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Title: correct role handling and S3FS bypass by ErinWeisbart · Pull Request #130 · DistributedScience/Distributed-CellProfiler · GitHub

Open Graph Title: correct role handling and S3FS bypass by ErinWeisbart · Pull Request #130 · DistributedScience/Distributed-CellProfiler

X Title: correct role handling and S3FS bypass by ErinWeisbart · Pull Request #130 · DistributedScience/Distributed-CellProfiler

Description: Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure. - correct role handling and S3FS bypass by ErinWeisbart · Pull Request #130 · DistributedScience/Distributed-CellProfiler

Open Graph Description: Correct credential handling to enable AWS IAM role usage.

X Description: Correct credential handling to enable AWS IAM role usage.

Opengraph URL: https://github.com/DistributedScience/Distributed-CellProfiler/pull/130

X: @github

direct link

Domain: github.com

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role_fixhttps://github.com/DistributedScience/Distributed-CellProfiler/tree/role_fix
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correct role handling and S3FS bypasshttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130#top
ErinWeisbarthttps://github.com/ErinWeisbart
masterhttps://github.com/DistributedScience/Distributed-CellProfiler/tree/master
role_fixhttps://github.com/DistributedScience/Distributed-CellProfiler/tree/role_fix
https://github.com/ErinWeisbart
ErinWeisbarthttps://github.com/ErinWeisbart
Jun 16, 2022https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#issue-1274085454
Please reload this pagehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130
ErinWeisbarthttps://github.com/ErinWeisbart
June 16, 2022 14:07https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#commits-pushed-0417e7d
https://github.com/ErinWeisbart
correct role handlinghttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/0417e7d2a0bc5d446f9af4418a96755964304a6a
0417e7dhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/0417e7d2a0bc5d446f9af4418a96755964304a6a
https://github.com/ErinWeisbart
update generate_task_definitionhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/526411d3e8979468ed3550757177f2e527a62c9f
526411dhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/526411d3e8979468ed3550757177f2e527a62c9f
https://github.com/ErinWeisbart
import configparser in run.pyhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/38df4c92021bdf8e386e8aa3b16f1d14deba6be3
38df4c9https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/38df4c92021bdf8e386e8aa3b16f1d14deba6be3
https://github.com/ErinWeisbart
enable separate source and destination bucketshttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/80a8c5b2c0cacd87a04bd6e37928beaa3ada76ef
80a8c5bhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/80a8c5b2c0cacd87a04bd6e37928beaa3ada76ef
https://github.com/ErinWeisbart
oops shouldnt have deleted thosehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/549871062f2bad6a5ca1fe950f56767f74dbef20
5498710https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/549871062f2bad6a5ca1fe950f56767f74dbef20
https://github.com/ErinWeisbart
fix multibucket handlinghttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/e657f11343a06f21d89ab6a4ffe67df80cb54a5a
e657f11https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/e657f11343a06f21d89ab6a4ffe67df80cb54a5a
https://github.com/ErinWeisbart
move source destination buckets to confighttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/cefd9e0a3db65b5a5868aa350002a2c569063385
cefd9e0https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/cefd9e0a3db65b5a5868aa350002a2c569063385
https://github.com/ErinWeisbart
switched in and not inhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/865d515c92e284ae616531b4571a882e25ad499b
865d515https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/865d515c92e284ae616531b4571a882e25ad499b
https://github.com/ErinWeisbart
fix s3fs bybasshttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/f7919b87390523492d317125122b243dc054992b
f7919b8https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/f7919b87390523492d317125122b243dc054992b
https://github.com/ErinWeisbart
ErinWeisbarthttps://github.com/ErinWeisbart
Aug 4, 2022https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#issuecomment-1205513160
#132https://github.com/DistributedScience/Distributed-CellProfiler/issues/132
#114https://github.com/DistributedScience/Distributed-CellProfiler/issues/114
Please reload this pagehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130
ErinWeisbarthttps://github.com/ErinWeisbart
