Background data check - #99

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gdurif wants to merge 82 commits into

Commits on Apr 26, 2021

update sidebar menu depending on chosen mode (diyabc-rf analysis or data generation)
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bfd21f9
remove useless (deprecated) home page ui
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a927836
rename home page ui and server
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e2cd1de
disable analysis and data generations modules, ready to refactor the app using global environment
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7ab8d8d
simplify file name (replace page denomination by module)
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e92aa27
use proj_name and proj_dir in environment
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27631f3
check if reactive values before using reactive values to list function
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12234d4
use variables from global environment
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1c481f6
WIP: refactoring analysis module (TODO: setup, training set simulation and random forest analysis)
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e69a4e9
use shinyFeedback package
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4e45426
rewrite global environment and rectiveValues in global environment definition and initialization
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c6a6d8b
rewrite project name module with global environment update
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e2eaa88
use shinyFeedback + reset project environment when starting new project
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9c7fca9
WIP: refactoring analysis module, DONE: using new version of project name module
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304f1ea
move help regarding project type in helper
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c07e7ee
provide initial value for locus_type and seq_mode
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c9ea9a4
update corresponding global environment when selecting data type
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2df2236
log project directory
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02a82a7
move clean on exit to main analysis module + rename proj name module + use new data type module
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dc686a7
WIP: writing project type module (to choose between new, existing or example)
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571e918
reformat project type/file help + manage project file input with potential warnings (TODO: project file check)
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aff2dd2
update version number for the app refactoring
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0639a70

Commits on Apr 29, 2021

inline doc minor edition + WIP modification of project input file management in a dedicated source file
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9b0b03f
WIP: analysis project file input management + corresponding tests (zip file input is ok)
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eff44e4
manage project file input (+tests)
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45bc5dd
test function + WIP parsing statobs
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5b02db9
parse and check statobs file (+test)
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d120a0a
WIP: rewriting project input file reading, parsing and checking
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42a0412
fix typo in file names
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2bc4cfd

Commits on Apr 30, 2021

parse scenario in header file OK + WIP read header file (and TODO read reftable)
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b35baa0
check prior extracted from header file
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4560ee6
check condition extracted from header file
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7e66331
check loci description extracted from header file
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73a7f71
remove useless lines + init at FALSE before branching checks
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e884c68
new regex (to extract 1E10 notation) + tests
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c187023
check MSS group prior
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5d8c708
forgot notation 1e12
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594442d
easier debugging
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9645aae
additional check case
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ed6c435
useless file
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b065000
implement header reader and related functions
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3619f1d
remove old functions to parse project header
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4022458

Commits on May 3, 2021

function to read reftable header
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7d2e81e
remove commented lines regarding header reader unused internal function
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eedcbee
fix typo
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adee449
function to test all input files (except the data file) from a project
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4959b02
manage project file input for existing project
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8a56734
feedback when uploading files to an existing project
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c6a35b4
function to clean the current project directory
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7a98246
move the bin dir cleaning function with other directory related functions
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c764cf3
additional environment reactive values storing project related metadata
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03d846c
add counter for file modification in project directory in environment reactive values
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3a24d0d
dedicated module to input files for an existing project (WIP, todo: file check)
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110502e
function to update project file list and modification counter
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71336a8
additional dependencies
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718549b

Commits on May 4, 2021

init global env sooner at startup + fix issue with datagen env init
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3935028
ui to list project files (WIP: ui to check project files and ui for example projects)
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3468f01
example proj ui + fix proj cleaning in existing proj ui
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44284cc
change naming convention for number of summary stats
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a41ffa9
change naming convention for number of scenarii
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3a1ae8b
save header file name
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42115a7

Commits on May 5, 2021

get number of parameters per scenario when reading header file
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8032936
verify consistency between header and reftable
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2224699
project configuration setup check (TODO: manage data file)
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e2988e2
data file input (TODO: data file check)
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7333605
WIP: preparation for data file check refactoring
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7f567f9
fix typo
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ad9de24

Commits on May 6, 2021

Commits on May 7, 2021