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authorFrederick Muriuki Muriithi2022-07-08 10:39:19 +0300
committerFrederick Muriuki Muriithi2022-07-19 04:59:59 +0300
commit3038c5166aad408d7255f83668b78d635878d3d3 (patch)
treed9384464a1f3c92b50db747346e74cfbc8396119 /qc_app/dbinsert.py
parent7a3a54ec40fac9071a513487602957f8418f163e (diff)
downloadgn-uploader-3038c5166aad408d7255f83668b78d635878d3d3.tar.gz
Implement select study
Implement the select study UI
Diffstat (limited to 'qc_app/dbinsert.py')
-rw-r--r--qc_app/dbinsert.py36
1 files changed, 35 insertions, 1 deletions
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index ea47806..e506175 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -53,6 +53,23 @@ def genechips():
return {}
+def studies_by_species_and_platform(speciesid:int, genechipid:int) -> tuple:
+ "Retrieve the studies by the related species and gene platform"
+ with database_connection() as conn:
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ query = (
+ "SELECT Species.SpeciesId, ProbeFreeze.* "
+ "FROM Species INNER JOIN InbredSet "
+ "ON Species.SpeciesId=InbredSet.SpeciesId "
+ "INNER JOIN ProbeFreeze "
+ "ON InbredSet.InbredSetId=ProbeFreeze.InbredSetId "
+ "WHERE Species.SpeciesId = %s "
+ "AND ProbeFreeze.ChipId = %s")
+ cursor.execute(query, (speciesid, genechipid))
+ return tuple(cursor.fetchall())
+
+ return tuple()
+
@dbinsertbp.route("/platform", methods=["POST"])
def select_platform():
"Select the platform (GeneChipId) used for the data."
@@ -76,7 +93,24 @@ def select_platform():
@dbinsertbp.route("/study", methods=["POST"])
def select_study():
- return "Not implemented yet"
+ "View to select/create the study (ProbeFreeze) associated with the data."
+ form = request.form
+ try:
+ assert form.get("filename"), "filename"
+ assert form.get("filetype"), "filetype"
+ assert form.get("species"), "species"
+ assert form.get("genechipid"), "platform"
+
+ speciesid = form["species"]
+ genechipid = form["genechipid"]
+
+ the_studies = studies_by_species_and_platform(speciesid, genechipid)
+ return render_template(
+ "select_study.html", filename=form["filename"],
+ filetype=form["filetype"], species=speciesid, genechipid=genechipid,
+ studies=the_studies)
+ except AssertionError as aserr:
+ return render_error(f"Missing data: {aserr.args[0]}")
@dbinsertbp.route("/select-dataset", methods=["POST"])
def select_dataset():