feat: project setup, add method GET for contexts and terms TSV along with test files

.gitignore

+.venv/
+
+*.pyc
+__pycache__/
+
+instance/
+
+.pytest_cache/
+.coverage
+htmlcov/
+
+dist/
+build/
+*.egg-info/

README.md

-# GarganTools
+## About The project
 
+## Virtual environment
+
+Create a vitual environment
+```shell
+python3 -m venv .venv
+```
+
+enter environment
+```shell
+. .venv/bin/activate
+```
+
+exit environment
+```shell
+deactivate
+```
+
+## Install needed packages
+
+for executing web app :
+```shell
+pip install -r requirement.txt
+```
+
+for executing test and coverage : 
+```shell
+pip install -e .
+pip install -r requirement_test.txt
+```
+
+## Tests and Coverage
+
+Executing tests and coverage
+```shell
+coverage run -m pytest
+```
+
+View coverage report
+```shell
+coverage report
+coverage html
+```
+
+## Start Project
+
+```shell
+flask --app gargantools.py run
+```

gargantools/__init__.py

+import os
+
+from flask import Flask
+
+
+def create_app(test_config=None):
+    # create and configure the app
+    app = Flask(__name__, instance_relative_config=True)
+    app.config.from_mapping(
+        SECRET_KEY='dev'
+    )
+
+    if test_config is None:
+        # load the instance config, if it exists, when not testing
+        app.config.from_pyfile('config.py', silent=True)
+    else:
+        # load the test config if passed in
+        app.config.from_mapping(test_config)
+
+    # ensure the instance folder exists
+    try:
+        os.makedirs(app.instance_path)
+    except OSError:
+        pass
+
+    # will later become the homepage
+    @app.get('/')
+    def homepage():
+        return 'Welcome to GarganTools'
+
+    # a simple page that says hello
+    @app.get('/hello')
+    def hello():
+        return 'Hello, World!'
+
+    from . import contexts
+    from . import terms
+
+    app.register_blueprint(contexts.bp)
+
+    app.register_blueprint(terms.bp)
+
+    return app

gargantools/contexts.py

+import json
+from flask import Blueprint
+
+
+bp = Blueprint("contexts", __name__, url_prefix="/contexts")
+
+@bp.get('')
+def tsvTemplate():
+    return json.dumps({"Publication Day": 1, "Publication Month": 1, "Publication Year": 1, "Authors": "Some authors", "Title": "A title", "Abstract": "An abstract", "Source": "Some Source" }, indent=3)

gargantools/terms.py

+import json
+from flask import Blueprint
+
+
+bp = Blueprint("terms", __name__, url_prefix="/terms")
+
+@bp.get('')
+def termsTemplate():
+    return json.dumps({"status": "MapTerm", "label": "A term"}, indent=3)

gargantools/utils.py

+ALLOWED_EXTENSIONS = {'csv', 'tsv'}
+
+def allowed_file(filename):
+    return '.' in filename and \
+        filename.rsplit('.', 1)[1].lower() in ALLOWED_EXTENSIONS
+ 
\ No newline at end of file

