg]

In 5305:

References #1110: Support for Excel files as an alternative to tab-separated files

Added support for evaluating formulas when converting Excel file to CSV.

[Nicklas Nordborg]

In 5306:

References #1110: Support for Excel files as an alternative to tab-separated files

The Excel worksheet should be named ReExtractionLabels when creating labels for re-extraction from lysate.

[Nicklas Nordborg]

In 5307:

References #1110: Support for Excel files as an alternative to tab-separated files

Do not evaluate formulas by default since we do not have any use case that requires it yet.

[Nicklas Nordborg]

In 5308:

References #1110: Support for Excel files as an alternative to tab-separated files

The "Storage box creation wizard" now has support for Excel when downloading labels.

[Nicklas Nordborg]

In 5309:

References #1110: Support for Excel files as an alternative to tab-separated files

The "Download HE glass labels wizard" now has support for Excel when downloading labels.

[Nicklas Nordborg]

In 5310:

References #1110: Support for Excel files as an alternative to tab-separated files

The "Protocols and labels for sample outtakes wizard" now has support for Excel when downloading labels.

[Nicklas Nordborg]

In 5316:

References #1110: Support for Excel files as an alternative to tab-separated files

Added support for setting specific number and date formatter implementations to make sure that values come out in a predictable format. Without this we get a mix of the formatting used in the original document and locale-specific changes that can happen if the document was created with a different default locale than the server is using.

[Nicklas Nordborg]

In 5317:

References #1110: Support for Excel files as an alternative to tab-separated files

Adding DoubleFormatter. It should have been included in [5316].

[Nicklas Nordborg]

In 5338:

References #1110: Support for Excel files as an alternative to tab-separated files

Fixed an issue that caused JSON data to be appended to the output file when downloading labels. It was simply ignored when creating an Excel file, but the CSV file had an extra line at the end: {"status":"ok"}