fortran-lang · henilp105 · Nov 29, 2023 · Nov 12, 2023 · Nov 12, 2023 · Nov 14, 2023
diff --git a/.docker/docker-compose.yaml b/.docker/docker-compose.yaml
diff --git a/.gitignore b/.gitignore
@@ -1,11 +1,38 @@
+# See https://help.github.com/articles/ignoring-files/ for more about ignoring files.
+
 /.vscode/
 /.docker/
-/flask/__pycache__/
-/flask/.env
-/flask/vercel.json
-/flask/static/
-/flask/.vercel
-/frontend/node_modules/
-tests/__pycache__/
+
+# backend
+/backend/.env
+/backend/vercel.json
+/backend/static/*.tar.gz
+/backend/__pycache__/
+/backend/.vercel
+/backend/app.log
 /.DS_Store
-/flask/.DS_Store
+/backend/.DS_Store
+
+# dependencies
+/frontend/node_modules
+/frontend//.pnp
+/frontend/.pnp.js
+
+# testing
+.pytest_cache/
+/frontend/coverage
+tests/__pycache__/
+
+# production
+/frontend/build
+
+# misc
+/frontend/.DS_Store
+/frontend/.env.local
+/frontend/.env.development.local
+/frontend/.env.test.local
+/frontend/.env.production.local
+
+/frontend/npm-debug.log*
+/frontend/yarn-debug.log*
+/frontend/yarn-error.log*
diff --git a/README.md b/README.md
@@ -1,46 +1,45 @@
-# Registry for Fortran package manager
+# Registry for Fortran Package Manager
 
-Currently for the testing phase :
-1. backend APIs are hosted at:  http://registry-apis.vercel.app/
-2. frontend is hosted at: https://registry-frontend.vercel.app/
-3. Documentation for the APIs are available at: https://registry-apis.vercel.app/apidocs/
+We are currently in the testing phase of this registry.
+
+1. backend APIs are hosted at: https://fpm-registry.vercel.app/
+2. frontend is hosted at: https://registry-phi.vercel.app/
+3. Documentation for the APIs are available at: https://fpm-registry.vercel.app/apidocs/
 
 **Please note: the current registry is a playground: its database will be fully deleted once its functionality is established. Please do not use it for production yet! more information will follow then.**
 
 The fpm release [0.8.2](https://fortran-lang.discourse.group/t/fpm-version-0-8-2-released-centralized-registry-playground/5792) introduces fpm support for uploading packages to the fpm-registry server directly from the command-line interface, via
 
 ```
-fpm publish --token <token-here>
+fpm publish --token <upload-token-here>
 ```
 
-fpm will now interact with a web interface that will help to manage the namespaces & packages.
-
+fpm will now also interact with a web interface that will help to manage the namespaces & packages. detailed information regarding the fpm cli can be found here: [docs](https://fpm.fortran-lang.org/registry/index.html)
 
-## fpm - registry : Python Flask app with Nginx and Mongo database
+## Instructions to Deploy with docker containers
 
-backend Project structure:
 ```
-.
-├── compose.yaml
-├── flask
-│   ├── Dockerfile
-│   ├── requirements.txt
-│   └── server.py
-|   └── app.py
-|   └── auth.py
-|   └── mongo.py
-|   └── .env
-└── nginx
-    └── nginx.conf
-
+$ sudo chmod 666 /var/run/docker.sock  # for root access
 ```
 
-## Instructions for Deploy with docker compose
+## Environment variable configuration
+
+set the environment variables in .env file in backend directory or in the docker compose file (compose.yaml). MONGO_URI must be set in the environment to the URL value of the MongoDB to use. For example,If deploying to production, MONGO_URI should be set to mongo container address. set the following env variables in the .env file in the backend folder: 
+   - SALT
+   - MONGO_URI=MONGO_DB_ATLAS_UR
+   - MONGO_DB_NAME
+   - SUDO_PASSWORD
+   - MONGO_USER_NAME
+   - MONGO_PASSWORD
+   - HOST
+   - RESET_EMAIL 
+   - RESET_PASSWORD
+
+#### before building the docker containers, you must configure the environment variables ("RESET_EMAIL" and "RESET_PASSWORD") in the compose.yaml file .
 
 ```
-$ sudo chmod 666 /var/run/docker.sock  (for root access)
-$ docker compose up -d
-$ REACT_APP_REGISTRY_API_URL="http://127.0.0.1:9090"  npm start run
+$ docker compose -f "compose.yaml" up -d --build
+$ cd frontend && REACT_APP_REGISTRY_API_URL="http://127.0.0.1:80"  npm start run
 ```
 
