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-rw-r--r--uploader/datautils.py21
-rw-r--r--uploader/expression_data/__init__.py2
-rw-r--r--uploader/population/views.py2
-rw-r--r--uploader/samples/models.py19
-rw-r--r--uploader/samples/views.py (renamed from uploader/expression_data/samples.py)190
-rw-r--r--uploader/templates/base.html2
-rw-r--r--uploader/templates/populations/macro-display-population-card.html32
-rw-r--r--uploader/templates/populations/macro-select-population.html30
-rw-r--r--uploader/templates/populations/view-population.html6
-rw-r--r--uploader/templates/samples/base.html12
-rw-r--r--uploader/templates/samples/index.html21
-rw-r--r--uploader/templates/samples/list-samples.html114
-rw-r--r--uploader/templates/samples/select-population.html117
-rw-r--r--uploader/templates/samples/select-species.html30
-rw-r--r--uploader/templates/samples/upload-failure.html27
-rw-r--r--uploader/templates/samples/upload-progress.html22
-rw-r--r--uploader/templates/samples/upload-samples.html139
-rw-r--r--uploader/templates/samples/upload-success.html18
18 files changed, 371 insertions, 433 deletions
diff --git a/uploader/datautils.py b/uploader/datautils.py
new file mode 100644
index 0000000..b95a9e0
--- /dev/null
+++ b/uploader/datautils.py
@@ -0,0 +1,21 @@
+"""Generic data utilities: Rename module."""
+import math
+from functools import reduce
+
+def order_by_family(items: tuple[dict, ...],
+ family_key: str = "Family",
+ order_key: str = "FamilyOrderId") -> list:
+ """Order the populations by their families."""
+ def __family_order__(item):
+ orderval = item[order_key]
+ return math.inf if orderval is None else orderval
+
+ def __order__(ordered, current):
+ _key = (__family_order__(current), current[family_key])
+ return {
+ **ordered,
+ _key: ordered.get(_key, tuple()) + (current,)
+ }
+
+ return sorted(tuple(reduce(__order__, items, {}).items()),
+ key=lambda item: item[0][0])
diff --git a/uploader/expression_data/__init__.py b/uploader/expression_data/__init__.py
index b773bce..206a764 100644
--- a/uploader/expression_data/__init__.py
+++ b/uploader/expression_data/__init__.py
@@ -4,10 +4,8 @@ from flask import Blueprint
from .rqtl2 import rqtl2
from .index import indexbp
from .parse import parsebp
-from .samples import samples
exprdatabp = Blueprint("expression-data", __name__)
exprdatabp.register_blueprint(indexbp, url_prefix="/")
exprdatabp.register_blueprint(rqtl2, url_prefix="/rqtl2")
exprdatabp.register_blueprint(parsebp, url_prefix="/parse")
-exprdatabp.register_blueprint(samples, url_prefix="/sample")
diff --git a/uploader/population/views.py b/uploader/population/views.py
index 5be19ae..003787a 100644
--- a/uploader/population/views.py
+++ b/uploader/population/views.py
@@ -13,6 +13,7 @@ from flask import (flash,
from uploader.ui import make_template_renderer
from uploader.authorisation import require_login
from uploader.db_utils import database_connection
+from uploader.samples.views import samplesbp
from uploader.species.models import (all_species,
species_by_id,
order_species_by_family)
@@ -25,6 +26,7 @@ from .models import (save_population,
__active_link__ = "populations"
popbp = Blueprint("populations", __name__)
+popbp.register_blueprint(samplesbp, url_prefix="/")
render_template = make_template_renderer("populations")
diff --git a/uploader/samples/models.py b/uploader/samples/models.py
new file mode 100644
index 0000000..15e509e
--- /dev/null
+++ b/uploader/samples/models.py
@@ -0,0 +1,19 @@
+"""Functions for handling samples."""
