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Comments (4)

jorainer avatar jorainer commented on August 16, 2024

My options are:
A) use a global setting to switch from join to outer join.
B) customize the individual joins defined in the table specifying the joins (i.e. the .JOINS table).

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jorainer avatar jorainer commented on August 16, 2024

Use cases:

  • use transcripts to fetch all transcripts of a gene and add (if available) protein annotation: in this case we want to get all transcripts, also the non-coding ones. -> outer join.
  • get all genes with a certain protein domain. In this case we use genes with a ProtdomidFilter thus it should work with both types of joins.
  • use a proteins method to get all proteins and add e.g. gene_name as a column. In this case we don't want an outer join that joins the /tx/ and /protein/ tables. -> join.

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jorainer avatar jorainer commented on August 16, 2024

The only solution to solve point 3 above and don't run into an issue when joining the protein and uniprot tables (not every protein id is annotated to an uniprot id) is to use left outer join and specify the table from which the join should start (i.e. gene for genes, protein for proteins etc).

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jorainer avatar jorainer commented on August 16, 2024

This ends up in implementing a new join engine.

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