39 Commits

Author SHA1 Message Date
2920ba95ee Increased default timeout
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2025-03-14 16:48:16 +00:00
14d760a266 Added optional parameter to change timeout
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2025-03-14 16:09:01 +00:00
f8d92a4aad Added predetermined headers feature
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2025-03-14 14:26:43 +00:00
34bf02c75a Increased timeout to 5 minutes
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2025-03-13 18:37:33 +00:00
3cb10a4609 Added client error as acceptable exception
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2025-03-13 18:13:38 +00:00
1776f5aa51 Fixed exception syntax
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2025-03-13 16:51:15 +00:00
96d715fdcb Added a server disconnect error catch
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2025-03-13 16:27:59 +00:00
e088d1080b Added functionality to retry determining ST
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2025-03-13 16:13:14 +00:00
8ffc7c7fb5 Added retry functionality for allele variant determination
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2025-03-13 15:54:35 +00:00
62fdada9c1 Added original filename to csv output
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2025-03-13 14:17:08 +00:00
17932ecd71 Alleles IDs obtained from one sequence is named the ID of that sequence
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Instead of generating a tuple comprised of the one sequence ID repeated
2025-02-26 06:15:56 +00:00
4b34036d17 Fixed concurrent profile_multiple_strings implementation
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2025-02-26 05:16:24 +00:00
27ae89fde7 Replaced schema with scheme
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2025-02-26 04:50:54 +00:00
b8cebb8ba4 Infrastructure for concurrent processing implemented
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2025-02-19 15:49:46 +00:00
7384895578 Writing now uses named MLST profile
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2025-02-18 16:03:17 +00:00
5a03c7e8d8 Multiple string profiling now respects grouped queries (for non-WGS)
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2025-02-18 15:34:18 +00:00
d0318536b2 Changed FASTA reading to group based on file for merging partial targets 2025-02-14 14:35:53 +00:00
73aade2bde Merge branch 'features/improved-oop-architecture' into features/non-exact-notation 2025-02-12 17:07:51 +00:00
af8590baa7 Removed import of deleted feature 2025-02-12 17:07:10 +00:00
36bca1b70d Merge branch 'features/improved-oop-architecture' into features/non-exact-notation 2025-02-12 17:02:22 +00:00
09a693b696 Removed features being worked on in separate branch 2025-02-12 17:02:00 +00:00
ba606c35a9 conversion of collection of alleles to map now produces results with tuples instead of lists 2025-02-12 16:36:31 +00:00
4183840ba0 Added notation to indicate inexact matching in CSV 2025-02-12 15:59:19 +00:00
175a51f968 Replaced local profiler with a not implemented exception 2025-02-12 15:52:48 +00:00
e568e9fb2c Adapted latest merged reading codebase to current codebase 2025-02-11 19:13:29 +00:00
4b9eb8674d Merge branch 'develop' into features/local-typing 2025-02-11 17:55:34 +00:00
f75707e4fe CSV output column order is now predictable (sorted) 2025-02-11 17:54:48 +00:00
b4845fab34 Added automatic handling of strings instead of arrays of sequences to typing 2025-02-06 21:15:50 +00:00
fe999f1cab Added a unit test for multithreaded alignments 2025-02-06 18:01:50 +00:00
85946eb110 Fixed match metric difference between remote and local 2025-02-06 17:12:31 +00:00
a27e09da31 Added code to retrieve sequences and annotations from NCBI GenBank 2025-02-06 17:11:20 +00:00
ba2b688e89 Removed sorting as it seems unecessary 2025-02-05 22:06:50 +00:00
49f31b7943 Async aligner work tracking issue fixed 2025-02-05 21:47:51 +00:00
1c6e1cfb35 Fixed issue with hashing a ndarray by using tuple. 2025-02-05 20:43:53 +00:00
fb99526162 Updated iteration on asynchronous aligner 2025-02-05 17:17:37 +00:00
ff8a1aff08 Implemented annotated local typing method without testing 2025-02-04 16:19:00 +00:00
3e3898334f Began implementing LazyPersistentCachedBIGSdbMLSTProfiler 2025-01-27 22:03:49 +00:00
ba1f0aa318 Fixed potential memory leak 2025-01-27 22:02:52 +00:00
1773bb9dcb Updated naming (again). 2025-01-22 21:05:19 +00:00