Implement creation of new platform.

3 files changed, 119 insertions, 4 deletions

diff --git a/uploader/platforms/models.py b/uploader/platforms/models.py
index 4b690bb..199f2df 100644
--- a/uploader/platforms/models.py
+++ b/uploader/platforms/models.py
@@ -2,7 +2,7 @@
 from typing import Optional
 
 import MySQLdb as mdb
-from MySQLdb.cursors import DictCursor
+from MySQLdb.cursors import Cursor, DictCursor
 
 def platforms_by_species(
         conn: mdb.Connection,
@@ -29,6 +29,7 @@ def species_platforms_count(conn: mdb.Connection, species_id: int) -> int:
             (species_id,))
         return int(cursor.fetchone()["count"])
 
+
 def platform_by_id(conn: mdb.Connection, platformid: int) -> Optional[dict]:
     """Retrieve a platform by its ID"""
     with conn.cursor(cursorclass=DictCursor) as cursor:
@@ -39,3 +40,56 @@ def platform_by_id(conn: mdb.Connection, platformid: int) -> Optional[dict]:
             return dict(result)
 
     return None
+
+
+def platform_by_species_and_id(
+        conn: mdb.Connection, species_id: int, platformid: int
+) -> Optional[dict]:
+    """Retrieve a platform by its species and ID"""
+    with conn.cursor(cursorclass=DictCursor) as cursor:
+        cursor.execute("SELECT * FROM GeneChip WHERE SpeciesId=%s AND Id=%s",
+                       (species_id, platformid))
+        result = cursor.fetchone()
+        if bool(result):
+            return dict(result)
+
+    return None
+
+
+def save_new_platform(# pylint: disable=[too-many-arguments]
+        cursor: Cursor,
+        species_id: int,
+        geo_platform: str,
+        platform_name: str,
+        platform_shortname: str,
+        platform_title: str,
+        go_tree_value: Optional[str]
+) -> dict:
+    """Save a new platform to the database."""
+    params = {
+        "species_id": species_id,
+        "GeoPlatform": geo_platform,
+        "GeneChipName": platform_name,
+        "Name": platform_shortname,
+        "Title": platform_title,
+        "GO_tree_value": go_tree_value
+    }
+    cursor.execute("SELECT SpeciesId, GeoPlatform FROM GeneChip")
+    assert (species_id, geo_platform) not in (
+        (row["SpeciesId"], row["GeoPlatform"]) for row in cursor.fetchall())
+    cursor.execute(
+        "INSERT INTO "
+        "GeneChip(SpeciesId, GeneChipName, Name, GeoPlatform, Title, GO_tree_value) "
+        "VALUES("
+        "%(species_id)s, %(GeneChipName)s, %(Name)s, %(GeoPlatform)s, "
+        "%(Title)s, %(GO_tree_value)s"
+        ")",
+        params)
+    new_id = cursor.lastrowid
+    cursor.execute("UPDATE GeneChip SET GeneChipId=%s WHERE Id=%s",
+                   (new_id, new_id))
+    return {
+        **params,
+        "Id": new_id,
+        "GeneChipId": new_id
+    }
diff --git a/uploader/platforms/views.py b/uploader/platforms/views.py
index 1abf52e..1030b6c 100644
--- a/uploader/platforms/views.py
+++ b/uploader/platforms/views.py
@@ -1,4 +1,5 @@
 """The endpoints for the platforms"""
+from MySQLdb.cursors import DictCursor
 from flask import (
     flash,
     request,
@@ -13,7 +14,10 @@ from uploader.db_utils import database_connection
 from uploader.species.models import all_species, species_by_id
 from uploader.datautils import safe_int, order_by_family, enumerate_sequence
 
-from .models import platforms_by_species, species_platforms_count
+from .models import (save_new_platform,
+                     platforms_by_species,
+                     species_platforms_count,
+                     platform_by_species_and_id)
 
 platformsbp = Blueprint("platforms", __name__)
 render_template = make_template_renderer("platforms")
@@ -69,7 +73,8 @@ def list_platforms(species_id: int):
 @require_login
 def create_platform(species_id: int):
     """Create a new genetic sequencing platform."""
-    with database_connection(app.config["SQL_URI"]) as conn:
+    with (database_connection(app.config["SQL_URI"]) as conn,
+          conn.cursor(cursorclass=DictCursor) as cursor):
         species = species_by_id(conn, species_id)
         if not bool(species):
             flash("No species provided.", "alert-danger")
@@ -81,4 +86,39 @@ def create_platform(species_id: int):
                 species=species,
                 activelink="create-platform")
 
-        raise NotImplementedError("This still needs to be implemented.")
+        try:
+            form = request.form
+            new_platform = save_new_platform(
+                cursor,
+                species_id,
+                form["geo-platform"],
+                form["platform-name"],
+                form["platform-shortname"],
+                form["platform-title"],
+                form.get("go-tree-value") or None)
+        except KeyError as _kerr:
+            flash(f"Required value for field {_kerr.args[0]} was not provided.",
+                  "alert-danger")
+            return redirect(url_for("species.platforms.create_platform",
+                                    species_id=species_id))
+        except AssertionError as _aerr:
+            flash(f"Platform with GeoPlatform value of '{form['geo-platform']}'"
+                  f" already existst for species '{species['FullName']}'.",
+                  "alert-danger")
+            return redirect(url_for("species.platforms.create_platform",
+                                    species_id=species_id))
+
+    flash("Platform created successfully", "alert-success")
+    return redirect(url_for("species.platforms.view_platform",
+                            species_id=species_id,
+                            platform_id=new_platform["Id"]))
+
+
+@platformsbp.route("<int:species_id>/platforms/<int:platform_id>/view",
+                   methods=["GET"])
+@require_login
+def view_platform(species_id: int, platform_id: int):
+    """View details for a specific platform."""
+    with database_connection(app.config["SQL_URI"]) as conn:
+        return platform_by_species_and_id(
+            conn, species_id, platform_id)
diff --git a/uploader/templates/platforms/create-platform.html b/uploader/templates/platforms/create-platform.html
index b5961ce..0866d5e 100644
--- a/uploader/templates/platforms/create-platform.html
+++ b/uploader/templates/platforms/create-platform.html
@@ -90,6 +90,27 @@
     </div>
 
     <div class="form-group">
+      <label for="txt-go-tree-value" class="form-label">GO Tree Value</label>
+      <input type="text"
+             id="txt-go-tree-value"
+             name="go-tree-value"
+             class="form-control"  />
+      <small class="form-text text-muted">
+        <p>This is a Chip identification value useful for analysis with the
+          <strong>
+            <a href="https://www.geneweaver.org/"
+               title="Go to the GeneWeaver site."
+               target="_blank">GeneWeaver</a></strong>
+          and
+          <strong>
+            <a href="https://www.webgestalt.org/"
+               title="Go to the WEB-based GEne SeT AnaLysis Toolkit site."
+               target="_blank">WebGestalt</a></strong>
+          tools.<br />
+        This can be left blank for custom platforms.</p></small>
+    </div>
+
+    <div class="form-group">
       <input type="submit"
              value="create new platform"
              class="btn btn-primary"  />