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Develop merge for release 2.0.0 #201

Merged
merged 393 commits into from
Mar 1, 2024
Merged

Develop merge for release 2.0.0 #201

merged 393 commits into from
Mar 1, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Mar 8, 2023

  1. naming people naming!

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    GuilleGorines committed Mar 8, 2023
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  2. beauty change!

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  3. naming again

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  4. whole lotta naming

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  5. not quite sure about options display

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  6. not sure about letting the user choose the day

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  7. more choices!

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  8. changed choice to prompt in day selection

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  9. needed explanation

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  10. fixed type error

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  11. tiny changes

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  12. updated to take previous date into account

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  13. tunnel vision!

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  14. same typo as before

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  15. updated the number of months

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  16. typo

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  17. checking sthg

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  18. testing changes

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  19. god this is getting tedious

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  20. this should be working now

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  21. Clearer question

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  22. just a goof

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  23. updated code comments

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  24. change in api path to work locally

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  25. checking on api

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  26. testing the api

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  27. updated api query

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  28. change I forgot to add

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  29. checking

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  30. update ask date function

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  31. missed this pbby

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  32. added query by resolution id

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  33. missed the commas

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  34. customization!

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  35. update

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  36. update!

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  37. testing update

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  38. testing failed, back again

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  39. single quotes inside an f string!

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  40. F-strings are friends!!

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  41. slight update

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  42. palceholder for functions

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  43. import update

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  44. Update archive.py

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  45. missed commas

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  46. simple quotes

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  47. trying

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  48. Update archive.py

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  49. updated to match conf

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  50. getting it!

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  51. avoid python keywords

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  52. prints for testing

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  53. Further testing for the API

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  54. Update archive.py

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  55. result in a list so it can be parsed just like in batch

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  56. Update archive.py

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  57. Update archive.py

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  58. primer on md5 and tar functions

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  59. Update archive.py

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  60. typo on conf

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  61. Update archive.py

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  62. trying

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  63. Update archive.py

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  64. added followup prints

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  65. Update archive.py

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  66. Notification failed query in console

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  67. prettier docstring

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  68. managing for no services in date range

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  69. removed prints

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  70. checks for api results

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  71. corrected stderrs

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  72. linting!

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  73. linting

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  74. import

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  75. linting

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  76. linting

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  77. extension of archive functionality

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  78. targz, md5 and size updated in archive

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  79. prompt updated, completed size calculations

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  80. archive step update

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  81. I fail to see the point in a remove method by now

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  82. no need to compare dirs if all of them are going to be compressed

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  83. linting

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  84. Removed anchor code, added handling if compressed file already present

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  85. cleaning code

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  86. primed new attribute for failed services

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  87. updated query (wont work in other modules, just testing)

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  88. queries updated!!

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  89. new util: prompt service id

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  90. typo on url, pretty now

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  91. tar gz managing

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  92. messages updated, moved inner loop outside in tgz

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  93. fixed loop (it was continue, not break), print debugs removed, msgs f… 

    …ixed
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  94. added all potential options

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  95. now asking for service, not for resolution. Crash handling

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  96. more crash handling I missed

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  97. made reversible functions, removed redundant function

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  98. handling: destiny exists before rsync

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  99. linting, remodel of query function (temporary)

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  100. linting

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  101. feedback for user adjustments

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  102. targz directories now generates the appropriate structure

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  103. primer on untar functions

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  104. uncompress tar gz method updated

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  105. adjustments to variable names

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  106. typo on untargz function

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  107. delete function

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  108. options handling

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  109. missnamed variable

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  110. fixed loop in delete services

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  111. corrected flaws in the functioning

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  112. primer for delete non archived function

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  113. updated and integrated deletion of non_archived_dirs

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  114. added "remove dir if already archived" to options

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  115. full handling of delete non archived dirs

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  116. fixed extraction dir

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  117. linting

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  118. primer on date validation outside the input

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  119. reorganized date asking function

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  120. date management working through datetime now (cleaner)

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  121. clearer data

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  122. first question is now "research or not"

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  123. less confusing managing of init

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  124. linting

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  125. linting

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Commits on Mar 13, 2023

  1. Created e-mail template jinja

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  2. Updated all modules using get_request function and removed unnecessar… 

    …y print.
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  3. Updated default value

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  4. Renamed some utils variables to be more generic to be used in several… 

    … modules.
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  5. Added option to pass sender e-mail password through command line

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  6. Removed debugging prints

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  7. Added function to copy images to bioinfo_doc folder so html files and… 

    … PDFs work
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  8. Added images folder to clean function to remove it after everython ha… 

    …s been created
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  9. Created module to send e-mail and all the configuration variables. PD… 

    …F file is attached and cc option is given
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  10. Fixed black linting

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  11. Fixed error with TLS encryption

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    svarona committed Mar 13, 2023
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  12. Fixed error.

