Code

Dev#3

Code

Merged

jcasadogp merged 80 commits intomainmsysbio/bacterial_growth:mainfrom devmsysbio/bacterial_growth:devCopy head branch name to clipboardApr 27, 2023

+1,578-9,873

Commits

Commits on Apr 2, 2023

• separate bash files

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  bd9e4f9

• update on working notebooks - addExperiment

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  64b010a

• populate db improves, where clause added

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  95270b2

• updates on sql files

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  b080601

• change parser name again

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  d50d4ef

• change location of bash files

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  19b1ad4

• separate reactor dictionary

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• ch

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• ch

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Commits on Apr 4, 2023

• changes in bash scripts and functions

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  cb1879f

• errors and warnings in the execute db function

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  58c57bb

• get all records unified function

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  98fe7f9

Commits on Apr 10, 2023

• changes in bash running

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  b9007dc

Commits on Apr 11, 2023

• DB functions SQL files

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  3c1be03

• changes in working notebooks

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  7c1502d

• remove echo variables

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  1ce0bb3

• add plotting parser

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  6e3c295

• check no empty filtered dataframe goes to db

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  e6d4236

• separate user input funcitons into new script

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  3aa697d

• add plotting script and changes needed in other scripts for plot

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  586c1fa

• intermediate files

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  32cad8c

Commits on Apr 17, 2023

• changes in working notebooks, bacterial plots

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  f0b43a5

• changes in the create db query, add unique fields in experiment table

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  fd5c50f

• chnge plot options

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  2931b14

• remove specific messages and add choose plot option

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  4c02700

• add get records

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  7e9e6b7

• change getWhereClause so it add IS NULL

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  44a8ff5

Commits on Apr 19, 2023

• advances in plot with the legends

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  a10fced

• working notebooks

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  7be3804

• changes in count Records, add get where clause function there

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  29440fd

• get where clause if no args or if arg is null and change get mean std more advanced

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  8ecc7e6

• Update .gitignore

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• add y label

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  e60c960

• Merge branch 'dev' of https://github.com/jcasadogp/bacterial_growth into dev

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  edac2c3

• changes in working notebook

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  5da669f

• changes in parser

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  d80eb8a

• add regex expressions to the constants file

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• ch

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  0a533f4

Commits on Apr 21, 2023

• add advanced queries

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  c274622

• update the db functions and add the supplementary db functions in this script

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  054e341

• remove supplementary db functions from this script

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  76a99f5

• change getAllRecords agrs to dictionary and add pert 0 option

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  522e75e

• add pert 0 option and add name of variables in function callings

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  e768d4f

Commits on Apr 22, 2023

• remove unnecesary imports

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  0ab186c

• changes in Notebooks

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  9649897

• cleaning repository to final code

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  76c1bac

• remove files for clean final repo

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  2b828e4

• Change env name

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  d32765c

• Add environment set up

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  4339bbe

Commits on Apr 24, 2023

• change count records return

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  a2c1eaf

• add try except error in reading yml file

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  22cf24e

• add try except error in reading yml file

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  c8de52a

• remove error comments

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  7c59471

• add local directory to the yml files

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  a2be66e

• put regex constants on the constants file

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  f73fad3

• add more constants

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  99a19b7

• remove commands file

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  81ff2fa

• create script

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  4902599

• put db_field as directory

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  e1e6ee0

Commits on Apr 25, 2023

• add posibility perturbation is 0

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  1ce24df

• error if no parameters are passed to get results file

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  8258f94

• add posibility perturbation is 0

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  e5272bd

• change get records header and add get In Clause

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  6804840

• final chnages, add zip file

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  7835d6c

• back to commands

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  96e36ee

• make experiment table smaller

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  353a34a

• change error in plotting perturbation arguments

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  d115aec

• change loops order so no error if id_args is empty

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  188ce13

• change .md for .txt

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  52cb054

• remove print args

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  31aefd4

• add plate id, row and column to perturbations

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  3a4c7a2

• remove plate columns in perturbation pretty table

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  e697f70

Commits on Apr 27, 2023

• add zip file name and final documentation in the function headers

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  6136964

• add zip file name function

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  eabf445

• change lab analysis file name

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  733b27c

• change subparsers order

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  9cde922

• add functions documentation

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  2161f3b

• add functions documentation

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  3ffc118

• add functions documentation

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  94b9846

• remove bash file with echos

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  bebf191