Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_decompose_db_retrieval

6 files changed, 69 insertions, 8 deletions

diff --git a/README.md b/README.md
index c1acba1..c3a9848 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@ Simply load up the environment (for development purposes):
 guix environment --load=guix.scm
 ```
 
-Also, make sure you have the *guix-bioinformatics* channel set up.
+Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up.
 
 ```bash
 env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --load=guix.scm
@@ -22,9 +22,21 @@ python3
 Better run a proper container
 
 ```
-env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm 
+env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm
 ```
 
+If you get a Guix error, such as `ice-9/boot-9.scm:1669:16: In procedure raise-exception:
+error: python-sqlalchemy-stubs: unbound variable` it typically means an update to guix latest is required (i.e., guix pull):
+
+```
+guix pull
+source ~/.config/guix/current/etc/profile
+```
+
+and try again.
+
+See also instructions in [.guix.scm](.guix.scm).
+
 #### Running Tests
 
 (assuming you are in a guix container; otherwise use venv!)
@@ -49,12 +61,33 @@ mypy .
 
 #### Running the flask app
 
-To spin up the server:
+To spin up the server on its own (for development):
 
 ```bash
 env FLASK_DEBUG=1 FLASK_APP="main.py" flask run --port=8080
 ```
 
+And test with
+
+```
+curl localhost:8080/api/version
+"1.0"
+```
+
+To run with gunicorn
+
+```
+gunicorn --bind 0.0.0.0:8080 wsgi:app
+```
+
+consider the following options for development `--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload wsgi`.
+
+And for the scalable production version run
+
+```
+gunicorn --bind 0.0.0.0:8080 --workers 8 --keep-alive 6000 --max-requests 10 --max-requests-jitter 5 --timeout 1200 wsgi:app
+```
+
 ##### Using python-pip
 
 IMPORTANT NOTE: we do not recommend using pip tools, use Guix instead
@@ -71,7 +104,7 @@ virtualenv --python python3 venv
 
 ```bash
 # The --ignore-installed flag forces packages to
-# get installed in the venv even if they existed 
+# get installed in the venv even if they existed
 # in the global env
 pip install -r requirements.txt --ignore-installed
 ```
diff --git a/gn3/api/general.py b/gn3/api/general.py
index cebb2e3..86fb7b7 100644
--- a/gn3/api/general.py
+++ b/gn3/api/general.py
@@ -11,6 +11,9 @@ from gn3.commands import run_cmd
 
 general = Blueprint("general", __name__)
 
+@general.route("/version")
+def version():
+  return jsonify("1.0")
 
 @general.route("/metadata/upload/", methods=["POST"],
                strict_slashes=False)
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 85cccfa..f66ead3 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -7,7 +7,7 @@ from gn3.db.datasets import retrieve_trait_dataset
 def get_trait_csv_sample_data(conn: Any,
                               trait_name: int, phenotype_id: int):
     """Fetch a trait and return it as a csv string"""
-    sql = ("SELECT  Strain.Id, PublishData.Id, Strain.Name, "
+    sql = ("SELECT DISTINCT Strain.Id, PublishData.Id, Strain.Name, "
            "PublishData.value, "
            "PublishSE.error, NStrain.count FROM "
            "(PublishData, Strain, PublishXRef, PublishFreeze) "
diff --git a/guix.scm b/guix.scm
index efef9c1..f94fe1a 100644
--- a/guix.scm
+++ b/guix.scm
@@ -17,6 +17,17 @@
 ;;; You should have received a copy of the GNU General Public License
 ;;; along with genenetwork3. If not, see https://www.gnu.org/licenses/.
 
+;; To use this file to build HEAD of gemma:
+;;
+;;   env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix build -f guix.scm
+;;
+;; After checking out the git repo
+;;   cd ~ ; git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics
+;;
+;; To get a development container (e.g., run in emacs shell).
+;;
+;;   env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix environment -C -l guix.scm
+
 (use-modules
  (srfi srfi-1)
  (srfi srfi-26)
@@ -71,8 +82,9 @@
                       #:recursive? #t
                       #:select? git-file?))
   (propagated-inputs `(("coreutils" ,coreutils)
-                       ("gemma-wrapper" ,gemma-wrapper)
                        ("csvdiff" ,go-github-com-aswinkarthik-csvdiff)
+                       ("gemma-wrapper" ,gemma-wrapper)
+                       ("gunicorn" ,gunicorn)
                        ("python" ,python-wrapper)
                        ("python-bcrypt" ,python-bcrypt)
                        ("python-flask" ,python-flask)
diff --git a/main.py b/main.py
index e3ca41a..a587697 100644
--- a/main.py
+++ b/main.py
@@ -2,6 +2,8 @@
 
 from gn3.app import create_app
 
-
 app = create_app()
-app.run(host="0.0.0.0")
+
+if __name__ == '__main__':
+    print("Starting app...")
+    app.run()
diff --git a/wsgi.py b/wsgi.py
new file mode 100644
index 0000000..d30bc49
--- /dev/null
+++ b/wsgi.py
@@ -0,0 +1,11 @@
+# import main
+
+print("STARTING WSGI APP")
+
+from gn3.app import create_app
+
+app = create_app()
+
+if __name__ == "__main__":
+    print("Starting wsgi app...")
+    app.run()