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  13. Changed capitalization to fit in pep8 guidelines.

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Commits on Apr 20, 2023

  1. res id was not exact, changed to service_id

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  2. managing in case of not found services

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  3. size calculations now happen in init

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  4. update the table and wrap up for the session

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  5. primer on scouting method

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  6. completed inital scouting method

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  7. update tar.gz function

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  8. update move_directory

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  9. delete methods updated

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  10. archive works with service names, not resolutions

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  11. scouting revised and working

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  12. update to search by id based on testing

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  13. linting, wrap up for the day

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  14. update on logging + console feedback

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  15. reorganized service dictionary with all the entries from the beginning

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  16. primer on csv table

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  17. update on log and console feedback

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  18. reorganized script

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  19. added click options

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  20. archive linting

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  21. linting

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  22. linting!

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Commits on Sep 26, 2023

  1. Fixed api authentication method

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  2. Fixed new service with DB changes

    @svarona
    svarona committed Sep 26, 2023
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  3. fixed scratch rsync

    @svarona
    svarona committed Sep 26, 2023
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  4. Fixed data paths

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    svarona committed Sep 26, 2023
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  5. set defaults to none

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    svarona committed Sep 26, 2023
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  6. some refactoring and archive changges

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    svarona committed Sep 26, 2023
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  7. come changes

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    svarona committed Sep 26, 2023
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  8. Fixed black

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  9. Fixed function to get path

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  10. Merge pull request #161 from svarona/iskylims_isciiides 

    Fixed some API variables and errors
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    saramonzon authored Sep 26, 2023
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Commits on Sep 27, 2023

  1. Fixed some variables strings

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  2. Fixed for new rsync command format

    @svarona
    svarona committed Sep 27, 2023
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  3. Fixed variables to fit in DB

    @svarona
    svarona committed Sep 27, 2023
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  4. Clean some functions and code

    @svarona
    svarona committed Sep 27, 2023
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  5. Fixed database variables

    @svarona
    svarona committed Sep 27, 2023
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  6. Cleaning and fixes

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    svarona committed Sep 27, 2023
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  7. Fixed new rsync command

    @svarona
    svarona committed Sep 27, 2023
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  8. Removed duplicated entry

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    svarona committed Sep 27, 2023
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  9. Fixed black

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  10. Resolved suggestions

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Commits on Oct 3, 2023

  1. first modifications archive, funcs moved to utils

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  2. fixed class initialization and api requests for archive

    @saramonzon @svarona
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  3. debugged and fixed scouting

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  4. fixed tar.gz dir

    @saramonzon @svarona
    saramonzon authored and svarona committed Oct 3, 2023
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  5. linting

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    saramonzon authored and svarona committed Oct 3, 2023
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  6. fixed copy and uncompress

    @saramonzon @svarona
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  7. Added new parameter service_file (to be implemented), else working

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  8. service_file param implemented, several fixes with param combination

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  9. linting

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  10. removed left pdb

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  11. minor typos and added param for output path

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  12. linting

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Commits on Oct 23, 2023

  1. Included credentials in main for all processes

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    Shettland committed Oct 23, 2023
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  2. Included credentials instead of token

    @Shettland
    Shettland committed Oct 23, 2023
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  3. Included path to yaml file in user home

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  4. Included credentials and minor error handling

    @Shettland
    Shettland committed Oct 23, 2023
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  5. Included credentials and error handling

    @Shettland
    Shettland committed Oct 23, 2023
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  6. Included credentials in copy_sftp module

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    Shettland committed Oct 23, 2023
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  7. Included new credentials into drylab_api module and some error handling

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  8. Included credentials in new-service module

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  9. Included credentials and error handling into drylab_api module

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  10. Included credentials in module scratch

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  11. Included pyyaml package into requirements

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  12. Introduced new auxiliary functions to help credential extraction and … 

