Merge pull request #1254 from NASA-IMPACT/dev

merge bugfixes and ml integration to staging

Author: CarsonDavis

CHANGELOG.md

@@ -12,6 +12,24 @@ For each PR made, an entry should be added to this changelog. It should contain
   - etc.
 
 ## Changelog
+
+- 1209-bug-fix-document-type-creator-form
+  - Description: The dropdown on the pattern creation form needs to be set as multi as the default option since this is why the doc type creator form is used for the majority of multi-URL pattern creations. This should be applied to doc types, division types, and titles as well.
+  - Changes:
+    - Set the default value for `match_pattern_type` in `BaseMatchPattern` class is set to `2`
+    - Changed `test_create_simple_exclude_pattern` test within `TestDeltaExcludePatternBasics`
+    - Changed `test_create_division_pattern` and `test_create_document_type_pattern_single` within `TestFieldModifierPatternBasics`
+
+- 1052-update-cosmos-to-create-jobs-for-scrapers-and-indexers
+  - Description: The original automation set up to generate the scrapers and indexers automatically based on a collection workflow status change needed to be updated to more accurately reflect the curation workflow. It would also be good to generate the jobs during this process to streamline the same.
+  - Changes:
+    - Updated function nomenclature. Scrapers are Sinequa connector configurations that are used to scrape all the URLs prior to curation. Indexers are Sienqua connector configurations that are used to scrape the URLs post to curation, which would be used to index content on production. Jobs are used to trigger the connectors which are included as parts of joblists.
+    - Parameterized the convert_template_to_job method to include the job_source to streamline the value added to the `<Collection>` tag in the job XML.
+    - Updated the fields that are pertinenet to transfer from a scraper to an indexer. Also added a third level of XML processing to facilitate the same.
+    - scraper_template.xml and indexer_template.xml now contains the templates used for the respective configuration generation.
+    - Deleted the redundant webcrawler_initial_crawl.xml file.
+    - Added and updated tests on workflow status triggers.
+
 - 2889-serialize-the-tdamm-tags
   - Description: Have TDAMM serialzed in a specific way and exposed via the Curated URLs API to be consumed into SDE Test/Prod
   - Changes:
@@ -36,13 +54,38 @@ For each PR made, an entry should be added to this changelog. It should contain
     - Used regex to catch any HTML content comming in as an input to form fields
     - Called this class within the serializer for necessary fields
 
+- 1030-resolve-0-value-document-type-in-nasa_science
+  - Description: Around 2000 of the docs coming out of the COSMOS api for nasa_science have a doc type value of 0.
+  - Changes:
+    - Added `obj.document_type != 0` as a condition in the `get_document_type` method within the `CuratedURLAPISerializer`
+
+- 1014-add-logs-when-importing-urls-so-we-know-how-many-were-expected-how-many-succeeded-and-how-many-failed
+  - Description: When URLs of a given collection are imported into COSMOS, a Slack notification is sent. This notification includes the name of the collection imported,count of the existing curated URLs, total URLs count as per the server, URLs successfully imported from the server, delta URLs identified and delta URLs marked for deletion.
+  - Changes:
+    - The get_full_texts() function in sde_collections/sinequa_api.py is updated to yeild total_count along with rows.
+    - fetch_and_replace_full_text() function in sde_collections/tasks.py captures the total_server_count and triggers send_detailed_import_notification().
+    - Added a function send_detailed_import_notification() in sde_collections/utils/slack_utils.py to structure the notification to be sent.
+    - Updated the associated tests effected due to inclusion of this functionality.
+
+- 3228-bugfix-preserve-scroll-position--document-type-selection-behavior-on-individual-urls
+  - Description: Upon selecting a document type on any individual URL, the page refreshes and returns to the top. This is not necessarily a bug but an inconvenience, especially when working at the bottom of the page. Fix the JS code.
+  - Changes:
+    - Added a constant `scrollPosition` within `postDocumentTypePatterns` to store the y coordinate postion on the page
+    - Modified the ajax relaod to navigate to this position upon posting/saving the document type changes.
+
 - 3227-bugfix-title-patterns-selecting-multi-url-pattern-does-nothing
   - Description: When selecting options from the match pattern type filter, the system does not filter the results as expected. Instead of displaying only the chosen variety of patterns, it continues to show all patterns.
   - Changes:
     - In `title_patterns_table` definition, corrected the column reference
     - Made `match_pattern_type` searchable
     - Corrected the column references and made code consistent on all the other tables, i.e., `exclude_patterns_table`, `include_patterns_table`, `division_patterns_table` and `document_type_patterns_table`
 
