Bug: cubi-tk (isa-tab|sodar) add-ped is modifying previous Study Assay Data when --library-kit or --library-kit-catalogue-id is given

[your-highness]

Describe the bug
When updating samplesheets for sodar project 25a57a17-9bee-44b5-aeca-c4a322b71f51 , I found that previous entries in Assay Data - which are not given in the pedifle - are wrongly set to library kit given by parameters --library-kit or --library-kit-catalogue-id . This wrongly alters columns Value[Library kit] and Comment[Library kit catalogue ID] in Assay Data.

When using only one of the parameters, only this column, i.e. Value[Library kit] or Comment[Library kit catalogue ID] , is wrongly updated in Assay Data. **This leads to inconsistencies of the columns!

When not using any of the parameters, no wrong updates are done.

To Reproduce

cubi-tk isa-tab add-ped \
  --batch-no 19 \
  --library-layout PAIRED \
  --library-type WES \
  --platform ILLUMINA \
  --instrument-model "Illumina NovaSeq 6000" \
  --library-kit-catalogue-id "S33266340" \
  --library-kit "Agilent SureSelect Human All Exon V8" \
  samplesheet/i_Investigation.txt v8.ped

or

cubi-tk sodar add-ped \
  --batch-no 19 \
  --library-layout PAIRED \
  --library-type WES \
  --platform ILLUMINA \
  --instrument-model "Illumina NovaSeq 6000" \
  --library-kit-catalogue-id "S33266340" \
  --library-kit "Agilent SureSelect Human All Exon V8" \
  25a57a17-9bee-44b5-aeca-c4a322b71f51 v8.ped

Expected behavior
Only add / update the samples given in the ped file!

Additional context
Example of wrong update diff with 2 parameters set (see changes in columns Value[Library kit] and Comment[Library kit catalogue ID] ):

Sample Name    Protocol REF    Parameter Value[Concentration measurement]      Performer       Date    Extract Name    Characteristics[Concentration]  Unit    Term Source REF Term Accession Number   Protocol REF    Parameter Value[Provider name]  Parameter Value[Provider contact]      Parameter Value[Provider project ID]    Parameter Value[Provider sample ID]     Parameter Value[Provider QC status]     Parameter Value[Requestor contact]      Parameter Value[Requestor project]      Parameter Value[Requestor sample ID]    Parameter Value[Concentration measurement]     Parameter Value[Library source] Parameter Value[Library strategy]       Parameter Value[Library selection]      Parameter Value[Library layout] Parameter Value[Library kit]    Comment[Library kit catalogue ID]       Parameter Value[Target insert size]    Parameter Value[Wet-lab insert size]    Parameter Value[Barcode kit]    Parameter Value[Barcode kit catalogue ID]       Parameter Value[Barcode name]   Parameter Value[Barcode sequence]       Performer       Date    Library Name    Characteristics[Folder name]   Characteristics[Concentration]  Unit    Term Source REF Term Accession Number   Protocol REF    Parameter Value[Platform]       Parameter Value[Instrument model]       Parameter Value[Base quality encoding]  Parameter Value[Center name]    Parameter Value[Center contact]        Performer       Date    Raw Data File
-LB20_2553-N1   Nucleic acid extraction WES                             LB20_2553-N1-DNA1                                       Library construction WES                                                                                GENOMIC WXS     Hybrid Selection      PAIRED   Agilent SureSelect Human All Exon V6r2  S07604514                                                                       LB20_2553-N1-DNA1-WES1  LB20-2553                                       Nucleic acid sequencing WES     ILLUMINA        Illumina NovaSeq 6000 Phred+33                                                                                                                                                                                                                                                                        
-LB21_0274-N1   Nucleic acid extraction WES                             LB21_0274-N1-DNA1                                       Library construction WES                                                                                GENOMIC WXS     Hybrid Selection      PAIRED   Agilent SureSelect Human All Exon V6r2  S07604514                                                                       LB21_0274-N1-DNA1-WES1  LB21-0274                                       Nucleic acid sequencing WES     ILLUMINA        Illumina NovaSeq 6000 Phred+33                                                                                                                                                                                                                                                                        
+LB20_2553-N1   Nucleic acid extraction WES                             LB20_2553-N1-DNA1                                       Library construction WES                                                                                GENOMIC WXS     Hybrid Selection      PAIRED   Agilent SureSelect Human All Exon V8    S33266340                                                                       LB20_2553-N1-DNA1-WES1  LB20-2553                                       Nucleic acid sequencing WES     ILLUMINA        Illumina NovaSeq 6000 Phred+33                                                                                                                                                                                                                                                                        
+LB21_0274-N1   Nucleic acid extraction WES                             LB21_0274-N1-DNA1                                       Library construction WES                                                                                GENOMIC WXS     Hybrid Selection      PAIRED   Agilent SureSelect Human All Exon V8    S33266340                                                                       LB21_0274-N1-DNA1-WES1  LB21-0274                                       Nucleic acid sequencing WES     ILLUMINA        Illumina NovaSeq 6000 Phred+33

