diff options
| -rw-r--r-- | uploader/genotypes/views.py | 66 | ||||
| -rw-r--r-- | uploader/templates/genotypes/base.html | 7 | ||||
| -rw-r--r-- | uploader/templates/genotypes/index.html | 129 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-genotypes.html | 227 | ||||
| -rw-r--r-- | uploader/templates/genotypes/macro-display-dataset-card.html | 24 |
5 files changed, 207 insertions, 246 deletions
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()}} <li class="breadcrumb-item"> - <a href="{{url_for('species.populations.genotypes.list_genotypes', + <a href="{{url_for('species.populations.genotypes.index', species_id=species['SpeciesId'], population_id=population['Id'])}}"> 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%} + +<div class="row"> + <h2>Genotype Data</h2> + + <div class="row"> + <div class="col"> + <p> + <a href="#" + class="not-implemented btn btn-primary"> + Add genotype records + </a> + </p> + </div> + </div> + + <div class="table-responsive"> + <table id="tbl-genotype-records" class="table"> + <thead> + <tr> + <th title="">#</th> + <th title="">Index</th> + <th title="Locus of marker on the chromosome">Locus</th> + <th title="Chromosome">Chr</th> + <th title="Physical location of marker in centimorgans">cM</th> + <th title="Physical location of marker in megabasepairs">Mb</th> + {%for sample in samples%} + <th title="Data for sample {{sample}}">{{sample}}</th> + {%endfor%} + </tr> + </thead> + + <tbody> + {%for record in genotype_records%} + <tr> + <td> + <input type="checkbox" + id="chk-geno-record-{{record.Id}}" + name="geno_record_id" + value="{{record.Id}}" /> + </td> + <td>{{record.index}}</td> + <td>{{record.Name}}</td> + <td>{{record.Chr}}</td> + <td>{{record.cM}}</td> + <td>{{record.Mb}}</td> + {%for sample in samples%} + <td>{{record.data[sample]}}</td> + {%endfor%} + </tr> + {%else%} + <tr> + <td colspan="6" class="text-info"> + There are no records + </td> + </tr> + {%endfor%} + </tbody> + </table> + </div> +</div> + +<div class="row"> + <h2>Genotype Encoding</h2> + <p>The numerical values in the table above are mapped from the following allele symbols:</p> + + <table class="table"> + <thead> + <tr> + <th>Allele Type</th> + <th>Allele Symbol</th> + <th>Mapped To</th> + </tr> + </thead> + + <tbody> + {%for row in genocode%} + <tr> + <td {%if row.AlleleType == 'mat'%} + title="Maternal allele" + {%elif row.AlleleType == "pat"%} + title="Paternal allele" + {%elif row.AlleleType == "het"%} + title="Heterozygous allele" + {%else%} + title="Unknown allele" + {%endif%}> + {{row.AlleleType}}</td> + <td>{{row.AlleleSymbol}}</td> + <td>{{row.DatabaseValue if row.DatabaseValue is not none}}</td> + </tr> + {%else%} + <tr> + <td colspan="3" class="text-info"> + There is no genotype encoding defined for this data. + </td> + </tr> + {%endfor%} + </tbody> + </table> +</div> + +{%else%} + +<div class="row"> + <p>We need to create a dataset to hold the genotype information for this + species/population, before we can proceed to upload the genotype data.</p> + <p>Please click the button below to create the dataset.</p> + + <div class="col"> + <a href="{{url_for('species.populations.genotypes.create_dataset', species_id=species.SpeciesId, population_id=population.Id)}}" + class="btn btn-primary">create genotype dataset</a> + </div> +</div> + +{%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()}} - -<div class="row"> - <h2>Genotype Encoding</h2> - <p> - The genotype encoding used for the "{{population.FullName}}" population from - the "{{species.FullName}}" species is as shown in the table below. - </p> - <table class="table"> - - <thead> - <tr> - <th>Allele Type</th> - <th>Allele Symbol</th> - <th>Allele Value</th> - </tr> - </thead> - - <tbody> - {%for row in genocode%} - <tr> - <td>{{row.AlleleType}}</td> - <td>{{row.AlleleSymbol}}</td> - <td>{{row.DatabaseValue if row.DatabaseValue is not none else "NULL"}}</td> - </tr> - {%else%} - <tr> - <td colspan="7" class="text-info"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - There is no explicit genotype encoding defined for this population. - </td> - </tr> - {%endfor%} - </tbody> - </table> - - {%if genocode | length < 1%} - <div class="col"> - <a