 After the application starts, navigate to `http://localhost:80` in your web browser or run:
@@ -50,19 +49,6 @@ $ curl localhost:80
 Hello world, Mongo Flask
 ```
 
-set MONGO_URI=MONGO_DB_ATLAS_URL (in .env file in flask directory)
-The MONGO_URI must be set in the environment (or, alternatively, in the .env file in the flask directory) to the URL value of the MongoDB to use. For example,If deploying to production, MONGO_URI should be set to mongo container address.
-set the following env variables in the .env file in the flask folder: 
-   - SALT
-   - MONGO_URI
-   - MONGO_DB_NAME
-   - SUDO_PASSWORD
-   - MONGO_USER_NAME
-   - MONGO_PASSWORD
-   - HOST
-   - RESET_EMAIL 
-   - RESET_PASSWORD
-
 Stop and remove the containers
 
 ```

diff --git a/flask/app.py → backend/app.py b/flask/app.py → backend/app.py
diff --git a/flask/auth.py → backend/auth.py b/flask/auth.py → backend/auth.py
@@ -19,13 +19,15 @@
     sudo_password = os.getenv("SUDO_PASSWORD")
     fortran_email = os.getenv("RESET_EMAIL")
     fortran_password = os.getenv("RESET_PASSWORD")
+    is_ci = os.getenv("IS_CI", "false")
     host = os.getenv("HOST")
     env_var["host"] = host
     env_var["salt"] = salt
     env_var["sudo_password"] = sudo_password
-    smtp = smtplib.SMTP("smtp.gmail.com", 587)
-    smtp.starttls()
-    smtp.login(fortran_email, fortran_password)
+    if is_ci!="true":
+        smtp = smtplib.SMTP("smtp.gmail.com", 587)
+        smtp.starttls()
+        smtp.login(fortran_email, fortran_password)
 
 except KeyError as err:
     print("Add SALT to .env file")
@@ -60,7 +62,7 @@ def login():
     if not user:
         return jsonify({"message": "Invalid email or password", "code": 401}), 401
 
-    if not user["isverified"]:
+    if not user["isverified"] and is_ci!='true':    # TODO: Uncomment this line to enable email verification
         return jsonify({"message": "Please verify your email", "code": 401}), 401
 
     uuid = generate_uuid() if user["loggedCount"] == 0 else user["uuid"]
@@ -143,7 +145,7 @@ def signup():
         else:
             user["roles"] = ["user"]
         db.users.insert_one(user)
-        send_verify_email(email)
+        send_verify_email(email) if is_ci != 'true' else None
         return (
             jsonify(
                 {

diff --git a/flask/backend.Dockerfile → backend/docker/backend.Dockerfile b/flask/backend.Dockerfile → backend/docker/backend.Dockerfile
diff --git a/flask/validate_package.Dockerfile → backend/docker/validate_package.Dockerfile b/flask/validate_package.Dockerfile → backend/docker/validate_package.Dockerfile
@@ -15,7 +15,7 @@ USER root
 WORKDIR /home/registry
 
 # Set up fpm
-RUN wget https://github.com/fortran-lang/fpm/releases/download/v0.8.0/fpm-0.8.0-linux-x86_64 -4 -O fpm && \
+RUN wget https://github.com/fortran-lang/fpm/releases/download/v0.9.0/fpm-0.9.0-linux-x86_64 -4 -O fpm && \
     chmod u+x fpm
 
