diff options
| -rw-r--r-- | uploader/genotypes/views.py | 63 | ||||
| -rw-r--r-- | uploader/templates/genotypes/create-dataset.html | 10 | ||||
| -rw-r--r-- | uploader/templates/genotypes/list-genotypes.html | 73 | ||||
| -rw-r--r-- | uploader/templates/genotypes/select-population.html | 25 |
4 files changed, 101 insertions, 70 deletions
diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 0d8f983..3fa2131 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -1,5 +1,8 @@ """Views for the genotypes.""" +import logging + from MySQLdb.cursors import DictCursor +from pymonad.either import Left, Right, Either from gn_libs.mysqldb import database_connection from flask import (flash, request, @@ -25,6 +28,7 @@ from .models import (genotype_markers, genotype_markers_count, genocode_by_population) +logger = logging.getLogger(__name__) genotypesbp = Blueprint("genotypes", __name__) render_template = make_template_renderer("genotypes") @@ -126,21 +130,28 @@ def view_dataset(species_id: int, population_id: int, dataset_id: int): redirect_uri="species.populations.list_species_populations") def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable=[unused-argument] """Create a genotype dataset.""" + if request.method == "GET": + return render_template("genotypes/create-dataset.html", + species=species, + population=population, + activelink="create-dataset") + with (database_connection(app.config["SQL_URI"]) as conn, conn.cursor(cursorclass=DictCursor) as cursor): - if request.method == "GET": - return render_template("genotypes/create-dataset.html", - species=species, - population=population, - activelink="create-dataset") - - form = request.form - new_dataset = save_new_dataset( - cursor, - population["Id"], - form["geno-dataset-name"], - form["geno-dataset-fullname"], - form["geno-dataset-shortname"]) + + def __save_dataset__() -> Either: + form = request.form + try: + return Right(save_new_dataset( + cursor, + population["Id"], + form["geno-dataset-name"], + form["geno-dataset-fullname"], + form["geno-dataset-shortname"])) + except Exception: + msg = "Error adding new Genotype dataset to database." + logger.error(msg, exc_info=True) + return Left(Exception(msg)) def __success__(_success): flash("Successfully created genotype dataset.", "alert-success") @@ -149,18 +160,20 @@ def create_dataset(species: dict, population: dict, **kwargs):# pylint: disable= species_id=species["SpeciesId"], population_id=population["Id"])) - return oauth2_post( - "auth/resource/genotypes/create", - json={ - **dict(request.form), - "species_id": species["SpeciesId"], - "population_id": population["Id"], - "dataset_id": new_dataset["Id"], - "dataset_name": form["geno-dataset-name"], - "dataset_fullname": form["geno-dataset-fullname"], - "dataset_shortname": form["geno-dataset-shortname"], - "public": "on" - } + return __save_dataset__().then( + lambda new_dataset: oauth2_post( + "auth/resource/genotypes/create", + json={ + **dict(request.form), + "species_id": species["SpeciesId"], + "population_id": population["Id"], + "dataset_id": new_dataset["Id"], + "dataset_name": new_dataset["Name"], + "dataset_fullname": new_dataset["FullName"], + "dataset_shortname": new_dataset["ShortName"], + "public": "on" + } + ) ).either( make_either_error_handler( "There was an error creating the genotype dataset."), diff --git a/uploader/templates/genotypes/create-dataset.html b/uploader/templates/genotypes/create-dataset.html index 10331c1..5a6d3d2 100644 --- a/uploader/templates/genotypes/create-dataset.html +++ b/uploader/templates/genotypes/create-dataset.html @@ -35,7 +35,9 @@ id="txt-geno-dataset-name" name="geno-dataset-name" required="required" - class="form-control" /> + class="form-control" + value="{{population.Name}}Geno" + readonly="readonly" /> <small class="form-text text-muted"> <p>This is a short representative, but constrained name for the genotype dataset.<br /> @@ -50,7 +52,8 @@ id="txt-geno-dataset-fullname" name="geno-dataset-fullname" required="required" - class="form-control" /> + class="form-control" + value="{{population.Name}} Genotypes" /> <small class="form-text text-muted"> <p>This is a longer, more descriptive name for your dataset.</p></small> </div> @@ -61,7 +64,8 @@ <input type="text" id="txt-geno-dataset-shortname" name="geno-dataset-shortname" - class="form-control" /> + class="form-control" + value="{{population.Name}}Geno" /> <small class="form-text text-muted"> <p>A short name for your dataset. If you leave this field blank, the short name will be set to the same value as the diff --git a/uploader/templates/genotypes/list-genotypes.html b/uploader/templates/genotypes/list-genotypes.html index a2b98c8..be297a4 100644 --- a/uploader/templates/genotypes/list-genotypes.html +++ b/uploader/templates/genotypes/list-genotypes.html @@ -9,19 +9,6 @@ {{flash_all_messages()}} <div class="row"> - <h2>Genetic Markers</h2> - <p>There are a total of {{total_markers}} currently registered genetic markers - for the "{{species.FullName}}" species. You can click - <a href="{{url_for('species.populations.genotypes.list_markers', - species_id=species.SpeciesId, - population_id=population.Id)}}" - title="View genetic markers for species '{{species.FullName}}"> - this link to view the genetic markers - </a>. - </p> -</div> - -<div class="row"> <h2>Genotype Encoding</h2> <p> The genotype encoding used for the "{{population.FullName}}" population from @@ -56,14 +43,47 @@ </table> {%if genocode | length < 1%} - <a href="#add-genotype-encoding" - title="Add a genotype encoding system for this population" - class="btn btn-primary not-implemented"> - add genotype encoding + <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 class="subheading">Genetic Markers</h2> + + <table id="tbl-genetic-markers" class="table compact stripe cell-border" + data-genetic-markers='{{genetic_markers | tojson}}'> + <thead> + <tr> + <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> + </tr> + {%endfor%} + </tbody> + </table> +</div> + <div class="row text-danger"> <h3>Some Important Concepts to Consider/Remember</h3> <ul> @@ -130,3 +150,22 @@ all the rest.</p> </div> {%endblock%} + + +{%block javascript%} +<script type="text/javascript"> + $(function() { + var dtGeneticMarkers = buildDataTable( + "#tbl-genetic-markers", + JSON.parse($("#tbl-genetic-markers").attr("data-genetic-markers")), + [ + {data: 'index'}, + {data: 'Name'}, + {data: 'Chr'}, + {data: 'Mb'}, + {data: 'Source'}, + {data: 'Source2'} + ]); + }) +</script> +{%endblock%} diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html deleted file mode 100644 index acdd063..0000000 --- a/uploader/templates/genotypes/select-population.html +++ /dev/null @@ -1,25 +0,0 @@ -{%extends "genotypes/base.html"%} -{%from "flash_messages.html" import flash_all_messages%} -{%from "species/macro-display-species-card.html" import display_species_card%} -{%from "populations/macro-select-population.html" import select_population_form%} - -{%block title%}Genotypes{%endblock%} - -{%block pagetitle%}Genotypes{%endblock%} - - -{%block contents%} -{{flash_all_messages()}} - -<div class="row"> - {{select_population_form(url_for("species.populations.genotypes.select_population", species_id=species.SpeciesId), species, populations)}} -</div> -{%endblock%} - -{%block sidebarcontents%} -{{display_species_card(species)}} -{%endblock%} - -{%block javascript%} -<script type="text/javascript" src="/static/js/populations.js"></script> -{%endblock%} |