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HISTORY.txt
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# RCSB_UTILS_SEQ HISTORY
11-Dec-2018 - V0.10 Created module supporting PDB - UniProt mapping using SIFTS
19-Mar-2019 V0.11 Incorporate UniProt feature extraction tools.
22-Apr-2019 V0.12 Improve cache management, broaden test coverage
24-Jun-2019 V0.13 Update development workflow
14-Jul-2019 V0.14 Fix py27 minidom issue with 'in' operation.
9-Sep-2019 V0.15 Add SiftsUtils() -> SiftsSummaryProvider()
10-Sep-2019 V0.16 Convert case on PDB accession codes
18-Sep-2019 V0.17 Add alignment details to the cache file
18-Sep-2019 V0.18 Address Py27 dependency issue
19-Sep-2019 V0.19 Move SeqAlign() utility class to this module
23-Sep-2019 V0.20 Guarantee order and uniqueness from SiftsProvider.getIndentifiers()
6-Oct-2019 V0.21 Include GO in the abbreviated set
6-Oct-2019 V0.22 Make the content extracted subject to an API control to avoid Azure testing issues
12-Oct-2019 V0.23 Add method SiftsSummaryProvider.getLongestAlignments()
16-Oct-2019 V0.24 Address variable record length in reading SIFTS GO data.
16-Oct-2019 V0.25 Update handling of secondary reference assignment mapping
17-Oct-2019 V0.26 Include taxonomy with accession code mapping
23-Nov-2019 V0.27 Move pipeline to py38
6-Dec-2019 V0.28 Add rebuildMatchResultIndex() to refresh the match index.
9-Dec-2019 V0.29 Add reformat method to support ExDB schema spec.
14-Dec-2019 V0.30 Add method to provide unique UniProt accessions.
15-Dec-2019 V0.31 Add method to provide unique UniProt accessions for an entry subset
16-Dec-2019 V0.32 Correction in parser for feature sequence positions
16-Dec-2019 V0.33 Improved error handling for failed fetches.
16-Dec-2019 V0.34 Suppress tracebacks for some connection issues.
3-Feb-2020 V0.35 Update dependencies
4-Feb-2020 V0.36 Add stricter tests for failed lookup requests.
8-Feb-2020 V0.37 Add independent tests for failover, expose more parameter
controls to public methods.
13-Feb-2020 V0.38 Add further uniqueness checks in reformatting Uniprot features.
18-Feb-2020 V0.39 Add Pfam and InterPro annotation providers
18-Feb-2020 V0.40 Handle encoding issues for Py27
5-Apr-2020 V0.41 Adjust logging details for UniProt fetchlist
20-Jun-2020 V0.42 Add method fetchSequenceList() to fetch fasta sequences
22-Jun-2020 V0.43 Add methods to return SeqAlign() from SIFTS data.
23-Aug-2020 V0.43 Adjust InterPro ftp URL references.
9-Oct-2020 V0.44 Add organism host taxonomy
24-Oct-2020 V0.46 Adjust tests to handle Ubuntu 20.04 issues
30-Nov-2020 V0.47 add UniProtIdMappingProvider() and tests.
1-Dec-2020 V0.48 make UniProtIdMappingProvider() a singleton.
2-Dec-2020 V0.49 Add legacy id mapping data in UniProtIdMappingProvider()
10-Dec-2020 V0.50 Add 'tdd' format in UniProtIdMappingProvider() and improve save and load performance
10-Dec-2020 V0.51 Add to and from stash methods in UniProtIdMappingProvider()
22-Mar-2020 V0.52 Add backup and restore methods in UniProtIdMappingProvider()
23-Mar-2020 V0.53 Add clearCache methods and preserve loaded state across multiple instances of UniProtIdMappingProvider()
10-May-2021 V0.54 Add feature and gene lookup method in UniProtUtils()
10-May-2021 V0.55 Adjust return prototype for lookup functions
10-May-2021 V0.56 Add review option for doGeneLookup()
10-May-2021 V0.57 Adjustments to UniProt FASTA comment line parser
26-May-2021 V0.58 Add Pfam mapping methods and GlyGenProvider() and associated tests
27-May-2021 V0.59 Tweaking diagnostic output in GlyGenProvider()
28-May-2021 V0.60 Add read-only version of GlycanProvider() and associated tests
30-May-2021 V0.61 Add getVersion() method in PfamProvider().
30-Jun-2021 V0.62 Make GlycanProvider() a subclass of StashableBase(), update __docformat__
24-Jul-2021 V0.63 Make SiftsSummaryProvider() a subclass of StashableBase()
14-Mar-2022 V0.64 Adjust parsing logic of ParentChildTreeFile.txt in InterProProvider.__getInterProParents()
16-May-2022 V0.65 Update GlyGenProvider resource URL location
25-Jul-2022 V0.66 Adjust UniProtUtils to temporarily use the legacy baseUrl (legacy.uniprot.org) for API calls
4-Oct-2022 V0.67 Update UniProtUtils code to use new UniProt API
10-Oct-2022 V0.68 Update URLs to InterPro data, and add better error catching for InterPro provider tests
11-Oct-2022 V0.69 Only use secondary service site (EBI) for bulk UniProt XML requests
26-Nov-2022 V0.70 Fix UniProtUtils primary API fetching method
28-Nov-2022 V0.71 Add functionality to search primary service using secondary accession IDs (in case of obsoleted IDs)
9-Jan-2023 V0.72 Configuration changes to support tox 4
6-Feb-2023 V0.73 Resolve pylint issues
23-Feb-2023 V0.74 Fix UniProtUtils primary fetching service to handle cases with invalid UniProt IDs
9-Mar-2023 V0.75 Lower default maxChunkSize to 10 for UniProt requests (UniProt API having trouble streaming XML responses)
19-Sep-2023 V0.76 Use HTTP instead of FTP for InterPro and Pfam downloads;
RO-4033: Adjust logic used for processing and assigning sequence alignment details
3-Oct-2023 V0.77 Update PfamProvider to use new Pfam mapping file
14-Nov-2023 V0.78 Add SPARQL functionality and version information to GlyGenProvider
18-Mar-2024 V0.79 Add yeast and fruitfly datasets to GlyGenProvider
21-May-2024 V0.80 Fix pylinting
3-Jun-2024 V0.81 Update PfamProvider to use new Pfam mapping file
20-Aug-2024 V0.82 Disable default backup to fallback setting in UniProtIdMappingProvider;
Update GlyGenProvider
9-Dec-2024 V0.83 Update Azure pipelines to use latest macOS, Ubuntu, and python 3.10