 WORKDIR /home/registry
diff --git a/flask/documentation/add_namespace_admin.yaml → ...nd/documentation/add_namespace_admin.yaml b/flask/documentation/add_namespace_admin.yaml → ...nd/documentation/add_namespace_admin.yaml
diff --git a/...cumentation/add_namespace_maintainer.yaml → ...cumentation/add_namespace_maintainer.yaml b/...cumentation/add_namespace_maintainer.yaml → ...cumentation/add_namespace_maintainer.yaml
diff --git a/...documentation/add_package_maintainer.yaml → ...documentation/add_package_maintainer.yaml b/...documentation/add_package_maintainer.yaml → ...documentation/add_package_maintainer.yaml
diff --git a/flask/documentation/check_admin_user.yaml → backend/documentation/check_admin_user.yaml b/flask/documentation/check_admin_user.yaml → backend/documentation/check_admin_user.yaml
diff --git a/flask/documentation/create_namespace.yaml → backend/documentation/create_namespace.yaml b/flask/documentation/create_namespace.yaml → backend/documentation/create_namespace.yaml
diff --git a/...tation/create_namespace_upload_token.yaml → ...tation/create_namespace_upload_token.yaml b/...tation/create_namespace_upload_token.yaml → ...tation/create_namespace_upload_token.yaml
diff --git a/...entation/create_package_upload_token.yaml → ...entation/create_package_upload_token.yaml b/...entation/create_package_upload_token.yaml → ...entation/create_package_upload_token.yaml
diff --git a/flask/documentation/delete_namespace.yaml → backend/documentation/delete_namespace.yaml b/flask/documentation/delete_namespace.yaml → backend/documentation/delete_namespace.yaml
diff --git a/flask/documentation/delete_package.yaml → backend/documentation/delete_package.yaml b/flask/documentation/delete_package.yaml → backend/documentation/delete_package.yaml
diff --git a/...documentation/delete_package_version.yaml → ...documentation/delete_package_version.yaml b/...documentation/delete_package_version.yaml → ...documentation/delete_package_version.yaml
diff --git a/flask/documentation/delete_user.yaml → backend/documentation/delete_user.yaml b/flask/documentation/delete_user.yaml → backend/documentation/delete_user.yaml
diff --git a/flask/documentation/forgot_password.yaml → backend/documentation/forgot_password.yaml b/flask/documentation/forgot_password.yaml → backend/documentation/forgot_password.yaml
diff --git a/...k/documentation/get_namespace_admins.yaml → ...d/documentation/get_namespace_admins.yaml b/...k/documentation/get_namespace_admins.yaml → ...d/documentation/get_namespace_admins.yaml
diff --git a/...umentation/get_namespace_maintainers.yaml → ...umentation/get_namespace_maintainers.yaml b/...umentation/get_namespace_maintainers.yaml → ...umentation/get_namespace_maintainers.yaml
diff --git a/...documentation/get_namespace_packages.yaml → ...documentation/get_namespace_packages.yaml b/...documentation/get_namespace_packages.yaml → ...documentation/get_namespace_packages.yaml
diff --git a/flask/documentation/get_package.yaml → backend/documentation/get_package.yaml b/flask/documentation/get_package.yaml → backend/documentation/get_package.yaml
diff --git a/flask/documentation/get_tarball.yaml → backend/documentation/get_tarball.yaml b/flask/documentation/get_tarball.yaml → backend/documentation/get_tarball.yaml
diff --git a/flask/documentation/get_user_account.yaml → backend/documentation/get_user_account.yaml b/flask/documentation/get_user_account.yaml → backend/documentation/get_user_account.yaml
diff --git a/flask/documentation/get_user_profile.yaml → backend/documentation/get_user_profile.yaml b/flask/documentation/get_user_profile.yaml → backend/documentation/get_user_profile.yaml
diff --git a/flask/documentation/get_version.yaml → backend/documentation/get_version.yaml b/flask/documentation/get_version.yaml → backend/documentation/get_version.yaml
diff --git a/flask/documentation/login.yaml → backend/documentation/login.yaml b/flask/documentation/login.yaml → backend/documentation/login.yaml
diff --git a/flask/documentation/logout.yaml → backend/documentation/logout.yaml b/flask/documentation/logout.yaml → backend/documentation/logout.yaml
diff --git a/flask/documentation/package_maintainers.yaml → ...nd/documentation/package_maintainers.yaml b/flask/documentation/package_maintainers.yaml → ...nd/documentation/package_maintainers.yaml
diff --git a/flask/documentation/package_upload.yaml → backend/documentation/package_upload.yaml b/flask/documentation/package_upload.yaml → backend/documentation/package_upload.yaml
diff --git a/...documentation/remove_namespace_admin.yaml → ...documentation/remove_namespace_admin.yaml b/...documentation/remove_namespace_admin.yaml → ...documentation/remove_namespace_admin.yaml
diff --git a/...entation/remove_namespace_maintainer.yaml → ...entation/remove_namespace_maintainer.yaml b/...entation/remove_namespace_maintainer.yaml → ...entation/remove_namespace_maintainer.yaml
diff --git a/...umentation/remove_package_maintainer.yaml → ...umentation/remove_package_maintainer.yaml b/...umentation/remove_package_maintainer.yaml → ...umentation/remove_package_maintainer.yaml
diff --git a/flask/documentation/reset_password.yaml → backend/documentation/reset_password.yaml b/flask/documentation/reset_password.yaml → backend/documentation/reset_password.yaml
diff --git a/flask/documentation/search_packages.yaml → backend/documentation/search_packages.yaml b/flask/documentation/search_packages.yaml → backend/documentation/search_packages.yaml
diff --git a/flask/documentation/signup.yaml → backend/documentation/signup.yaml b/flask/documentation/signup.yaml → backend/documentation/signup.yaml
diff --git a/flask/documentation/transfer_account.yaml → backend/documentation/transfer_account.yaml b/flask/documentation/transfer_account.yaml → backend/documentation/transfer_account.yaml
diff --git a/flask/documentation/verify_user_role.yaml → backend/documentation/verify_user_role.yaml b/flask/documentation/verify_user_role.yaml → backend/documentation/verify_user_role.yaml
diff --git a/flask/mongo.py → backend/mongo.py b/flask/mongo.py → backend/mongo.py
diff --git a/flask/namespaces.py → backend/namespaces.py b/flask/namespaces.py → backend/namespaces.py
diff --git a/flask/packages.py → backend/packages.py b/flask/packages.py → backend/packages.py
@@ -7,17 +7,16 @@
 from datetime import datetime, timedelta
 from auth import generate_uuid
 from app import swagger
-import zipfile
 import tarfile
-import io
+import os
 import toml
+import shutil
 from flasgger.utils import swag_from
 from urllib.parse import unquote
 import math
 import semantic_version
 from license_expression import get_spdx_licensing
-from io import BytesIO
-# import validate_package
+# from validate_package import validate
 
