diff options
| -rw-r--r-- | uploader/phenotypes/models.py | 31 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 17 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/view-dataset.html | 82 |
3 files changed, 129 insertions, 1 deletions
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py index 1f72dbd..4ef674f 100644 --- a/uploader/phenotypes/models.py +++ b/uploader/phenotypes/models.py @@ -20,3 +20,34 @@ def datasets_by_population( "WHERE s.Id=%s AND iset.Id=%s;", (species_id, population_id)) return tuple(dict(row) for row in cursor.fetchall()) + + +def phenotypes_data(conn: mdb.Connection, + population_id: int, + dataset_id: int, + offset: int = 0, + limit: Optional[int] = None) -> tuple[dict, ...]: + """Fetch the data for the phenotypes.""" + #TODO: This query isn't exactly right, it misses some data. + # — Phenotype -> PublishXRef -> PublishData -> Strain -> PublishFreeze + _query = ("SELECT pxr.*, pd.*, str.* FROM PublishFreeze AS pf " + "INNER JOIN PublishXRef AS pxr ON pf.InbredSetId=pxr.InbredSetId " + "INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id " + "INNER JOIN Strain AS str ON pd.StrainId=str.Id " + "WHERE pf.InbredSetId=%s AND pf.Id=%s " + "ORDER BY pxr.DataId ASC, str.Id ASC") + ( + f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "") + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute(_query, (population_id, dataset_id)) + debug_query(cursor) + return tuple(dict(row) for row in cursor.fetchall()) + + +def phenotypes_se(conn: mdb.Connection, dataset_id: int) -> tuple[dict, ...]: + """Fetch the standard errors for the phenotypes.""" + return tuple() + + +def phenotypes_sample_counts(conn: mdb.Connection, dataset_id: int) -> tuple[dict, ...]: + """Fetch the standard errors for the phenotypes.""" + return tuple() diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 7ad32ad..88cb89c 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -14,7 +14,7 @@ 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 +from .models import datasets_by_population, phenotypes_data phenotypesbp = Blueprint("phenotypes", __name__) @@ -83,3 +83,18 @@ def list_datasets(species: int, population: int, **kwargs): species["SpeciesId"], population["Id"]), activelink="list-datasets") + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/view", + methods=["GET"]) +@require_login +@with_population(species_redirect_uri="species.populations.phenotypes.index", + redirect_uri="species.populations.phenotypes.select_population") +def view_dataset(species: int, population: int, dataset_id: int, **kwargs): + """View a specific dataset""" + with database_connection(app.config["SQL_URI"]) as conn: + from flask import jsonify + return jsonify(phenotypes_data( + conn, population["Id"], dataset_id, offset=0, limit=20)) diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html new file mode 100644 index 0000000..219e61e --- /dev/null +++ b/uploader/templates/phenotypes/view-dataset.html @@ -0,0 +1,82 @@ +{%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=="view-datasets"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('species.populations.phenotypes.view_datasets', + species_id=species.SpeciesId, + population_id=population.Id)}}">View Datasets</a> +</li> +{%endblock%} + +{%block contents%} +{{flash_all_messages()}} + +<div class="row"> + <p>The basic dataset details are:</p> + + <table class="table"> + <thead> + <tr> + <th>Name</th> + <th>Full Name</th> + <th>Short Name</th> + </tr> + </thead> + + <tbody> + <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> + </tbody> + </table> +</div> + +<div class="row"> + <h2>Phenotype Data</h2> + + <p>The dataset has the following phenotypes:</p> + + <table class="table"> + <thead> + <tr> + <th>#</th> + <th>Name</th> + <th>Full Name</th> + <th>Short Name</th> + </tr> + </thead> + + <tbody> + {%for pheno in phenotypes%} + <tr> + <td>{{pheno.sequence_number}}</td> + <td>{{pheno.Id}}</td> + <td>{{pheno.FullName}}</td> + <td>{{pheno.ShortName}}</td> + </tr> + {%else%} + <tr><td colspan="5"></td></tr> + {%endfor%} + </tbody> + </table> +</div> +{%endblock%} + +{%block sidebarcontents%} +{{display_population_card(species, population)}} +{%endblock%} |