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-rw-r--r--uploader/input_validation.py21
-rw-r--r--uploader/phenotypes/models.py28
-rw-r--r--uploader/phenotypes/views.py54
-rw-r--r--uploader/static/css/styles.css6
-rw-r--r--uploader/templates/phenotypes/create-dataset.html106
-rw-r--r--uploader/templates/phenotypes/list-datasets.html6
6 files changed, 219 insertions, 2 deletions
diff --git a/uploader/input_validation.py b/uploader/input_validation.py
index 88ffd8c..b84fca6 100644
--- a/uploader/input_validation.py
+++ b/uploader/input_validation.py
@@ -1,6 +1,11 @@
"""Input validation utilities"""
+import re
+import json
+import base64
from typing import Any
+from flask import request
+
def is_empty_string(value: str) -> bool:
"""Check whether as string is empty"""
return (isinstance(value, str) and value.strip() == "")
@@ -50,3 +55,19 @@ def is_valid_representative_name(repr_name: str) -> bool:
"""
pattern = re.compile(r"^[a-zA-Z]+[a-zA-Z0-9_-]*[a-zA-Z0-9]$")
return bool(pattern.match(repr_name))
+
+
+def encode_errors(errors: tuple[tuple[str, str], ...], form) -> str:
+ """Encode form errors into base64 string."""
+ return base64.b64encode(
+ json.dumps({
+ "errors": dict(errors),
+ "original_formdata": dict(form)
+ }).encode("utf8"))
+
+
+def decode_errors(errorstr) -> dict[str, dict]:
+ """Decode errors from base64 string"""
+ if not bool(errorstr):
+ return {"errors": {}, "original_formdata": {}}
+ return json.loads(base64.b64decode(errorstr.encode("utf8")).decode("utf8"))
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py
index be970ac..9324601 100644
--- a/uploader/phenotypes/models.py
+++ b/uploader/phenotypes/models.py
@@ -1,6 +1,7 @@
"""Database and utility functions for phenotypes."""
from typing import Optional
from functools import reduce
+from datetime import datetime
import MySQLdb as mdb
from MySQLdb.cursors import Cursor, DictCursor
@@ -202,3 +203,30 @@ def phenotypes_data(conn: mdb.Connection,
cursor.execute(_query, (population_id, dataset_id))
debug_query(cursor)
return tuple(dict(row) for row in cursor.fetchall())
+
+
+def save_new_dataset(cursor: Cursor,
+ population_id: int,
+ dataset_name: str,
+ dataset_fullname: str,
+ dataset_shortname: str) -> dict:
+ """Create a new phenotype dataset."""
+ params = {
+ "population_id": population_id,
+ "dataset_name": dataset_name,
+ "dataset_fullname": dataset_fullname,
+ "dataset_shortname": dataset_shortname,
+ "created": datetime.now().date().isoformat(),
+ "public": 2,
+ "confidentiality": 0,
+ "users": None
+ }
+ cursor.execute(
+ "INSERT INTO PublishFreeze(Name, FullName, ShortName, CreateTime, "
+ "public, InbredSetId, confidentiality, AuthorisedUsers) "
+ "VALUES(%(dataset_name)s, %(dataset_fullname)s, %(dataset_shortname)s, "
+ "%(created)s, %(public)s, %(population_id)s, %(confidentiality)s, "
+ "%(users)s)",
+ params)
+ debug_query(cursor)
+ return {**params, "Id": cursor.lastrowid}
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 47fbd51..c7bc965 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -1,6 +1,7 @@
"""Views handling ('classical') phenotypes."""
from functools import wraps
+from MySQLdb.cursors import DictCursor
from flask import (flash,
request,
url_for,
@@ -18,10 +19,14 @@ from uploader.request_checks import with_species, with_population
from uploader.datautils import safe_int, order_by_family, enumerate_sequence
from uploader.population.models import (populations_by_species,
population_by_species_and_id)
+from uploader.input_validation import (encode_errors,
+ decode_errors,
+ is_valid_representative_name)
from .models import (dataset_by_id,
phenotype_by_id,
phenotypes_count,
+ save_new_dataset,
dataset_phenotypes,
datasets_by_population)
@@ -222,3 +227,52 @@ def view_phenotype(# pylint: disable=[unused-argument]
make_either_error_handler(
"There was an error fetching the roles and privileges."),
lambda resp: resp)
+
+
+@phenotypesbp.route(
+ "<int:species_id>/populations/<int:population_id>/phenotypes/datasets/create",
+ methods=["GET", "POST"])
+@require_login
+@with_population(
+ species_redirect_uri="species.populations.phenotypes.index",
+ redirect_uri="species.populations.phenotypes.select_population")
+def create_dataset(species: dict, population: dict, **kwargs):
+ """Create a new phenotype dataset."""
