fix: Changes according to PR comments

.travis.yml

@@ -10,12 +10,13 @@ cache:
 # install dependencies
 install:
   - pip install pipenv
-  - pipenv install --dev
+  - pipenv install --skip-lock --dev
   - pipenv graph
 
 # run tests
 script:
   - cd tests
+  - export MANIFEST_SERVICE_CONFIG_PATH=../config.json
   - python -m pytest -v
 
 after_script:

Dockerfile

@@ -1,45 +1,47 @@
-# To run: docker run -v /path/to/wsgi.py:/var/www/manifest_service/wsgi.py --name=manifest_service -p 81:80 manifest_service
-# To check running container: docker exec -it manifest_service /bin/bash
+# To run: docker run -v /path/to/wsgi.py:/var/www/manifestservice/wsgi.py --name=manifestservice -p 81:80 manifestservice
+# To check running container: docker exec -it manifestservice /bin/bash
 
 
 FROM quay.io/cdis/python-nginx:master
 
-
-ENV appname=manifest_service
+RUN echo "7" && ls
+ENV appname=manifestservice
 
 # number of uwsgi worker processes
 ENV UWSGI_CHEAPER 2
 
+ENV WORKON_HOME=/.venv
+
 RUN apk update \
     && apk add postgresql-libs postgresql-dev libffi-dev libressl-dev \
     && apk add linux-headers musl-dev gcc \
     && apk add curl bash git vim
-
+RUN echo "17" && ls
 COPY . /$appname
 COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini
 COPY ./deployment/uwsgi/wsgi.py /$appname/wsgi.py
 COPY ./deployment/nginx/nginx.conf /etc/nginx/
 COPY ./deployment/nginx/uwsgi.conf /etc/nginx/conf.d/nginx.conf
 WORKDIR /$appname
+RUN echo "24" && ls
 
-RUN python -m pip install --upgrade pip \
-    && python -m pip install --upgrade setuptools \
-    && pip install -r requirements.txt --src /usr/local/lib/python3.6/site-packages/
+RUN python -m pip install --upgrade pip && pip install pipenv && pipenv install
 
+RUN echo "26" && ls
 RUN mkdir -p /var/www/$appname \
     && mkdir -p /var/www/.cache/Python-Eggs/ \
     && mkdir /run/nginx/ \
     && ln -sf /dev/stdout /var/log/nginx/access.log \
     && ln -sf /dev/stderr /var/log/nginx/error.log \
     && chown nginx -R /var/www/.cache/Python-Eggs/ \
     && chown nginx /var/www/$appname
-
+RUN echo "34" && ls
 EXPOSE 80
-
+RUN echo "36"
 RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/version_data.py \
     && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/version_data.py \
     && python setup.py install
 
 WORKDIR /var/www/$appname
-
+RUN echo "42" && ls
 CMD /$appname/dockerrun.bash

Pipfile

@@ -4,14 +4,18 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
-pytest="*"
-pytest-mock = "*"
-pytest-flask = "*"
+codacy-coverage = "*"
+pytest="~=4.3"
+pytest-mock="~=1.10"
+pytest-flask="~=0.14.0"
 
 [packages]
-flask = "*"
-authutils = "*"
-boto3 = "*"
+flask="~=0.10"
+authutils="~=3.0"
+boto3="~=1.9"
 
 [requires]
-python_version = "3.7"
+python_version = "3.6"
+
+[pipenv]
+allow_prereleases = true

README.md

@@ -2,21 +2,35 @@
 ### Overview
 This service handles reading from and writing to a user's s3 folder containing their manifests. A manifest is a JSON file that lists records a researcher may be interested in analyzing. This service stores a manifest to a user folder in an s3 bucket and delivers it for later use, such as when the researcher wants to mount the manifest in their workspace. 
 
+Manifest files should contain JSON of the form 
+
+    [
+      {
+        "object_id": "757508f5-2697-4700-a69f-89d173a4c514",
+        "subject_id": "da6a14a0-6498-4941-a1b2-bbe45a2ccac2"
+      },
+      {
+        "object_id": "835db5c6-5cc8-4d70-a3b2-9a18ad4912cd",
+        "subject_id": "da6a14a0-6498-4941-a1b2-bbe45a2ccac2"
+      },
+      ...
+    ]
+
 ### Endpoints
 
-For all endpoints, the request cookie should contain an access_token. The user needs read access and read-storage access
+For all endpoints, the request must contain an Authorization header with an access_token. The user needs read access and read-storage access
 on at least one project in order to use this service.
 
