From 6986e90351bca4071ea61387bee1f52f1125aceb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Boris=20Cl=C3=A9net?= <boris.clenet@inria.fr>
Date: Thu, 31 Aug 2023 14:35:10 +0200
Subject: [PATCH 1/6] [BUG] inside unit_tests workflow

---
 .github/workflows/unit_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
index 20f20ea3..d0097882 100644
--- a/.github/workflows/unit_tests.yml
+++ b/.github/workflows/unit_tests.yml
@@ -34,7 +34,7 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v3
 
-   - name: Load configuration for self-hosted runner
+    - name: Load configuration for self-hosted runner
       run: cp /home/neuro/local_testing_config.toml narps_open/utils/configuration/testing_config.toml
 
     - name: Install dependencies

From 2cc3c8048e92bd2c054a0a35cc7d337b34803eee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Boris=20Cl=C3=A9net?= <boris.clenet@inria.fr>
Date: Fri, 22 Sep 2023 17:33:02 +0200
Subject: [PATCH 2/6] Browsing all issues pages from Github API

---
 narps_open/utils/status.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/narps_open/utils/status.py b/narps_open/utils/status.py
index cc4eb8a7..333a046e 100644
--- a/narps_open/utils/status.py
+++ b/narps_open/utils/status.py
@@ -18,10 +18,18 @@
 def get_opened_issues():
     """ Return a list of opened issues and pull requests for the NARPS Open Pipelines project """
     request_url = 'https://api.github.com/repos/Inria-Empenn/narps_open_pipelines/issues'
-    response = get(request_url, timeout = 2)
-    response.raise_for_status()
-
-    return response.json()
+    request_url += '?page={page_number}'
+
+    issues = {}
+    page = True # Will later be replaced by a dict
+    page_number = 0
+    while bool(page) :
+        response = get(request_url.format(page_number = str(page_number)), timeout = 2)
+        response.raise_for_status()
+        page = response.json()
+        issues += page
+
+    return issues
 
 def get_teams_with_pipeline_files():
     """ Return a set of teams having a file for their pipeline in the repository """

From 01845d9df9b50b5011b198797916e3e81b0d9b54 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Boris=20Cl=C3=A9net?= <boris.clenet@inria.fr>
Date: Mon, 25 Sep 2023 11:26:37 +0200
Subject: [PATCH 3/6] Get all pages of GitHub issues

---
 narps_open/utils/status.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/narps_open/utils/status.py b/narps_open/utils/status.py
index 333a046e..e70e984d 100644
--- a/narps_open/utils/status.py
+++ b/narps_open/utils/status.py
@@ -20,10 +20,11 @@ def get_opened_issues():
     request_url = 'https://api.github.com/repos/Inria-Empenn/narps_open_pipelines/issues'
     request_url += '?page={page_number}'
 
-    issues = {}
+    issues = []
     page = True # Will later be replaced by a dict
-    page_number = 0
-    while bool(page) :
+    page_number = 1 # According to the doc, first page is not page 0
+    # https://docs.github.com/en/rest/issues/issues#list-repository-issues
+    while page : # TODO check if page is empty
         response = get(request_url.format(page_number = str(page_number)), timeout = 2)
         response.raise_for_status()
         page = response.json()

From 6a8472cfe20ddee796590daf3ad1b7ed8f3a5545 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Boris=20Cl=C3=A9net?= <boris.clenet@inria.fr>
Date: Mon, 25 Sep 2023 14:34:31 +0200
Subject: [PATCH 4/6] [TEST] Updating test for status module

---
 docs/status.md             |  2 +-
 narps_open/utils/status.py |  4 ++--
 tests/utils/test_status.py | 14 ++++++++++++--
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/docs/status.md b/docs/status.md
index f323cc8f..7fde8239 100644
--- a/docs/status.md
+++ b/docs/status.md
@@ -36,7 +36,7 @@ print(pipeline_info['status'])
 report.markdown() # Returns a string containing the markdown
 ```
 
-You can also use the command-line tool as so. Option `-t` is for the team id, option `-d` allows to print only one of the sub parts of the description among : `general`, `exclusions`, `preprocessing`, `analysis`, and `categorized_for_analysis`.
+You can also use the command-line tool as so.
 