+- 1190-add-tests-for-job-generation-pipeline
+  - Description: Tests have been added to enhance coverage for the config and job creation pipeline, alongside comprehensive tests for XML processing.
+  - Changes:
+    - Added config_generation/tests/test_config_generation_pipeline.py which tests the config and job generation pipeline, ensuring all components interact correctly
+    - config_generation/tests/test_db_to_xml.py is updated to include comprehensive tests for XML Processing
+
 - 1001-tests-for-critical-functionalities
   - Description: Critical functionalities have been identified and listed, and critical areas lacking tests listed
   - Changes:
@@ -65,3 +108,32 @@ For each PR made, an entry should be added to this changelog. It should contain
     - Added universal search functionality tests
     - Created search pane filter tests
     - Added pattern application form tests with validation checks
+
+- 1101-bug-fix-quotes-not-escaped-in-titles
+  - Description: Title rules that include single quotes show up correctly in the sinequa frontend (and the COSMOS api) but not in the delta urls page.
+  - Changes:
+    - Added `escapeHtml` function in the `delta_url_list.js` file to handle special character escaping correctly.
+    - Called this function while retrieving the titles in `getGeneratedTitleColumn()` and `getCuratedGeneratedTitleColumn()` functions.
+
+- 1240-fix-code-scanning-alert-inclusion-of-functionality-from-an-untrusted-source
+  - Description: Ensured all external resources load securely by switching to HTTPS and adding Subresource Integrity (SRI) checks.
+  - Changes:
+    - Replaced protocol‑relative URLs with HTTPS.
+    - Added SRI (integrity) and crossorigin attributes to external script tags.
+
+- 1196-arrange-the-show-100-csv-customize-columns-boxes-to-be-in-one-line-on-the-delta-urls-page
+  changelog-update-Issue-1001
+  - Description: Formatting the buttons - 'Show 100','CSV' and 'Customize Columns' to be on a single line for an optimal use of space.
+  - Changes:
+    - Updated delta_url_list.css and delta_url_list.js files with necessary modifications
+
+- 1246-minor-enhancement-document-type-pattern-form-require-document-type-or-show-appropriate-error
+  - Description: In the Document Type Pattern Form, if the user does not select a Document Type while filling out the form, an appropriate error message is displayed.
+  - Changes:
+    - Added a JavaScript validation check on form submission to ensure the document type (stored in a hidden input) is not empty.
+    - Display an error message and prevent form submission if the field is empty.
+
+- 1249-add-https-link-to-cors_allowed_origins-for-sde-lrm
+  - Description: The feedback form API was throwing CORS errors and to rectify that, we need to add the apt https link for sde-lrm.
+  - Changes:
+    - Added `https://sde-lrm.nasa-impact.net` to `CORS_ALLOWED_ORIGINS` in the base settings.

compose/local/django/start

@@ -1,3 +1,4 @@
+#compose/local/django/start
 #!/bin/bash
 
 set -o errexit

compose/production/django/Dockerfile

@@ -1,3 +1,4 @@
+# compose/production/django/Dockerfile
 # define an alias for the specfic python version used in this file.
 FROM python:3.10.14-slim-bullseye AS python
 