href="#add-genotype-encoding" - title="Add a genotype encoding system for this population" - class="btn btn-primary not-implemented"> - define genotype encoding - </a> - </div> - {%endif%} -</div> - -<div class="row"> - <h2>Genotype Dataset</h2> -</div> - -{%if dataset is not none%} - -<div class="row"> - <h3>Dataset Details</h3> - <table class="table"> - <thead> - <tr> - <th>Name</th> - <th>Full Name</th> - </tr> - </thead> - - <tbody> - <tr> - <td>{{dataset.Name}}</td> - <td><a href="{{url_for('species.populations.genotypes.view_dataset', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}" - title="View details regarding and manage dataset '{{dataset.FullName}}'" - target="_blank"> - {{dataset.FullName}}</a></td> - </tr> - </tbody> - </table> - - <p> - 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.</p> -</div> - -<div class="row"> - <h3>Genotype Markers</h3> -</div> - -<div class="row"> - <p> - 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. - </p> - <table id="tbl-genetic-markers" class="table compact stripe cell-border"> - <thead> - <tr> - <th title="">#</th> - <th title="">Index</th> - <th title="">Marker Name</th> - <th title="Chromosome">Chr</th> - <th title="Physical location of the marker in megabasepairs"> - Location (Mb)</th> - <th title="">Source</th> - <th title="">Source2</th> - </thead> - - <tbody> - {%for marker in markers%} - <tr> - <td></td> - <td></td> - <td></td> - <td></td> - <td></td> - <td></td> - <td></td> - </tr> - {%endfor%} - </tbody> - </table> -</div> - -{%else%} - -<div class="row"> - <p> - Your genotype data will need to be under a dataset. Unfortunately there is - currently no dataset defined for this population. - </p> - - <p class="text-warning"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - Click the button below to define the genotype dataset for this population. - </p> - <p> - <a href="{{url_for('species.populations.genotypes.create_dataset', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species." - class="btn btn-primary"> - create new genotype dataset</a></p> -</div> - -{%endif%} - -<div class="row"> - <h2>Notes</h2> - <div class="row text-danger"> - <h3>Genetic Markers: Some Important Concepts to Consider/Remember</h3> - <ul> - <li>Reference vs. Non-reference alleles</li> - <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li> - </ul> - <h3>Possible references</h3> - <ul> - <li>https://mr-dictionary.mrcieu.ac.uk/term/genotype/</li> - <li>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/</li> - </ul> - </div> - - <div class="row text-warning"> - <h3>Genotype Dataset</h3> - <p> - <span class="glyphicon glyphicon-exclamation-sign"></span> - <strong>NOTE</strong>: 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. - </p> - </div> -</div> - -{%endblock%} - - -{%block javascript%} -<script type="text/javascript"> - - $(function() { - var dtGeneticMarkers = buildDataTable( - "#tbl-genetic-markers", - [], - [ - { - data: function(marker) { - return `<input type="checkbox" name="selected-markers" ` + - `id="chk-selected-markers-${marker.Id}-${marker.GenoFreezeId}" ` + - `value="${marker.Id}_${marker.GenoFreezeId}" ` + - `class="chk-row-select" />`; - } - }, - {data: 'index'}, - {data: "Name", searchable: true}, - {data: "Chr", searchable: true}, - {data: "Mb", searchable: true}, - {data: "Source", searchable: true}, - {data: "Source2", searchable: true} - ], - { - ajax: { - url: "{{url_for('species.populations.genotypes.list_markers', species_id=species.SpeciesId, population_id=population.Id, dataset_id=dataset.Id)}}", - dataSrc: "markers" - }, - paging: true, - scroller: true, - scrollY: "50vh", - scrollCollapse: true, - layout: { - top: "info", - topStart: null, - topEnd: null, - bottom: null, - bottomStart: null, - bottomEnd: null - } - }); - }); - -</script> -{%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)}} +<div class="row"> + <table class="table"> + <caption>Current genotype dataset</caption> + <tbody> + <tr> + <th>Name</th> + <td>{{dataset.Name}}</td> + </tr> + <tr> + <th>Full Name</th> + <td>{{dataset.FullName}}</td> + </tr> + <tr> + <th>Short Name</th> + <td>{{dataset.ShortName}}</td> + </tr> + </tbody> + </table> +</div> +{%endmacro%} |