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-rw-r--r--uploader/__init__.py2
-rw-r--r--uploader/dbinsert.py1
-rw-r--r--uploader/expression_data/index.py2
-rw-r--r--uploader/expression_data/rqtl2.py1
-rw-r--r--uploader/expression_data/samples.py1
-rw-r--r--uploader/species/__init__.py2
-rw-r--r--uploader/species/models.py (renamed from uploader/db/species.py)4
-rw-r--r--uploader/species/views.py91
-rw-r--r--uploader/templates/base.html10
-rw-r--r--uploader/templates/species/base.html11
-rw-r--r--uploader/templates/species/create-species.html116
-rw-r--r--uploader/templates/species/list-species.html68
12 files changed, 305 insertions, 4 deletions
diff --git a/uploader/__init__.py b/uploader/__init__.py
index 941765d..347f170 100644
--- a/uploader/__init__.py
+++ b/uploader/__init__.py
@@ -10,6 +10,7 @@ from flask_session import Session
from uploader.oauth2.client import user_logged_in, authserver_authorise_uri
from .base_routes import base
+from .species import speciesbp
from .dbinsert import dbinsertbp
from .oauth2.views import oauth2
from .expression_data import exprdatabp
@@ -81,6 +82,7 @@ def create_app():
# setup blueprints
app.register_blueprint(base, url_prefix="/")
app.register_blueprint(oauth2, url_prefix="/oauth2")
+ app.register_blueprint(speciesbp, url_prefix="/species")
app.register_blueprint(dbinsertbp, url_prefix="/dbinsert")
app.register_blueprint(exprdatabp, url_prefix="/expression-data")
diff --git a/uploader/dbinsert.py b/uploader/dbinsert.py
index 559dc5e..328ccc8 100644
--- a/uploader/dbinsert.py
+++ b/uploader/dbinsert.py
@@ -14,6 +14,7 @@ from flask import (
from uploader.authorisation import require_login
from uploader.db_utils import with_db_connection, database_connection
from uploader.db import species, species_by_id, populations_by_species
+from uploader.species.models import species_by_id, all_species as species
from . import jobs
diff --git a/uploader/expression_data/index.py b/uploader/expression_data/index.py
index 799989e..db23136 100644
--- a/uploader/expression_data/index.py
+++ b/uploader/expression_data/index.py
@@ -14,7 +14,7 @@ from flask import (
render_template,
current_app as app)
-from uploader.db import species
+from uploader.species.models import all_species as species
from uploader.authorisation import require_login
from uploader.db_utils import with_db_connection
diff --git a/uploader/expression_data/rqtl2.py b/uploader/expression_data/rqtl2.py
index 48df66c..975fc1f 100644
--- a/uploader/expression_data/rqtl2.py
+++ b/uploader/expression_data/rqtl2.py
@@ -41,6 +41,7 @@ from uploader.db import (
save_population,
populations_by_species,
population_by_species_and_id,)
+from uploader.species.models import species_by_id
from uploader.db.datasets import (
geno_dataset_by_id,
geno_datasets_by_species_and_population,
diff --git a/uploader/expression_data/samples.py b/uploader/expression_data/samples.py
index 95b9b73..0715d14 100644
--- a/uploader/expression_data/samples.py
+++ b/uploader/expression_data/samples.py
@@ -34,6 +34,7 @@ from uploader.db import (
population_by_id,
populations_by_species,
species as fetch_species)
+from uploader.species.models import species_by_id, all_species as fetch_species
samples = Blueprint("samples", __name__)
diff --git a/uploader/species/__init__.py b/uploader/species/__init__.py
new file mode 100644
index 0000000..83f2165
--- /dev/null
+++ b/uploader/species/__init__.py
@@ -0,0 +1,2 @@
+"""Package to handle creation and management of species."""
+from .views import speciesbp
diff --git a/uploader/db/species.py b/uploader/species/models.py
index 653e59b..98337a3 100644
--- a/uploader/db/species.py
+++ b/uploader/species/models.py
@@ -2,12 +2,12 @@
import MySQLdb as mdb
from MySQLdb.cursors import DictCursor
-def species(conn: mdb.Connection) -> tuple:
+def all_species(conn: mdb.Connection) -> tuple:
"Retrieve the species from the database."
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName, "
- "FullName FROM Species")
+ "FullName, TaxonomyId FROM Species")
return tuple(cursor.fetchall())
return tuple()
diff --git a/uploader/species/views.py b/uploader/species/views.py
new file mode 100644
index 0000000..af66de3
--- /dev/null
+++ b/uploader/species/views.py
@@ -0,0 +1,91 @@
+"""Endpoints handling species."""
+from flask import (flash,
+ request,
+ url_for,
+ redirect,
+ Blueprint,
+ current_app as app,
+ render_template as flask_render_template)
+
+from uploader.db_utils import database_connection
+
+from .models import all_species, save_species, species_by_id
+
+
+speciesbp = Blueprint("species", __name__)
+
+
+def render_template(template, **kwargs):
+ """Render template for species."""
