Merge branch 'release/2024-11-12_3647ris_3573article_autocheck_3838_n…

…osuchapplication'

README.md

@@ -4,6 +4,12 @@
 This repository provides the software which drives the DOAJ website and the DOAJ 
 directory.
 
+## CI Status
+
+**develop**   [![CircleCI](https://dl.circleci.com/status-badge/img/gh/DOAJ/doaj/tree/develop.svg?style=svg)](https://dl.circleci.com/status-badge/redirect/gh/DOAJ/doaj/tree/develop)
+
+**master**   [![CircleCI](https://dl.circleci.com/status-badge/img/gh/DOAJ/doaj/tree/master.svg?style=svg)](https://dl.circleci.com/status-badge/redirect/gh/DOAJ/doaj/tree/master)
+
 ## Reporting issues
 
 Please feel free to use the issue tracker on https://github.com/DOAJ/doaj/issues for any bug 

doajtest/fixtures/accounts.py

@@ -85,9 +85,12 @@ def create_publisher_a():
     return publisher
 
 
-def create_maned_a():
+def create_maned_a(save=False):
     from portality import models
     maned = models.Account(**AccountFixtureFactory.make_managing_editor_source())
+    maned.set_password("password")
+    if save:
+        maned.save(blocking=True)
     return maned
 
 

doajtest/fixtures/v2/common.py

@@ -25,7 +25,7 @@
 }
 
 SEAL_FORM_EXPANDED = {
-    "doaj_seal": False,
+    "doaj_seal": [],
 }
 
 JOURNAL_LIKE_BIBJSON = {

doajtest/helpers.py

@@ -149,6 +149,7 @@ class DoajTestCase(TestCase):
     @classmethod
     def create_app_patch(cls):
         return {
+            'AUTOCHECK_INCOMING': False,  # old test cases design and depend on work flow of autocheck disabled
             "STORE_IMPL": "portality.store.StoreLocal",
             "STORE_LOCAL_DIR": paths.rel2abs(__file__, "..", "tmp", "store", "main", cls.__name__.lower()),
             "STORE_TMP_DIR": paths.rel2abs(__file__, "..", "tmp", "store", "tmp", cls.__name__.lower()),
@@ -436,9 +437,9 @@ def assert_expected_dict(test_case: TestCase, target, expected: dict):
     test_case.assertDictEqual(actual, expected)
 
 
-def login(app_client, username, password, follow_redirects=True):
+def login(app_client, email, password, follow_redirects=True):
     return app_client.post(url_for('account.login'),
-                           data=dict(user=username, password=password),
+                           data=dict(user=email, password=password),
                            follow_redirects=follow_redirects)
 
 

doajtest/testbook/public_site/public_search.yml

@@ -186,4 +186,13 @@ tests:
   - step: click spacebar to check the filter
     results:
       - filter is applied
-
+- title: Export article in RIS format
+  context:
+    role: anonymous
+  steps:
+  - step: Go to the DOAJ search page at /search/articles
+    results:
+      - Only articles are shown in the results
+  - step: Click on 'Export RIS' of any article
+    results:
+      - A RIS file is downloaded

doajtest/unit/api_tests/test_api_crud_returnvalues.py

@@ -1,3 +1,4 @@
+from doajtest import helpers
 from doajtest.helpers import DoajTestCase, with_es
 from portality import models
 from doajtest.fixtures import ApplicationFixtureFactory, ArticleFixtureFactory, JournalFixtureFactory
@@ -205,9 +206,7 @@ def test_04_article_structure_exceptions(self):
 
     @staticmethod
     def login(app, username, password):
-        return app.post('/account/login',
-                        data=dict(username=username, password=password),
-                        follow_redirects=True)
+        return helpers.login(app, username, password)
 
     @staticmethod
     def logout(app):

doajtest/unit/application_processors/test_maned_journal_review.py

@@ -148,7 +148,7 @@ def test_04_maned_review_doaj_seal(self):
         )
 
         # set the seal to False using the form
-        fc.form.doaj_seal.data = False
+        fc.form.doaj_seal.data = []
 
         # run the crosswalk, don't test it at all in this test
         fc.form2target()
@@ -162,7 +162,7 @@ def test_04_maned_review_doaj_seal(self):
         fc.source.set_seal(True)
         fc.source2form()
 
