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authorMuriithi Frederick Muriuki2021-08-08 11:06:35 +0300
committerMuriithi Frederick Muriuki2021-08-08 11:06:35 +0300
commit0ec39e6c5058f4f06bfb5f763f51cd9dc176cb35 (patch)
tree2c9ea26f67e2a451343f4003fb67478baeb17ec2
parenta73d1ce388012758ce3b0d789f008e4184e6a38e (diff)
parente0476d51603432f60b6412b65486166deabe9e08 (diff)
downloadgenenetwork3-0ec39e6c5058f4f06bfb5f763f51cd9dc176cb35.tar.gz
Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_decompose_db_retrieval
-rw-r--r--README.md41
-rw-r--r--gn3/api/general.py3
-rw-r--r--gn3/db/traits.py2
-rw-r--r--guix.scm14
-rw-r--r--main.py6
-rw-r--r--wsgi.py11
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()