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def samples_by_species_and_population(
+ conn: mdb.Connection,
+ species_id: int,
+ population_id: int
+) -> tuple[dict, ...]:
+ """Fetch the samples by their species and population."""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ "SELECT iset.InbredSetId, s.* FROM InbredSet AS iset "
+ "INNER JOIN StrainXRef AS sxr ON iset.InbredSetId=sxr.InbredSetId "
+ "INNER JOIN Strain AS s ON sxr.StrainId=s.Id "
+ "WHERE s.SpeciesId=%(species_id)s "
+ "AND iset.InbredSetId=%(population_id)s",
+ {"species_id": species_id, "population_id": population_id})
+ return tuple(cursor.fetchall())
diff --git a/uploader/expression_data/samples.py b/uploader/samples/views.py
index d430aa9..6af90f4 100644
--- a/uploader/expression_data/samples.py
+++ b/uploader/samples/views.py
@@ -22,124 +22,106 @@ from functional_tools import take
from uploader import jobs
from uploader.files import save_file
+from uploader.datautils import order_by_family
from uploader.authorisation import require_login
from uploader.input_validation import is_integer_input
from uploader.db_utils import (
with_db_connection,
database_connection,
with_redis_connection)
-from uploader.species.models import species_by_id, all_species as fetch_species
+from uploader.species.models import (all_species,
+ species_by_id,
+ order_species_by_family)
from uploader.population.models import(save_population,
population_by_id,
populations_by_species)
-samples = Blueprint("samples", __name__)
+from .models import samples_by_species_and_population
-@samples.route("/upload/species", methods=["GET", "POST"])
-@require_login
-def select_species():
- """Select the species."""
- if request.method == "GET":
- return render_template("samples/select-species.html",
- species=with_db_connection(fetch_species))
-
- index_page = redirect(url_for("expression-data.index.upload_file"))
- species_id = request.form.get("species_id")
- if bool(species_id):
- species_id = int(species_id)
- species = with_db_connection(
- lambda conn: species_by_id(conn, species_id))
- if bool(species):
- return redirect(url_for(
- "samples.select_population", species_id=species_id))
- flash("Invalid species selected!", "alert-error")
- flash("You need to select a species", "alert-error")
- return index_page
+samplesbp = Blueprint("samples", __name__)
+
+@samplesbp.route("/samples", methods=["GET"])
+def index():
+ """Direct entry-point for uploading/handling the samples."""
+ with database_connection(app.config["SQL_URI"]) as conn:
+ if not bool(request.args.get("species_id")):
+ return render_template(
+ "samples/index.html",
+ species=order_species_by_family(all_species(conn)),
+ activelink="samples")
+ species = species_by_id(conn, request.args.get("species_id"))
+ if not bool(species):
+ flash("No such species!", "alert-danger")
+ return redirect(url_for("species.populations.samples.index"))
+ return redirect(url_for("species.populations.samples.select_population",
+ species_id=species["SpeciesId"]))
-@samples.route("/upload/species/<int:species_id>/create-population",
- methods=["POST"])
-@require_login
-def create_population(species_id: int):
- """Create new grouping/population."""
- if not is_integer_input(species_id):
- flash("You did not provide a valid species. Please select one to "
- "continue.",
- "alert-danger")
- return redirect(url_for("expression-data.samples.select_species"))
- species = with_db_connection(lambda conn: species_by_id(conn, species_id))
- if not bool(species):
- flash("Species with given ID was not found.", "alert-danger")
- return redirect(url_for("expression-data.samples.select_species"))
- species_page = redirect(url_for("expression-data.samples.select_species"), code=307)
+@samplesbp.route("<int:species_id>/samples/select-population", methods=["GET"])
+def select_population(species_id: int):
+ """Select the population to use for the samples."""