 ```bash
 python narps_open/utils/status -h
diff --git a/narps_open/utils/status.py b/narps_open/utils/status.py
index e70e984d..e919b0fc 100644
--- a/narps_open/utils/status.py
+++ b/narps_open/utils/status.py
@@ -21,10 +21,10 @@ def get_opened_issues():
     request_url += '?page={page_number}'
 
     issues = []
-    page = True # Will later be replaced by a dict
+    page = True # Will later be replaced by a table
     page_number = 1 # According to the doc, first page is not page 0
     # https://docs.github.com/en/rest/issues/issues#list-repository-issues
-    while page : # TODO check if page is empty
+    while bool(page) is True : # Test if the page is empty
         response = get(request_url.format(page_number = str(page_number)), timeout = 2)
         response.raise_for_status()
         page = response.json()
diff --git a/tests/utils/test_status.py b/tests/utils/test_status.py
index 0e98ef83..49c13a6f 100644
--- a/tests/utils/test_status.py
+++ b/tests/utils/test_status.py
@@ -36,7 +36,7 @@ def mock_api_issue(mocker):
     """
     response = Response()
     response.status_code = 200
-    def json_func():
+    def json_func_page_0():
         return [
             {
                 "html_url": "url_issue_2",
@@ -50,7 +50,13 @@ def json_func():
                 "title" : "Pull request for pipeline 2T6S",
                 "pull_request" : {},
                 "body" : "Work has been done."
-            },
+            }
+        ]
+
+    json_func_page_1 = json_func_page_0
+
+    def json_func_page_2():
+        return [
             {
                 "html_url": "url_issue_4",
                 "number": 4,
@@ -64,6 +70,10 @@ def json_func():
                 "body" : "Something about 2T6S."
             }
         ]
+
+    def json_func_page_3():
+        return []
+
     response.json = json_func
     mocker.patch('narps_open.utils.status.get', return_value = response)
     mocker.patch(

From e18ea00a378335217dec12b07b637b5dcd6e0e23 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Boris=20Cl=C3=A9net?= <boris.clenet@inria.fr>
Date: Tue, 26 Sep 2023 12:03:46 +0200
Subject: [PATCH 5/6] [TEST] fetch several issues

---
 narps_open/utils/status.py |   3 +-
 tests/utils/test_status.py | 133 +++++++++++++++++++++----------------
 2 files changed, 79 insertions(+), 57 deletions(-)

diff --git a/narps_open/utils/status.py b/narps_open/utils/status.py
index e919b0fc..fef7708d 100644
--- a/narps_open/utils/status.py
+++ b/narps_open/utils/status.py
@@ -18,7 +18,7 @@
 def get_opened_issues():
     """ Return a list of opened issues and pull requests for the NARPS Open Pipelines project """
     request_url = 'https://api.github.com/repos/Inria-Empenn/narps_open_pipelines/issues'
-    request_url += '?page={page_number}'
+    request_url += '?page={page_number}?per_page=100'
 
     issues = []
     page = True # Will later be replaced by a table
@@ -29,6 +29,7 @@ def get_opened_issues():
         response.raise_for_status()
         page = response.json()
         issues += page
+        page_number += 1
 
