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Develop merge for release 2.0.0 #201

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merged 393 commits into from
Mar 1, 2024
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1f5b85b
naming people naming!
GuilleGorines Jan 26, 2023
4088c66
beauty change!
GuilleGorines Jan 26, 2023
401bb22
naming again
GuilleGorines Jan 26, 2023
f4ac048
whole lotta naming
GuilleGorines Jan 26, 2023
9457154
not quite sure about options display
GuilleGorines Jan 26, 2023
513be45
not sure about letting the user choose the day
GuilleGorines Jan 26, 2023
7d79eb6
more choices!
GuilleGorines Jan 26, 2023
e03b067
changed choice to prompt in day selection
GuilleGorines Jan 26, 2023
e86b2dc
needed explanation
GuilleGorines Jan 26, 2023
c3070e0
fixed type error
GuilleGorines Jan 26, 2023
0d77f3f
tiny changes
GuilleGorines Jan 26, 2023
0ab8dd1
updated to take previous date into account
GuilleGorines Jan 26, 2023
350f193
tunnel vision!
GuilleGorines Jan 26, 2023
b7a7e1e
same typo as before
GuilleGorines Jan 26, 2023
a70c839
updated the number of months
GuilleGorines Jan 26, 2023
0e9e9f6
typo
GuilleGorines Jan 26, 2023
ef469db
checking sthg
GuilleGorines Jan 26, 2023
46d6a96
testing changes
GuilleGorines Jan 26, 2023
0c640e5
god this is getting tedious
GuilleGorines Jan 26, 2023
8bcac28
this should be working now
GuilleGorines Jan 26, 2023
1086069
Clearer question
GuilleGorines Jan 26, 2023
49427a0
just a goof
GuilleGorines Jan 26, 2023
6e2e5cd
updated code comments
GuilleGorines Jan 26, 2023
529f9df
change in api path to work locally
GuilleGorines Jan 26, 2023
f0652d6
checking on api
GuilleGorines Jan 26, 2023
60b7ec2
testing the api
GuilleGorines Jan 26, 2023
8b86146
updated api query
GuilleGorines Jan 26, 2023
b068ad6
change I forgot to add
GuilleGorines Jan 26, 2023
b66f6b3
checking
GuilleGorines Jan 26, 2023
58896c5
update ask date function
GuilleGorines Jan 26, 2023
d1b5d79
missed this pbby
GuilleGorines Jan 26, 2023
a88eafb
added query by resolution id
GuilleGorines Jan 26, 2023
4b1f84c
missed the commas
GuilleGorines Jan 26, 2023
cd703be
customization!
GuilleGorines Jan 26, 2023
46bf548
update
GuilleGorines Jan 26, 2023
a3b5d19
update!
GuilleGorines Jan 26, 2023
56190ff
testing update
GuilleGorines Jan 26, 2023
a214bf4
testing failed, back again
GuilleGorines Jan 26, 2023
ba6afba
single quotes inside an f string!
GuilleGorines Jan 26, 2023
6b18375
F-strings are friends!!
GuilleGorines Jan 26, 2023
7bccbc4
slight update
GuilleGorines Jan 30, 2023
e061cb1
palceholder for functions
GuilleGorines Jan 30, 2023
b2ca0ee
import update
GuilleGorines Jan 30, 2023
16ef055
Update archive.py
GuilleGorines Jan 30, 2023
e414513
missed commas
GuilleGorines Jan 30, 2023
96dc0f3
simple quotes
GuilleGorines Jan 30, 2023
48c5cd2
trying
GuilleGorines Jan 30, 2023
e814781
Update archive.py
GuilleGorines Jan 30, 2023
10caa41
updated to match conf
GuilleGorines Jan 30, 2023
b9cb442
getting it!
GuilleGorines Jan 30, 2023
d9e7c8c
avoid python keywords
GuilleGorines Jan 30, 2023
d5608ea
prints for testing
GuilleGorines Jan 30, 2023
02cd829
Further testing for the API
GuilleGorines Jan 30, 2023
b61969a
Update archive.py
GuilleGorines Jan 30, 2023
404d49d
result in a list so it can be parsed just like in batch
GuilleGorines Jan 30, 2023
71f1651
Update archive.py
GuilleGorines Jan 30, 2023
dac6513
Update archive.py
GuilleGorines Jan 30, 2023
3f53b01
primer on md5 and tar functions
GuilleGorines Jan 30, 2023
7721739
Update archive.py
GuilleGorines Jan 31, 2023
