Merge branch 'develop' into feature/3619_publisher_csv_validator

.gitignore

@@ -11,7 +11,11 @@ src*
 build/*
 dist/*
 tmp/*
+
 *.zip
+!doajtest/unit/resources/*.zip
+!doajtest/preservation_upload_test_package/*.zip
+
 scratch.py
 .coverage
 htmlcov/*

doajtest/mocks/preservation.py

@@ -226,3 +226,227 @@ class PreservationMock:
         "es_type": "article"
     }
 
+    ARTICLE_DATA_JOURNAL2 = {
+        "index": {
+            "issn": [
+                "2673-611X"
+            ],
+            "date": "2016-10-01T00:00:00Z",
+            "date_toc_fv_month": "2016-10-01T00:00:00Z",
+            "subject": [
+                "Science: Natural history (General): General. Including nature conservation, geographical distribution"
+            ],
+            "schema_subject": [
+                "LCC:Neurology. Diseases of the nervous system"
+            ],
+            "classification": [
+                "Neurology. Diseases of the nervous system"
+            ],
+            "publisher": [
+                "Frontiers Media S.A."
+            ],
+            "license": [
+                "CC BY"
+            ],
+            "language": [
+                "English"
+            ],
+            "country": "United Kingdom",
+            "schema_code": [
+                "LCC:RC346-429"
+            ],
+            "classification_paths": [
+                "Medicine: Internal medicine: Neurosciences. Biological psychiatry. Neuropsychiatry: Neurology. Diseases of the nervous system"
+            ],
+            "unpunctitle": "Variation in TMEM106B in chronic traumatic encephalopathy",
+            "asciiunpunctitle": "Variation in TMEM106B in chronic traumatic encephalopathy",
+            "has_seal": "Yes",
+            "doi": "10.3389/fcosc.2022.1028295",
+            "fulltext": "https://frontiersin.org/articles/10.3389/fcosc.2022.1028295",
+            "schema_codes_tree": [
+                "LCC:RC31-1245",
+                "LCC:RC346-429",
+                "LCC:RC321-571",
+                "LCC:R"
+            ]
+        },
+        "last_updated": "2020-11-24T21:55:20Z",
+        "admin": {
+            "in_doaj": "true",
+            "seal": "true"
+        },
+        "created_date": "2018-11-04T12:37:46Z",
+        "id": "00005741594643f4996e2666a01e0310",
+        "bibjson": {
+            "title": "Variation in TMEM106B in chronic traumatic encephalopathy",
+            "year": "2018",
+            "month": "11",
+            "start_page": "1",
+            "end_page": "9",
+            "abstract": "Abstract The genetic basis of chronic traumatic encephalopathy (CTE) is poorly understood. Variation in transmembrane protein 106B (TMEM106B) has been associated with enhanced neuroinflammation during aging and with TDP-43-related neurodegenerative disease, and rs3173615, a missense coding SNP in TMEM106B, has been implicated as a functional variant in these processes. Neuroinflammation and TDP-43 pathology are prominent features in CTE. The purpose of this study was to determine whether genetic variation in TMEM106B is associated with CTE risk, pathological features, and ante-mortem dementia. Eighty-six deceased male athletes with a history of participation in American football, informant-reported Caucasian, and a positive postmortem diagnosis of CTE without comorbid neurodegenerative disease were genotyped for rs3173615. The minor allele frequency (MAF = 0.42) in participants with CTE did not differ from previously reported neurologically normal controls (MAF = 0.43). However, in a case-only analysis among CTE cases, the minor allele was associated with reduced phosphorylated tau (ptau) pathology in the dorsolateral frontal cortex (DLFC) (AT8 density, odds ratio [OR] of increasing one quartile = 0.42, 95% confidence interval [CI] 0.22–0.79, p = 0.008), reduced neuroinflammation in the DLFC (CD68 density, OR of increasing one quartile = 0.53, 95% CI 0.29–0.98, p = 0.043), and increased synaptic protein density (β = 0.306, 95% CI 0.065–0.546, p = 0.014). Among CTE cases, TMEM106B minor allele was also associated with reduced ante-mortem dementia (OR = 0.40, 95% CI 0.16–0.99, p = 0.048), but was not associated with TDP-43 pathology. All case-only models were adjusted for age at death and duration of football play. Taken together, variation in TMEM106B may have a protective effect on CTE-related outcomes.",
+            "journal": {
+                "volume": "6",
+                "number": "1",
+                "publisher": "BMC",
+                "title": "Acta Neuropathologica Communications",
+                "country": "GB",
+                "license": [
+                    {
+                        "title": "CC BY",
+                        "type": "CC BY",
