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Dev #3

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merged 80 commits into from
Apr 27, 2023
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bd9e4f9
separate bash files
jcasadogp Apr 2, 2023
64b010a
update on working notebooks - addExperiment
jcasadogp Apr 2, 2023
95270b2
populate db improves, where clause added
jcasadogp Apr 2, 2023
b080601
updates on sql files
jcasadogp Apr 2, 2023
d50d4ef
change parser name again
jcasadogp Apr 2, 2023
19b1ad4
change location of bash files
jcasadogp Apr 2, 2023
5bc57e8
separate reactor dictionary
jcasadogp Apr 2, 2023
7f109e0
ch
jcasadogp Apr 2, 2023
0907433
ch
jcasadogp Apr 2, 2023
cb1879f
changes in bash scripts and functions
jcasadogp Apr 4, 2023
58c57bb
errors and warnings in the execute db function
jcasadogp Apr 4, 2023
98fe7f9
get all records unified function
jcasadogp Apr 4, 2023
b9007dc
changes in bash running
jcasadogp Apr 10, 2023
3c1be03
DB functions SQL files
jcasadogp Apr 11, 2023
7c1502d
changes in working notebooks
jcasadogp Apr 11, 2023
1ce0bb3
remove echo variables
jcasadogp Apr 11, 2023
6e3c295
add plotting parser
jcasadogp Apr 11, 2023
e6d4236
check no empty filtered dataframe goes to db
jcasadogp Apr 11, 2023
3aa697d
separate user input funcitons into new script
jcasadogp Apr 11, 2023
586c1fa
add plotting script and changes needed in other scripts for plot
jcasadogp Apr 11, 2023
32cad8c
intermediate files
jcasadogp Apr 11, 2023
f0b43a5
changes in working notebooks, bacterial plots
jcasadogp Apr 17, 2023
fd5c50f
changes in the create db query, add unique fields in experiment table
jcasadogp Apr 17, 2023
2931b14
chnge plot options
jcasadogp Apr 17, 2023
4c02700
remove specific messages and add choose plot option
jcasadogp Apr 17, 2023
7e9e6b7
add get records
jcasadogp Apr 17, 2023
44a8ff5
change getWhereClause so it add IS NULL
jcasadogp Apr 17, 2023
a10fced
advances in plot with the legends
jcasadogp Apr 19, 2023
7be3804
working notebooks
jcasadogp Apr 19, 2023
29440fd
changes in count Records, add get where clause function there
jcasadogp Apr 19, 2023
8ecc7e6
get where clause if no args or if arg is null and change get mean std…
jcasadogp Apr 19, 2023
996e1fa
Update .gitignore
jcasadogp Apr 19, 2023
e60c960
add y label
jcasadogp Apr 19, 2023
edac2c3
Merge branch 'dev' of https://github.com/jcasadogp/bacterial_growth i…
jcasadogp Apr 19, 2023
5da669f
changes in working notebook
jcasadogp Apr 19, 2023
d80eb8a
changes in parser
jcasadogp Apr 19, 2023
3231e8b
add regex expressions to the constants file
jcasadogp Apr 19, 2023
0a533f4
ch
jcasadogp Apr 19, 2023
c274622
add advanced queries
jcasadogp Apr 21, 2023
054e341
update the db functions and add the supplementary db functions in thi…
jcasadogp Apr 21, 2023
76a99f5
remove supplementary db functions from this script
jcasadogp Apr 21, 2023
522e75e
change getAllRecords agrs to dictionary and add pert 0 option
jcasadogp Apr 21, 2023
e768d4f
add pert 0 option and add name of variables in function callings
jcasadogp Apr 21, 2023
0ab186c
remove unnecesary imports
jcasadogp Apr 22, 2023
9649897
changes in Notebooks
jcasadogp Apr 22, 2023
76c1bac
cleaning repository to final code
jcasadogp Apr 22, 2023
2b828e4
remove files for clean final repo
jcasadogp Apr 22, 2023
d32765c
Change env name
jcasadogp Apr 22, 2023
4339bbe
Add environment set up
jcasadogp Apr 22, 2023
a2c1eaf
change count records return
jcasadogp Apr 24, 2023
22cf24e
add try except error in reading yml file
jcasadogp Apr 24, 2023
c8de52a
add try except error in reading yml file
jcasadogp Apr 24, 2023
7c59471
remove error comments
jcasadogp Apr 24, 2023
a2be66e
add local directory to the yml files
jcasadogp Apr 24, 2023
f73fad3
put regex constants on the constants file
jcasadogp Apr 24, 2023
99a19b7
add more constants
jcasadogp Apr 24, 2023
81ff2fa
remove commands file
jcasadogp Apr 24, 2023
4902599
create script
jcasadogp Apr 24, 2023
e1e6ee0
put db_field as directory
jcasadogp Apr 24, 2023
1ce24df
add posibility perturbation is 0
jcasadogp Apr 25, 2023
8258f94
error if no parameters are passed to get results file
jcasadogp Apr 25, 2023
e5272bd
add posibility perturbation is 0
jcasadogp Apr 25, 2023
6804840
change get records header and add get In Clause
jcasadogp Apr 25, 2023
7835d6c
final chnages, add zip file
jcasadogp Apr 25, 2023
96e36ee
back to commands
jcasadogp Apr 25, 2023
353a34a
make experiment table smaller
jcasadogp Apr 25, 2023
d115aec
change error in plotting perturbation arguments
jcasadogp Apr 25, 2023
188ce13
change loops order so no error if id_args is empty
jcasadogp Apr 25, 2023
52cb054
change .md for .txt
jcasadogp Apr 25, 2023
31aefd4
remove print args
jcasadogp Apr 25, 2023
3a4c7a2
add plate id, row and column to perturbations
jcasadogp Apr 25, 2023
e697f70
remove plate columns in perturbation pretty table
jcasadogp Apr 25, 2023
6136964
add zip file name and final documentation in the function headers
jcasadogp Apr 27, 2023
eabf445
add zip file name function
jcasadogp Apr 27, 2023
733b27c
change lab analysis file name
jcasadogp Apr 27, 2023
9cde922
change subparsers order
jcasadogp Apr 27, 2023
2161f3b
add functions documentation
jcasadogp Apr 27, 2023
3ffc118
add functions documentation
jcasadogp Apr 27, 2023
94b9846
add functions documentation
jcasadogp Apr 27, 2023
bebf191
remove bash file with echos
jcasadogp Apr 27, 2023
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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
Data/
DataParsed/
DataParsed.zip
MyExperiment*/

