fix: prevented pmid,pmcid,doi from being undefined during ingestion o…

compose/neurosynth-frontend/cypress/e2e/pages/EditStudyPage.cy.tsx

@@ -12,9 +12,7 @@ describe(PAGE_NAME, () => {
         cy.intercept('GET', `https://api.semanticscholar.org/**`, {
             fixture: 'semanticScholar',
         }).as('semanticScholarFixture');
-    });
 
-    it('should load', () => {
         cy.intercept('GET', `**/api/studies/mock-study-id*`, { fixture: 'study' }).as(
             'studyFixture'
         );
@@ -25,12 +23,44 @@ describe(PAGE_NAME, () => {
             'annotationFixture'
         );
         cy.intercept('GET', `**/api/studysets/*`, { fixture: 'studyset' }).as('studysetFixture');
+
+        cy.intercept('POST', `https://www.google-analytics.com/*/**`, {}).as(
+            'googleAnalyticsFixture'
+        );
+
         cy.login('mocked').visit(PATH);
+    });
+
+    it('should load', () => {
         cy.visit(PATH)
             .wait('@studyFixture')
             .wait('@projectFixture')
             .wait('@annotationFixture')
             .wait('@semanticScholarFixture')
             .wait('@studysetFixture');
     });
+
+    it('should save and set study with doi and pmid undefined if they are empty', () => {
+        cy.intercept('PUT', '**/api/studies/mock-study-id').as('editStudy');
+
+        // ARRANGE
+        cy.visit(PATH)
+            .wait('@studyFixture')
+            .wait('@projectFixture')
+            .wait('@annotationFixture')
+            .wait('@semanticScholarFixture')
+            .wait('@studysetFixture');
+
+        // ACT
+        cy.get('div').contains('(name, authors, description, doi, pmid, etc)').click();
+        cy.contains('label', 'doi').next().clear();
+        cy.contains('label', 'pmid').next().clear();
+        cy.contains('label', 'pmcid').next().clear();
+        cy.contains('button', 'save').click();
+
+        // ASSERT
+        cy.get('@editStudy').its('request.body').should('not.have.a.property', 'doi');
+        cy.get('@editStudy').its('request.body').should('not.have.a.property', 'pmid');
+        cy.get('@editStudy').its('request.body').should('not.have.a.property', 'pmcid');
+    });
 });

compose/neurosynth-frontend/cypress/e2e/workflows/ingestion/Ingestion.cy.tsx

@@ -0,0 +1,60 @@
+/// <reference types="cypress" />
+
+const PATH = '/projects/mock-project-id/curation';
+
+describe('Ingestion', () => {
+    beforeEach(() => {
+        cy.clearLocalStorage().clearSessionStorage();
+        cy.intercept('GET', 'https://api.appzi.io/**', { fixture: 'appzi' }).as('appziFixture');
+        cy.intercept('GET', `**/api/meta-analyses*`, { fixture: 'metaAnalyses' }).as(
+            'metaAnalysesFixture'
+        );
+
+        cy.intercept('POST', `https://www.google-analytics.com/*/**`, {}).as(
+            'googleAnalyticsFixture'
+        );
+
+        cy.intercept('GET', `**/api/projects/*`, {
+            fixture: 'IngestionFixtures/projectFixture',
+        }).as('projectFixture');
+        cy.intercept('PUT', `**/api/projects/*`, {
+            fixture: 'IngestionFixtures/projectPutFixture',
+        });
+
+        cy.intercept('POST', `**/api/studysets/`, {
+            fixture: 'IngestionFixtures/studysetFixture',
+        }).as('studysetFixture');
+        cy.intercept('PUT', `**/api/studysets/*`, {
+            fixture: 'IngestionFixtures/studysetPutFixture',
+        });
+        cy.intercept('GET', `**/api/studysets/*`, {
+            fixture: 'IngestionFixtures/studysetFixture',
+        }).as('studysetFixture');
+
+        cy.intercept('POST', `**/api/annotations/*`, {
+            fixture: 'IngestionFixtures/annotationsFixture',
+        }).as('annotationFixture');
+        cy.intercept('PUT', `**/api/annotations/*`, {
+            fixture: 'IngestionFixtures/annotationsPutFixture',
+        }).as('annotationPutFixture');
+        cy.intercept('GET', `**/api/annotations/*`, {
+            fixture: 'IngestionFixtures/annotationsPutFixture',
+        }).as('annotationFixture');
+
+        cy.intercept('POST', `**/api/base-studies/`, {
+            fixture: 'IngestionFixtures/baseStudiesFixture',
+        }).as('baseStudiesFixture');
+    });
+
+    it('should show the dialog', () => {
+        cy.login('mocked').visit(PATH);
+        cy.contains('button', 'Move To Extraction Phase').click();
+
+        cy.contains('button', 'extraction: get started').click();
+        cy.contains('button', 'NEXT').click();
+
+        cy.get('@baseStudiesFixture').its('request.body').should('not.have.a.property', 'doi');
+        cy.get('@baseStudiesFixture').its('request.body').should('not.have.a.property', 'pmid');
+        cy.get('@baseStudiesFixture').its('request.body').should('not.have.a.property', 'pmcid');
+    });
+});