211b388
typo on conf
GuilleGorines Jan 31, 2023
d47670c
Update archive.py
GuilleGorines Jan 31, 2023
5009e3d
trying
GuilleGorines Jan 31, 2023
a4fb785
Update archive.py
GuilleGorines Jan 31, 2023
b867418
added followup prints
GuilleGorines Jan 31, 2023
d782b20
Update archive.py
GuilleGorines Jan 31, 2023
e97b1dc
Notification failed query in console
GuilleGorines Feb 1, 2023
8757b0c
prettier docstring
GuilleGorines Feb 1, 2023
0ac2bb1
managing for no services in date range
GuilleGorines Feb 1, 2023
527193e
removed prints
GuilleGorines Feb 1, 2023
802acf9
checks for api results
GuilleGorines Feb 1, 2023
06bd945
corrected stderrs
GuilleGorines Feb 1, 2023
d7f2cb5
linting!
GuilleGorines Feb 15, 2023
fa0eb92
linting
GuilleGorines Feb 28, 2023
325933f
import
GuilleGorines Feb 28, 2023
595eccd
linting
GuilleGorines Feb 28, 2023
cd5dab5
linting
GuilleGorines Feb 28, 2023
7d25f3d
extension of archive functionality
GuilleGorines Mar 1, 2023
f9b1cae
targz, md5 and size updated in archive
GuilleGorines Mar 1, 2023
3c8466e
prompt updated, completed size calculations
GuilleGorines Mar 1, 2023
05d1a17
archive step update
GuilleGorines Mar 1, 2023
ba99ab7
I fail to see the point in a remove method by now
GuilleGorines Mar 1, 2023
1139ee1
no need to compare dirs if all of them are going to be compressed
GuilleGorines Mar 1, 2023
0d931f8
linting
GuilleGorines Mar 1, 2023
742e72e
Removed anchor code, added handling if compressed file already present
GuilleGorines Mar 2, 2023
2e5172d
cleaning code
GuilleGorines Mar 2, 2023
b584cc8
primed new attribute for failed services
GuilleGorines Mar 2, 2023
2ad3324
updated query (wont work in other modules, just testing)
GuilleGorines Mar 2, 2023
d4cb90c
queries updated!!
GuilleGorines Mar 2, 2023
43d211c
new util: prompt service id
GuilleGorines Mar 2, 2023
8a00820
typo on url, pretty now
GuilleGorines Mar 2, 2023
ada80b0
tar gz managing
GuilleGorines Mar 2, 2023
cc076b1
messages updated, moved inner loop outside in tgz
GuilleGorines Mar 2, 2023
c5c964b
fixed loop (it was continue, not break), print debugs removed, msgs f…
GuilleGorines Mar 2, 2023
2c35a04
added all potential options
GuilleGorines Mar 2, 2023
c99faa4
now asking for service, not for resolution. Crash handling
GuilleGorines Mar 2, 2023
dfdfc87
more crash handling I missed
GuilleGorines Mar 2, 2023
dbafbce
made reversible functions, removed redundant function
GuilleGorines Mar 2, 2023
bd24c9d
handling: destiny exists before rsync
GuilleGorines Mar 2, 2023
eeee3e9
linting, remodel of query function (temporary)
GuilleGorines Mar 2, 2023
9210f2c
linting
GuilleGorines Mar 2, 2023
73826ef
feedback for user adjustments
GuilleGorines Mar 3, 2023
7ba90fe
targz directories now generates the appropriate structure
GuilleGorines Mar 3, 2023
cd8cd78
primer on untar functions
GuilleGorines Mar 3, 2023
9d7d74f
uncompress tar gz method updated
GuilleGorines Mar 3, 2023
b887556
adjustments to variable names
GuilleGorines Mar 3, 2023
4a8baba
typo on untargz function
GuilleGorines Mar 3, 2023
64432ae
delete function
GuilleGorines Mar 3, 2023
d78bd98
options handling
GuilleGorines Mar 3, 2023
4f521cd
missnamed variable
GuilleGorines Mar 3, 2023
361c999
fixed loop in delete services
GuilleGorines Mar 3, 2023
2bbc6cb
corrected flaws in the functioning
GuilleGorines Mar 3, 2023
d82d93d
primer for delete non archived function
GuilleGorines Mar 3, 2023
b60375f
updated and integrated deletion of non_archived_dirs
GuilleGorines Mar 3, 2023
91f0667
added "remove dir if already archived" to options