     return issues
 
diff --git a/tests/utils/test_status.py b/tests/utils/test_status.py
index 49c13a6f..6c16279b 100644
--- a/tests/utils/test_status.py
+++ b/tests/utils/test_status.py
@@ -34,48 +34,62 @@ def mock_api_issue(mocker):
         which is actually imported as `get` inside the `narps_open.utils.status` module.
         Hence, we patch the `narps_open.utils.status.get` method.
     """
-    response = Response()
-    response.status_code = 200
-    def json_func_page_0():
-        return [
-            {
-                "html_url": "url_issue_2",
-                "number": 2,
-                "title" : "Issue for pipeline UK24",
-                "body" : "Nothing to add here."
-            },
-            {
-                "html_url": "url_pull_3",
-                "number": 3,
-                "title" : "Pull request for pipeline 2T6S",
-                "pull_request" : {},
-                "body" : "Work has been done."
-            }
-        ]
-
-    json_func_page_1 = json_func_page_0
-
-    def json_func_page_2():
-        return [
-            {
-                "html_url": "url_issue_4",
-                "number": 4,
-                "title" : None,
-                "body" : "This is a malformed issue about C88N."
-            },
-            {
-                "html_url": "url_issue_5",
-                "number": 5,
-                "title" : "Issue about 2T6S",
-                "body" : "Something about 2T6S."
-            }
-        ]
-
-    def json_func_page_3():
-        return []
-
-    response.json = json_func
-    mocker.patch('narps_open.utils.status.get', return_value = response)
+
+    # Create a method to mock requests.get
+    def mocked_requests_get(url, params=None, **kwargs):
+
+        response = Response()
+        response.status_code = 200
+        def json_func_page_0():
+            return [
+                {
+                    "html_url": "url_issue_2",
+                    "number": 2,
+                    "title" : "Issue for pipeline UK24",
+                    "body" : "Nothing to add here."
+                },
+                {
+                    "html_url": "url_pull_3",
+                    "number": 3,
+                    "title" : "Pull request for pipeline 2T6S",
+                    "pull_request" : {},
+                    "body" : "Work has been done."
+                }
+            ]
+
+        json_func_page_1 = json_func_page_0
+
+        def json_func_page_2():
+            return [
+                {
+                    "html_url": "url_issue_4",
+                    "number": 4,
+                    "title" : None,
+                    "body" : "This is a malformed issue about C88N."
+                },
+                {
+                    "html_url": "url_issue_5",
+                    "number": 5,
+                    "title" : "Issue about 2T6S",
+                    "body" : "Something about 2T6S."
+                }
+            ]
+
+        def json_func_page_3():
+            return []
+
+        if '?page=1' in url:
+            response.json = json_func_page_1
+        elif '?page=2' in url:
+            response.json = json_func_page_2
+        elif '?page=3' in url:
+            response.json = json_func_page_3
+        else:
+            response.json = json_func_page_0
+
+        return response
+
+    mocker.patch('narps_open.utils.status.get', side_effect = mocked_requests_get)
     mocker.patch(
         'narps_open.utils.status.get_teams_with_pipeline_files',
         return_value = ['2T6S', 'UK24', 'Q6O0']
@@ -104,8 +118,6 @@ def test_get_issues(mocker):
             which is actually imported as `get` inside the `narps_open.utils.status` module.
             Hence, we patch the `narps_open.utils.status.get` method.
         """
-        get_opened_issues()
-
         # Create a mock API response for 404 error
         response = Response()
         response.status_code = 404
@@ -124,18 +136,27 @@ def json_func():
         assert len(get_opened_issues()) == 0
 
         # Create a mock API response for the general usecase
-        response = Response()
-        response.status_code = 200
-        def json_func():
-            return [
-                {
-                    "html_url": "urls",
-                    "number": 2,
-                }
-            ]
-        response.json = json_func
-
-        mocker.patch('narps_open.utils.status.get', return_value = response)
+        def mocked_requests_get(url, params=None, **kwargs):
+            response = Response()
+            response.status_code = 200
+            def json_func_page_1():
+                return [
+                    {
+                        "html_url": "urls",
+                        "number": 2,
+                    }
+                ]
+            def json_func_page_2():
+                return []
+
+            if '?page=2' in url:
+                response.json = json_func_page_2
+            else:
+                response.json = json_func_page_1
+
+            return response
+
+        mocker.patch('narps_open.utils.status.get', side_effect = mocked_requests_get)
         issues = get_opened_issues()
         assert len(issues) == 1
         assert issues[0]['html_url'] == 'urls'

From f9f7a550dc509c690f92c967aee0b6093a2d61ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Boris=20Cl=C3=A9net?= <boris.clenet@inria.fr>
Date: Fri, 29 Sep 2023 10:10:46 +0200
Subject: [PATCH 6/6] Dealing with single page of issues

---
 narps_open/utils/status.py |  13 ++-
 tests/utils/test_status.py | 233 ++++++++++++++++++++++---------------
 2 files changed, 154 insertions(+), 92 deletions(-)

diff --git a/narps_open/utils/status.py b/narps_open/utils/status.py
index fef7708d..56b64052 100644
--- a/narps_open/utils/status.py
+++ b/narps_open/utils/status.py
@@ -17,8 +17,15 @@
 
 def get_opened_issues():
     """ Return a list of opened issues and pull requests for the NARPS Open Pipelines project """
+    # First get the number of issues of the project
+    request_url = 'https://api.github.com/repos/Inria-Empenn/narps_open_pipelines'
+    response = get(request_url, timeout = 2)
+    response.raise_for_status()
+    nb_issues = response.json()['open_issues']
+
+    # Get all opened issues
     request_url = 'https://api.github.com/repos/Inria-Empenn/narps_open_pipelines/issues'
-    request_url += '?page={page_number}?per_page=100'
+    request_url += '?page={page_number}?per_page=30'
 
     issues = []
     page = True # Will later be replaced by a table
@@ -31,6 +38,10 @@ def get_opened_issues():
         issues += page
         page_number += 1
 
