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Topic/repetitive measurements2#5233

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lukasmueller wants to merge 109 commits intomastersolgenomics/sgn:masterfrom topic/repetitive_measurements2solgenomics/sgn:topic/repetitive_measurements2Copy head branch name to clipboard

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Commits

Commits on Feb 27, 2024

• retrieve more term props; refactor into get_term_props function.

  lukasmueller

  committed
  4a9d453

Commits on Feb 28, 2024

• add some comments how the system should work with multiple phenotypico observations.

  lukasmueller

  committed
  9cf7ba3

Commits on Mar 1, 2024

• add trait_repeat_type to the load_trait_props.pl script and its backend.

  lukasmueller

  committed
  a8cf000

• adjust storing logic to trait_repeat_type parameter.

  lukasmueller

  committed
  a8d6236

• fix some issues with variable declarations.

  lukasmueller

  committed
  343188c

Commits on Mar 3, 2024

• fix issue with query parameters.

  lukasmueller

  committed
  b441938

Commits on Mar 5, 2024

• fix typo in variable name

  lukasmueller

  committed
  a03f71f

• add support for multiple measurements.

  lukasmueller

  committed
  21c7f4d

• add support for multiple observations.

  lukasmueller

  committed
  b57d07b

• fix typo in variable name.

  lukasmueller

  committed
  ad1be34

Commits on Mar 8, 2024

• implement multiple values features.

  lukasmueller

  committed
  3570705

Commits on Mar 13, 2024

• add support for multiple measurements for native search in phenotype matrix.

  lukasmueller

  committed
  66132e9

• comment out debug info.

  lukasmueller

  committed
  aab1ed3

• add missing Perl module CXGN::Trial.

  lukasmueller

  committed
  479501f

Commits on Mar 15, 2024

• remove debug messages.

  lukasmueller

  committed
  4d4dde8

Commits on Mar 25, 2024

• Merge branch 'master' into topic/repetitive_measurements

  lukasmueller

  committed
  7277658

Commits on Mar 29, 2024

• add phenotype matrix test.

  lukasmueller

  committed
  24b7f2a

Commits on Mar 31, 2024

• add trait_repeat_type to trait properties add function.

  lukasmueller

  committed
  1a97caf

• Merge branch 'master' into topic/repetitive_measurements

  lukasmueller

  committed
  822dcc8

Commits on Apr 1, 2024

• add repetitive_measurements key and tweak pod.

  lukasmueller

  committed
  d7b849b

• prevent errors when there are no observations.

  lukasmueller

  committed
  30260e0

• fix typo in assignment.

  lukasmueller

  committed
  ceb1fc7

• add new accessor for repetitive measurements.

  lukasmueller

  committed
  bab60c9

• rename multiple_observations_treatment to repetitive_measurements; add UI elements for downloads; adapt code to changes.

  lukasmueller

  committed
  917c998

Commits on Apr 2, 2024

• add trait repeat prop cvterm and transfer timestamps to correct field.

  lukasmueller

  committed
  4e79541

Commits on May 23, 2024

• add time based queries to phenotype download in the wizard

  lukasmueller

  committed
  4b3a0b5

Commits on May 24, 2024

• add date related queries to downloads.

  lukasmueller

  committed
  25a058d

Commits on Nov 1, 2024

• resolve conflicts.

  lukasmueller

  committed
  e5d96fc

• add separate section for repetitve measurements in trial detail page

  Sri-2023

  committed
  6bc876b

• fix the ID names; and fix indentation in repetitive_measurement options

  Sri-2023

  committed
  07752bb

• add value attributes to reptitive values in search page

  Sri-2023

  committed
  f74c9d4

• Fix ID names for repetitive options in download phenotypes dialog

  Sri-2023

  committed
  ff1fb0c

• swap 'phenotype_raw_data' and 'phenotype_summary_statistics' sections on the trial detail page

  Sri-2023

  committed
  20f9d1e

Commits on Nov 2, 2024

• add date range option and slider to phenotype summary stats section to filter trait values accordingly

  Sri-2023

  committed
  c5d93d5

• add start_date, and end_date params to the trait_pheno and pheno_summary methods

  Sri-2023

  committed
  6c43e6c

Commits on Nov 3, 2024

• add trial_collect_date_range endpoint to retrieve trial start and end date

  Sri-2023

  committed
  cc88f3b

• add start_date and end_date to search query

  Sri-2023

  committed
  66c6264

• refactor to use the consistent trial_id

  Sri-2023

  committed
  0da16d5

Commits on Nov 4, 2024

• add small line graph to see trend, and zoomable large graph to view

  Sri-2023

  committed
  0dc88f9

• fix typo

  Sri-2023

  committed
  57b9872

• add title to line_graph

  Sri-2023

  committed
  1eaf2e0

• correct repetitive_params in download_phenotypes_action

  Sri-2023

  committed
  afb829f

• add seperate section to show # of phenotypes recorded in a trial; and also, filter the trait values based on the obs_level