 Lists a user's manifests: 
 
     GET /
-    Returns: { "manifests" : [ "filename-1.json", "filename-2.json", ... ] }
+    Returns: { "manifests" : [ { "filename" : "manifest-2019-02-27T11-44-20.548126.json", "last_modified" : "2019-02-27 17:44:21" }, ... ] }
 
 Create a manifest file in the user's folder:
 
     POST /
     Post body: The contents of the manifest.json file to be created.
-    Returns: { "filename" : "the-timestamped-filename-generated-by-the-service.json" }
+    Returns: { "filename" : "manifest-2019-03-09T21-47-04.041499.json" }
 
 Read the contents of a manifest file in the user's folder:
 
@@ -28,11 +42,10 @@ On failure, the above endpoints all return JSON in the form
     { "error" : "error-message" }
 
 ### Running the service locally
-If you want to run this service locally, fill out manifest_service/dev_settings.py with the correct values and then run:
+If you want to run this service locally, fill out the config.json file with the correct values and then run:
 
-    virtualenv -p python3 ~/manifest_service_env
-    source ~/manifest_service_env/bin/activate
-    pip3 install  -r requirements.txt
+    pipenv shell --python 3.6
+    pipenv install --skip-lock --dev
     python3 run.py
 
 And then GET and POST to http://localhost:5000/

build_openapi.py

@@ -4,7 +4,7 @@
 from flasgger import Swagger, Flasgger
 from yaml.representer import Representer
 
-from manifest_service.api import app
+from manifestservice.api import app
 from openapi.app_info import app_info
 
 

config.json

@@ -0,0 +1,6 @@
+{
+    "aws_access_key_id": "",
+    "aws_secret_access_key": "",
+    "manifest_bucket_name" : "",
+    "hostname": ""
+}

deployment/nginx/uwsgi.conf

@@ -5,25 +5,30 @@ server {
         uwsgi_param REMOTE_ADDR $http_x_forwarded_for if_not_empty;
         uwsgi_param REMOTE_USER $http_x_userid if_not_empty;
 
+        ## GEN3_REQUEST_TIMESTAMP and GEN3_TIMEOUT_SECONDS
+        # These two together aligns the HARAKIRI timeout in uWSGI with NGINX
+        # See also https://github.com/uc-cdis/cdis-python-utils#uwsgi
+        uwsgi_param GEN3_REQUEST_TIMESTAMP $msec;
+        uwsgi_param GEN3_TIMEOUT_SECONDS '20';
+
         include uwsgi_params;
-        uwsgi_pass unix:/var/www/manifest_service/uwsgi.sock;
+        uwsgi_pass unix:/var/www/manifestservice/uwsgi.sock;
         uwsgi_read_timeout 20s;
         uwsgi_send_timeout 20s;
     }
 
     location /_status {
-        uwsgi_param REMOTE_ADDR $http_x_forwarded_for if_not_empty;
-        uwsgi_param REMOTE_USER $http_x_userid if_not_empty;
-
         include uwsgi_params;
-        uwsgi_pass unix:/var/www/manifest_service/uwsgi.sock;
+        uwsgi_pass unix:/var/www/manifestservice/uwsgi.sock;
         uwsgi_read_timeout 20s;
-        uwsgi_send_timeout 20s;
+        uwsgi_param GEN3_REQUEST_TIMESTAMP $msec;
+        uwsgi_param GEN3_TIMEOUT_SECONDS $arg_timeout;
+        uwsgi_ignore_client_abort on;
         access_log off;
     }
 
     error_page 504 /504.html;
     location /504.html {
         return 504 '{"error": {"Request Timeout"}}';
     }
-}
+}

deployment/uwsgi/uwsgi.ini

@@ -1,20 +1,40 @@
 [uwsgi]
 protocol = uwsgi
-socket = /var/www/manifest_service/uwsgi.sock
+socket = /var/www/manifestservice/uwsgi.sock
 buffer-size = 32768
 chmod-socket = 666
 master = true
 harakiri-verbose = 20
 disable-logging = true
-wsgi-file=/manifest_service/wsgi.py
+wsgi-file=/manifestservice/wsgi.py
 plugins = python3
 vacuum = true
-chdir = /manifest_service/
+chdir = /manifestservice/
 uid = nginx
 gid = nginx
+# pythonpath = /usr/local/lib/site-packages/
+virtualenv = $(VENV)
 pythonpath = /usr/local/lib/python3.6/site-packages/
 
 
+# [uwsgi]
+# protocol = uwsgi
+# socket = /var/www/wts/uwsgi.sock
+# buffer-size = 32768
+# chmod-socket = 666
+# master = true
+# harakiri-verbose = 20
+# disable-logging = true
+# wsgi-file=/wts/wsgi.py
+# plugins = python3
+# vacuum = true
+# chdir = /wts/
+# uid = nginx
+# gid = nginx
+# virtualenv = $(VENV)
+# pythonpath = /usr/local/lib/python3.6/site-packages/
+
+
 # Use this to initialize application in worker processes, not master. This
 # prevents the workers from all trying to open the same database
 # connections at startup:

deployment/uwsgi/wsgi.py

@@ -1,2 +1,2 @@
-from manifest_service.api import app
+from manifestservice.api import app
 application = app

dockerrun.bash

@@ -1,7 +1,8 @@
 #!/bin/bash
 
+cd /$appname
+export VENV=$(pipenv --venv)
 cd /var/www/$appname
-
 #
 # Update certificate authority index -
 # environment may have mounted more authorities
@@ -10,6 +11,7 @@ update-ca-certificates
 #
 # Enable debug flag based on GEN3_DEBUG environment
 #
+
 if [[ -f ./wsgi.py && "$GEN3_DEBUG" == "True" ]]; then
   echo -e "\napplication.debug=True\n" >> ./wsgi.py
 fi