From bfb581115cb5306cf2b95bb940d22b4c1dfca7d3 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Thu, 10 Sep 2026 14:13:26 -0500 Subject: PoC: UI for genotype records. Implement a proof-of-concept (PoC) UI for genotype records. --- uploader/templates/genotypes/base.html | 7 +- uploader/templates/genotypes/index.html | 129 ++++++++++++ uploader/templates/genotypes/list-genotypes.html | 227 --------------------- .../genotypes/macro-display-dataset-card.html | 24 +++ 4 files changed, 159 insertions(+), 228 deletions(-) create mode 100644 uploader/templates/genotypes/index.html delete mode 100644 uploader/templates/genotypes/list-genotypes.html create mode 100644 uploader/templates/genotypes/macro-display-dataset-card.html (limited to 'uploader/templates') diff --git a/uploader/templates/genotypes/base.html b/uploader/templates/genotypes/base.html index 8d1b951..c2abc63 100644 --- a/uploader/templates/genotypes/base.html +++ b/uploader/templates/genotypes/base.html @@ -1,10 +1,11 @@ {%extends "populations/base.html"%} {%from "populations/macro-display-population-card.html" import display_sui_population_card%} +{%from "genotypes/macro-display-dataset-card.html" import display_dataset_card%} {%block breadcrumbs%} {{super()}}
  • - genotype @@ -14,5 +15,9 @@ {%block sidebarcontents%} +{%if dataset is defined and dataset is not none%} +{{display_dataset_card(species, population, dataset)}} +{%else%} {{display_sui_population_card(species, population)}} +{%endif%} {%endblock%} diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html new file mode 100644 index 0000000..1d44e26 --- /dev/null +++ b/uploader/templates/genotypes/index.html @@ -0,0 +1,129 @@ +{%extends "genotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} + +{%block title%}Genotypes{%endblock%} + +{%block pagetitle%}Genotypes{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + + +{%if dataset is defined and dataset is not none%} + +
    +

    Genotype Data

    + +
    +
    +

    + + Add genotype records + +

    +
    +
    + +
    + + + + + + + + + + {%for sample in samples%} + + {%endfor%} + + + + + {%for record in genotype_records%} + + + + + + + + {%for sample in samples%} + + {%endfor%} + + {%else%} + + + + {%endfor%} + +
    #IndexLocusChrcMMb{{sample}}
    + + {{record.index}}{{record.Name}}{{record.Chr}}{{record.cM}}{{record.Mb}}{{record.data[sample]}}
    + There are no records +
    +
    +
    + +
    +

    Genotype Encoding

    +

    The numerical values in the table above are mapped from the following allele symbols:

    + + + + + + + + + + + + {%for row in genocode%} + + + + + + {%else%} + + + + {%endfor%} + +
    Allele TypeAllele SymbolMapped To
    + {{row.AlleleType}}{{row.AlleleSymbol}}{{row.DatabaseValue if row.DatabaseValue is not none}}
    + There is no genotype encoding defined for this data. +
    +
    + +{%else%} + +
    +

    We need to create a dataset to hold the genotype information for this + species/population, before we can proceed to upload the genotype data.

    +

    Please click the button below to create the dataset.

    + +
    + create genotype dataset +
    +
    + +{%endif%} + +{%endblock%} diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html deleted file mode 100644 index a7e8ba4..0000000 --- a/uploader/templates/genotypes/list-genotypes.html +++ /dev/null @@ -1,227 +0,0 @@ -{%extends "genotypes/base.html"%} -{%from "flash_messages.html" import flash_all_messages%} - -{%block title%}Genotypes{%endblock%} - -{%block pagetitle%}Genotypes{%endblock%} - -{%block contents%} -{{flash_all_messages()}} - -
    -

    Genotype Encoding

    -

    - The genotype encoding used for the "{{population.FullName}}" population from - the "{{species.FullName}}" species is as shown in the table below. -

    - - - - - - - - - - - - {%for row in genocode%} - - - - - - {%else%} - - - - {%endfor%} - -
    Allele TypeAllele SymbolAllele Value
    {{row.AlleleType}}{{row.AlleleSymbol}}{{row.DatabaseValue if row.DatabaseValue is not none else "NULL"}}
    - - There is no explicit genotype encoding defined for this population. -
    - - {%if genocode | length < 1%} -
    - - define genotype encoding - -
    - {%endif%} -
    - -
    -

    Genotype Dataset

    -
    - -{%if dataset is not none%} - -
    -

    Dataset Details

    - - - - - - - - - - - - - - -
    NameFull Name
    {{dataset.Name}} - {{dataset.FullName}}
    - -

    - To see more information regarding this dataset (e.g. which markers have - sample allele data, the allele data itself, etc) click on the "Full Name" - link above.

    -
    - -
    -

    Genotype Markers

    -
    - -
    -

    - The table below lists all of the markers that exist for species - {{species.SpeciesName}} ({{species.FullName}}), regardless of whether - (or not) we have corresponding sample allele data for a particular marker. -

    - - - - - - - - - - - - - - {%for marker in markers%} - - - - - - - - - - {%endfor%} - -
    #IndexMarker NameChr - Location (Mb)SourceSource2
    -
    - -{%else%} - -
    -

    - Your genotype data will need to be under a dataset. Unfortunately there is - currently no dataset defined for this population. -

    - -

    - - Click the button below to define the genotype dataset for this population. -

    -

    - - create new genotype dataset

    -
    - -{%endif%} - -
    -

    Notes

    -
    -

    Genetic Markers: Some Important Concepts to Consider/Remember

    -
      -
    • Reference vs. Non-reference alleles
      • -
    • In GenoCode table, items are ordered by InbredSet
      • -
    -

    Possible references

    -
      -
    • https://mr-dictionary.mrcieu.ac.uk/term/genotype/
      • -
    • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/
      • -
    -
    - -
    -

    Genotype Dataset

    -

    - - NOTE: Currently the GN2 (and related) system(s) expect a - single genotype dataset per population. If there is more than one, the - system apparently fails in unpredictable ways. -

    -
    -
    - -{%endblock%} - - -{%block javascript%} - -{%endblock%} diff --git a/uploader/templates/genotypes/macro-display-dataset-card.html b/uploader/templates/genotypes/macro-display-dataset-card.html new file mode 100644 index 0000000..2b197d4 --- /dev/null +++ b/uploader/templates/genotypes/macro-display-dataset-card.html @@ -0,0 +1,24 @@ +{%from "populations/macro-display-population-card.html" import display_sui_population_card%} + +{%macro display_dataset_card(species, population, dataset)%} +{{display_sui_population_card(species, population)}} +
    + + + + + + + + + + + + + + + + +
    Current genotype dataset
    Name{{dataset.Name}}
    Full Name{{dataset.FullName}}
    Short Name{{dataset.ShortName}}
    +
    +{%endmacro%} -- cgit 1.4.1