compose/production/django/start

@@ -1,3 +1,4 @@
+# compose/production/django/start
 #!/bin/bash
 
 set -o errexit

compose/production/traefik/traefik.yml

@@ -1,3 +1,4 @@
+# compose/production/traefik/traefik.yml
 log:
   level: INFO
 

config/celery.py

@@ -0,0 +1,24 @@
+# config/celery.py
+import os
+
+from celery import Celery
+from celery.schedules import crontab
+
+# Set the default Django settings module
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "config.settings.local")
+
+app = Celery("cosmos")
+
+# Configure Celery using Django settings
+app.config_from_object("django.conf:settings", namespace="CELERY")
+
+# Load task modules from all registered Django app configs
+app.autodiscover_tasks()
+
+app.conf.beat_schedule = {
+    "process-inference-queue": {
+        "task": "inference.tasks.process_inference_job_queue",
+        # Only run between 6pm and 7am
+        "schedule": crontab(minute="*/5", hour="18-23,0-6"),
+    },
+}

config/settings/base.py

@@ -84,6 +84,7 @@
     "feedback",
     "sde_collections",
     "sde_indexing_helper.users",
+    "inference",
 ]
 
 # https://docs.djangoproject.com/en/dev/ref/settings/#installed-apps
@@ -92,6 +93,7 @@
 CORS_ALLOWED_ORIGINS = [
     "http://localhost:3000",
     "http://sde-lrm.nasa-impact.net",
+    "https://sde-lrm.nasa-impact.net",
     "https://sde-qa.nasa-impact.net",
     "https://sciencediscoveryengine.test.nasa.gov",
     "https://sciencediscoveryengine.nasa.gov",
@@ -288,11 +290,9 @@
 # https://docs.celeryq.dev/en/stable/userguide/configuration.html#std:setting-result_serializer
 CELERY_RESULT_SERIALIZER = "json"
 # https://docs.celeryq.dev/en/stable/userguide/configuration.html#task-time-limit
-# TODO: set to whatever value is adequate in your circumstances
-CELERY_TASK_TIME_LIMIT = 5 * 60
+CELERY_TASK_TIME_LIMIT = 30 * 60
 # https://docs.celeryq.dev/en/stable/userguide/configuration.html#task-soft-time-limit
-# TODO: set to whatever value is adequate in your circumstances
-CELERY_TASK_SOFT_TIME_LIMIT = 60
+CELERY_TASK_SOFT_TIME_LIMIT = 25 * 60
 # https://docs.celeryq.dev/en/stable/userguide/configuration.html#beat-scheduler
 CELERY_BEAT_SCHEDULER = "django_celery_beat.schedulers:DatabaseScheduler"
 # https://docs.celeryq.dev/en/stable/userguide/configuration.html#worker-send-task-events
@@ -349,3 +349,5 @@
 LRM_QA_PASSWORD = env("LRM_QA_PASSWORD")
 LRM_DEV_TOKEN = env("LRM_DEV_TOKEN")
 XLI_TOKEN = env("XLI_TOKEN")
+INFERENCE_API_URL = env("INFERENCE_API_URL", default="http://host.docker.internal:8000")
+TDAMM_CLASSIFICATION_THRESHOLD = env("TDAMM_CLASSIFICATION_THRESHOLD", default="0.5")

config_generation/db_to_xml.py

@@ -148,35 +148,51 @@ def convert_template_to_scraper(self, collection) -> None:
         scraper_config = self.update_config_xml()
         return scraper_config
 
-    def convert_template_to_plugin_indexer(self, scraper_editor) -> None:
+    def convert_template_to_job(self, collection, job_source) -> None:
         """
-        assuming this class has been instantiated with the scraper_template.xml
+        assuming this class has been instantiated with the job_template.xml
+        """
+        self.update_or_add_element_value("Collection", f"/{job_source}/{collection.config_folder}/")
+        job_config = self.update_config_xml()
+        return job_config
+
+    def convert_template_to_indexer(self, scraper_editor) -> None:
+        """
+        assuming this class has been instantiated with the final_config_template.xml
         """
 