# Files that will be filled in by the user
src/yml_info_files/
Expand Down
93 changes: 0 additions & 93 deletions DB_scripts/OldDBScripts/create_tables.sql

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74 changes: 0 additions & 74 deletions DB_scripts/OldDBScripts/create_tables_v2.sql

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9 changes: 0 additions & 9 deletions DB_scripts/TmpDBScripts/create_file_paths_db.sql

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47 changes: 0 additions & 47 deletions DB_scripts/TmpDBScripts/insert_bacteria.sql

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21 changes: 0 additions & 21 deletions DB_scripts/TmpDBScripts/insert_exp.sql

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8 changes: 0 additions & 8 deletions DB_scripts/TmpDBScripts/insert_precultivation.sql

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8 changes: 0 additions & 8 deletions DB_scripts/TmpDBScripts/insert_reactor.sql

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8 changes: 0 additions & 8 deletions DB_scripts/create_precultivation.sql

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77 changes: 0 additions & 77 deletions DB_scripts/create_tables_v3.sql

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10 changes: 0 additions & 10 deletions IntermediateFiles/experiments_info.txt

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9 changes: 0 additions & 9 deletions IntermediateFiles/experiments_info_mod.txt

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1 change: 0 additions & 1 deletion IntermediateFiles/lab_experiment_names.txt

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9 changes: 0 additions & 9 deletions IntermediateFiles/lab_files_headers.txt

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