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[GSoC 2024] Integrating KinFin Proteome Cluster analyses into Genome Browsing environments #9

Merged
merged 148 commits into from
Aug 27, 2024
Merged

[GSoC 2024] Integrating KinFin Proteome Cluster analyses into Genome Browsing environments #9

merged 148 commits into from
Aug 27, 2024

Commits on May 31, 2024

  1. chore: Remove build artifacts from version control

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  2. chore: update requirements.txt file

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  3. update: switch 'iteritems()' to 'items()' for Python 3 compatibility

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  4. refactor: Remove file download logic from kinfin script

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Commits on Jun 14, 2024

  1. refactor: modularize the install script

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  2. feat: replace --outprefix with --output_path for clarity and flexibility

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  3. chore: Add type hint ignore comment for PyQt4 import

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  4. refactor: Remove unused assignments from DataFactory

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  5. fix: get_major_ticks() is now get_majorticklabels() to access labels

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  6. feat: create new entrypoint for kinfin

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Commits on Jun 16, 2024

  1. feat: add util to check whether file exists if filepath provided

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  2. feat: added check for whether required data files exists

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  3. feat: added classes to store input data

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  4. feat: added constants to config.py file

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  5. feat: added argument parsing using argparse

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  6. feat: added function to validate CLI args

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  7. feat: map arguments to input class

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  8. feat: defined class to store attribute level data

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  9. feat: defined class to store ALO collections

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  10. feat: added method to compute proteomes grouped by levels for each at… 

    …tribute
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  11. feat: added method to create ALO objects for each attribute and level

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  12. feat: added util function to read file line by line

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  13. feat: added logic to parse attributes from config file

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  14. feat: added logic to get lineage of taxonomic identifier

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  15. feat: added util function to show progress

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  16. feat: added logic to parse nodesdb file

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  17. feat: added logic to add taxonomic attributes from nodesdb file

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  18. feat: added logic to parse tree from nwk file

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  19. feat: added function to build AloCollection from CLI input

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  20. feat: added logic to parse attributes from json list and taxon-idx ma… 

    …pping
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  21. feat: added function to build AloCollection from API input

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  22. feat: initialize AloCollection inside data store

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  23. feat: added class to store individual protein data

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  24. feat: added class to store collection of proteins

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  25. fix: spelling correction ALoCollection -> AloCollection

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  26. feat: added docstring to 'build_AloCollection_from_json' function

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  27. feat: added util function to read fasta file

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  28. feat: added logic to parse fasta directory and get lengths by protein id

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  29. feat: added logic to parse pFam mapping file

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  30. feat: added logic to parse ipr mapping file

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  31. feat: added logic to parse go mapping file

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  32. feat: added method to add annotations to protein

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  33. feat: added function to parse domains from functional annotations file

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  34. feat: initialize ProteinCollection inside data store

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  35. feat: added class to store Cluster data

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  36. feat: added class to store Cluster Collection data

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  37. feat: added function to identify singleton clusters

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  38. fix: add functional annotations to protein collections

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  39. feat: added function to parse cluster file to create cluster objects

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  40. feat: initialize ClusterCollection inside data store

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  41. feat: add method to setup directories to store output

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  42. feat: added util functions to calculate mean, median, sd and perform … 

    …statistical tests
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  43. feat: added logic to compute protein IDs grouped by proteome IDs

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  44. feat: added method to calculate stats based on protein lengths

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  45. fix: addded return type to mean, median, sd utils

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  46. feat: addded logic to determine cluster type: singleton, shared, spec… 

    …ific
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  47. feat: addded logic to determine cardinality type

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  48. feat: addded more properties to cluster class

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  49. feat: addded 'add_cluster' method to AttributeLevel class

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  50. feat: added 'analyse_cluster' method to DataFactory class

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  51. feat: added 'analyse_clusters' method to DataFactory class

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  52. feat: added method to generate header for a node

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  53. feat: added method to generate histogram chart for a node

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  54. feat: added method to plot and save texual representation of nwk tree

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  55. feat: added method to plot and save graphical representation of nwk tree

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  56. feat: added method to write tree data to files

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  57. feat: added method to compute rarefaction data

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  58. feat: added method to plot cluster sizes

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  59. feat: added method to generate a header line based on the specified f… 

    …iletype and attribute
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  60. feat: added method to conduct pairwise representation test

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  61. feat: added method to retrieve ALO metrics

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  62. feat: added method to compute protein length stats

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  63. feat: added method to compute secreted cluster coverage

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  64. feat: added method to compute domain aggregated domain counts by doma… 

    …in source for set of protein IDs
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Commits on Jun 17, 2024

  1. feat: added method to compute entropy of domain groups

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  2. feat: added method to generate volcano plots

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  3. feat: added method to generate cluster metrics and write them into files

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  4. fix: remove unused ALO property: self.rarefaction_data = {}

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  5. feat: added method to generate output from the input data

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  6. feat: added method to count proteins for a cluster type

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  7. feat: added method to count clusters of specific status and type

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  8. feat: added method to get span of proteins for particular cluster type

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  9. feat: added method to get count of clusters by cardinality and type

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  10. feat: added method to get sorted string of proteomes

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Commits on Jun 18, 2024

  1. fix: add type to datastore methods

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  2. feat: added option to perform analysis in CLI mode

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  3. feat: add a session manager class for api

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  4. feat: define endpoint to init API session

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  5. feat: added option to perform analysis in API mode

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  6. fix: remove unnecessary print statement

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  7. feat: basic script to compare outputs

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Commits on Jun 24, 2024

  1. Update .gitignore

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Commits on Jun 25, 2024

  1. fix: use log base of 2

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  2. mkae domain counts in sorted order for easier testing

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  3. feat: add tests to ensure consistent output