         transfer_fields = [
-            "KeepHashFragmentInUrl",
-            "CorrectDomainCookies",
-            "IgnoreSessionCookies",
-            "DownloadImages",
-            "DownloadMedia",
-            "DownloadCss",
-            "DownloadFtp",
-            "DownloadFile",
-            "IndexJs",
-            "FollowJs",
-            "CrawlFlash",
-            "NormalizeSecureSchemesWhenTestingVisited",
-            "RetryCount",
-            "RetryPause",
-            "AddBaseHref",
-            "AddMetaContentType",
-            "NormalizeUrls",
+            "Throttle",
         ]
 
         double_transfer_fields = [
-            ("UrlAccess", "AllowXPathCookies"),
             ("UrlAccess", "UseBrowserForWebRequests"),
-            ("UrlAccess", "UseHttpClientForWebRequests"),
+            ("UrlAccess", "BrowserForWebRequestsReadinessThreshold"),
+            ("UrlAccess", "BrowserForWebRequestsInitialDelay"),
+            ("UrlAccess", "BrowserForWebRequestsMaxTotalDelay"),
+            ("UrlAccess", "BrowserForWebRequestsMaxResourcesDelay"),
+            ("UrlAccess", "BrowserForWebRequestsLogLevel"),
+            ("UrlAccess", "BrowserForWebRequestsViewportWidth"),
+            ("UrlAccess", "BrowserForWebRequestsViewportHeight"),
+            ("UrlAccess", "BrowserForWebRequestsAdditionalJavascript"),
+            ("UrlAccess", "PostLoginUrl"),
+            ("UrlAccess", "PostLoginData"),
+            ("UrlAccess", "GetBeforePostLogin"),
+            ("UrlAccess", "PostLoginAutoRedirect"),
+            ("UrlAccess", "ReLoginCount"),
+            ("UrlAccess", "ReLoginDelay"),
+            ("UrlAccess", "DetectHtmlLoginPattern"),
+            ("IndexerClient", "RetryTimeout"),
+            ("IndexerClient", "RetrySleep"),
+        ]
+
+        triple_transfer_fields = [
+            ("UrlAccess", "BrowserLogin", "Activate"),
+            ("UrlAccess", "BrowserLogin", "RemoteDebuggingPort"),
+            ("UrlAccess", "BrowserLogin", "BrowserLogLevel"),
+            ("UrlAccess", "BrowserLogin", "ShowDevTools"),
+            ("UrlAccess", "BrowserLogin", "SuccessCondition"),
+            ("UrlAccess", "BrowserLogin", "CookieFilter"),
         ]
 
         for field in transfer_fields:
@@ -187,18 +203,15 @@ def convert_template_to_plugin_indexer(self, scraper_editor) -> None:
                 f"{parent}/{child}", scraper_editor.get_tag_value(f"{parent}/{child}", strict=True)
             )
 
+        for grandparent, parent, child in triple_transfer_fields:
+            self.update_or_add_element_value(
+                f"{grandparent}/{parent}/{child}",
+                scraper_editor.get_tag_value(f"{grandparent}/{parent}/{child}", strict=True),
+            )
+
         scraper_config = self.update_config_xml()
         return scraper_config
 
-    def convert_template_to_indexer(self, collection) -> None:
-        """
-        assuming this class has been instantiated with the indexer_template.xml
-        """
-        self.update_or_add_element_value("Collection", f"/SDE/{collection.config_folder}/")
-        indexer_config = self.update_config_xml()
-
-        return indexer_config
-
     def _mapping_exists(self, new_mapping: ET.Element):
         """
         Check if the mapping with given parameters already exists in the XML tree

