From 41b78a32c20df5c84d1b2910d8b84f301429f1d7 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Fri, 13 Dec 2024 15:08:10 -0600 Subject: Rename template Rename original template to indicate it uses the R/qtl2 bundle format. --- .../add-phenotypes-with-rqtl2-bundle.html | 231 +++++++++++++++++++++ uploader/templates/phenotypes/add-phenotypes.html | 231 --------------------- 2 files changed, 231 insertions(+), 231 deletions(-) create mode 100644 uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html delete mode 100644 uploader/templates/phenotypes/add-phenotypes.html (limited to 'uploader') diff --git a/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html new file mode 100644 index 0000000..2bd5fab --- /dev/null +++ b/uploader/templates/phenotypes/add-phenotypes-with-rqtl2-bundle.html @@ -0,0 +1,231 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-table-pagination.html" import table_pagination%} +{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +
  • + Add Phenotypes +
    • +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +
    +
    + Add New Phenotypes + +
    +

    Select the zip file bundle containing information on the phenotypes you + wish to upload, then click the "Upload Phenotypes" button below to + upload the data.

    +

    See the File Formats section below + to get an understanding of what is expected of the bundle files you + upload.

    +

    This will not update any existing phenotypes!

    +
    + +
    + + +
    + +
    + +
    +
    +
    + +
    +

    File Formats

    +

    We accept an extended form of the + + input files' format used with the R/qtl2 software as a single ZIP + file

    +

    The files that are used for this feature are: +

    +

    +

    Other files within the bundle will be ignored, for this feature.

    +

    The following section will detail the expectations for each of the + different file types within the uploaded ZIP file bundle for phenotypes:

    + +

    Control File

    +

    There MUST be one, and only one file that acts + as the control file. This file can be: +

    +

    + +

    The control file is useful for defining things about the bundle such as:

    + + +

    pheno File(s)

    +

    These files are the main data files. You must have at least one of these + files in your bundle for it to be valid for this step.

    +

    The data is a matrix of individuals × phenotypes by default, as + below:
    + + id,10001,10002,10003,10004,…
    + BXD1,61.400002,54.099998,483,49.799999,…
    + BXD2,49,50.099998,403,45.5,…
    + BXD5,62.5,53.299999,501,62.900002,…
    + BXD6,53.099998,55.099998,403,NA,…
    + ⋮
     +

    +

    If the pheno_transposed value is set to True, + then the data will be a phenotypes × individuals matrix as in the + example below:
    + + id,BXD1,BXD2,BXD5,BXD6,…
    + 10001,61.400002,49,62.5,53.099998,…
    + 10002,54.099998,50.099998,53.299999,55.099998,…
    + 10003,483,403,501,403,…
    + 10004,49.799999,45.5,62.900002,NA,…
    + ⋮ +     +

    + + +

    phenocovar File(s)

    +

    At least one phenotypes metadata file with the metadata values such as + descriptions, PubMed Identifier, publication titles (if present), etc.

    +

    The data in this/these file(s) is a matrix of + phenotypes × phenotypes-covariates. The first column is always the + phenotype names/identifiers — same as in the R/qtl2 format.

    +

    phenocovar files should never be transposed!

    +

    This file MUST be present in the bundle, and have data for + the bundle to be considered valid by our system for this step.
    + In addition to that, the following are the fields that must be + present, and + have values, in the file before the file is considered valid: +

    + +

    The following optional fields can also be provided: +

    +

    +

    These files will be marked up in the control file with the + phenocovar key, as in the examples below: +

      +
    1. JSON: single file
      + {
      +   ⋮,
      +   "phenocovar": "your_covariates_file.csv",
      +   ⋮
      + } +       +
      2. +
    2. JSON: multiple files
      + {
      +   ⋮,
      +   "phenocovar": [
      +     "covariates_file_01.csv",
      +     "covariates_file_01.csv",
      +     ⋮
      +   ],
      +   ⋮
      + } +       +
      3. +
    3. YAML: single file or
      + + ⋮
      + phenocovar: your_covariates_file.csv
      + ⋮ +       +
      4. +
    4. YAML: multiple files
      + + ⋮
      + phenocovar:
      + - covariates_file_01.csv
      + - covariates_file_02.csv
      + - covariates_file_03.csv
      + …
      + ⋮ +       +
      5. +
    +

    + +

    phenose and phenonum File(s)

    +

    These are extensions to the R/qtl2 standard, i.e. these types ofs file are + not supported by the original R/qtl2 file format

    +

    We use these files to upload the standard errors (phenose) when + the data file (pheno) is average data. In that case, the + phenonum file(s) contains the number of individuals that were + involved when computing the averages.

    +

    Both types of files are matrices of individuals × phenotypes by + default. Like the related pheno files, if + pheno_transposed: True, then the file will be a matrix of + phenotypes × individuals.

    +
    + +
    +

    Notes for Devs (well… Fred, really.)