 
 parameters = {
@@ -252,39 +251,21 @@ def upload():
         {"name": package_name, "namespace": namespace_doc["_id"]}
     )
 
-    if tarball.content_type not in ["application/gzip", "application/zip","application/octet-stream"]:
+    if tarball.content_type not in ["application/gzip", "application/zip","application/octet-stream","application/x-tar"]:
         return jsonify({"code": 400, "message": "Invalid file type"}), 400
 
     tarball_name = "{}-{}.tar.gz".format(package_name, package_version)
-    # Upload the tarball to the Grid FS storage.
-
-    # try: TODO: Enable this after Validation is Enabled
-    #     zipball, tarball = get_file_object(tarball)
-    # except Exception as e:
-    #     return jsonify({"code": 400, "message": "Invalid package tarball."}), 400
-
-    # zipfile_object_id = file_storage.put(
-    #     zipball, content_type=zipball.content_type, filename=tarball_name + ".zip"
-    # )
-    # tarfile_object_id = file_storage.put(
-    #     tarball, content_type=tarball.content_type, filename=tarball_name + ".tar.gz"
-    # )
-    file_object_id = file_storage.put(
-        tarball, content_type=tarball.content_type, filename=tarball_name
-    )
 
-    # Extract the package metadata from the tarball's fpm.toml file.
-    try:
-        package_data = extract_fpm_toml(tarball)
-    except Exception as e:
-        return jsonify({"code": 400, "message": "Invalid package tarball."}), 400
 
-    # TODO: Uncomment this when the package validation is enabled
+    package_data = extract_toml(tarball)
     # validate the package with fpm
+    # valid_package, package_data = validate(tarball,"{}-{}".format(package_name, package_version))  # TODO: Enable this after Validation is Enabled
+
+
+    # if not valid_package: # TODO: Enable this after Validation is Enabled
+    #     return jsonify({"code": 400, "message": "Invalid package"}), 400    
 
-    # valid_package = validate_package.validate_package(tarball,"{}-{}".format(package_name, package_version))
-    # if not valid_package:
-    #     return jsonify({"status": "error", "message": "Invalid package", "code": 400}), 400
+    file_object_id = file_storage.put(tarball, content_type=tarball.content_type, filename=tarball_name)
 