compose/neurosynth-frontend/cypress/fixtures/IngestionFixtures/annotationsFixture.json

@@ -0,0 +1,18 @@
+{
+    "id": "DVwyM6Qg5iaw",
+    "user": "auth0|666c39a8b281fda9ff9699e9",
+    "username": "test user 5",
+    "created_at": "2024-07-22T17:09:51.521370+00:00",
+    "updated_at": null,
+    "studyset": "hQFjozWL9v8Q",
+    "notes": [],
+    "source": null,
+    "source_id": null,
+    "source_updated_at": null,
+    "note_keys": {
+        "included": "boolean"
+    },
+    "metadata": null,
+    "name": "Annotation for studyset hQFjozWL9v8Q",
+    "description": ""
+}

compose/neurosynth-frontend/cypress/fixtures/IngestionFixtures/annotationsPutFixture.json

@@ -0,0 +1,18 @@
+{
+    "id": "DVwyM6Qg5iaw",
+    "user": "auth0|666c39a8b281fda9ff9699e9",
+    "username": "test user 5",
+    "created_at": "2024-07-22T17:09:51.521370+00:00",
+    "updated_at": null,
+    "studyset": "hQFjozWL9v8Q",
+    "notes": [],
+    "source": null,
+    "source_id": null,
+    "source_updated_at": null,
+    "note_keys": {
+        "included": "boolean"
+    },
+    "metadata": null,
+    "name": "Annotation for studyset hQFjozWL9v8Q",
+    "description": ""
+}

compose/neurosynth-frontend/cypress/fixtures/IngestionFixtures/baseStudiesFixture.json

@@ -0,0 +1,29 @@
+[
+    {
+        "id": "CtGJ5aaN5AeK",
+        "user": "auth0|666c39a8b281fda9ff9699e9",
+        "username": "test user 5",
+        "created_at": "2024-07-22T17:09:51.627184+00:00",
+        "updated_at": null,
+        "metadata": null,
+        "versions": [
+            {
+                "id": "ZR6H8F6c2aKX",
+                "user": "auth0|666c39a8b281fda9ff9699e9",
+                "username": "test user 5",
+                "created_at": "2024-07-22T17:09:51.627184+00:00",
+                "updated_at": null,
+                "source": null
+            }
+        ],
+        "name": "New study",
+        "description": "",
+        "publication": "",
+        "doi": null,
+        "pmid": null,
+        "pmcid": null,
+        "authors": "",
+        "year": 0,
+        "level": "group"
+    }
+]

compose/neurosynth-frontend/cypress/fixtures/IngestionFixtures/projectFixture.json