  Sri-2023

  committed
  bdad8ea

• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

  committed
  fbcff9c

• add 'sum' option to the repetitive_values

  Sri-2023

  committed
  539e153

• handle sum values

  Sri-2023

  committed
  5dae445

Commits on Nov 5, 2024

• comment out alter messages

  Sri-2023

  committed
  dc9442a

• two options to retrieve all values: single line and multi line

  Sri-2023

  committed
  5ebe930

• fix BrApi phenotyping test

  Sri-2023

  committed
  caf981f

• parse the time-series repetitive values

  Sri-2023

  committed
  2c79bd3

• handle collect_date in Native search

  Sri-2023

  committed
  4a7ffd9

• add package for storing phenotype additional info and references

  Sri-2023

  committed
  5da8d4b

• add accessors to max, min, duplicates, value_count

  Sri-2023

  committed
  4f0a173

Commits on Nov 7, 2024

• modify POD

  Sri-2023

  committed
  4fd9b51

• missing true value

  Sri-2023

  committed
  7f863de

Commits on Nov 8, 2024

• add date params get_phennotypes_for_trait function

  Sri-2023

  committed
  42e1f9b

• refactor phenotypes in-progress

  Sri-2023

  committed
  bedbe71

Commits on Nov 11, 2024

• add the sum_observations method repetitive_values; fix indent

  Sri-2023

  committed
  15771e4

• fix phenotype_multi_categories test

  Sri-2023

  committed
  07f0303

• update PhenotypeMatrix test with all_values_single_line and sum params

  Sri-2023

  committed
  23cfc93

• refactor phenotypes to store the multiple measurement values

  Sri-2023

  committed
  0b90a30

Commits on Nov 12, 2024

• fix the BrAPI phenotying test

  Sri-2023

  committed
  6908c3e

• refactor phenotypes

  Sri-2023

  committed
  c8d4183

• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

  committed
  bc189ff

• fix ValidateNIRS test.

  lukasmueller

  committed
  8d46891

Commits on Nov 13, 2024

• exlude notes from trait check.

  lukasmueller

  committed
  898bfbd

• update the default end date to the current date

  Sri-2023

  committed
  2b5da46

• fix indent

  Sri-2023

  committed
  4571f3c

• exclude notes from normal phenotype storage.

  lukasmueller

  committed
  24c4eb4

• make test labels distinct.

  lukasmueller

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  dd9c667

Commits on Nov 14, 2024

• fix a test, one more to go.

  lukasmueller

  committed
  ced594f

• fix typo (oops) and fix last test.

  lukasmueller

  committed
  2b3c491

Commits on Nov 15, 2024

• remove duplicated repeat_type

  Sri-2023

  committed
  83c8c59

• filter the values based on the timestamp

  Sri-2023

  committed
  77f5907

Commits on Nov 19, 2024

• make the values of end_date inclusive, when they select the last date; sort the values as per the date

  Sri-2023

  committed
  2488cf9

• comment the sorting values by date from line_graph package

  Sri-2023

  committed
  61557ec

Commits on Nov 21, 2024

• sort observations by date; and use latest(last) date as timestamp for avg and sum values

  Sri-2023

  committed
  a169caf

• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

  committed
  8899f08

Commits on Nov 22, 2024

• add timestamp check for the avg and sum options

  Sri-2023

  committed
  da35fb7

• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

  committed
  ac38f76

Commits on Dec 3, 2024

• modify the phenotype_matrix function to retrieve reptitive values in multi-line

  Sri-2023

  committed
  23f68c2

• modify note field to store multiple entries for repetitive_measurements

  Sri-2023

  committed
  3809678

• typo

  Sri-2023

  committed
  ac590c9

• use clean_up_db to clean up some tests; in SGN::Test::Fixture, also clean cvtermprop in clean_up_db function.

  lukasmueller

  committed
  5e90e90

Commits on Dec 4, 2024

• clean up db after some tests and also re-run matviews so they are correct for the following tests.

  lukasmueller

  committed
  4efa217

• try to fix tests.

  lukasmueller

  committed
  600276b

Commits on Dec 6, 2024

• hmmm... changing the order of the values may not help in the long run...

  lukasmueller

  committed
  d092c16

• more sustainable approach is to sort the returned data before checking.

  lukasmueller

  committed
  10b6046

• more attempts to make tests pass...

  lukasmueller

  committed
  31d80c3

• Merge branch 'master' into topic/repetitive_measurements2

  lukasmueller

  authored
  d5ea2c8

Commits on Dec 12, 2024

• fix upload_phenotype tests to handle potential delays

  Sri-2023

  committed
  a6f8ba0

• add strict and warnings options

  Sri-2023

  committed
  46ff305

• add ability to load multiple phenotypic values by pushing on an array in generic simple upload.

  

  Production User

  committed
  ed4cc06

• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

  committed
  4479cc8

• Merge remote-tracking branch 'origin/topic/repetitive_measurements2' into topic/repetitive_measurements2

  Sri-2023

  committed
  2a6aea6

• fix lint issues

  Sri-2023

  committed
  666d1bb

• make Phenotype_with_multi_categories.t test pass more reliably by checking substring of returned error.

  lukasmueller

  committed
  a32aa30

Commits on Dec 13, 2024

• fix all linting issues

  Sri-2023

  committed
  487986a

• update branch

  Sri-2023

  committed
  55dca30

• fix this last lint issue

  Sri-2023

  committed
  66076d9

Commits on Dec 16, 2024

• update the manual with repetitive_measurements

  Sri-2023

  committed
  39e79b9

• update bookdown docs

  

  github-actions

  committed
  406823c

Commits on Dec 17, 2024

• make trait values dynamic as trait option changes

  Sri-2023

  committed
  ad285fc

• update bookdown docs

  

  github-actions

  committed
  1356040

• requested to make a defualt option - as Average on UI under repetitive_measurements option

  Sri-2023

  committed
  55af6b1

• typo in passing the type param

  Sri-2023

  committed
  47ebabf

• update bookdown docs

  

  github-actions

  committed
  4bb21d0

Commits on Dec 22, 2024

• add a conversion file for ncsu excel format.

  lukasmueller

  committed
  873a49c

• update bookdown docs

  

  github-actions

  committed
  7fdb481