+        # Leave if there is only one page (in this case, the `page` query parameter has no effect)
+        if nb_issues < 30:
+            break
+
     return issues
 
 def get_teams_with_pipeline_files():
diff --git a/tests/utils/test_status.py b/tests/utils/test_status.py
index 6c16279b..41143bbf 100644
--- a/tests/utils/test_status.py
+++ b/tests/utils/test_status.py
@@ -25,6 +25,118 @@
     PipelineStatusReport
     )
 
+mocked_issues_4 = [
+    {
+        "html_url": "url_issue_2",
+        "number": 2,
+        "title" : "Issue for pipeline UK24",
+        "body" : "Nothing to add here."
+    },
+    {
+        "html_url": "url_pull_3",
+        "number": 3,
+        "title" : "Pull request for pipeline 2T6S",
+        "pull_request" : {},
+        "body" : "Work has been done."
+    },
+    {
+        "html_url": "url_issue_4",
+        "number": 4,
+        "title" : None,
+        "body" : "This is a malformed issue about C88N."
+    },
+    {
+        "html_url": "url_issue_5",
+        "number": 5,
+        "title" : "Issue about 2T6S",
+        "body" : "Something about 2T6S."
+    }
+]
+
+mocked_issues_40_1 = [
+    {
+        "html_url": "url_issue_55",
+        "number": i,
+        "title" : "Issue for pipeline UK24",
+        "body" : "Nothing to add here."
+    } for i in range(0,30)
+]
+
+mocked_issues_40_2 = [
+    {
+        "html_url": "url_issue_55",
+        "number": i,
+        "title" : "Issue for pipeline UK24",
+        "body" : "Nothing to add here."
+    } for i in range(0,10)
+]
+
+mocked_repo_info_0 = {
+    "open_issues": 0
+}
+
+mocked_repo_info_4 = {
+    "open_issues": 4
+}
+
+mocked_repo_info_40 = {
+    "open_issues": 40
+}
+
+def mocked_requests_get_0(url, params=None, **kwargs):
+    """ Create a method to mock requests.get in case there are no issues """
+
+    response = Response()
+    response.status_code = 200
+
+    if 'issues' not in url:
+        def mocked_json():
+            return mocked_repo_info_0
+    else:
+        def mocked_json():
+            return []
+
+    response.json = mocked_json
+    return response
+
+def mocked_requests_get_4(url, params=None, **kwargs):
+    """ Create a method to mock requests.get in case there are less than 30 issues """
+
+    response = Response()
+    response.status_code = 200
+
+    if 'issues' not in url:
+        def mocked_json():
+            return mocked_repo_info_4
+    else:
+        def mocked_json():
+            return mocked_issues_4
+
+    response.json = mocked_json
+    return response
+
+def mocked_requests_get_40(url, params=None, **kwargs):
+    """ Create a method to mock requests.get in case there are more than 30 issues """
+
+    response = Response()
+    response.status_code = 200
+
+    if 'issues' not in url:
+        def mocked_json():
+            return mocked_repo_info_40
+    elif '?page=1' in url:
+        def mocked_json():
+            return mocked_issues_40_1
+    elif '?page=2' in url:
+        def mocked_json():
+            return mocked_issues_40_2
+    else:
+        def mocked_json():
+            return []
+
+    response.json = mocked_json
+    return response
+
 @fixture
 def mock_api_issue(mocker):
     """ Create a mock GitHub API response for successful query on open issues
@@ -34,62 +146,6 @@ def mock_api_issue(mocker):
         which is actually imported as `get` inside the `narps_open.utils.status` module.
         Hence, we patch the `narps_open.utils.status.get` method.
     """
-
-    # Create a method to mock requests.get
-    def mocked_requests_get(url, params=None, **kwargs):
-
-        response = Response()
-        response.status_code = 200
-        def json_func_page_0():
-            return [
-                {
-                    "html_url": "url_issue_2",
-                    "number": 2,
-                    "title" : "Issue for pipeline UK24",
-                    "body" : "Nothing to add here."
-                },
-                {
-                    "html_url": "url_pull_3",
-                    "number": 3,
-                    "title" : "Pull request for pipeline 2T6S",
-                    "pull_request" : {},
-                    "body" : "Work has been done."
-                }
-            ]
-
-        json_func_page_1 = json_func_page_0
-
-        def json_func_page_2():
-            return [
-                {
-                    "html_url": "url_issue_4",
-                    "number": 4,
-                    "title" : None,
-                    "body" : "This is a malformed issue about C88N."
-                },
-                {
-                    "html_url": "url_issue_5",
-                    "number": 5,
-                    "title" : "Issue about 2T6S",
-                    "body" : "Something about 2T6S."
-                }
-            ]
-
-        def json_func_page_3():
-            return []
-
-        if '?page=1' in url:
-            response.json = json_func_page_1
-        elif '?page=2' in url:
-            response.json = json_func_page_2
-        elif '?page=3' in url:
-            response.json = json_func_page_3
-        else:
-            response.json = json_func_page_0
-
-        return response
-
-    mocker.patch('narps_open.utils.status.get', side_effect = mocked_requests_get)
     mocker.patch(
         'narps_open.utils.status.get_teams_with_pipeline_files',
         return_value = ['2T6S', 'UK24', 'Q6O0']
@@ -118,7 +174,7 @@ def test_get_issues(mocker):
             which is actually imported as `get` inside the `narps_open.utils.status` module.
             Hence, we patch the `narps_open.utils.status.get` method.
         """
-        # Create a mock API response for 404 error
+        # Behavior for 404 error
         response = Response()
         response.status_code = 404
 
