UI: Select ProbeSet study.

5 files changed, 199 insertions, 41 deletions

diff --git a/qc_app/db/__init__.py b/qc_app/db/__init__.py
index 270f1a0..36e93e8 100644
--- a/qc_app/db/__init__.py
+++ b/qc_app/db/__init__.py
@@ -5,4 +5,4 @@ from .populations import (
     population_by_id,
     populations_by_species,
     population_by_species_and_id)
-from .datasets import geno_dataset_by_species_and_population
+from .datasets import geno_datasets_by_species_and_population
diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
index 8122cfa..086c103 100644
--- a/qc_app/db/datasets.py
+++ b/qc_app/db/datasets.py
@@ -2,7 +2,7 @@
 import MySQLdb as mdb
 from MySQLdb.cursors import DictCursor
 
-def geno_dataset_by_species_and_population(
+def geno_datasets_by_species_and_population(
         conn: mdb.Connection,
         speciesid: int,
         populationid: int) -> tuple[dict, ...]:
@@ -21,3 +21,31 @@ def geno_dataset_by_id(conn: mdb.Connection, dataset_id: int) -> dict:
         cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s",
                        (dataset_id,))
         return dict(cursor.fetchone())
+
+def probeset_studies_by_species_and_population(
+        conn: mdb.Connection,
+        speciesid: int,
+        populationid: int) -> tuple[dict, ...]:
+    """Retrieve all probesets"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute(
+            "SELECT pf.* FROM InbredSet AS iset INNER JOIN ProbeFreeze AS pf "
+            "ON iset.InbredSetId=pf.InbredSetId "
+            "WHERE iset.SpeciesId=%(sid)s AND iset.InbredSetId=%(pid)s",
+            {"sid": speciesid, "pid": populationid})
+        return tuple(dict(row) for row in cursor.fetchall())
+
+def probeset_datasets_by_study(conn: mdb.Connection,
+                               studyid: int) -> tuple[dict, ...]:
+    """Retrieve all probeset databases by study."""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM ProbeSetFreeze WHERE ProbeFreezeId=%s",
+                       (studyid,))
+        return tuple(dict(row) for row in cursor.fetchall())
+
+def probe_study_by_id(conn: mdb.Connection, studyid: int) -> dict:
+    """Retrieve ProbeSet study by ID"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM ProbeFreeze WHERE Id=%s",
+                       (studyid,))
+        return dict(cursor.fetchone())
diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html
new file mode 100644
index 0000000..c0c6401
--- /dev/null
+++ b/qc_app/templates/rqtl2/select-probeset-dataset.html
@@ -0,0 +1,17 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Phenotype(ProbeSet) Dataset</h2>
+
+<div class="explainer">
+  <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
+    file(s). This data needs to be organised under a dataset..</p>
+  <p>This page gives you the ability to do that.</p>
+</div>
+
+<p style="color: red; font-weight: bold;">Under Construction</p>
+
+{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-probeset-study-id.html b/qc_app/templates/rqtl2/select-probeset-study-id.html
new file mode 100644
index 0000000..bb31fde
--- /dev/null
+++ b/qc_app/templates/rqtl2/select-probeset-study-id.html
@@ -0,0 +1,59 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Phenotype(ProbeSet) Study</h2>
+
+<div class="explainer">
+  <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
+    file(s). This data needs to be organised under a study.</p>
+  <p>This page gives you the ability to do that.</p>
+</div>
+
+<form method="POST"
+      action="#">
+  <legend class="heading">Select from existing ProbeSet datasets</legend>
+
+  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+  <input type="hidden" name="population_id"
+	 value="{{population.InbredSetId}}" />
+  <input type="hidden" name="rqtl2_bundle_file"
+	 value="{{rqtl2_bundle_file}}" />
+  <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+
+  <fieldset>
+    <label for="select:probe-study">Study</label>
+    <select id="select:probe-study"
+	    name="probe-study-id"
+	    required="required"
+	    {%if studies | length == 0%}disabled="disabled"{%endif%}>
+      <option value="">Select a study</option>
+      {%for study in studies%}
+      <option value={{study.Id}}>
+	{{study.Name}}
+	{%if study.FullName%}
+	 -- ({{study.FullName}})
+	{%endif%}
+      </option>
+      {%endfor%}
+    </select>
+  </fieldset>
+
+  <fieldset>
+    <input type="submit"
+	   value="select study"
+	   class="btn btn-main form-col-2" />
+  </fieldset>
+</form>
+
+<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+
+<form method="POST"
+      action="#">
+  <legend class="heading">Create new ProbeSet dataset</legend>
+  <strong style="color: red;font-weight:bold;">Under construction</strong>
+</form>
+
+{%endblock%}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 6ddc83f..3411f98 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -25,7 +25,11 @@ from qc_app.db import (
     populations_by_species,
     population_by_species_and_id,)
 from qc_app.db.datasets import (
-    geno_dataset_by_id,  geno_dataset_by_species_and_population)
+    geno_dataset_by_id,
+    geno_datasets_by_species_and_population,
+
+    probeset_datasets_by_study,
+    probeset_studies_by_species_and_population)
 
 rqtl2 = Blueprint("rqtl2", __name__)
 