@@ -0,0 +1,148 @@
+{
+    "created_at": "2024-07-22T17:06:27.161543+00:00",
+    "description": "",
+    "draft": true,
+    "id": "5uEqnaad4Hfe",
+    "meta_analyses": [],
+    "name": "Untitled",
+    "neurostore_study": {
+        "created_at": "2024-07-22T17:06:27.172187+00:00",
+        "exception": null,
+        "neurostore_id": "teTeQPRAe7E5",
+        "status": "PENDING",
+        "traceback": null,
+        "updated_at": "2024-07-22T17:06:27.177339+00:00"
+    },
+    "neurostore_url": "https://neurostore.org/api/studies/teTeQPRAe7E5",
+    "provenance": {
+        "curationMetadata": {
+            "columns": [
+                {
+                    "id": "0ac133d9-f994-434e-9d93-352f40e7d266",
+                    "name": "not included",
+                    "stubStudies": []
+                },
+                {
+                    "id": "38eec6d4-4c07-4a11-aff9-afe2de91116e",
+                    "name": "included",
+                    "stubStudies": [
+                        {
+                            "abstractText": "",
+                            "articleLink": "",
+                            "articleYear": "",
+                            "authors": "",
+                            "doi": "",
+                            "exclusionTag": null,
+                            "id": "c70a3df6-dd10-4789-b3f3-41743061fb6f",
+                            "identificationSource": {
+                                "id": "neurosynth_pubmed_id_source",
+                                "label": "PubMed"
+                            },
+                            "journal": "",
+                            "keywords": "",
+                            "pmcid": "",
+                            "pmid": "",
+                            "tags": [
+                                {
+                                    "id": "a71d283c-fb05-496d-a005-551cdfe3cd8e",
+                                    "isAssignable": true,
+                                    "isExclusionTag": false,
+                                    "label": "MANUAL_CREATE-2024-07-22T17:09:16.238Z"
+                                }
+                            ],
+                            "title": "New study"
+                        }
+                    ]
+                }
+            ],
+            "exclusionTags": [
+                {
+                    "id": "neurosynth_exclude_exclusion",
+                    "isAssignable": true,
+                    "isExclusionTag": true,
+                    "label": "Exclude"
+                },
+                {
+                    "id": "neurosynth_duplicate_exclusion",
+                    "isAssignable": true,
+                    "isExclusionTag": true,
+                    "label": "Duplicate"
+                }
+            ],
+            "identificationSources": [
+                {
+                    "id": "neurosynth_neurostore_id_source",
+                    "label": "Neurostore"
+                },
+                {
+                    "id": "neurosynth_pubmed_id_source",
+                    "label": "PubMed"
+                },
+                {
+                    "id": "neurosynth_scopus_id_source",
+                    "label": "Scopus"
+                },
+                {
+                    "id": "neurosynth_web_of_science_id_source",
+                    "label": "Web of Science"
+                },
+                {
+                    "id": "neurosynth_psycinfo_id_source",
+                    "label": "PsycInfo"
+                },
+                {
+                    "id": "neurosynth_sleuth_id_source",
+                    "label": "Sleuth"
+                }
+            ],
+            "infoTags": [
+                {
+                    "id": "neurosynth_untagged_tag",
+                    "isAssignable": false,
+                    "isExclusionTag": false,
+                    "label": "Untagged studies"
+                },
+                {
+                    "id": "neurosynth_uncategorized_tag",
+                    "isAssignable": false,
+                    "isExclusionTag": false,
+                    "label": "Uncategorized Studies"
+                },
+                {
+                    "id": "neurosynth_needs_review_tag",
+                    "isAssignable": false,
+                    "isExclusionTag": false,
+                    "label": "Needs Review"
+                },
+                {
+                    "id": "a71d283c-fb05-496d-a005-551cdfe3cd8e",
+                    "isAssignable": true,
+                    "isExclusionTag": false,
+                    "label": "MANUAL_CREATE-2024-07-22T17:09:16.238Z"
+                }
+            ],
+            "prismaConfig": {
+                "eligibility": {
+                    "exclusionTags": []
+                },
+                "identification": {
+                    "exclusionTags": []
+                },
+                "isPrisma": false,
+                "screening": {
+                    "exclusionTags": []
+                }
+            }
+        },
+        "extractionMetadata": {
+            "studyStatusList": []
+        },
+        "metaAnalysisMetadata": {
+            "canEditMetaAnalyses": false
+        }
+    },
+    "public": true,
+    "updated_at": "2024-07-22T17:09:24.932504+00:00",
+    "user": "auth0|62e0e6c9dd47048572613b4d",
+    "username": "test user 5"
+}