diff options
| -rw-r--r-- | uploader/phenotypes/models.py | 22 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 22 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/list-datasets.html | 63 |
3 files changed, 107 insertions, 0 deletions
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py new file mode 100644 index 0000000..1f72dbd --- /dev/null +++ b/uploader/phenotypes/models.py @@ -0,0 +1,22 @@ +"""Database and utility functions for phenotypes.""" +from typing import Optional + +import MySQLdb as mdb +from MySQLdb.cursors import DictCursor + +from uploader.db_utils import debug_query + +def datasets_by_population( + conn: mdb.Connection, + species_id: int, + population_id: int +) -> tuple[dict, ...]: + """Retrieve all of a population's phenotype studies.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT s.SpeciesId, pf.* FROM Species AS s " + "INNER JOIN InbredSet AS iset ON s.Id=iset.SpeciesId " + "INNER JOIN PublishFreeze AS pf ON iset.Id=pf.InbredSetId " + "WHERE s.Id=%s AND iset.Id=%s;", + (species_id, population_id)) + return tuple(dict(row) for row in cursor.fetchall()) diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 9185f4c..7ad32ad 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -14,6 +14,8 @@ from uploader.request_checks import with_species, with_population from uploader.population.models import (populations_by_species, population_by_species_and_id) +from .models import datasets_by_population + phenotypesbp = Blueprint("phenotypes", __name__) @phenotypesbp.route("/phenotypes", methods=["GET"]) @@ -61,3 +63,23 @@ def select_population(species: dict, **kwargs): return redirect(url_for("species.populations.phenotypes.list_datasets", species_id=species["SpeciesId"], population_id=population["Id"])) + + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets", + methods=["GET"]) +@require_login +@with_population(species_redirect_uri="species.populations.phenotypes.index", + redirect_uri="species.populations.phenotypes.select_population") +def list_datasets(species: int, population: int, **kwargs): + """List available phenotype datasets.""" + with database_connection(app.config["SQL_URI"]) as conn: + return render_template("phenotypes/list-datasets.html", + species=species, + population=population, + datasets=datasets_by_population( + conn, + species["SpeciesId"], + population["Id"]), + activelink="list-datasets") diff --git a/uploader/templates/phenotypes/list-datasets.html b/uploader/templates/phenotypes/list-datasets.html new file mode 100644 index 0000000..360fd2c --- /dev/null +++ b/uploader/templates/phenotypes/list-datasets.html @@ -0,0 +1,63 @@ +{%extends "phenotypes/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "populations/macro-display-population-card.html" import display_population_card%} + +{%block title%}Phenotypes{%endblock%} + +{%block pagetitle%}Phenotypes{%endblock%} + +{%block lvl4_breadcrumbs%} +<li {%if activelink=="list-datasets"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.list_datasets', + species_id=species.SpeciesId, + population_id=population.Id)}}">List Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + {%if datasets | length > 0%} + <p>The dataset(s) available for this population is/are:</p> + + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + <th>Short Name</th> + </tr> + </thead> + + <tbody> + {%for dataset in datasets%} + <tr> + <td><a href="{{url_for('species.populations.phenotypes.view_dataset', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}">{{dataset.Name}}</a></td> + <td>{{dataset.FullName}}</td> + <td>{{dataset.ShortName}}</td> + </tr> + {%endfor%} + </tbody> + </table> + {%else%} + <p class="text-warning"> + <span class="glyphicon glyphicon-exclamation-sign"></span> + There is no dataset for this population!</p> + <p><a href="#" + class="not-implemented btn btn-primary" + title="Create a new phenotype dataset.">create dataset</a></p> + {%endif%} +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} |