+                        "url": "https://actaneurocomms.biomedcentral.com/submission-guidelines/copyright",
+                        "open_access": "true"
+                    }
+                ],
+                "language": [
+                    "EN"
+                ],
+                "issns": [
+                    "2673-611X"
+                ]
+            },
+            "identifier": [
+                {
+                    "type": "doi",
+                    "id": "10.1186/s40478-018-0619-9"
+                },
+                {
+                    "type": "eissn",
+                    "id": "2051-5960"
+                }
+            ],
+            "keywords": [
+                "Chronic traumatic encephalopathy",
+                "TMEM106B",
+                "Neuroinflammation",
+                "Football",
+                "Traumatic brain injury",
+                "Tau"
+            ],
+            "link": [
+                {
+                    "type": "fulltext",
+                    "url": "http://link.springer.com/article/10.1186/s40478-018-0619-9",
+                    "content_type": "HTML"
+                }
+            ],
+            "subject": [
+                {
+                    "scheme": "LCC",
+                    "term": "Neurology. Diseases of the nervous system",
+                    "code": "RC346-429"
+                }
+            ],
+            "author": [
+                {
+                    "name": "Jonathan D. Cherry",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Jesse Mez",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "John F. Crary",
+                    "affiliation": "Department of Pathology, Fishberg Department of Neuroscience, Friedman Brain Institute, Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai School"
+                },
+                {
+                    "name": "Yorghos Tripodis",
+                    "affiliation": "Department of Biostatistics, Boston University School of Public Health"
+                },
+                {
+                    "name": "Victor E. Alvarez",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Ian Mahar",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Bertrand R. Huber",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Michael L. Alosco",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Raymond Nicks",
+                    "affiliation": "Department of Veterans Affairs Medical Center"
+                },
+                {
+                    "name": "Bobak Abdolmohammadi",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Patrick T. Kiernan",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Laney Evers",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Sarah Svirsky",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Katharine Babcock",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Hannah M. Gardner",
+                    "affiliation": "VA Boston Healthcare System"
+                },
+                {
+                    "name": "Gaoyuan Meng",
+                    "affiliation": "VA Boston Healthcare System"
+                },
+                {
+                    "name": "Christopher J. Nowinski",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Brett M. Martin",
+                    "affiliation": "Department of Biostatistics, Boston University School of Public Health"
+                },
+                {
+                    "name": "Brigid Dwyer",
+                    "affiliation": "Department of Neurology, Boston University School of Medicine"
+                },
+                {
+                    "name": "Neil W. Kowall",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Robert C. Cantu",
+                    "affiliation": "Department of Anatomy and Neurobiology, Boston University School of Medicine"
+                },
+                {
+                    "name": "Lee E. Goldstein",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Douglas I. Katz",
+                    "affiliation": "Department of Neurology, Boston University School of Medicine"
+                },
+                {
+                    "name": "Robert A. Stern",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Lindsay A. Farrer",
+                    "affiliation": "Department of Neurology, Boston University School of Medicine"
+                },
+                {
+                    "name": "Ann C. McKee",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                },
+                {
+                    "name": "Thor D. Stein",
+                    "affiliation": "Boston University Alzheimer’s Disease and CTE Center, Boston University School of Medicine"
+                }
+            ]
+        },
+        "es_type": "article"
+    }