August 4, 2022 09:52https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#commits-pushed-b9f8916
https://github.com/ErinWeisbart
remove multibucket from job filehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/b9f89162c94a63f214ee7d34b6a9a5c5fbd1e67f
b9f8916https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/b9f89162c94a63f214ee7d34b6a9a5c5fbd1e67f
https://github.com/ErinWeisbart
remove changes to run_batch_generalhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/3d8cc82a121337877a7693379d0e666dd6d5ee1e
3d8cc82https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/3d8cc82a121337877a7693379d0e666dd6d5ee1e
https://github.com/ErinWeisbart
csv handling to keep structurehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/fad0284233b07206a1575d23308162bcafdf31eb
fad0284https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/fad0284233b07206a1575d23308162bcafdf31eb
https://github.com/ErinWeisbart
pipelines path and run command fixeshttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/c840b4448a35610a596957ec7c30a485f98f461d
c840b44https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/c840b4448a35610a596957ec7c30a485f98f461d
https://github.com/ErinWeisbart
ErinWeisbarthttps://github.com/ErinWeisbart
Aug 5, 2022https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#event-7133113452
https://github.com/ErinWeisbart
ErinWeisbarthttps://github.com/ErinWeisbart
Aug 5, 2022https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#issuecomment-1206055925
Please reload this pagehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130
ErinWeisbarthttps://github.com/ErinWeisbart
August 4, 2022 22:28https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#commits-pushed-8f57047
https://github.com/ErinWeisbart
output, destination, same differencehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/8f5704769e7ab5dac6de3420ccff996a0e02fa70
8f57047https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/8f5704769e7ab5dac6de3420ccff996a0e02fa70
https://github.com/ErinWeisbart
add upload flagshttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/4ff6463d2ccec65639b4ae89aef021ffc4ac0063
4ff6463https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/4ff6463d2ccec65639b4ae89aef021ffc4ac0063
https://github.com/ErinWeisbart
ErinWeisbarthttps://github.com/ErinWeisbart
Aug 5, 2022https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#issuecomment-1206748532
Please reload this pagehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130
ErinWeisbarthttps://github.com/ErinWeisbart
August 5, 2022 12:03https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#commits-pushed-22abe35
https://github.com/ErinWeisbart
but what if it doesn't existhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/22abe35b765c1bf7b0d9070933f43fca42f78767
22abe35https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/22abe35b765c1bf7b0d9070933f43fca42f78767
https://github.com/ErinWeisbart
more things in task definitionhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/e774d411defed750cd131bb1f37033cdca92f20f
e774d41https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/e774d411defed750cd131bb1f37033cdca92f20f
https://github.com/ErinWeisbart
stash changeshttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/7d8f4c84c72350ebf2dc148bfcc1d6df4edcbf39
7d8f4c8https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/7d8f4c84c72350ebf2dc148bfcc1d6df4edcbf39
https://github.com/ErinWeisbart
ErinWeisbarthttps://github.com/ErinWeisbart
Sep 20, 2022 https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#ref-issue-1327870976
DOWNLOAD_FILES doesn't fully bypass S3FS #132 https://github.com/DistributedScience/Distributed-CellProfiler/issues/132
https://github.com/bethac07
bethac07https://github.com/bethac07
Sep 20, 2022https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#event-7425373776
DOWNLOAD_FILES doesn't fully bypass S3FS #132 https://github.com/DistributedScience/Distributed-CellProfiler/issues/132
ErinWeisbarthttps://github.com/ErinWeisbart
September 21, 2022 13:20https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#commits-pushed-e907c6a
https://github.com/ErinWeisbart
update to AWS CLI2https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/e907c6a438d99a5c5b899ad151cb9d9ca044edef
e907c6ahttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/e907c6a438d99a5c5b899ad151cb9d9ca044edef
https://github.com/ErinWeisbart
the right way to check for variable, finallyhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/c66de9e9c7602484204a28cead1012c61d1b5eb3
c66de9ehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/c66de9e9c7602484204a28cead1012c61d1b5eb3
https://github.com/ErinWeisbart