-        assert fc.form.doaj_seal.data is True
+        assert 'y' in fc.form.doaj_seal.data
 
     def test_05_maned_review_continuations(self):
         # construct it from form data (with a known source)

doajtest/unit/test_crosswalks_article_ris.py

@@ -0,0 +1,43 @@
+import unittest
+
+from doajtest.fixtures import ArticleFixtureFactory
+from portality import models
+from portality.crosswalks.article_ris import ArticleRisXWalk
+
+
+class TestArticleRisXWalk(unittest.TestCase):
+    def test_article2ris(self):
+        article = ArticleFixtureFactory.make_article_source()
+        article = models.Article(**article)
+        article.bibjson().abstract = "abstract"
+        ris = ArticleRisXWalk.article2ris(article)
+        assert ris.type == 'JOUR'
+        assert ris['T1'] == [article.data['bibjson']['title']]
+        assert ris.to_text().split() == """
+TY  - JOUR
+T1  - Article Title
+AU  - The Author
+PY  - 1991
+JF  - The Title
+PB  - The Publisher
+VL  - 1
+IS  - 99
+SP  - 3
+EP  - 21
+UR  - http://www.example.com/article
+AB  - abstract
+KW  - word
+KW  - key
+DO  - 10.0000/SOME.IDENTIFIER
+LA  - EN
+LA  - FR
+ER  - 
+        """.split()
+
+    def test_article2ris__only_title(self):
+        ris = ArticleRisXWalk.article2ris({"bibjson": {"title": "Article Title"}})
+        assert ris.to_text().split() == """
+TY  - JOUR
+T1  - Article Title
+ER  - 
+        """.split()

doajtest/unit/test_ris.py

@@ -0,0 +1,66 @@
+from unittest import TestCase
+
+from portality.lib.ris import RisEntry
+
+
+class TestRisEntry(TestCase):
+
+    def test_get_set_item(self):
+        test_value = 'value_a'
+        entry = RisEntry()
+        entry['A1'] = test_value
+        assert entry['A1'] == [test_value]
+
+    def test_append(self):
+        entry = RisEntry()
+        entry.append('A1', '1')
+        entry['A1'].append('2')
+        assert entry['A1'] == ['1', '2']
+
+        entry['A1'] = '9'
+        assert entry['A1'] == ['9']
+
+    def test_getitem__valid_undefined(self):
+        entry = RisEntry()
+        assert entry['A1'] == []
+
+    def test_setitem__raise_field_not_found(self):
+        entry = RisEntry()
+        with self.assertRaises(ValueError):
+            entry['qoidjqowijdkncoiqw'] = 'value_a'
+
+    def test_getitem__raise_field_not_found(self):
+        entry = RisEntry()
+        with self.assertRaises(ValueError):
+            print(entry['qoidjqowijdkncoiqw'])
+
+    def test_to_text(self):
+        entry = RisEntry()
+        entry['A1'] = 'value_a'
+        entry['A2'] = 'value_b'
+        entry['TY'] = 'JOUR'
+
+        expected = """
+TY  - JOUR
+A1  - value_a
+A2  - value_b
+ER  -
+        """.strip() + ' \n'
+
+        assert entry.to_text() == expected
+
+    def test_from_text(self):
+        expected = """
+        TY  - JOUR
+        A1  - value_a
+        A2  - value_b
+        ER  -
+                """.strip() + ' \n'
+
+        entry = RisEntry.from_text(expected)
+        assert entry.type == 'JOUR'
+        assert dict(entry.data) == {
+            'TY': ['JOUR'],
+            'A1': ['value_a'],
+            'A2': ['value_b'],
+        }

doajtest/unit/test_view_admin.py

@@ -0,0 +1,37 @@
+import json
+
+from doajtest import helpers
+from doajtest.fixtures import JournalFixtureFactory
+from doajtest.fixtures.accounts import create_maned_a
+from doajtest.helpers import DoajTestCase
+from portality import models
+from portality.util import url_for
+
+
+class TestViewAdmin(DoajTestCase):
+
+    def setUp(self):
+        super().setUp()
+        self.acc = create_maned_a(save=True)
+
+    def test_journal_article_info(self):
+        journal = models.Journal(
+            **JournalFixtureFactory.make_journal_source()
+        )
+        journal.save(blocking=True)
+        models.Journal.refresh()
+
+        with self.app_test.test_client() as client:
+            resp = helpers.login(client, self.acc.email, 'password')
+            assert resp.status_code == 200
+
+            resp = client.get(url_for("admin.journal_article_info", journal_id=journal.id))
+            assert resp.status_code == 200
+            assert json.loads(resp.data) == {'n_articles': 0}
+
+    def test_journal_article_info__not_found(self):
+        with self.app_test.test_client() as client:
+            helpers.login(client, self.acc.email, 'password')
+
+            resp = client.get(url_for("admin.journal_article_info", journal_id='aksjdlaksjdlkajsdlkajsdlk'))
+            assert resp.status_code == 404