GuilleGorines Mar 3, 2023
c7c360d
full handling of delete non archived dirs
GuilleGorines Mar 3, 2023
c2a6b35
fixed extraction dir
GuilleGorines Mar 3, 2023
c98166f
linting
GuilleGorines Mar 3, 2023
f261e2f
primer on date validation outside the input
GuilleGorines Mar 8, 2023
b51dc6d
reorganized date asking function
GuilleGorines Mar 8, 2023
187fe15
date management working through datetime now (cleaner)
GuilleGorines Mar 8, 2023
48ac6c8
clearer data
GuilleGorines Mar 8, 2023
61817de
first question is now "research or not"
GuilleGorines Mar 8, 2023
79e8244
less confusing managing of init
GuilleGorines Mar 8, 2023
916adab
linting
GuilleGorines Mar 8, 2023
51bbb2c
linting
GuilleGorines Mar 8, 2023
40d4064
Created e-mail template jinja
svarona Mar 10, 2023
2e6494f
Updated all modules using get_request function and removed unnecessar…
svarona Mar 10, 2023
dd3aca8
Updated default value
svarona Mar 10, 2023
1efb8c0
Renamed some utils variables to be more generic to be used in several…
svarona Mar 10, 2023
407b1b7
Added option to pass sender e-mail password through command line
svarona Mar 10, 2023
aeead35
Removed debugging prints
svarona Mar 10, 2023
9254415
Added function to copy images to bioinfo_doc folder so html files and…
svarona Mar 10, 2023
0923e16
Added images folder to clean function to remove it after everython ha…
svarona Mar 10, 2023
92eb58c
Created module to send e-mail and all the configuration variables. PD…
svarona Mar 10, 2023
93dca5c
Fixed black linting
svarona Mar 10, 2023
18978e3
Fixed error with TLS encryption
svarona Mar 10, 2023
2673616
Fixed error.
svarona Mar 10, 2023
7630e88
Changed capitalization to fit in pep8 guidelines.
svarona Mar 13, 2023
0f498e1
res id was not exact, changed to service_id
GuilleGorines Mar 8, 2023
d306ac1
managing in case of not found services
GuilleGorines Mar 8, 2023
ff501fa
size calculations now happen in init
GuilleGorines Mar 8, 2023
f314d9f
update the table and wrap up for the session
GuilleGorines Mar 8, 2023
905cdeb
primer on scouting method
GuilleGorines Mar 8, 2023
dff5743
completed inital scouting method
GuilleGorines Mar 9, 2023
d0845c1
update tar.gz function
GuilleGorines Mar 9, 2023
a19f785
update move_directory
GuilleGorines Mar 9, 2023
20e2bc4
delete methods updated
GuilleGorines Mar 9, 2023
c0056ec
archive works with service names, not resolutions
GuilleGorines Mar 9, 2023
897bca9
scouting revised and working
GuilleGorines Mar 9, 2023
00fa9ad
update to search by id based on testing
GuilleGorines Mar 9, 2023
15d0083
linting, wrap up for the day
GuilleGorines Mar 9, 2023
5ac9f76
update on logging + console feedback
GuilleGorines Mar 17, 2023
18fbc0f
reorganized service dictionary with all the entries from the beginning
GuilleGorines Mar 17, 2023
8f40509
primer on csv table
GuilleGorines Mar 21, 2023
9521572
update on log and console feedback
GuilleGorines Mar 22, 2023
05e5279
reorganized script
GuilleGorines Mar 30, 2023
db43ff4
added click options
GuilleGorines Mar 30, 2023
9b848fd
archive linting
GuilleGorines Apr 18, 2023
d87f505
linting
GuilleGorines Apr 18, 2023
ca39cc2
linting!
GuilleGorines Apr 18, 2023
17aed43
Fixed api authentication method
svarona Sep 26, 2023
76a3dde
Fixed new service with DB changes
svarona Sep 26, 2023
7dad22c
fixed scratch rsync
svarona Sep 26, 2023
c1032d1
Fixed data paths
svarona Sep 26, 2023
b7421aa
set defaults to none
svarona Sep 26, 2023
8e79205
some refactoring and archive changges
svarona Sep 26, 2023
ee757d5
come changes
svarona Sep 26, 2023
8bda683