ErinWeisbarthttps://github.com/ErinWeisbart
January 6, 2023 23:01https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#event-8172995187
https://github.com/ErinWeisbart
ErinWeisbarthttps://github.com/ErinWeisbart
bethac07https://github.com/bethac07
January 6, 2023 23:01https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#event-8172995440
https://github.com/ErinWeisbart
ErinWeisbarthttps://github.com/ErinWeisbart
Jan 6, 2023https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#issuecomment-1374237900
Please reload this pagehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130
Please reload this pagehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130
https://github.com/ErinWeisbart
Merge branch 'master' into role_fixhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/8cb1390e60d98ecc7f7418464454708e1368a842
8cb1390https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/8cb1390e60d98ecc7f7418464454708e1368a842
https://github.com/bethac07
bethac07https://github.com/bethac07
Jan 20, 2023 https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#pullrequestreview-1264477306
View reviewed changes https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/files/8cb1390e60d98ecc7f7418464454708e1368a842
files/exampleJob.jsonhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/files/8cb1390e60d98ecc7f7418464454708e1368a842#diff-3385d388778ca204e23be93215f18417dcf111612511341f4426fb8a15fd85e3
Please reload this pagehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130
https://github.com/bethac07
bethac07https://github.com/bethac07
Jan 20, 2023 https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#pullrequestreview-1264480192
View reviewed changes https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/files/8cb1390e60d98ecc7f7418464454708e1368a842
bethac07https://github.com/bethac07
https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#pullrequestreview-1264480192
Learn morehttps://docs.github.com/articles/managing-disruptive-comments/#hiding-a-comment
Please reload this pagehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130
https://github.com/bethac07
bethac07https://github.com/bethac07
Jan 20, 2023 https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#ref-pullrequest-747793356
Completely avoid S3FS #119 https://github.com/DistributedScience/Distributed-CellProfiler/pull/119
https://github.com/ErinWeisbart
Update exampleJob.jsonhttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/2b95a3692e4a46ed9b9f82f00c1dc5410db55835
2b95a36https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/commits/2b95a3692e4a46ed9b9f82f00c1dc5410db55835
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Jan 21, 2023https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#issuecomment-1399108835
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Please reload this pagehttps://github.com/DistributedScience/Distributed-CellProfiler/pull/130
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63a409ahttps://github.com/DistributedScience/Distributed-CellProfiler/commit/63a409a7e1ceaca31239a4c59fc2451c72affc66
Jan 21, 2023https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#event-8326168348
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January 21, 2023 00:59https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#event-8326168737
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Jan 23, 2023https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#event-8337318344
Make DCP use roles better, not just passing around credentials #114 https://github.com/DistributedScience/Distributed-CellProfiler/issues/114
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Jan 23, 2023 https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#ref-issue-736221517
Make DCP use roles better, not just passing around credentials #114 https://github.com/DistributedScience/Distributed-CellProfiler/issues/114
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bethac07https://github.com/bethac07
Dec 4, 2024 https://github.com/DistributedScience/Distributed-CellProfiler/pull/130#ref-pullrequest-2716090169
bypass S3FS if downloading #187 https://github.com/DistributedScience/Distributed-CellProfiler/pull/187
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https://github.com/DistributedScience/Distributed-CellProfiler/pull/130/files/8cb1390e60d98ecc7f7418464454708e1368a842
DOWNLOAD_FILES doesn't fully bypass S3FS https://github.com/DistributedScience/Distributed-CellProfiler/issues/132
Make DCP use roles better, not just passing around credentials https://github.com/DistributedScience/Distributed-CellProfiler/issues/114
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