config_generation/tests/test_config_generation_pipeline.py

@@ -0,0 +1,90 @@
+from unittest.mock import MagicMock, call, patch
+
+from django.test import TestCase
+
+from sde_collections.models.collection import Collection
+from sde_collections.models.collection_choice_fields import WorkflowStatusChoices
+
+"""
+Workflow status change → Opens template → Applies XML transformation → Writes to GitHub.
+
+- When the `workflow_status` changes, it triggers the relevant config creation method.
+- The method reads an template and processes it using `XmlEditor`.
+- `XmlEditor` modifies the template by injecting collection-specific values and transformations.
+- The generated XML is passed to `_write_to_github()`, which commits it directly to GitHub.
+
+Note: This test verifies that the correct methods are triggered and XML content is passed to GitHub.
+The actual XML structure and correctness are tested separately in `test_db_xml.py`.
+"""
+
+
+class TestConfigCreation(TestCase):
+    def setUp(self):
+        self.collection = Collection.objects.create(
+            name="Test Collection", division="1", workflow_status=WorkflowStatusChoices.RESEARCH_IN_PROGRESS
+        )
+
+    @patch("sde_collections.utils.github_helper.GitHubHandler")  # Mock GitHubHandler
+    @patch("sde_collections.models.collection.Collection._write_to_github")
+    @patch("sde_collections.models.collection.XmlEditor")
+    def test_ready_for_engineering_triggers_config_and_job_creation(
+        self, MockXmlEditor, mock_write_to_github, MockGitHubHandler
+    ):
+        """
+        When the collection's workflow status is updated to READY_FOR_ENGINEERING,
+        it should trigger the creation of scraper configuration and job files.
+        """
+        # Mock GitHubHandler to avoid actual API calls
+        mock_github_instance = MockGitHubHandler.return_value
+        mock_github_instance.create_file.return_value = None
+        mock_github_instance.create_or_update_file.return_value = None
+
+        # Set up the XmlEditor mock for both config and job
+        mock_editor_instance = MockXmlEditor.return_value
+        mock_editor_instance.convert_template_to_scraper.return_value = "<scraper_config>config_data</scraper_config>"
+        mock_editor_instance.convert_template_to_job.return_value = "<scraper_job>job_data</scraper_job>"
+
+        # Simulate the status change to READY_FOR_ENGINEERING
+        self.collection.workflow_status = WorkflowStatusChoices.READY_FOR_ENGINEERING
+        self.collection.save()
+
+        # Verify that the XML for both config and job are generated and written to GitHub
+        expected_calls = [
+            call(self.collection._scraper_config_path, "<scraper_config>config_data</scraper_config>", False),
+            call(self.collection._scraper_job_path, "<scraper_job>job_data</scraper_job>", False),
+        ]
+        mock_write_to_github.assert_has_calls(expected_calls, any_order=True)
+
+    @patch("sde_collections.models.collection.GitHubHandler")  # Mock GitHubHandler in the correct module path
+    @patch("sde_collections.models.collection.Collection._write_to_github")
+    @patch("sde_collections.models.collection.XmlEditor")
+    def test_ready_for_curation_triggers_indexer_config_and_job_creation(
+        self, MockXmlEditor, mock_write_to_github, MockGitHubHandler
+    ):
+        """
+        When the collection's workflow status is updated to READY_FOR_CURATION,
+        it should trigger indexer config and job creation methods.
+        """
+        # Mock GitHubHandler to avoid actual API calls
+        mock_github_instance = MockGitHubHandler.return_value
+        mock_github_instance.check_file_exists.return_value = True  # Assume scraper exists
+        mock_github_instance._get_file_contents.return_value = MagicMock()
+        mock_github_instance._get_file_contents.return_value.decoded_content = (
+            b"<scraper_config>Mock Data</scraper_config>"
+        )
+
+        # Set up the XmlEditor mock for both config and job
+        mock_editor_instance = MockXmlEditor.return_value
+        mock_editor_instance.convert_template_to_indexer.return_value = "<indexer_config>config_data</indexer_config>"
+        mock_editor_instance.convert_template_to_job.return_value = "<indexer_job>job_data</indexer_job>"
+
+        # Simulate the status change to READY_FOR_CURATION
+        self.collection.workflow_status = WorkflowStatusChoices.READY_FOR_CURATION
+        self.collection.save()
+
+        # Verify that the XML for both indexer config and job are generated and written to GitHub
+        expected_calls = [
+            call(self.collection._indexer_config_path, "<indexer_config>config_data</indexer_config>", True),
+            call(self.collection._indexer_job_path, "<indexer_job>job_data</indexer_job>", False),
+        ]
+        mock_write_to_github.assert_has_calls(expected_calls, any_order=True)