+ with (database_connection(app.config["SQL_URI"]) as conn,
+ conn.cursor(cursorclass=DictCursor) as cursor):
+ if request.method == "GET":
+ return render_template("phenotypes/create-dataset.html",
+ activelink="create-dataset",
+ species=species,
+ population=population,
+ **decode_errors(
+ request.args.get("error_values", "")))
+
+ form = request.form
+ _errors = tuple()
+ if not is_valid_representative_name(
+ (form.get("dataset-name") or "").strip()):
+ _errors = _errors + (("dataset-name", "Invalid dataset name."),)
+
+ if not bool((form.get("dataset-fullname") or "").strip()):
+ _errors = _errors + (("dataset-fullname",
+ "You must provide a value for 'Full Name'."),)
+
+ if bool(_errors) > 0:
+ return redirect(url_for(
+ "species.populations.phenotypes.create_dataset",
+ species_id=species["SpeciesId"],
+ population_id=population["Id"],
+ error_values=encode_errors(_errors, form)))
+
+ dataset_shortname = (
+ form["dataset-shortname"] or form["dataset-name"]).strip()
+ pheno_dataset = save_new_dataset(
+ cursor,
+ population["Id"],
+ form["dataset-name"].strip(),
+ form["dataset-fullname"].strip(),
+ dataset_shortname)
+ return redirect(url_for("species.populations.phenotypes.list_datasets",
+ species_id=species["SpeciesId"],
+ population_id=population["Id"]))
diff --git a/uploader/static/css/styles.css b/uploader/static/css/styles.css
index 574f53e..0e9a029 100644
--- a/uploader/static/css/styles.css
+++ b/uploader/static/css/styles.css
@@ -125,3 +125,9 @@ input[type="submit"], .btn {
border-color: #AAAAAA;
background-color: #EFEFEF;
}
+
+.danger {
+ color: #A94442;
+ border-color: #DCA7A7;
+ background-color: #F2DEDE;
+}
diff --git a/uploader/templates/phenotypes/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html
new file mode 100644
index 0000000..93de92f
--- /dev/null
+++ b/uploader/templates/phenotypes/create-dataset.html
@@ -0,0 +1,106 @@
+{%extends "phenotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "macro-table-pagination.html" import table_pagination%}
+{%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=="create-dataset"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.phenotypes.create_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}">Create Datasets</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <p>Create a new phenotype dataset.</p>
+</div>
+
+<div class="row">
+ <form id="frm-create-pheno-dataset"
+ action="{{url_for('species.populations.phenotypes.create_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}"
+ method="POST">
+
+ <div class="form-group">
+ <label class="form-label" for="txt-dataset-name">Name</label>
+ {%if errors["dataset-name"] is defined%}
+ <small class="form-text text-muted danger">
+ <p>{{errors["dataset-name"]}}</p></small>
+ {%endif%}
+ <input type="text"
+ name="dataset-name"
+ id="txt-dataset-name"
+ value="{{original_formdata.get('dataset-name') or (population.InbredSetCode + 'Publish')}}"
+ {%if errors["dataset-name"] is defined%}
+ class="form-control danger"
+ {%else%}
+ class="form-control"
+ {%endif%}
+ required="required" />
+ <small class="form-text text-muted">
+ <p>A short representative name for the dataset.</p>
+ <p>Recommended: Use the population code and append "Publish" at the end.
+ <br />This field will only accept names composed of
+ letters ('A-Za-z'), numbers (0-9), hyphens and underscores.</p>
+ </small>
+ </div>
+
+ <div class="form-group">
+ <label class="form-label" for="txt-dataset-fullname">Full Name</label>
+ {%if errors["dataset-fullname"] is defined%}
+ <small class="form-text text-muted danger">
+ <p>{{errors["dataset-fullname"]}}</p></small>
+ {%endif%}
+ <input id="txt-dataset-fullname"
+ name="dataset-fullname"
+ type="text"
+ value="{{original_formdata.get('dataset-fullname', '')}}"
+ {%if errors["dataset-fullname"] is defined%}
+ class="form-control danger"
+ {%else%}
+ class="form-control"
+ {%endif%}
+ required="required" />
+ <small class="form-text text-muted">
+ <p>A longer, descriptive name for the dataset &mdash; useful for humans.
+ </p></small>
+ </div>
+
+ <div class="form-group">
+ <label class="form-label" for="txt-dataset-shortname">Short Name</label>
+ <input id="txt-dataset-shortname"
+ name="dataset-shortname"
+ type="text"
+ class="form-control"
+ value="{{original_formdata.get('dataset-shortname') or (population.InbredSetCode + ' Publish')}}" />
+ <small class="form-text text-muted">
+ <p>An optional, short name for the dataset. <br />
+ If this is not provided, it will default to the value provided for the
+ <strong>Name</strong> field above.</p></small>
+ </div>
+
+ <div class="form-group">
+ <input type="submit"
+ class="btn btn-primary"
+ value="create phenotype dataset" />
+ </div>
+
+ </form>
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}
diff --git a/uploader/templates/phenotypes/list-datasets.html b/uploader/templates/phenotypes/list-datasets.html
index 360fd2c..2eaf43a 100644
--- a/uploader/templates/phenotypes/list-datasets.html
+++ b/uploader/templates/phenotypes/list-datasets.html
@@ -51,8 +51,10 @@
<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"
+ <p><a href="{{url_for('species.populations.phenotypes.create_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}"
+ class="btn btn-primary"
title="Create a new phenotype dataset.">create dataset</a></p>
{%endif%}
</div>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-05 16:30:49 +0000