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  4. Merge branch 'master' into rohan/basic-endpoint

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  5. chore: update requirements.txt

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  6. chore: add dependencies for developing features

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  7. chore: add fastapi as dependency

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Commits on Jun 26, 2024

  1. fix: replace 'id' with '_id' to avoid python keyword conflict

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  2. fix: update request method from GET to POST

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  3. feat: update API request to return cluster_size_distribution.png file

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  4. renmae: 'session_path' variable to 'result_dir' variable

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    rohan-b-84 committed Jun 26, 2024
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  5. feat: add environment variables for server

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    rohan-b-84 committed Jun 26, 2024
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  6. feat: add .env.example file

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    rohan-b-84 committed Jun 26, 2024
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  7. feat: added endpoint to retrieve plots from results

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    rohan-b-84 committed Jun 26, 2024
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  8. feat: use 'logging' module for logs

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    rohan-b-84 committed Jun 26, 2024
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Commits on Jun 28, 2024

  1. fix: add '-r requirements.txt' at start of requirements-dev.txt file

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    rohan-b-84 committed Jun 28, 2024
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  2. chore: Add docstrings to all the functions

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    rohan-b-84 committed Jun 28, 2024
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  3. feat: update testing logic and move them to tests directory

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    rohan-b-84 committed Jun 28, 2024
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  4. feat: made analyse function run asynchronously in background; added d… 

    …ocstrings
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    rohan-b-84 committed Jun 28, 2024
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  5. refactor: initialize output array as header line

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    rohan-b-84 committed Jun 28, 2024
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  6. refactor: output line to be concatanated instead of appended and join… 

    …ed from array
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    rohan-b-84 committed Jun 28, 2024
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Commits on Jun 30, 2024

  1. fix: implement sourcery changes

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    rohan-b-84 committed Jun 30, 2024
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  2. fix: more sourcery manual fixes; breaking functions into smaller comp… 

    …onents
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    rohan-b-84 committed Jun 30, 2024
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Commits on Jul 2, 2024

  1. fix: sourcery error for analyse_cluster method

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    rohan-b-84 committed Jul 2, 2024
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  2. fix: sourcery error for plot_count_comparisons_volcano method

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    rohan-b-84 committed Jul 2, 2024
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  3. fix: most of the flake8 errors (except E501-line length)

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    rohan-b-84 committed Jul 2, 2024
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  4. fix: use logging module

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    rohan-b-84 committed Jul 2, 2024
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Commits on Jul 7, 2024

  1. fix: all sourcery errors and warnings

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    rohan-b-84 committed Jul 7, 2024
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  2. feat: added docstrings :)

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    rohan-b-84 committed Jul 7, 2024
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  3. feat: tests show missing files if any

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    rohan-b-84 committed Jul 7, 2024
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  4. feat: more list comprehensions

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    rohan-b-84 committed Jul 7, 2024
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Commits on Jul 8, 2024

  1. fix: comment 'Offending SequenceID' error message

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    rohan-b-84 committed Jul 8, 2024
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  2. Merge branch 'master' into rohan/basic-endpoint

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    rohan-b-84 committed Jul 8, 2024
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  3. fix: avoid escaping quotes

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    rohan-b-84 committed Jul 8, 2024
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  4. fix: unterminated string literal warning

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    rohan-b-84 committed Jul 8, 2024
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  5. fix: linting errors

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    rohan-b-84 committed Jul 8, 2024
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Commits on Jul 9, 2024

  1. fix: update function return types for API handlers

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    rohan-b-84 committed Jul 9, 2024
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  2. feat: update setup.py

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    rohan-b-84 committed Jul 9, 2024
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Commits on Jul 27, 2024

  1. feat: save logs in file

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    rohan-b-84 committed Jul 27, 2024
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  2. feat: use asyncio and subprocesses instead of fastapi's background tasks

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    rohan-b-84 committed Jul 27, 2024
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Commits on Aug 1, 2024

  1. feat: use query sessions instead of user sessions

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    rohan-b-84 committed Aug 1, 2024
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  2. fix: linting and sourcery

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    rohan-b-84 committed Aug 1, 2024
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Commits on Aug 6, 2024

  1. refactor: use results_base_dir env directly only for API

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    rohan-b-84 committed Aug 6, 2024
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  2. feat: added example taxon_idx_mapping file

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    rohan-b-84 committed Aug 6, 2024
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  3. fix: set plot format to png for API

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    rohan-b-84 committed Aug 6, 2024
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  4. fix: set content-disposition to inline instead of attachment for plots

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    rohan-b-84 committed Aug 6, 2024
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  5. feat: added endpoint to get run summary in JSON format

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    rohan-b-84 committed Aug 6, 2024
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  6. feat: prefix kinfin endpoints with /kinfin

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    rohan-b-84 committed Aug 6, 2024
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  7. feat: added counts-by-taxon endpoint

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    rohan-b-84 committed Aug 6, 2024
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Commits on Aug 19, 2024

  1. feat: make output deterministic; rename attribute as

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    rohan-b-84 committed Aug 19, 2024
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  2. feat: refactor endpoints.py; added wrapper; endpoints to get availabl… 

    …e attributes and taxon_sets; endpoint to get status; uniform response format; sorting and filtering; pagination
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    rohan-b-84 committed Aug 19, 2024
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  3. feat: some curl examples for KaaS

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    rohan-b-84 committed Aug 19, 2024
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  4. fix: sourcery magic

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    rohan-b-84 committed Aug 19, 2024
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  5. fix: isort

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    rohan-b-84 committed Aug 19, 2024
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  6. fix: remove unnecessary print statements

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    rohan-b-84 committed Aug 19, 2024
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  7. chore: remove testing data from version control

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    rohan-b-84 committed Aug 19, 2024
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