openapi.yaml

+openapi: '3.0.3'
+info:
+  title: GarganTools
+  version: '1.0.0'
+  description: Are listed here all methods related to the web application GarganTools used to convert any documents format to a format compatible with GarganText.
+servers:
+  - url: http://127.0.0.1:5000
+tags:
+  - name: contexts
+    description: Convertion from any format to TSV
+  - name: terms
+    description: Convertion from any format to terms TSV
+  - name: api
+    description: API using tools
+paths:
+  /contexts:
+    get:
+      tags:
+        - contexts
+      summary: Get the columns that should be in a documents CSV file
+      description: .
+      operationId: tsvTemplate
+      responses:
+        '200':
+          description: successful operation
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/CSV'
+        '404':
+          description: Not Found
+    post:
+      tags:
+        - contexts
+      summary: Operation on one or multiple files of different origin
+      description: .
+      operationId: tsvOperation
+      parameters:
+        - in: query
+          name: from
+          schema:
+            type: string
+            enum:
+              - Harzing
+              - RIS
+              - Element
+              - MultivacTwitterX
+              - Europresse
+              - Prospéro
+              - PDF
+      requestBody:
+        content:
+          multipart/form-data:
+            schema:
+              type: object
+              required:
+                - file
+              properties:
+                newFileName:
+                  type: string
+                  default: ''
+                file:
+                  $ref: '#/components/schemas/File'
+                headerMapping:
+                  $ref: '#/components/schemas/CSVmapping'
+      responses:
+        '200':
+          description: TSV file or ZIP of TSV files
+          content:
+            application/octet-stream:
+              schema:
+                $ref: '#/components/schemas/File'
+        '400':
+          description: Bad Request
+        '404':
+          description: Not Found
+        '422':
+          description: Unprocessable Content
+        '500':
+          description: Unexpected Error
+  /contexts/pdf:
+    post:
+      tags:
+        - contexts
+      summary: Operation on one or multiple PDF files
+      description: .
+      operationId: anyPDFtoTSV
+      parameters:
+        - in: query
+          name: split
+          schema:
+              type: integer
+              example: 7
+              default: 7
+              maximum: 15
+      requestBody:
+        content:
+          multipart/form-data:
+            schema:
+              type: object
+              required:
+                - file
+              properties:
+                newFileName:
+                  type: string
+                  default: ''
+                file:
+                  $ref: '#/components/schemas/File'
+                metadata:
+                  type: string
+                  format: binary
+      responses:
+        '200':
+          description: TSV file or ZIP of TSV files
+          content:
+            application/octet-stream:
+              schema:
+                $ref: '#/components/schemas/File'
+        '400':
+          description: Bad Request
+        '404':
+          description: Not Found
+        '422':
+          description: Unprocessable Content
+        '500':
+          description: Unexpected Error
+  /contexts/pdf/scientific:
+    post:
+      tags:
+        - contexts
+      summary: Operation on one or multiple PDF files
+      description: .
+      operationId: scientificPDFtoTSV
+      parameters:
+        - in: query
+          name: select
+          schema:
+            type: array
+            items:
+              type: string
+      requestBody:
+        content:
+          multipart/form-data:
+            schema:
+              type: object
+              required:
+                - file
+              properties:
+                newFileName:
+                  type: string
+                  default: ''
+                file:
+                  $ref: '#/components/schemas/File'
+                metadata:
+                  type: string
+                  format: binary
+      responses:
+        '200':
+          description: TSV file or ZIP of TSV files
+          content:
+            application/octet-stream:
+              schema:
+                $ref: '#/components/schemas/File'
+        '400':
+          description: Bad Request
+        '404':
+          description: Not Found
+        '422':
+          description: Unprocessable Content
+        '500':
+          description: Unexpected Error
+  /terms:
+    get:
+      tags:
+        - terms
+      summary: Get the columns that should be in a terms CSV file
+      description: .
+      operationId: termsTemplate
+      responses:
+        '200':
+          description: successful operation
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/Terms'
+        '404':
+          description: Not Found
+    post:
+      tags:
+        - terms
+      summary: Operation on one or multiple files concerning terms
+      description: .
+      operationId: termsOperation
+      parameters:
+        - in: query
+          name: from
+          schema:
+            type: string
+            enum:
+              - TXT
+              - Prospero
+              - GarganTextGEXF
+      requestBody:
+        content:
+          multipart/form-data:
+            schema:
+              type: object
+              required:
+                - file
+              properties:
+                newFileName:
+                  type: string
+                  default: ''
+                file:
+                  $ref: '#/components/schemas/File'
+                headerMapping:
+                  $ref: '#/components/schemas/TermsMapping'
+      responses:
+        '200':
+          description: terms TSV file or ZIP of terms TSV files
+          content:
+            application/octet-stream:
+              schema:
+                $ref: '#/components/schemas/File'
+        '400':
+          description: Bad Request
+        '404':
+          description: Not Found
+        '422':
+          description: Unprocessable Content
+        '500':
+          description: Unexpected Error
+  /api:
+    post:
+      tags:
+        - api
+      summary: Operation concerning API
+      description: .
+      operationId: apiOperation
+      parameters:
+        - in: query
+          name: language
+          schema:
+            type: string
+            enum:
+              - en
+              - fr
+              - es
+        - in: query
+          name: from
+          schema:
+            type: string
+            enum:
+              - Isidore
+      requestBody:
+        content:
+          multipart/form-data:
+            schema:
+              type: object
+              required:
+                - file
+              properties:
+                newFileName:
+                  type: string
+                  default: ''
+                file:
+                  $ref: '#/components/schemas/File'
+      responses:
+        '200':
+          description: TSV file
+          content:
+            application/octet-stream:
+              schema:
+                $ref: '#/components/schemas/File'
+        '400':
+          description: Bad Request
+        '404':
+          description: Not Found
+        '500':
+          description: Unexpected Error
+
+components:
+  schemas:
+    File:
+      type: string
+      format: binary
+    CSV:
+      type: object
+      properties:
+        Publication Day:
+          type: integer
+          minimum: 1
+          maximum: 31
+          example: 1
+        Publication Month:
+          type: integer
+          minimum: 1
+          maximum: 12
+          example: 1
+        Publication Year:
+          type: integer
+          minimum: 1
+          example: 1
+        Authors:
+          type: string
+          example: Some authors
+        Title:
+          type: string
+          example: A title
+        Abstract:
+          type: string
+          example: An abstract
+        Source:
+          type: string
+          example: Some Source
+    CSVmapping:
+      type: object
+      properties:
+        Publication Day:
+          type: string
+          example: my column name
+        Publication Month:
+          type: string
+          example: my column name
+        Publication Year:
+          type: string
+          example: my column name
+        Authors:
+          type: string
+          example: my column name
+        Title:
+          type: string
+          example: my column name
+        Abstract:
+          type: string
+          example: my column name
+        Source:
+          type: string
+          example: my column name
+    Terms:
+      type: object
+      properties:
+        status:
+          type: string
+          pattern: '^(Mapterm|CandidateTerm|StopTerm)$'
+          example: MapTerm
+        label:
+          type: string
+          example: A term
+    TermsMapping:
+      type: object
+      properties:
+        status:
+          type: string
+          example: my column name
+        label:
+          type: string
+          example: my column name
+                    
\ No newline at end of file