    …validation
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  13. Included credentials as validation method, linting

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  14. Minor typo changes

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  15. Commented a pseudo-coded function

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  16. Included extended docstrings for the most recent functions

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  17. Minor changes for consistency

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  18. Included srun_settings fields in scratch_copy

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  19. Changed the rsync to be executed using slurm's srun

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  20. Changed the rsync to be executed using srun from SLURM

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  21. Included new field scratch_path in config

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  22. Included srun in the scratch_copy process

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Commits on Oct 30, 2023

  1. Fixed cases

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  2. Fixed capitalization of variables

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  3. Fixed PyPDF2 functions new version

    @svarona @saramonzon
    svarona authored and saramonzon committed Oct 30, 2023
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  4. Fixed database capitalization

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  5. Fixed linting

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  6. Fixed black

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  7. Fixed DB variables capitalization

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  8. Fixed jinja templates

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  9. Updated README

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  10. Fixed variables capitalization

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  11. Allow to only send available PDFs

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  12. Fixed error when making tree

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  13. Made code to ask to continue if markdowns do not exist.

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  14. Fixed path, md must be markdown

    @svarona @saramonzon
    svarona authored and saramonzon committed Oct 30, 2023
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  15. Fixed black

    @svarona @saramonzon
    svarona authored and saramonzon committed Oct 30, 2023
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  16. Merge branch 'develop' into iskylims_isciiides

    @svarona
    svarona committed Oct 30, 2023
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  17. Fixed black

    @svarona
    svarona committed Oct 30, 2023
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  18. Fixed SFTP path

    @svarona
    svarona committed Oct 30, 2023
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  19. Fixed tamplet when no samples in service

    @svarona
    svarona committed Oct 30, 2023
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Commits on Oct 31, 2023

  1. Merge pull request #171 from svarona/iskylims_isciiides 

    Merge branch 'develop' into iskylims_isciiides
    @svarona
    svarona authored Oct 31, 2023
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Commits on Nov 3, 2023

  1. added gubbins to snippy template

    @saramonzon
    saramonzon committed Nov 3, 2023
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Commits on Dec 28, 2023

  1. Merge remote-tracking branch 'origin/develop' into iskylims_isciiides

    @svarona
    svarona committed Dec 28, 2023
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  2. Created template for freebayes_outbreak

    @svarona
    svarona committed Dec 28, 2023
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  3. Added freebayes outbreak

    @svarona
    svarona committed Dec 28, 2023
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Commits on Jan 8, 2024

  1. Merge pull request #175 from svarona/iskylims_isciiides 

    Merged develop into Iskylims isciiides
    @svarona
    svarona authored Jan 8, 2024
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Commits on Jan 15, 2024

  1. Merge pull request #181 from BU-ISCIII/iskylims_isciiides 

    Merge iskylims_isciiides into develop
    @svarona
    svarona authored Jan 15, 2024
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Commits on Feb 1, 2024

  1. Merge pull request #194 from BU-ISCIII/main 

    Merge changes from main into develop
    @saramonzon
    saramonzon authored Feb 1, 2024
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Commits on Feb 29, 2024

  1. Prepare Release 2.0.0

    @Shettland
    Shettland committed Feb 29, 2024
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  2. Prepare Release 2.0.0 .

    @Shettland
    Shettland committed Feb 29, 2024
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  3. Prepare Release 2.0.0. Linting

    @Shettland
    Shettland committed Feb 29, 2024
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Commits on Mar 1, 2024

  1. Updated iskylims api url to v2

    @Shettland @saramonzon
    Shettland authored and saramonzon committed Mar 1, 2024
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  2. Included IRMA template

    @Shettland @saramonzon
    Shettland authored and saramonzon committed Mar 1, 2024
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  3. Fixed bug when executing rsync through srun

    @Shettland @saramonzon
    Shettland authored and saramonzon committed Mar 1, 2024
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  4. Prepared CHANGELOG for new release 2.0.0

    @Shettland @saramonzon
    Shettland authored and saramonzon committed Mar 1, 2024
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  5. Fixed bug when executing rsync through srun

    @Shettland @saramonzon
    Shettland authored and saramonzon committed Mar 1, 2024
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  6. Updated CHANGELOG.md with latest changes

    @Shettland @saramonzon
    Shettland authored and saramonzon committed Mar 1, 2024
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