with database_connection(app.config["SQL_URI"]) as conn:
species = species_by_id(conn, species_id)
- pop_name = request.form.get("inbredset_name", "").strip()
- pop_fullname = request.form.get("inbredset_fullname", "").strip()
-
if not bool(species):
- flash("Invalid species!", "alert-error error-create-population")
- return species_page
- if (not bool(pop_name)) or (not bool(pop_fullname)):
- flash("You *MUST* provide a grouping/population name",
- "alert-error error-create-population")
- return species_page
-
- pop = save_population(conn, {
- "SpeciesId": species["SpeciesId"],
- "Name": pop_name,
- "InbredSetName": pop_fullname,
- "FullName": pop_fullname,
- "Family": request.form.get("inbredset_family") or None,
- "Description": request.form.get("description") or None
- })
-
- flash("Grouping/Population created successfully.", "alert-success")
- return redirect(url_for("samples.upload_samples",
- species_id=species_id,
- population_id=pop["population_id"]))
+ flash("Invalid species!", "alert-danger")
+ return redirect(url_for("species.populations.samples.index"))
+
+ if not bool(request.args.get("population_id")):
+ return render_template("samples/select-population.html",
+ species=species,
+ populations=order_by_family(
+ populations_by_species(
+ conn,
+ species_id),
+ order_key="FamilyOrder"),
+ activelink="samples")
+
+ population = population_by_id(conn, request.args.get("population_id"))
+ if not bool(population):
+ flash("Population not found!", "alert-danger")
+ return redirect(url_for(
+ "species.populations.samples.select_population",
+ species_id=species_id))
-@samples.route("/upload/species/<int:species_id>/population",
- methods=["GET", "POST"])
-@require_login
-def select_population(species_id: int):
- """Select from existing groupings/populations."""
- if not is_integer_input(species_id):
- flash("You did not provide a valid species. Please select one to "
- "continue.",
- "alert-danger")
- return redirect(url_for("expression-data.samples.select_species"))
- species = with_db_connection(lambda conn: species_by_id(conn, species_id))
- if not bool(species):
- flash("Species with given ID was not found.", "alert-danger")
- return redirect(url_for("expression-data.samples.select_species"))
+ return redirect(url_for("species.populations.samples.list_samples",
+ species_id=species_id,
+ population_id=population["Id"]))
+
+@samplesbp.route("<int:species_id>/populations/<int:population_id>/samples")
+def list_samples(species_id: int, population_id: int):
+ """
+ List the samples in a particular population and give the ability to upload
+ new ones.
+ """
+ with database_connection(app.config["SQL_URI"]) as conn:
+ species = species_by_id(conn, species_id)
+ if not bool(species):
+ flash("Invalid species!", "alert-danger")
+ return redirect(url_for("species.populations.samples.index"))
- if request.method == "GET":
- return render_template(
- "samples/select-population.html",
- species=species,
- populations=with_db_connection(
- lambda conn: populations_by_species(conn, species_id)))
-
- population_page = redirect(url_for(
- "samples.select_population", species_id=species_id), code=307)
- _population_id = request.form.get("inbredset_id")
- if not is_integer_input(_population_id):
- flash("You did not provide a valid population. Please select one to "
- "continue.",
- "alert-danger")
- return population_page
- population = with_db_connection(
- lambda conn: population_by_id(conn, _population_id))
- if not bool(population):
- flash("Invalid grouping/population!",
- "alert-error error-select-population")
- return population_page
+ population = population_by_id(conn, population_id)
+ if not bool(population):
+ flash("Population not found!", "alert-danger")
+ return redirect(url_for(
+ "species.populations.samples.select_population",
+ species_id=species_id))
+
+ all_samples = samples_by_species_and_population(
+ conn, species_id, population_id)
+ total_samples = len(all_samples)
+ offset = int(request.args.get("from") or 0)
+ if offset < 0:
+ offset = 0
+ count = int(request.args.get("count") or 10)
+ return render_template("samples/list-samples.html",
+ species=species,
+ population=population,
+ samples=all_samples[offset:offset+count],
+ offset=offset,
+ count=count,
+ total_samples=total_samples,
+ activelink="list-samples")
- return redirect(url_for("samples.upload_samples",
- species_id=species_id,
- population_id=_population_id),
- code=307)
def read_samples_file(filepath, separator: str, firstlineheading: bool, **kwargs) -> Iterator[dict]:
"""Read the samples file."""
@@ -154,6 +136,7 @@ def read_samples_file(filepath, separator: str, firstlineheading: bool, **kwargs
for row in reader:
yield row
+
def save_samples_data(conn: mdb.Connection,
speciesid: int,
file_data: Iterator[dict]):
@@ -174,6 +157,7 @@ def save_samples_data(conn: mdb.Connection,
total += len(batch)
print(f"\tSaved {total} samples total so far.")