doajtest/testbook/articles_preservation/user_test_script.yml → doajtest/testbook/articles_preservation/upload_preservation_files.yml

@@ -1,6 +1,6 @@
 # ~~ ArticlesPreservation:FunctionalTest -> Preservation:Feature ~~
 suite: Articles Preservation
-testset: User Test Script
+testset: Upload Preservation Files
 tests:
 - title: Publisher without preservation role
   context:
@@ -22,7 +22,8 @@ tests:
   steps:
   - step: Ensure that the archive package has been created with correct structure
   - step: Go to preservation area /publisher/preservation
-  - step: Select 'Browse' and select the paaackage zip file
+  - step: Select 'Browse' and select the package zip file
+    resource: /preservation_upload_test_package/valid_article.zip
   - step: click 'Upload'
     results:
     - 'A flash message appears at the top of the screen: File uploaded and waiting
@@ -40,7 +41,8 @@ tests:
   steps:
   - step: Create a incorrect or junk file that does not have articles
   - step: Go to preservation area /publisher/preservation
-  - step: Select 'Browse' and select the paaackage zip file
+  - step: Select 'Browse' and select the package zip file
+    resource: /preservation_upload_test_package/invalid_article.zip
   - step: click 'Upload'
     results:
     - 'A flash message appears at the top of the screen: File uploaded and waiting
@@ -56,9 +58,11 @@ tests:
   context:
     role: publisher
   steps:
-  - step: Create a incorrect or junk file that does not have articles
+  - step: Make sure not to login as admin user as admin does not have restrictions. Login as publisher.
+  - step: Ensure that the archive package has been created with correct structure but the article does not own by the logged in user.
   - step: Go to preservation area /publisher/preservation
-  - step: Select 'Browse' and select the paaackage zip file
+  - step: Select 'Browse' and select the package zip file
+    resource: /preservation_upload_test_package/valid_article.zip
   - step: click 'Upload'
     results:
     - 'A flash message appears at the top of the screen: File uploaded and waiting
@@ -75,11 +79,47 @@ tests:
     - if the status is 'partially success', show details link will be displayed. When
       clicked on the link details of how many articles successful and how many not
       successful will be displayed
+- title: Upload correctly structured file with multiple journals and it is processed correctly
+  context:
+    role: publisher
+  setup:
+    - Have a publisher account which is the owner of 3 journals that are in DOAJ, and which have articles
+      uploaded for them
+    - Select 1 article from each journal and note its DOI
+    - Download the multi_journals.zip test package (see link below in second step)
+    - Unzip the multi_journals.zip test package
+    - In the identifiers.csv file in the root of the test package, put each of the DOIs from your articles
+      next to one of the article directory names listed (removing the existing test DOIs that are present in that
+      file already).  For example you will have a line which reads "article1,10.1224/mydoi/3" where the DOI
+      is the one from your article.
+    - Re-zip the multi_journals.zip package.  This wil be the file you will upload for testing in the below script
+  steps:
+  - step: Ensure that the archive package has been created with correct structure
+  - step: Ensure that the archive package contains more than one article with different journals. 
+          A sample zip file is available for testing purpose. If there are no articles with the DOIs specified in the indentifiers.csv
+          file in your DSoace instance, 
+          the results may not be as expected. In that case unzip the file and update the identifiers.csv file with appropriate identifiers for the articles.
+    resource: /preservation_upload_test_package/multi_journals.zip
+  - step: Go to preservation area /publisher/preservation
+  - step: Select 'Browse' and select the package zip file
+  - step: click 'Upload'
+    results:
+    - 'A flash message appears at the top of the screen: File uploaded and waiting
+      to be processed.'
+    - Upload status is shown in 'History of uploads' with status processing
+  - step: wait a short amount of time for the job to process, then reload the page
+      (do not re-submit the form data).  If the job remains in "pending", reload the
+      page until the status changes.
+    results:
+    - Upload status in 'History of uploads' changes to 'successfully processed' and
+      the 'Notes' shows as 'uploaded to archive server'
+    - The 'Notes' has the label 'UPLOADED PACKAGES'
+    - Under the label 'UPLOADED PACKAGES', details of the packages that were uploaded are displayed in the format <journal_id>_<Date>.tar.gz
 - title: Test maintenance mode for 'Upload preservation file' tab
   context:
     role: publisher
   steps:
   - step: Set the value of 'PRESERVATION_PAGE_UNDER_MAINTENANCE' to True in the configuration file (app.cfg/dev.cfg/test.cfg)
   - step: Go to preservation area /publisher/preservation
     results:
-    - Maintenance page should be displayed with the content as 'This page is currently offline for maintenance'
+    - Maintenance page should be displayed with the content as 'This page is currently offline for maintenance'

doajtest/unit/resources/invalid_article.zip

@@ -0,0 +1 @@
+../../preservation_upload_test_package/invalid_article.zip

doajtest/unit/resources/multi_journals.zip

@@ -0,0 +1 @@
+../../preservation_upload_test_package/multi_journals.zip

doajtest/unit/resources/valid_article.zip

@@ -0,0 +1 @@
+../../preservation_upload_test_package/valid_article.zip