Fixed black
svarona Sep 26, 2023
3529b1e
Fixed function to get path
svarona Sep 26, 2023
f7febd7
Merge pull request #161 from svarona/iskylims_isciiides
saramonzon Sep 26, 2023
e7d69ed
Fixed some variables strings
svarona Sep 27, 2023
b096bb3
Fixed for new rsync command format
svarona Sep 27, 2023
733b0d4
Fixed variables to fit in DB
svarona Sep 27, 2023
706d554
Clean some functions and code
svarona Sep 27, 2023
33ed7f7
Fixed database variables
svarona Sep 27, 2023
b2ac5de
Cleaning and fixes
svarona Sep 27, 2023
8668e53
Fixed new rsync command
svarona Sep 27, 2023
776ea80
Removed duplicated entry
svarona Sep 27, 2023
91ca429
Fixed black
svarona Sep 27, 2023
f422677
Resolved suggestions
svarona Sep 27, 2023
37af41f
first modifications archive, funcs moved to utils
saramonzon Sep 27, 2023
3defa36
fixed class initialization and api requests for archive
saramonzon Sep 29, 2023
d153bb0
debugged and fixed scouting
saramonzon Sep 29, 2023
f72af07
fixed tar.gz dir
saramonzon Oct 3, 2023
f842d4e
linting
saramonzon Oct 3, 2023
9d28ab9
fixed copy and uncompress
saramonzon Oct 3, 2023
35c679a
Added new parameter service_file (to be implemented), else working
saramonzon Oct 3, 2023
3f7d7ad
service_file param implemented, several fixes with param combination
saramonzon Oct 3, 2023
9fb2362
linting
saramonzon Oct 3, 2023
94145cb
removed left pdb
saramonzon Oct 3, 2023
e142a57
minor typos and added param for output path
saramonzon Oct 3, 2023
1b6c552
linting
saramonzon Oct 3, 2023
9c3d883
Included credentials in main for all processes
Shettland Oct 18, 2023
f3d2e9c
Included credentials instead of token
Shettland Oct 18, 2023
7a1c6f6
Included path to yaml file in user home
Shettland Oct 18, 2023
11c15b8
Included credentials and minor error handling
Shettland Oct 18, 2023
dea26a9
Included credentials and error handling
Shettland Oct 18, 2023
707d698
Included credentials in copy_sftp module
Shettland Oct 18, 2023
54a5787
Included new credentials into drylab_api module and some error handling
Shettland Oct 18, 2023
e663c8a
Included credentials in new-service module
Shettland Oct 18, 2023
1f299d7
Included credentials and error handling into drylab_api module
Shettland Oct 18, 2023
9235a49
Included credentials in module scratch
Shettland Oct 18, 2023
c9b00aa
Included pyyaml package into requirements
Shettland Oct 18, 2023
41b529b
Introduced new auxiliary functions to help credential extraction and …
Shettland Oct 18, 2023
397a7a7
Included credentials as validation method, linting
Shettland Oct 18, 2023
72b6098
Minor typo changes
Shettland Oct 19, 2023
9771c9f
Commented a pseudo-coded function
Shettland Oct 19, 2023
4410865
Included extended docstrings for the most recent functions
Shettland Oct 19, 2023
ff92005
Minor changes for consistency
Shettland Oct 19, 2023
ca59f9a
Included srun_settings fields in scratch_copy
Shettland Oct 19, 2023
a8c76fd
Changed the rsync to be executed using slurm's srun
Shettland Oct 19, 2023
e8fc4c8
Changed the rsync to be executed using srun from SLURM
Shettland Oct 19, 2023
a7a9766
Included new field scratch_path in config
Shettland Oct 20, 2023
0c09f94
Included srun in the scratch_copy process
Shettland Oct 20, 2023
1785788
Fixed cases
svarona Oct 23, 2023
db0f7f3
Fixed capitalization of variables
svarona Oct 24, 2023
c0d9c2f
Fixed PyPDF2 functions new version
svarona Oct 24, 2023
8f8f8af
Fixed database capitalization
svarona Oct 24, 2023
c5bc1c9
Fixed linting
svarona Oct 24, 2023
333bfb9
Fixed black
svarona Oct 24, 2023
b0ee35c
Fixed DB variables capitalization