+ return flask_render_template(template, **kwargs, activelink="species")
+
+
+@speciesbp.route("/", methods=["GET"])
+def list_species():
+ """List and display all the species in the database."""
+ with database_connection(app.config["SQL_URI"]) as conn:
+ return render_template("species/list-species.html",
+ allspecies=all_species(conn))
+
+@speciesbp.route("/<int:species_id>", methods=["GET"])
+def view_species(species_id: int):
+ """View details of a particular species and menus to act upon it."""
+ with database_connection(app.config["SQL_URI"]) as conn:
+ return species_by_id(conn, species_id)
+
+@speciesbp.route("/create", methods=["GET", "POST"])
+def create_species():
+ """Create a new species."""
+ # We can use uniprot's API to fetch the details with something like
+ # https://rest.uniprot.org/taxonomy/<taxonID> e.g.
+ # https://rest.uniprot.org/taxonomy/6239
+ if request.method == "GET":
+ return render_template("species/create-species.html")
+
+ with (database_connection(app.config["SQL_URI"]) as conn,
+ conn.cursor() as cursor):
+ error = False
+ taxon_id = request.form.get("taxon_id", "").strip() or None
+
+ common_name = request.form.get("common_name", "").strip()
+ if not bool(common_name):
+ flash("The common species name MUST be provided.", "alert-danger")
+ error = True
+
+ scientific_name = request.form.get("scientific_name", "").strip()
+ if not bool(scientific_name):
+ flash("The species' scientific name MUST be provided.",
+ "alert-danger")
+ error = True
+
+ parts = tuple(name.strip() for name in scientific_name.split(" "))
+ if len(parts) != 2 or not all(bool(name) for name in parts):
+ flash("The scientific name you provided is invalid.", "alert-danger")
+ error = True
+
+ cursor.execute(
+ "SELECT * FROM Species WHERE FullName=%s", (scientific_name,))
+ res = cursor.fetchone()
+ if bool(res):
+ flash("A species already exists with the provided scientific name.",
+ "alert-danger")
+ error = True
+
+ if bool(taxon_id):
+ cursor.execute(
+ "SELECT * FROM Species WHERE TaxonomyId=%s", (taxon_id,))
+ res = cursor.fetchone()
+ if bool(res):
+ flash("A species already exists with the provided scientific name.",
+ "alert-danger")
+ error = True
+
+ if error:
+ return redirect(url_for("species.create_species",
+ common_name=common_name,
+ scientific_name=scientific_name,
+ taxon_id=taxon_id))
+
+ species = save_species(conn, common_name, scientific_name, taxon_id)
+ flash("Species saved successfully!", "alert-success")
+ return redirect(url_for("species.view_species", species_id=species["species_id"]))
diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index 58227f4..7431767 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -44,6 +44,7 @@
<aside id="nav-sidebar" class="container-fluid">
<ul class="nav flex-column">
<li><a href="/" >Home</a></li>
+ <li><a href="{{url_for('species.list_species')}}" >Species</a></li>
<li><a href="{{url_for('expression-data.index.index')}}" >Expression Data</a></li>
</ul>
</aside>
@@ -54,7 +55,14 @@
<h1>GN Uploader: {%block pagetitle%}{%endblock%}</h1>
<nav>
<ol class="breadcrumb">
- {%block breadcrumb%}{%endblock%}
+ <li {%if activelink is not defined or activelink=="home"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('base.index')}}">Home</a>
+ </li>
+ {%block breadcrumbs%}{%endblock%}
</ol>
</nav>
</div>
diff --git a/uploader/templates/species/base.html b/uploader/templates/species/base.html
new file mode 100644
index 0000000..b77cc8b
--- /dev/null
+++ b/uploader/templates/species/base.html
@@ -0,0 +1,11 @@
+{%extends "base.html"%}
+
+{%block breadcrumbs%}
+<li {%if activelink=="species"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.list_species')}}">Species</a>
+</li>
+{%endblock%}
diff --git a/uploader/templates/species/create-species.html b/uploader/templates/species/create-species.html
new file mode 100644
index 0000000..b96e2d3
--- /dev/null
+++ b/uploader/templates/species/create-species.html
@@ -0,0 +1,116 @@
+{%extends "species/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Create Species{%endblock%}
+
+{%block pagetitle%}Create Species{%endblock%}
+
+{%block breadcrumbs%}
+<li {%if activelink=="create-species"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.create_species')}}">Species</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+<div class="row">
+ <form id="frm-create-species"
+ method="POST"
+ action="{{url_for('species.create_species')}}">
+ <legend>Create Species</legend>
+
+ {{flash_all_messages()}}
+
+ <div class="form-group">
+ <label for="txt-taxonomy-id" class="form-label">
+ Taxonomy ID</label>
+ <div class="input-group">
+ <input id="txt-taxonomy-id"
+ name="species_taxonomy_id"
+ type="text"
+ class="form-control" />
+ <span class="input-group-btn">
+ <button id="btn-search-taxonid" class="btn btn-info">Search</button>
+ </span>
+ </div>
+ <small class="form-text text-small text-muted">Provide the taxonomy ID for
+ your species that can be used to link to external sites like NCBI. Enter
+ the taxonomy ID and click "Search" to auto-fill the form with data.