@@ -126,41 +182,27 @@ def test_get_issues(mocker):
         with raises(HTTPError):
             get_opened_issues()
 
-        # Create a mock API response for the no issues case
-        response = Response()
-        response.status_code = 200
-        def json_func():
-            return []
-        response.json = json_func
-        mocker.patch('narps_open.utils.status.get', return_value = response)
+        # No issues case
+        mocker.patch('narps_open.utils.status.get', side_effect = mocked_requests_get_0)
         assert len(get_opened_issues()) == 0
 
-        # Create a mock API response for the general usecase
-        def mocked_requests_get(url, params=None, **kwargs):
-            response = Response()
-            response.status_code = 200
-            def json_func_page_1():
-                return [
-                    {
-                        "html_url": "urls",
-                        "number": 2,
-                    }
-                ]
-            def json_func_page_2():
-                return []
-
-            if '?page=2' in url:
-                response.json = json_func_page_2
-            else:
-                response.json = json_func_page_1
-
-            return response
-
-        mocker.patch('narps_open.utils.status.get', side_effect = mocked_requests_get)
+        # General usecase 4 issues
+        mocker.patch('narps_open.utils.status.get', side_effect = mocked_requests_get_4)
         issues = get_opened_issues()
-        assert len(issues) == 1
-        assert issues[0]['html_url'] == 'urls'
+        assert len(issues) == 4
+        assert issues[0]['html_url'] == 'url_issue_2'
         assert issues[0]['number'] == 2
+        assert issues[0]['title'] == 'Issue for pipeline UK24'
+        assert issues[0]['body'] == 'Nothing to add here.'
+
+        # General usecase 40 issues
+        mocker.patch('narps_open.utils.status.get', side_effect = mocked_requests_get_40)
+        issues = get_opened_issues()
+        assert len(issues) == 40
+        assert issues[0]['html_url'] == 'url_issue_55'
+        assert issues[0]['number'] == 0
+        assert issues[0]['title'] == 'Issue for pipeline UK24'
+        assert issues[0]['body'] == 'Nothing to add here.'
 
     @staticmethod
     @mark.unit_test
@@ -175,9 +217,12 @@ def test_get_teams():
 
     @staticmethod
     @mark.unit_test
-    def test_generate(mock_api_issue):
+    def test_generate(mock_api_issue, mocker):
         """ Test generating a PipelineStatusReport """
 
+        # Mock requests.get
+        mocker.patch('narps_open.utils.status.get', side_effect = mocked_requests_get_4)
+
         # Test the generation
         report = PipelineStatusReport()
         report.generate()
@@ -223,9 +268,12 @@ def test_generate(mock_api_issue):
 
     @staticmethod
     @mark.unit_test
-    def test_markdown(mock_api_issue):
+    def test_markdown(mock_api_issue, mocker):
         """ Test writing a PipelineStatusReport as Markdown """
 
+        # Mock requests.get
+        mocker.patch('narps_open.utils.status.get', side_effect = mocked_requests_get_4)
+
         # Generate markdown from report
         report = PipelineStatusReport()
         report.generate()
@@ -241,9 +289,12 @@ def test_markdown(mock_api_issue):
 
     @staticmethod
     @mark.unit_test
-    def test_str(mock_api_issue):
+    def test_str(mock_api_issue, mocker):
         """ Test writing a PipelineStatusReport as JSON """
 
+        # Mock requests.get
+        mocker.patch('narps_open.utils.status.get', side_effect = mocked_requests_get_4)
+
         # Generate report
         report = PipelineStatusReport()
         report.generate()