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Default nucleotide and amino acid sequence #454

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Taepper opened this issue May 29, 2024 · 0 comments · Fixed by #510 or #514

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Taepper commented May 29, 2024

The default nucleotide and amino acid sequence, that is used when it is omitted in queries, should be better configurable.

it is not possible to set a default amino acid sequence. This should be added to the database config.
the default nucleotide sequence is main. The default should be unset. A null should be treated as unset.
It should be verified that the default sequence exists in the provided dataset.

The text was updated successfully, but these errors were encountered:

Taepper mentioned this issue

Validate that the default sequence name is present in the database at startup #475

Closed

fengelniederhammer self-assigned this

fengelniederhammer added a commit that referenced this issue


          refactor: split out method to read DatabaseConfig from a string

63ef978

So that we can bring the testdata closer to the test.
Having separate files for every test case seems tedious.

Refs: #454

fengelniederhammer added a commit that referenced this issue


          refactor: improve error messages

069edd8

Refs: #454

fengelniederhammer added a commit that referenced this issue


          feat: have no default sequence by default, implement default amino ac…

963a63c

…id sequence from config

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: throw error in preprocessing when default sequence is not in re…

ffbe3be

…ference genomes

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: set the default sequence when there is only a single sequence i…

60865b2

…n the reference genomes

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: have no default sequence by default, implement default amino ac…

16898ff

…id sequence from config

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: throw error in preprocessing when default sequence is not in re…

1f7b77f

…ference genomes

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: set the default sequence when there is only a single sequence i…

…n the reference genomes

closes #454

fengelniederhammer mentioned this issue

default nucleotide and amino acid sequence #510

Merged

1 task

fengelniederhammer added a commit that referenced this issue


          feat: throw error in preprocessing when default sequence is not in re…

4c76b08

…ference genomes

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: set the default sequence when there is only a single sequence i…

f92a472

…n the reference genomes

closes #454

fengelniederhammer added a commit that referenced this issue


          refactor: split out method to read DatabaseConfig from a string

e499e12

So that we can bring the testdata closer to the test.
Having separate files for every test case seems tedious.

Refs: #454

fengelniederhammer added a commit that referenced this issue


          refactor: improve error messages

25105f2

Refs: #454

fengelniederhammer added a commit that referenced this issue


          feat: have no default sequence by default, implement default amino ac…

d1638eb

…id sequence from config

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: throw error in preprocessing when default sequence is not in re…

6d98358

…ference genomes

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: set the default sequence when there is only a single sequence i…

05a167e

…n the reference genomes

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: throw error in preprocessing when default sequence is not in re…

6565b0b

…ference genomes

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: set the default sequence when there is only a single sequence i…

d39b48b

…n the reference genomes

closes #454

fengelniederhammer added a commit that referenced this issue


          refactor: split out method to read DatabaseConfig from a string

f8c1feb

So that we can bring the testdata closer to the test.
Having separate files for every test case seems tedious.

Refs: #454

fengelniederhammer added a commit that referenced this issue


          refactor: improve error messages

2c7f3b9

Refs: #454

fengelniederhammer added a commit that referenced this issue


          feat: have no default sequence by default, implement default amino ac…

448a6de

…id sequence from config

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: throw error in preprocessing when default sequence is not in re…

c739ad6

…ference genomes

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: set the default sequence when there is only a single sequence i…

092c65b

…n the reference genomes

closes #454

fengelniederhammer closed this as completed in #510

fengelniederhammer added a commit that referenced this issue


          refactor: split out method to read DatabaseConfig from a string

9a00e37

So that we can bring the testdata closer to the test.
Having separate files for every test case seems tedious.

Refs: #454

fengelniederhammer added a commit that referenced this issue


          refactor: improve error messages

b420504

Refs: #454

fengelniederhammer added a commit that referenced this issue


          feat: have no default sequence by default, implement default amino ac…

2edf924

…id sequence from config

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: throw error in preprocessing when default sequence is not in re…

287bb8b

…ference genomes

closes #454

fengelniederhammer added a commit that referenced this issue


          feat: set the default sequence when there is only a single sequence i…

0ae4022

…n the reference genomes

closes #454

This was referenced Jul 18, 2024

chore(main): release 0.2.9 #514

Merged

chore(main): release 0.2.10 #520

Merged

davidgicev pushed a commit that referenced this issue


          refactor: split out method to read DatabaseConfig from a string

88f8149

So that we can bring the testdata closer to the test.
Having separate files for every test case seems tedious.

Refs: #454

davidgicev pushed a commit that referenced this issue


          refactor: improve error messages

9b06377

Refs: #454

davidgicev pushed a commit that referenced this issue


          feat: have no default sequence by default, implement default amino ac…

491b16b

…id sequence from config

closes #454

davidgicev pushed a commit that referenced this issue


          feat: throw error in preprocessing when default sequence is not in re…

…ference genomes

closes #454

davidgicev pushed a commit that referenced this issue


          feat: set the default sequence when there is only a single sequence i…

895767b

…n the reference genomes

closes #454

github-actions bot mentioned this issue

Update to Clang tidy 20 #535

Merged

2 tasks

github-actions bot mentioned this issue

chore(main): release 0.2.17 #553

Merged

This was referenced Sep 12, 2024

Panic utilities improvements: ensure DEBUG_ASSERT compiles, add ASSERT_EQ etc., add tests #571

Merged

chore(main): release 0.2.19 #573

Merged

github-actions bot mentioned this issue

chore(main): release 0.2.22 #598

Merged

github-actions bot mentioned this issue

chore(main): release 0.3.2 #631

Merged

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