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-rw-r--r--qc_app/db/datasets.py7
-rw-r--r--qc_app/db/species.py10
-rw-r--r--qc_app/templates/rqtl2/summary-info.html26
-rw-r--r--qc_app/upload/rqtl2.py20
4 files changed, 51 insertions, 12 deletions
diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
index 3a27706..8122cfa 100644
--- a/qc_app/db/datasets.py
+++ b/qc_app/db/datasets.py
@@ -14,3 +14,10 @@ def geno_dataset_by_species_and_population(
"WHERE iset.SpeciesId=%(sid)s AND iset.InbredSetId=%(pid)s",
{"sid": speciesid, "pid": populationid})
return tuple(dict(row) for row in cursor.fetchall())
+
+def geno_dataset_by_id(conn: mdb.Connection, dataset_id: int) -> dict:
+ """Retrieve genotype dataset by ID"""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s",
+ (dataset_id,))
+ return dict(cursor.fetchone())
diff --git a/qc_app/db/species.py b/qc_app/db/species.py
index 7006d15..653e59b 100644
--- a/qc_app/db/species.py
+++ b/qc_app/db/species.py
@@ -6,8 +6,8 @@ def 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 "
- "FROM Species")
+ "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName, "
+ "FullName FROM Species")
return tuple(cursor.fetchall())
return tuple()
@@ -16,9 +16,7 @@ def species_by_id(conn: mdb.Connection, speciesid) -> dict:
"Retrieve the species from the database by id."
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
- (
- "SELECT "
- "SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName "
- "FROM Species WHERE SpeciesId=%s"),
+ "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName, "
+ "FullName FROM Species WHERE SpeciesId=%s",
(speciesid,))
return cursor.fetchone()
diff --git a/qc_app/templates/rqtl2/summary-info.html b/qc_app/templates/rqtl2/summary-info.html
new file mode 100644
index 0000000..c3a2ac0
--- /dev/null
+++ b/qc_app/templates/rqtl2/summary-info.html
@@ -0,0 +1,26 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Summary</h2>
+
+<div class="explainer">
+ <p>This is the information you have provided to accompany the R/qtl2 bundle
+ you have uploaded. Please verify the information is correct before
+ proceeding.</p>
+</div>
+
+<dl>
+ <dt>Species</dt>
+ <dd>{{species.SpeciesName}} ({{species.FullName}})</dd>
+
+ <dt>Population</dt>
+ <dd>{{population.InbredSetName}}</dd>
+
+ <dt>Genotype Dataset</dt>
+ <dd>{{geno_dataset.Name}} ({{geno_dataset.FullName}})</dd>
+</dl>
+
+{%endblock%}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 7db005c..9bed4f1 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -23,8 +23,9 @@ from qc_app.db import (
species_by_id,
save_population,
populations_by_species,
- population_by_species_and_id,
- geno_dataset_by_species_and_population)
+ population_by_species_and_id,)
+from qc_app.db.datasets import (
+ geno_dataset_by_id, geno_dataset_by_species_and_population)
rqtl2 = Blueprint("rqtl2", __name__)
@@ -214,20 +215,27 @@ def select_dataset_info(species_id: int, population_id: int):
if bool(error_page):
return error_page
+ species = species_by_id(conn, species_id)
+ population = population_by_species_and_id(
+ conn, species_id, population_id)
thefile = fullpath(form["rqtl2_bundle_file"])
with ZipFile(str(thefile), "r") as zfile:
cdata = r_qtl2.control_data(zfile)
if "geno" in cdata and not bool(form.get("geno-dataset-id")):
return render_template(
"rqtl2/select-geno-dataset.html",
- species=species_by_id(conn, species_id),
- population=population_by_species_and_id(
- conn, species_id, population_id),
+ species=species,
+ population=population,
rqtl2_bundle_file=thefile.name,
datasets=geno_dataset_by_species_and_population(
conn, species_id, population_id))
- return "All data points collected. Should proceed to launching the job."
+ geno_dataset = geno_dataset_by_id(conn, form["geno-dataset-id"])
+
+ return render_template("rqtl2/summary-info.html",
+ species=species,
+ population=population,
+ geno_dataset=geno_dataset)
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
"/rqtl2-bundle/select-geno-dataset"),