+
def cross_reference_samples(conn: mdb.Connection,
species_id: int,
population_id: int,
@@ -218,6 +202,7 @@ def cross_reference_samples(conn: mdb.Connection,
print(f"\t{total} total samples cross-referenced to the population "
"so far.")
+
def build_sample_upload_job(# pylint: disable=[too-many-arguments]
speciesid: int,
populationid: int,
@@ -233,7 +218,8 @@ def build_sample_upload_job(# pylint: disable=[too-many-arguments]
f"--quotechar={quotechar}"
] + (["--firstlineheading"] if firstlineheading else [])
-@samples.route("/upload/species/<int:species_id>/populations/<int:population_id>/samples",
+
+@samplesbp.route("/upload/species/<int:species_id>/populations/<int:population_id>/samples",
methods=["GET", "POST"])
@require_login
def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-many-return-statements]
@@ -312,7 +298,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma
return redirect(url_for(
"samples.upload_status", job_id=the_job["jobid"]))
-@samples.route("/upload/status/<uuid:job_id>", methods=["GET"])
+@samplesbp.route("/upload/status/<uuid:job_id>", methods=["GET"])
def upload_status(job_id: uuid.UUID):
"""Check on the status of a samples upload job."""
job = with_redis_connection(lambda rconn: jobs.job(
@@ -339,7 +325,7 @@ def upload_status(job_id: uuid.UUID):
return render_template("no_such_job.html", job_id=job_id), 400
-@samples.route("/upload/failure/<uuid:job_id>", methods=["GET"])
+@samplesbp.route("/upload/failure/<uuid:job_id>", methods=["GET"])
def upload_failure(job_id: uuid.UUID):
"""Display the errors of the samples upload failure."""
job = with_redis_connection(lambda rconn: jobs.job(
diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index 5c7f123..d68c6c0 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -50,7 +50,7 @@
title="Upload Genotype data.">Genotype Data</a></li>
<li><a href="{{url_for('species.populations.index')}}"
title="View and manage species populations.">Populations</a></li>
- <li><a href="#"
+ <li><a href="{{url_for('species.populations.samples.index')}}"
title="Upload population samples.">Samples</a></li>
<li><a href="{{url_for('expression-data.index.index')}}"
title="Upload expression data.">Expression Data</a></li>
diff --git a/uploader/templates/populations/macro-display-population-card.html b/uploader/templates/populations/macro-display-population-card.html
new file mode 100644
index 0000000..e68f8e3
--- /dev/null
+++ b/uploader/templates/populations/macro-display-population-card.html
@@ -0,0 +1,32 @@
+{%from "species/macro-display-species-card.html" import display_species_card%}
+
+{%macro display_population_card(species, population)%}
+{{display_species_card(species)}}
+
+<div class="card">
+ <div class="card-body">
+ <h5 class="card-title">Population</h5>
+ <div class="card-text">
+ <dl>
+ <dt>Name</dt>
+ <dd>{{population.Name}}</dd>
+
+ <dt>Full Name</dt>
+ <dd>{{population.FullName}}</dd>
+
+ <dt>Code</dt>
+ <dd>{{population.InbredSetCode}}</dd>
+
+ <dt>Genetic Type</dt>
+ <dd>{{population.GeneticType}}</dd>
+
+ <dt>Family</dt>
+ <dd>{{population.Family}}</dd>
+
+ <dt>Description</dt>
+ <dd>{{population.Description or "-"}}</dd>
+ </dl>
+ </div>
+ </div>
+</div>
+{%endmacro%}
diff --git a/uploader/templates/populations/macro-select-population.html b/uploader/templates/populations/macro-select-population.html
new file mode 100644
index 0000000..af4fd3a
--- /dev/null
+++ b/uploader/templates/populations/macro-select-population.html
@@ -0,0 +1,30 @@
+{%macro select_population_form(form_action, populations)%}
+<form method="GET" action="{{form_action}}">
+ <legend>Select Population</legend>
+
+ <div class="form-group">
+ <label for="select-population" class="form-label">Select Population</label>
+ <select id="select-population"
+ name="population_id"
+ class="form-control"
+ required="required">
+ <option value="">Select Population</option>
+ {%for family in populations%}
+ <optgroup {%if family[0][1] is not none%}
+ label="{{family[0][1]}}"
+ {%else%}
+ label="Undefined"
+ {%endif%}>
+ {%for population in family[1]%}
+ <option value="{{population.Id}}">{{population.FullName}}</option>
+ {%endfor%}
+ </optgroup>
+ {%endfor%}
+ </select>
+ </div>
+
+ <div class="form-group">