@@ -199,44 +203,16 @@ def check_errors(conn, *args, **kwargs):
                                 pgsrc="error"),
                         code=307)
 
-    return None
-
-@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
-              "/rqtl2-bundle/dataset-info"),
-             methods=["POST"])
-def select_dataset_info(species_id: int, population_id: int):
-    """
-    If `geno` files exist in the R/qtl2 bundle, prompt user to provide the
-    dataset the genotypes belong to.
-    """
-    form = request.form
-    with database_connection(app.config["SQL_URI"]) as conn:
-        error_page = check_errors(conn, "species", "population", "rqtl2_bundle_file")
-        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,
-                    population=population,
-                    rqtl2_bundle_file=thefile.name,
-                    datasets=geno_dataset_by_species_and_population(
-                        conn, species_id, population_id))
-
-            geno_dataset = geno_dataset_by_id(
-                conn, int(form["geno-dataset-id"]))
+    if ("probe-study-id" in args and
+        not bool(request.form.get("probe-study-id"))):
+        flash("No probeset study was selected!", "alert-error alert-rqtl2")
+        return redirect(url_for("upload.rqtl2.select_probeset_study",
+                                species_id=species_id,
+                                population_id=population_id,
+                                pgsrc="error"),
+                        code=307)
 
-    return render_template("rqtl2/summary-info.html",
-                           species=species,
-                           population=population,
-                           geno_dataset=geno_dataset)
+    return None
 
 @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
               "/rqtl2-bundle/select-geno-dataset"),
@@ -249,7 +225,7 @@ def select_geno_dataset(species_id: int, population_id: int):
         if bool(error):
             return error
 
-        geno_dset = geno_dataset_by_species_and_population(
+        geno_dset = geno_datasets_by_species_and_population(
             conn, species_id, population_id)
         if not bool(geno_dset):
             flash("No genotype dataset was provided!",
@@ -321,3 +297,81 @@ def create_geno_dataset(species_id: int, population_id: int):
                     conn, species_id, population_id),
                 rqtl2_bundle_file=request.form["rqtl2_bundle_file"],
                 geno_dataset={**new_dataset, "id": cursor.lastrowid})
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+              "/rqtl2-bundle/select-probeset-study"),
+             methods=["POST"])
+def select_probeset_study(species_id: int, population_id: int):
+    """Select or create a probeset study."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        error = check_errors(
+            conn, "species", "population", "rqtl2_bundle_file", "geno-dataset",
+            "probe-study-id")
+        if bool(error):
+            return error
+
+        summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
+                                        species=species_by_id(conn, species_id),
+                                        population=population_by_species_and_id(
+                                            conn, species_id, population_id)),
+                                code=307)
+        if not bool(probe_study_by_id(conn, int(request.form["probe-study-id"]))):
+            flash("Invalid study selected!", "alert-error alert-rqtl2")
+            return summary_page
+
+        return summary_page
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+              "/rqtl2-bundle/dataset-info"),
+             methods=["POST"])
+def select_dataset_info(species_id: int, population_id: int):
+    """
+    If `geno` files exist in the R/qtl2 bundle, prompt user to provide the
+    dataset the genotypes belong to.
+    """
+    form = request.form
+    with database_connection(app.config["SQL_URI"]) as conn:
+        error_page = check_errors(conn, "species", "population", "rqtl2_bundle_file")
+        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,
+                    population=population,
+                    rqtl2_bundle_file=thefile.name,
+                    datasets=geno_datasets_by_species_and_population(
+                        conn, species_id, population_id))
+            geno_dataset = geno_dataset_by_id(conn, int(form["geno-dataset-id"]))
+
+            if "pheno" in cdata and not bool(form.get("probe-study-id")):
+                return render_template(
+                    "rqtl2/select-probeset-study-id.html",
+                    species=species,
+                    population=population,
+                    rqtl2_bundle_file=thefile.name,
+                    geno_dataset=geno_dataset,
+                    studies=probeset_studies_by_species_and_population(
+                            conn, species_id, population_id))
+
+            if "pheno" in cdata and not bool(form.get("probe-dataset-id")):
+                    return render_template(
+                        "rqtl2/select-probeset-dataset.html",
+                        species=species,
+                        population=population,
+                        rqtl2_bundle_file=thefile.name,
+                        geno_dataset=geno_dataset,
+                        datasets=probeset_datasets_by_study(
+                            conn, int(form["probe-study-id"])))
+
+    return render_template("rqtl2/summary-info.html",
+                           species=species,
+                           population=population,
+                           geno_dataset=geno_dataset)