svarona Oct 24, 2023
736fe80
Fixed jinja templates
svarona Oct 24, 2023
aafffba
Updated README
svarona Oct 27, 2023
486b932
Fixed variables capitalization
svarona Oct 27, 2023
c7a6189
Allow to only send available PDFs
svarona Oct 27, 2023
fecab2d
Fixed error when making tree
svarona Oct 27, 2023
7da784b
Made code to ask to continue if markdowns do not exist.
svarona Oct 27, 2023
fddac14
Fixed path, md must be markdown
svarona Oct 27, 2023
c1af994
Fixed black
svarona Oct 27, 2023
490c8d8
Merge branch 'develop' into iskylims_isciiides
svarona Oct 30, 2023
64105a8
Fixed black
svarona Oct 30, 2023
2de3dc6
Fixed SFTP path
svarona Oct 30, 2023
eced4e0
Fixed tamplet when no samples in service
svarona Oct 30, 2023
44cdd27
Merge pull request #171 from svarona/iskylims_isciiides
svarona Oct 31, 2023
6814155
added gubbins to snippy template
saramonzon Nov 3, 2023
9ccbb1d
Merge remote-tracking branch 'origin/develop' into iskylims_isciiides
svarona Dec 28, 2023
6db38ca
Created template for freebayes_outbreak
svarona Dec 28, 2023
0e3d06f
Added freebayes outbreak
svarona Dec 28, 2023
aa93319
Merge pull request #175 from svarona/iskylims_isciiides
svarona Jan 8, 2024
f4efe59
Merge pull request #181 from BU-ISCIII/iskylims_isciiides
svarona Jan 15, 2024
c1a51c1
Merge pull request #194 from BU-ISCIII/main
saramonzon Feb 1, 2024
42253b5
Prepare Release 2.0.0
Shettland Feb 29, 2024
a2c45ac
Prepare Release 2.0.0 .
Shettland Feb 29, 2024
e1cce2c
Prepare Release 2.0.0. Linting
Shettland Feb 29, 2024
f61e1da
Updated iskylims api url to v2
Shettland Mar 1, 2024
ae31c6e
Included IRMA template
Shettland Mar 1, 2024
41aaa90
Fixed bug when executing rsync through srun
Shettland Mar 1, 2024
1ad2d53
Prepared CHANGELOG for new release 2.0.0
Shettland Mar 1, 2024
90a3d26
Fixed bug when executing rsync through srun
Shettland Mar 1, 2024
f9f46fe
Updated CHANGELOG.md with latest changes
Shettland Mar 1, 2024
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63 changes: 42 additions & 21 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,47 @@ All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [Unreleased]
## [2.1.0dev] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.1.X

## [2.0.0dev] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.0.0
### Credits

Code contributions to the hotfix:

### Template fixes and updates

### Modules

#### Added enhancements

#### Fixes

#### Changed

#### Removed

### Requirements

## [2.X.1hot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.1

### Credits

Code contributions to the hotfix:

### Template fixes and updates

### Modules

#### Added enhancements

#### Fixes

#### Changed

#### Removed

### Requirements

## [2.0.0] - 2024-03-01 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.0.0

### Credits

Expand All @@ -33,6 +71,8 @@ Code contributions to the release:
- Added finish module
- Added json files: sftp_user.json
- Added delivery jinja templates
- Added IRMA template to services.json
- Scratch module now executes rsync using SLURM's srun

#### Fixes

Expand All @@ -47,25 +87,6 @@ Code contributions to the release:

- Added PyYAML

## [1.0.2hot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/1.0.2

### Credits

Code contributions to the hotfix:

### Template fixes and updates

### Modules

#### Added enhancements

#### Fixes

#### Changed

#### Removed

### Requirements

## [1.0.1] - 2024-02-01 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/1.0.1

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