pyproject.toml

+[project]
+name = "gargantools"
+version = "1.0.0"
+description = "A web application for converting data from different format to a GarganText format"
+dependencies = [
+    "flask",
+]
+
+[build-system]
+requires = ["flit_core<4"]
+build-backend = "flit_core.buildapi"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[tool.coverage.run]
+branch = true
+source = ["gargantools"]

requirement.txt

+Flask==3.1.0
\ No newline at end of file

requirement_test.txt

+pytest==8.3.4
+coverage==7.6.10
\ No newline at end of file

tests/conftest.py

+import pytest
+from gargantools import create_app
+
+
+@pytest.fixture
+def app():
+
+    app = create_app({
+        'TESTING': True,
+    })
+
+    yield app
+    
+
+@pytest.fixture
+def client(app):
+    return app.test_client()
+
+@pytest.fixture
+def runner(app):
+    return app.test_cli_runner()

tests/test_factory.py

+from gargantools import create_app
+
+
+def test_config():
+    assert not create_app().testing
+    assert create_app({'TESTING': True}).testing
+
+def test_homepage(client):
+    response = client.get('/')
+    assert response.status_code == 200
+
+def test_hello(client):
+    response = client.get('/hello')
+    assert response.data == b'Hello, World!'
+    assert response.status_code == 200

tests/test_templates.py

+import json
+
+
+def test_tsvTemplate(client):
+    expected_response = str(json.dumps({"Publication Day": 1, "Publication Month": 1, "Publication Year": 1, "Authors": "Some authors", "Title": "A title", "Abstract": "An abstract", "Source": "Some Source"}, indent=3)).encode(encoding="utf-8")
+    response = client.get('/contexts')
+    assert response.data == expected_response
+    assert response.status_code == 200
+
+def test_termsTemplate(client):
+    expected_response = str(json.dumps({"status": "MapTerm", "label": "A term"}, indent=3)).encode(encoding="utf-8")
+    response = client.get('/terms')
+    assert response.data == expected_response
+    assert response.status_code == 200