     # No previous recorded versions of the package found.
     if not package_doc:
@@ -295,12 +276,12 @@ def upload():
                 "description": package_data["description"],
                 "homepage": package_data["homepage"],
                 "repository": package_data["repository"],
+                "copyright": package_data["copyright"],
                 "license": package_license,
                 "createdAt": datetime.utcnow(),
                 "updatedAt": datetime.utcnow(),
                 "author": user["_id"],
                 "maintainers": [user["_id"]],
-                "copyright": package_data["copyright"],
                 "tags": ["fortran", "fpm"],
                 "isDeprecated": False,
             }
@@ -321,8 +302,7 @@ def upload():
             "dependencies": "Test dependencies",
             "createdAt": datetime.utcnow(),
             "isDeprecated": False,
-            # "download_url_zip": f"/tarballs/{zipfile_object_id}",  TODO: Uncomment this when the package validation is enabled
-            # "download_url_tar": f"/tarballs/{tarfile_object_id}",
+            "download_url": f"/tarballs/{file_object_id}"
         }
 
         package_obj["versions"] = []
@@ -331,7 +311,7 @@ def upload():
         package_obj["versions"].append(version_obj)
 
         if dry_run:
-            return jsonify({"message": "Dry run Successful.", "code": 200})
+            return jsonify({"message": "Dry run Successful.", "code": 200}), 200
 
         db.packages.insert_one(package_obj)
 
@@ -805,53 +785,19 @@ def checkUserUnauthorizedForNamespaceTokenCreation(user_id, namespace_doc):
     return str_user_id not in admins_id_list and str_user_id not in maintainers_id_list
 
 
-def extract_fpm_toml(file_obj):
-    binary_stream = BytesIO()
-    binary_stream.write(file_obj.getbuffer())
-    binary_stream.seek(0)
-    tar = tarfile.open(fileobj=binary_stream, mode='r')
-    fpm_toml_file = None
-    for file in tar.getmembers():
-        if file.name == 'fpm.toml':
-            fpm_toml_file = file
-            break
-
-    if fpm_toml_file is None:
-        raise ValueError("fpm.toml file not found in the tarball.")
-
-    extracted_file = tar.extractfile(fpm_toml_file)
-    toml_data = extracted_file.read()
-    tar.close()
-    parsed_toml = toml.loads(str(toml_data, 'utf-8'))
-    return parsed_toml
-
-def convert_zip_to_tar(zip_file):
-    tar_file = io.BytesIO()
-    with zipfile.ZipFile(zip_file, 'r') as zip_ref:
-        with tarfile.open(fileobj=tar_file, mode='w') as tar_ref:
-            for file_name in zip_ref.namelist():
-                file_data = zip_ref.read(file_name)
-                tar_info = tarfile.TarInfo(name=file_name)
-                tar_info.size = len(file_data)
-                tar_ref.addfile(tar_info, fileobj=io.BytesIO(file_data))
-
-    tar_file.seek(0)  # Reset the file position for reading    
-    return tar_file
-
-
-def convert_to_zip(file_obj):
-    with tarfile.open(file_obj, "r:gz") as tar:
-        tar.extractall()
-        with zipfile.ZipFile("package.zip", "w") as zip_ref:
-            zip_ref.write("fpm.toml")
-            zip_ref.write("package")
-    return zip_ref
-
-
-def get_file_object(file_obj):
-    if file_obj.content_type == "application/zip":
-        return file_obj, convert_zip_to_tar(file_obj)
-    elif file_obj.content_type == "application/gzip":
-        return convert_to_zip(file_obj), file_obj
-    else:
-        raise Exception("Invalid file type")
+def extract_toml(file):
+    with open('static/temp/temp.tar.gz', 'wb') as f:
+        f.write(file.read())
+    with tarfile.open('static/temp/temp.tar.gz', "r") as tar:
+        tar.extractall("static/temp")
+
+    for root, dirs, files in os.walk('static/temp'):
+        file_name = 'fpm.toml'
+        if file_name in files:
+            file_path = os.path.join(root, file_name)
+            with open(file_path, 'r') as file:
+                file_content = file.read()
+            shutil.rmtree('static/temp')
+            os.makedirs('static/temp', exist_ok=True)
+            parsed_toml = toml.loads(file_content)
+            return parsed_toml
diff --git a/flask/requirements.txt → backend/requirements.txt b/flask/requirements.txt → backend/requirements.txt