+ <input type="submit" value="Select" class="btn btn-primary" />
+ </div>
+</form>
+{%endmacro%}
diff --git a/uploader/templates/populations/view-population.html b/uploader/templates/populations/view-population.html
index 52dadc4..31db54f 100644
--- a/uploader/templates/populations/view-population.html
+++ b/uploader/templates/populations/view-population.html
@@ -59,7 +59,11 @@
<nav class="nav">
<ul>
<li>
- <a href="#" title="Upload samples">upload samples</a>
+ <a href="{{url_for('species.populations.samples.list_samples',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}"
+ title="Manage samples: Add new or delete existing.">
+ manage samples</a>
</li>
<li>
<a href="#" title="Upload expression data">upload expression data</a>
diff --git a/uploader/templates/samples/base.html b/uploader/templates/samples/base.html
new file mode 100644
index 0000000..291782b
--- /dev/null
+++ b/uploader/templates/samples/base.html
@@ -0,0 +1,12 @@
+{%extends "populations/base.html"%}
+
+{%block lvl3_breadcrumbs%}
+<li {%if activelink=="samples"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.samples.index')}}">Samples</a>
+</li>
+{%block lvl4_breadcrumbs%}{%endblock%}
+{%endblock%}
diff --git a/uploader/templates/samples/index.html b/uploader/templates/samples/index.html
new file mode 100644
index 0000000..7c88c01
--- /dev/null
+++ b/uploader/templates/samples/index.html
@@ -0,0 +1,21 @@
+{%extends "samples/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "species/macro-select-species.html" import select_species_form%}
+
+{%block title%}Populations{%endblock%}
+
+{%block pagetitle%}Populations{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <p>Here, you can upload the samples/individuals that were used in your
+ experiments.</p>
+ <p>Since the samples are linked to specific species and populations, we will
+ need to first select them in the next few steps.</p>
+
+ {{select_species_form(url_for("species.populations.samples.index"), species)}}
+</div>
+{%endblock%}
diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html
new file mode 100644
index 0000000..a29dc1c
--- /dev/null
+++ b/uploader/templates/samples/list-samples.html
@@ -0,0 +1,114 @@
+{%extends "samples/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "populations/macro-select-population.html" import select_population_form%}
+{%from "populations/macro-display-population-card.html" import display_population_card%}
+
+{%block title%}Samples &mdash; List Samples{%endblock%}
+
+{%block pagetitle%}Samples &mdash; List Samples{%endblock%}
+
+{%block lvl4_breadcrumbs%}
+<li {%if activelink=="list-samples"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.samples.list_samples',
+ species_id=species.SpeciesId,
+ population_id=population.Id)}}">List</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <p>
+ Samples for population "{{population.FullName}}" from the
+ "{{species.FullName}}" species.
+ </p>
+
+ {%if samples | length > 0%}
+ <div class="row">
+ <div class="col-md-2">
+ {%if offset > 0:%}
+ <a href="{{url_for('species.populations.samples.list_samples',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ from=offset-count,
+ count=count)}}">
+ <span class="glyphicon glyphicon-backward"></span>
+ Previous
+ </a>
+ {%endif%}
+ </div>
+
+ <div class="col-md-8" style="text-align: center;">
+ Samples {{offset}} &mdash; {{offset+(count if offset + count < total_samples else total_samples - offset)}} / {{total_samples}}
+ </div>
+
+ <div class="col-md-2">
+ {%if offset + count < total_samples:%}
+ <a href="{{url_for('species.populations.samples.list_samples',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ from=offset+count,
+ count=count)}}">
+ Next
+ <span class="glyphicon glyphicon-forward"></span>
+ </a>
+ {%endif%}
+ </div>
+ </div>
+ <table class="table">
+ <thead>
+ <tr>
+ <th>Name</th>
+ <th>Auxilliary Name</th>
+ <th>Symbol</th>
+ <th>Alias</th>
+ </tr>
+ </thead>
+
+ <tbody>
+ {%for sample in samples%}
+ <tr>
+ <td>{{sample.Name}}</td>
+ <td>{{sample.Name2}}</td>
+ <td>{{sample.Symbol or "-"}}</td>
+ <td>{{sample.Alias or "-"}}</td>
+ </tr>
+ {%endfor%}
+ </tbody>
+ </table>
+
+ <p>
+ <a href="#"
+ title="Add samples for population '{{population.FullName}}' from species
+ '{{species.FullName}}'."