Example of wrong update diff with only ID given (see inconsistency in Value[Library kit] and Comment[Library kit catalogue ID] ):

Sample Name    Protocol REF    Parameter Value[Concentration measurement]      Performer       Date    Extract Name    Characteristics[Concentration]  Unit    Term Source REF Term Accession Number   Protocol REF    Parameter Value[Provider name]  Parameter Value[Provider contact]      Parameter Value[Provider project ID]    Parameter Value[Provider sample ID]     Parameter Value[Provider QC status]     Parameter Value[Requestor contact]      Parameter Value[Requestor project]      Parameter Value[Requestor sample ID]    Parameter Value[Concentration measurement]     Parameter Value[Library source] Parameter Value[Library strategy]       Parameter Value[Library selection]      Parameter Value[Library layout] Parameter Value[Library kit]    Comment[Library kit catalogue ID]       Parameter Value[Target insert size]    Parameter Value[Wet-lab insert size]    Parameter Value[Barcode kit]    Parameter Value[Barcode kit catalogue ID]       Parameter Value[Barcode name]   Parameter Value[Barcode sequence]       Performer       Date    Library Name    Characteristics[Folder name]   Characteristics[Concentration]  Unit    Term Source REF Term Accession Number   Protocol REF    Parameter Value[Platform]       Parameter Value[Instrument model]       Parameter Value[Base quality encoding]  Parameter Value[Center name]    Parameter Value[Center contact]        Performer       Date    Raw Data File
-LB20_2553-N1   Nucleic acid extraction WES                             LB20_2553-N1-DNA1                                       Library construction WES                                                                                GENOMIC WXS     Hybrid Selection      PAIRED   Agilent SureSelect Human All Exon V6r2  S07604514                                                                       LB20_2553-N1-DNA1-WES1  LB20-2553                                       Nucleic acid sequencing WES     ILLUMINA        Illumina NovaSeq 6000 Phred+33                                                                                                                                                                                                                                                                        
-LB21_0274-N1   Nucleic acid extraction WES                             LB21_0274-N1-DNA1                                       Library construction WES                                                                                GENOMIC WXS     Hybrid Selection      PAIRED   Agilent SureSelect Human All Exon V6r2  S07604514                                                                       LB21_0274-N1-DNA1-WES1  LB21-0274                                       Nucleic acid sequencing WES     ILLUMINA        Illumina NovaSeq 6000 Phred+33                                                                                                                                                                                                                                                                        
+LB20_2553-N1   Nucleic acid extraction WES                             LB20_2553-N1-DNA1                                       Library construction WES                                                                                GENOMIC WXS     Hybrid Selection      PAIRED   Agilent SureSelect Human All Exon V6r2  S33266340                                                                       LB20_2553-N1-DNA1-WES1  LB20-2553                                       Nucleic acid sequencing WES     ILLUMINA        Illumina NovaSeq 6000 Phred+33                                                                                                                                                                                                                                                                        
+LB21_0274-N1   Nucleic acid extraction WES                             LB21_0274-N1-DNA1                                       Library construction WES                                                                                GENOMIC WXS     Hybrid Selection      PAIRED   Agilent SureSelect Human All Exon V6r2  S33266340                                                                       LB21_0274-N1-DNA1-WES1  LB21-0274                                       Nucleic acid sequencing WES     ILLUMINA        Illumina NovaSeq 6000 Phred+33

[Nicolai-vKuegelgen]

This issue is still present and should be solved

[Nicolai-vKuegelgen]

okay, I think I have a fix for this.
And just have it noted: the add-ped function is coded in a pretty complicated way so any fixes or functionality changes here will be slow coming.

[Nicolai-vKuegelgen]

@your-highness

Fix incoming, I hope the issue is solved with the newest version