    +

    Use the following resources for automated retrieval of certain data

    + +
    + +{%endblock%} + +{%block sidebarcontents%} +{{display_pheno_dataset_card(species, population, dataset)}} +{%endblock%} diff --git a/uploader/templates/phenotypes/add-phenotypes.html b/uploader/templates/phenotypes/add-phenotypes.html deleted file mode 100644 index 2bd5fab..0000000 --- a/uploader/templates/phenotypes/add-phenotypes.html +++ /dev/null @@ -1,231 +0,0 @@ -{%extends "phenotypes/base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "macro-table-pagination.html" import table_pagination%} -{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%} - -{%block title%}Phenotypes{%endblock%} - -{%block pagetitle%}Phenotypes{%endblock%} - -{%block lvl4_breadcrumbs%} -
  • - Add Phenotypes -
    • -{%endblock%} - -{%block contents%} -{{flash_all_messages()}} - -
    -
    - Add New Phenotypes - -
    -

    Select the zip file bundle containing information on the phenotypes you - wish to upload, then click the "Upload Phenotypes" button below to - upload the data.

    -

    See the File Formats section below - to get an understanding of what is expected of the bundle files you - upload.

    -

    This will not update any existing phenotypes!

    -
    - -
    - - -
    - -
    - -
    -
    -
    - -
    -

    File Formats

    -

    We accept an extended form of the - - input files' format used with the R/qtl2 software as a single ZIP - file

    -

    The files that are used for this feature are: -

    -

    -

    Other files within the bundle will be ignored, for this feature.

    -

    The following section will detail the expectations for each of the - different file types within the uploaded ZIP file bundle for phenotypes:

    - -

    Control File

    -

    There MUST be one, and only one file that acts - as the control file. This file can be: -

    -

    - -

    The control file is useful for defining things about the bundle such as:

    - - -

    pheno File(s)

    -

    These files are the main data files. You must have at least one of these - files in your bundle for it to be valid for this step.

    -

    The data is a matrix of individuals × phenotypes by default, as - below:
    - - id,10001,10002,10003,10004,…
    - BXD1,61.400002,54.099998,483,49.799999,…
    - BXD2,49,50.099998,403,45.5,…
    - BXD5,62.5,53.299999,501,62.900002,…
    - BXD6,53.099998,55.099998,403,NA,…
    - ⋮
     -

    -

    If the pheno_transposed value is set to True, - then the data will be a phenotypes × individuals matrix as in the - example below:
    - - id,BXD1,BXD2,BXD5,BXD6,…
    - 10001,61.400002,49,62.5,53.099998,…
    - 10002,54.099998,50.099998,53.299999,55.099998,…
    - 10003,483,403,501,403,…
    - 10004,49.799999,45.5,62.900002,NA,…
    - ⋮ -     -

    - - -

    phenocovar File(s)

    -

    At least one phenotypes metadata file with the metadata values such as - descriptions, PubMed Identifier, publication titles (if present), etc.

    -

    The data in this/these file(s) is a matrix of - phenotypes × phenotypes-covariates. The first column is always the - phenotype names/identifiers — same as in the R/qtl2 format.

    -

    phenocovar files should never be transposed!

    -

    This file MUST be present in the bundle, and have data for - the bundle to be considered valid by our system for this step.
    - In addition to that, the following are the fields that must be - present, and - have values, in the file before the file is considered valid: -

    - -

    The following optional fields can also be provided: -

    -

    -

    These files will be marked up in the control file with the - phenocovar key, as in the examples below: -

      -
    1. JSON: single file
      - {
      -   ⋮,
      -   "phenocovar": "your_covariates_file.csv",
      -   ⋮
      - } -       -
      2. -
    2. JSON: multiple files
      - {
      -   ⋮,
      -   "phenocovar": [
      -     "covariates_file_01.csv",
      -     "covariates_file_01.csv",
      -     ⋮
      -   ],
      -   ⋮
      - } -       -
      3. -
    3. YAML: single file or
      - - ⋮
      - phenocovar: your_covariates_file.csv
      - ⋮ -       -
      4. -
    4. YAML: multiple files
      - - ⋮
      - phenocovar:
      - - covariates_file_01.csv
      - - covariates_file_02.csv
      - - covariates_file_03.csv
      - …
      - ⋮ -       -
      5. -
    -

    - -

    phenose and phenonum File(s)

    -

    These are extensions to the R/qtl2 standard, i.e. these types ofs file are - not supported by the original R/qtl2 file format

    -

    We use these files to upload the standard errors (phenose) when - the data file (pheno) is average data. In that case, the - phenonum file(s) contains the number of individuals that were - involved when computing the averages.

    -

    Both types of files are matrices of individuals × phenotypes by - default. Like the related pheno files, if - pheno_transposed: True, then the file will be a matrix of - phenotypes × individuals.

    -
    - -
    -

    Notes for Devs (well… Fred, really.)

    -

    Use the following resources for automated retrieval of certain data

    - -
    - -{%endblock%} - -{%block sidebarcontents%} -{{display_pheno_dataset_card(species, population, dataset)}} -{%endblock%} -- cgit v1.2.3