+ class="btn btn-danger">
+ delete all samples
+ </a>
+ </p>
+ {%else%}
+ <p class="text-danger">
+ <span class="glyphicon glyphicon-exclamation-sign"></span>
+ There are no samples for this population at this time.
+ </p>
+
+ <p>
+ <a href="#"
+ title="Add samples for population '{{population.FullName}}' from species
+ '{{species.FullName}}'."
+ class="btn btn-primary">
+ add samples
+ </a>
+ </p>
+ {%endif%}
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}
+
diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html
index da19ddc..8e22ac1 100644
--- a/uploader/templates/samples/select-population.html
+++ b/uploader/templates/samples/select-population.html
@@ -1,99 +1,34 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
+{%extends "samples/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "populations/macro-select-population.html" import select_population_form%}
+{%from "species/macro-display-species-card.html" import display_species_card%}
-{%block title%}Select Grouping/Population{%endblock%}
+{%block title%}Samples &mdash; Select Population{%endblock%}
-{%block contents%}
-<h1 class="heading">Select grouping/population</h1>
-
-<div>
- <p>We organise the samples/cases/strains in a hierarchichal form, starting
- with <strong>species</strong> at the very top. Under species, we have a
- grouping in terms of the relevant population
- (e.g. Inbred populations, cell tissue, etc.)</p>
-</div>
-
-<form method="POST" action="{{url_for('samples.select_population',
- species_id=species.SpeciesId)}}">
- <legend class="heading">select grouping/population</legend>
- {{flash_messages("error-select-population")}}
-
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
-
- <div class="form-group">
- <label for="select:inbredset" class="form-label">grouping/population</label>
- <select id="select:inbredset"
- name="inbredset_id"
- required="required"
- class="form-control">
- <option value="">Select a grouping/population</option>
- {%for pop in populations%}
- <option value="{{pop.InbredSetId}}">
- {{pop.InbredSetName}} ({{pop.FullName}})</option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit" class="btn btn-primary">select population</button>
-</form>
-
-<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
-
-<form method="POST" action="{{url_for('samples.create_population',
- species_id=species.SpeciesId)}}">
- <legend class="heading">create new grouping/population</legend>
- {{flash_messages("error-create-population")}}
+{%block pagetitle%}Samples &mdash; Select Population{%endblock%}
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <div class="form-group">
- <legend>mandatory</legend>
- <label for="txt:inbredset-name" class="form-label">name</label>
- <input id="txt:inbredset-name"
- name="inbredset_name"
- type="text"
- required="required"
- placeholder="Enter grouping/population name"
- class="form-control" />
-
- <label for="txt:" class="form-label">full name</label>
- <input id="txt:inbredset-fullname"
- name="inbredset_fullname"
- type="text"
- required = "required"
- placeholder="Enter the grouping/population's full name"
- class="form-control" />
- </div>
- <div class="form-group">
- <legend>Optional</legend>
-
- <label for="num:public" class="form-label">public?</label>
- <input id="num:public"
- name="public"
- type="number"
- min="0" max="2" value="2"
- class="form-control" />
-
- <label for="txt:inbredset-family" class="form-label">family</label>
- <input id="txt:inbredset-family"
- name="inbredset_family"
- type="text"
- placeholder="I am not sure what this is about."
