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/genotypes/views.py | 66 ++++-- 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 +++ 5 files changed, 207 insertions(+), 246 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 diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index f27671c..c18c330 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -4,11 +4,13 @@ import logging from MySQLdb.cursors import DictCursor from pymonad.either import Left, Right, Either from gn_libs.mysqldb import database_connection +from werkzeug.exceptions import UnsupportedMediaType from flask import (flash, request, jsonify, redirect, Blueprint, + make_response, render_template, current_app as app) @@ -16,17 +18,16 @@ from uploader.flask_extensions import url_for from uploader.ui import make_template_renderer from uploader.oauth2.client import oauth2_post from uploader.authorisation import require_login -from uploader.route_utils import generic_select_population -from uploader.datautils import safe_int, enumerate_sequence -from uploader.species.models import all_species, species_by_id +from uploader.species.models import species_by_id from uploader.monadic_requests import make_either_error_handler from uploader.population.models import population_by_species_and_id -from uploader.request_checks import with_species, with_dataset, with_population +from uploader.request_checks import with_population + from .models import (genotype_markers, + genotype_records, genotype_dataset, save_new_dataset, - genotype_markers_count, genocode_by_population) logger = logging.getLogger(__name__) @@ -40,20 +41,49 @@ render_template = make_template_renderer("genotypes") @require_login @with_population(species_redirect_uri="species.list_species", redirect_uri="species.populations.list_species_populations") -def list_genotypes(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] - """List genotype details for species and population.""" +def index(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] + """Entry-point to the genotypes management section.""" with database_connection(app.config["SQL_URI"]) as conn: - return render_template("genotypes/list-genotypes.html", - species=species, - population=population, - genocode=genocode_by_population( - conn, population["Id"]), - total_markers=genotype_markers_count( - conn, species["SpeciesId"]), - dataset=genotype_dataset(conn, - species["SpeciesId"], - population["Id"]), - activelink="list-genotypes") + offset = int(request.args.get("start", "0")) + number_of_records = int(request.args.get("count", "10")) + _markers, _total_markers, = genotype_markers( + conn, species["SpeciesId"], population["Id"]) + _genotype_records, _count = genotype_records( + conn, + species["SpeciesId"], + population["Id"], + offset, + number_of_records) + _genotype_records = tuple( + {**_record, "index": _idx} + for _idx, _record + in enumerate(_genotype_records, start=offset+1)) + + ## Order these correctly + _samples = tuple(_genotype_records[0]["data"].keys()) + + if "application/json" in request.headers["Accept"]: + return make_response( + jsonify({ + "genotype_records": _genotype_records, + "total_genotype_records": _count, + "fetched_genotype_records": len(_genotype_records), + "sample_order": _samples + }), 200) + + if "text/html" in request.headers["Accept"]: + return render_template( + "genotypes/index.html", + species=species, + population=population, + genocode=genocode_by_population(conn, population["Id"]), + dataset=genotype_dataset( + conn, species["SpeciesId"], population["Id"]), + genotype_records=_genotype_records, + samples=_samples, + activelink="list-genotypes") + + raise UnsupportedMediaType("This endpoint can only server HTML or JSON") @genotypesbp.route( 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