doajtest/unit/test_view_doajservices.py

@@ -0,0 +1,28 @@
+from doajtest.fixtures import ArticleFixtureFactory
+from doajtest.helpers import DoajTestCase
+from portality.crosswalks.article_ris import ArticleRisXWalk
+from portality.models import Article
+from portality.util import url_for
+
+
+class TestDoajservices(DoajTestCase):
+
+    def test_export_article_ris(self):
+        article = Article(**ArticleFixtureFactory.make_article_source())
+        article.save(blocking=True)
+        Article.refresh()
+
+        ris = ArticleRisXWalk.article2ris(article).to_text()
+
+        with self.app_test.test_client() as t_client:
+            url = url_for('doajservices.export_article_ris', article_id=article.id, fmt='ris')
+            response = t_client.get(url)
+            assert response.status_code == 200
+            assert response.get_data(as_text=True) == ris
+
+    def test_export_article_ris__not_found(self):
+        with self.app_test.test_client() as t_client:
+            url = url_for('doajservices.export_article_ris',
+                          article_id='article_id_that_does_not_exist', fmt='ris')
+            response = t_client.get(url)
+            assert response.status_code == 404

doajtest/unit/test_view_publisher.py

@@ -0,0 +1,21 @@
+from doajtest import helpers
+from doajtest.helpers import DoajTestCase
+from portality import models, constants
+from portality.util import url_for
+
+
+class TestViewPublisher(DoajTestCase):
+
+    def test_delete_application__no_such_object(self):
+        pwd = 'password'
+        un = 'publisher_a'
+        acc = models.Account.make_account(un + "@example.com", un, "Publisher " + un, [constants.ROLE_PUBLISHER])
+        acc.set_password(pwd)
+        acc.save(blocking=True)
+
+        with self.app_test.test_client() as t_client:
+            resp = helpers.login(t_client, acc.email, pwd)
+            assert resp.status_code == 200
+
+            resp = t_client.get(url_for("publisher.delete_application", application_id='no_such_id'))
+            assert resp.status_code == 404

docs/dictionary.md

@@ -1,11 +1,11 @@
-| Short   | Description                  |
-|---------|------------------------------|
-| bgjob   | background job               |
-| noti    | notification                 |
-| noqa    | NO-QA (NO Quality Assurance) |
-| inst    | instance                     |
-| fmt     | format                       |
-| exparam | extra parameter              |
-| maned   | Managing Editor              |
-| gsheet  | Google Sheet                 |
-| svc     | service                      |
+| Short    | Description                  |
+|----------|------------------------------|
+| bgjob    | background job               |
+| noti     | notification                 |
+| noqa     | NO-QA (NO Quality Assurance) |
+| inst     | instance                     |
+| fmt      | format                       |
+| exparam  | extra parameter              |
+| maned    | Managing Editor              |
+| gsheet   | Google Sheet                 |
+| svc,serv | service                      |

portality/crosswalks/article_ris.py

@@ -0,0 +1,50 @@
+from typing import Union
+
+from portality import models
+from portality.lib import jsonpath_utils
+from portality.lib.ris import RisEntry
+
+
+def extra_author_names(article) -> list:
+    query = '$.bibjson.author[*].name'
+    values = jsonpath_utils.find_values(query, article)
+    return sorted(set(values))
+
+
+RIS_ARTICLE_MAPPING = {
+    'T1': '$.bibjson.title',
+    'AU': extra_author_names,
+    'PY': '$.bibjson.year',
+    'JF': '$.bibjson.journal.title',
+    'PB': '$.bibjson.journal.publisher',
+    'VL': '$.bibjson.journal.volume',
+    'IS': '$.bibjson.journal.number',
+    'SP': '$.bibjson.start_page',
+    'EP': '$.bibjson.end_page',
+    'UR': '$.bibjson.link[*].url',
+    'AB': '$.bibjson.abstract',
+    'KW': '$.bibjson.keywords[*]',
+    'DO': '$.bibjson.identifier[?(@.type == "doi")].id',
+    'SN': '$.bibjson.journal.issns[*]',
+    'LA': '$.bibjson.journal.language[*]',
+}
+
+
+class ArticleRisXWalk:
+
+    @classmethod
+    def article2ris(cls, article: Union[models.Article, dict]) -> RisEntry:
+        if isinstance(article, models.Article):
+            article = article.data
+
+        entry = RisEntry(type_of_reference='JOUR')
+        for tag, query in RIS_ARTICLE_MAPPING.items():
+            if callable(query):
+                values = query(article)
+            else:
+                values = jsonpath_utils.find_values(query, article)
+
+            for v in values:
+                entry[tag].append(v)
+
+        return entry

portality/crosswalks/journal_form.py

@@ -289,7 +289,7 @@ def form2admin(cls, form, obj):
                 obj.set_editor(editor)
 
         if getattr(form, "doaj_seal", None):
-            obj.set_seal(form.doaj_seal.data)
+            obj.set_seal('y' in form.doaj_seal.data)
 
     @classmethod
     def bibjson2form(cls, bibjson, forminfo):
@@ -457,7 +457,7 @@ def admin2form(cls, obj, forminfo):
         if obj.editor is not None:
             forminfo['editor'] = obj.editor
 
-        forminfo['doaj_seal'] = obj.has_seal()
+        forminfo['doaj_seal'] = ['y'] if obj.has_seal() else []
 
 
 class JournalFormXWalk(JournalGenericXWalk):