- class="form-control" />
-
- <label for="txtarea:" class="form-label">Description</label>
- <textarea id="txtarea:description"
- name="description"
- rows="5"
- placeholder="Enter a description of this grouping/population"
- class="form-control"></textarea>
- </div>
-
- <button type="submit" class="btn btn-primary">create grouping/population</button>
-</form>
+{%block contents%}
+{{flash_all_messages()}}
+<div class="row">
+ <p>Select the population to use with your samples:</p>
+ {{select_population_form(
+ url_for("species.populations.samples.select_population", species_id=species.SpeciesId),
+ populations)}}
+</div>
+<div class="row">
+ <p><strong>Cannot find your population in the list?</strong></p>
+
+ <p>If you cannot find the population you want in the drop-down above, you can
+ instead,
+ <a href="{{url_for('species.populations.create_population',
+ species_id=species.SpeciesId)}}"
+ title="Create a new population for species '{{species.FullName}},">
+ create a new population</a>.
+</div>
{%endblock%}
-
-{%block javascript%}
+{%block sidebarcontents%}
+{{display_species_card(species)}}
{%endblock%}
diff --git a/uploader/templates/samples/select-species.html b/uploader/templates/samples/select-species.html
deleted file mode 100644
index aa64ecf..0000000
--- a/uploader/templates/samples/select-species.html
+++ /dev/null
@@ -1,30 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_all_messages%}
-
-{%block title%}Select Grouping/Population{%endblock%}
-
-{%block contents%}
-<h2 class="heading">upload samples/cases</h2>
-
-<p>We need to know what species your data belongs to.</p>
-
-{{flash_all_messages()}}
-
-<form method="POST" action="{{url_for('expression-data.samples.select_species')}}">
- <legend class="heading">upload samples</legend>
- <div class="form-group">
- <label for="select_species02" class="form-label">Species</label>
- <select id="select_species02"
- name="species_id"
- required="required"
- class="form-control">
- <option value="">Select species</option>
- {%for spec in species%}
- <option value="{{spec.SpeciesId}}">{{spec.MenuName}}</option>
- {%endfor%}
- </select>
- </div>
-
- <button type="submit" class="btn btn-primary">submit</button>
-</form>
-{%endblock%}
diff --git a/uploader/templates/samples/upload-failure.html b/uploader/templates/samples/upload-failure.html
deleted file mode 100644
index 09e2ecf..0000000
--- a/uploader/templates/samples/upload-failure.html
+++ /dev/null
@@ -1,27 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Samples Upload Failure{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job.job_name}}</h2>
-
-<p>There was a failure attempting to upload the samples.</p>
-
-<p>Here is some information to help with debugging the issue. Provide this
- information to the developer/maintainer.</p>
-
-<h3>Debugging Information</h3>
-<ul>
- <li><strong>job id</strong>: {{job.job_id}}</li>
- <li><strong>status</strong>: {{job.status}}</li>
- <li><strong>job type</strong>: {{job["job-type"]}}</li>
-</ul>
-
-<h4>stdout</h4>
-{{cli_output(job, "stdout")}}
-
-<h4>stderr</h4>
-{{cli_output(job, "stderr")}}
-
-{%endblock%}
diff --git a/uploader/templates/samples/upload-progress.html b/uploader/templates/samples/upload-progress.html
deleted file mode 100644
index 7bb02be..0000000
--- a/uploader/templates/samples/upload-progress.html
+++ /dev/null
@@ -1,22 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block extrameta%}
-<meta http-equiv="refresh" content="5">
-{%endblock%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job.job_name}}</h2>
-
-<p>
-<strong>status</strong>:
-<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br />
-</p>
-
-<p>saving to database...</p>
-
-{{cli_output(job, "stdout")}}
-
-{%endblock%}
diff --git a/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html
deleted file mode 100644
index e62de57..0000000
--- a/uploader/templates/samples/upload-samples.html
+++ /dev/null
@@ -1,139 +0,0 @@
-{%extends "base.html"%}
-{%from "flash_messages.html" import flash_messages%}
-
-{%block title%}Upload Samples{%endblock%}
-
-{%block css%}{%endblock%}
-
-{%block contents%}
-<h1 class="heading">upload samples</h1>
-
-{{flash_messages("alert-success")}}
-
-<p>You can now upload a character-separated value (CSV) file that contains