+ <br />
+ While it is recommended to provide a value for this field, doing so is
+ optional.
+ </small>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-species-name" class="form-label">Common Name</label>
+ <input id="txt-species-name"
+ name="common_name"
+ type="text"
+ class="form-control"
+ required="required" />
+ <small class="form-text text-muted">Provide the common, possibly
+ non-scientific name for the species here, e.g. Human, Mouse, etc.</small>
+ </div>
+
+ <div class="form-group">
+ <label for="txt-species-scientific" class="form-label">
+ Scientific Name</label>
+ <input id="txt-species-scientific"
+ name="scientific_name"
+ type="text"
+ class="form-control"
+ required="required" />
+ <small class="form-text text-muted">Provide the scientific name for the
+ species you are creating, e.g. Homo sapiens, Mus musculus, etc.</small>
+ </div>
+
+ <div class="form-group">
+ <input type="submit"
+ value="create new species"
+ class="btn btn-primary" />
+ </div>
+
+ </form>
+</div>
+{%endblock%}
+
+{%block javascript%}
+<script>
+ var lastTaxonId = null;
+
+ var fetch_taxonomy = (taxonId) => {
+ var uri = (
+ "https://rest.uniprot.org/taxonomy/" + encodeURIComponent(taxonId));
+ $.get(
+ uri,
+ {},
+ (data, textStatus, jqXHR) => {
+ if(textStatus == "success") {
+ lastTaxonId = taxonId;
+ $("#txt-species-scientific").val(data.scientificName);
+ $("#txt-species-name").val(data.commonName);
+ return false;
+ }
+ msg = (
+ "Request to '${uri}' failed with message '${textStatus}'. "
+ + "Please try again later, or fill the details manually.");
+ alert(msg);
+ console.error(msg, data, textStatus);
+ return false;
+ },
+ "json");
+ };
+
+ $("#btn-search-taxonid").on("click", (event) => {
+ event.preventDefault();
+ taxonId = $("#txt-taxonomy-id").val();
+ if((taxonId !== "") && (taxonId !== lastTaxonId)) {
+ fetch_taxonomy(taxonId);
+ }
+ });
+</script>
+{%endblock%}
diff --git a/uploader/templates/species/list-species.html b/uploader/templates/species/list-species.html
new file mode 100644
index 0000000..42094c1
--- /dev/null
+++ b/uploader/templates/species/list-species.html
@@ -0,0 +1,68 @@
+{%extends "species/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}List Species{%endblock%}
+
+{%block pagetitle%}List Species{%endblock%}
+
+{%block contents%}
+<div class="row">
+ <p>
+ All data in GeneNetwork revolves around species. This is the core of the
+ system.</p>
+ <p>Here you can see a list of all the species available in GeneNetwork.
+ Click on the link besides each species to view greater detail on the species,
+ and access further operations that are possible for said species.</p>
+</div>
+
+<div class="row">
+ <p>If you cannot find the species you are looking for below, click the button
+ below to create it</p>
+ <p><a href="{{url_for('species.create_species')}}"
+ title="Add a new species to GeneNetwork"
+ class="btn btn-danger">Create Species</a></p>
+</div>
+
+<div class="row">
+ <table class="table">
+ <caption>Available Species</caption>
+ <thead>
+ <tr>
+ <th>Common Name</th>
+ <th>Scientific Name</th>
+ <th>TaxonId</th>
+ <th>Use</th>
+ </tr>
+ </thead>
+ <tbody>
+ {%for species in allspecies%}
+ <tr>
+ <td>{{species["SpeciesName"]}}</td>
+ <td>{{species["FullName"]}}</td>
+ <td>
+ <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={{species['TaxonomyId']}}"
+ title="View species details on NCBI"
+ target="_blank">{{species["TaxonomyId"]}}</a>
+ </td>
+ <td>
+ <a href="{{url_for('species.view_species',
+ species_id=species['SpeciesId'])}}"
+ title="">
+ {{species["SpeciesName"]}} ({{species["FullName"]}})
+ </a>
+ </td>
+ </tr>
+ {%else%}
+ <tr>
+ <td colspan="3">
+ <p class="text-danger">
+ <span class="glyphicon glyphicon-exclamation-mark"></span>
+ There were no species found!
+ </p>
+ </td>
+ </tr>
+ {%endfor%}
+ </tbody>
+ </table>
+</div>
+{%endblock%}
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-26 10:27:07 +0000