- details about your samples. The CSV file should have the following fields:
- <dl>
- <dt>Name</dt>
- <dd>The primary name for the sample</dd>
-
- <dt>Name2</dt>
- <dd>A secondary name for the sample. This can simply be the same as
- <strong>Name</strong> above. This field <strong>MUST</strong> contain a
- value.</dd>
-
- <dt>Symbol</dt>
- <dd>A symbol for the sample. Can be an empty field.</dd>
-
- <dt>Alias</dt>
- <dd>An alias for the sample. Can be an empty field.</dd>
- </dl>
-</p>
-
-<form id="form-samples"
- method="POST"
- action="{{url_for('samples.upload_samples',
- species_id=species.SpeciesId,
- population_id=population.InbredSetId)}}"
- enctype="multipart/form-data">
- <legend class="heading">upload samples</legend>
-
- <div class="form-group">
- <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
- <label class="form-label">species:</label>
- <span class="form-text">{{species.SpeciesName}} [{{species.MenuName}}]</span>
- </div>
-
- <div class="form-group">
- <input type="hidden" name="inbredset_id" value="{{population.InbredSetId}}" />
- <label class="form-label">grouping/population:</label>
- <span class="form-text">{{population.Name}} [{{population.FullName}}]</span>
- </div>
-
- <div class="form-group">
- <label for="file-samples" class="form-label">select file</label>
- <input type="file" name="samples_file" id="file:samples"
- accept="text/csv, text/tab-separated-values"
- class="form-control" />
- </div>
-
- <div class="form-group">
- <label for="select:separator" class="form-label">field separator</label>
- <select id="select:separator"
- name="separator"
- required="required"
- class="form-control">
- <option value="">Select separator for your file: (default is comma)</option>
- <option value="&#x0009;">TAB</option>
- <option value="&#x0020;">Space</option>
- <option value=",">Comma</option>
- <option value=";">Semicolon</option>
- <option value="other">Other</option>
- </select>
- <input id="txt:separator"
- type="text"
- name="other_separator"
- class="form-control" />
- <small class="form-text text-muted">
- If you select '<strong>Other</strong>' for the field separator value,
- enter the character that separates the fields in your CSV file in the form
- field below.
- </small>
- </div>
-
- <div class="form-group form-check">
- <input id="chk:heading"
- type="checkbox"
- name="first_line_heading"
- class="form-check-input" />
- <label for="chk:heading" class="form-check-label">
- first line is a heading?</label>
- <small class="form-text text-muted">
- Select this if the first line in your file contains headings for the
- columns.
- </small>
- </div>
-
- <div class="form-group">
- <label for="txt:delimiter" class="form-label">field delimiter</label>
- <input id="txt:delimiter"
- type="text"
- name="field_delimiter"
- maxlength="1"
- class="form-control" />
- <small class="form-text text-muted">
- If there is a character delimiting the string texts within particular
- fields in your CSV, provide the character here. This can be left blank if
- no such delimiters exist in your file.
- </small>
- </div>
-
- <button type="submit"
- class="btn btn-primary">upload samples file</button>
-</form>
-
-<table id="tbl:samples-preview" class="table">
- <caption class="heading">preview content</caption>
-
- <thead>
- <tr>
- <th>Name</th>
- <th>Name2</th>
- <th>Symbol</th>
- <th>Alias</th>
- </tr>
- </thead>
-
- <tbody>
- <tr id="default-row">
- <td colspan="4">
- Please make some selections to preview the data.</td>
- </tr>
- </tbody>
-</table>
-
-{%endblock%}
-
-
-{%block javascript%}
-<script src="/static/js/upload_samples.js" type="text/javascript"></script>
-{%endblock%}
diff --git a/uploader/templates/samples/upload-success.html b/uploader/templates/samples/upload-success.html
deleted file mode 100644
index cb745c3..0000000
--- a/uploader/templates/samples/upload-success.html
+++ /dev/null
@@ -1,18 +0,0 @@
-{%extends "base.html"%}
-{%from "cli-output.html" import cli_output%}
-
-{%block title%}Job Status{%endblock%}
-
-{%block contents%}
-<h1 class="heading">{{job.job_name}}</h2>
-
-<p>
-<strong>status</strong>:
-<span>{{job["status"]}} ({{job.get("message", "-")}})</span><br />
-</p>
-
-<p>Successfully uploaded the samples.</p>
-
-{{cli_output(job, "stdout")}}
-
-{%endblock%}