Merge pull request #40 from aanil/fix_git

Fix for reading dotenv file
NationalGenomicsInfrastructure · May 15, 2024 · 002caa9 · 002caa9
2 parents d19b4e7 + 1178350
commit 002caa9
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diff --git a/daily_read/__init__.py b/daily_read/__init__.py
@@ -1,3 +1,4 @@
-import daily_read.config
+""" DailyRead version
+"""
 
-config_values = daily_read.config.Config()
+__version__ = "0.0.1"
diff --git a/daily_read/__main__.py b/daily_read/__main__.py
@@ -21,52 +21,57 @@
 import daily_read.utils
 
 
-config_values = daily_read.config.Config()
+@click.group(context_settings=dict(help_option_names=["-h", "--help"]))
+@click.option("--env_file_path", type=click.Path())
+@click.pass_context
+def daily_read_cli(ctx, env_file_path):
+    config_values = daily_read.config.Config(env_file_path=env_file_path)
+    if ctx.obj is None:
+        ctx.obj = dict()
+    ctx.obj["config_values"] = config_values
 
-rich_handler = RichHandler()
-rich_handler.setFormatter(logging.Formatter("%(message)s"))
-LOG_FORMAT = "%(asctime)s - %(name)s - %(levelname)s - Commit: %(commit)s - %(message)s"
+    rich_handler = RichHandler()
+    rich_handler.setFormatter(logging.Formatter("%(message)s"))
+    LOG_FORMAT = "%(asctime)s - %(name)s - %(levelname)s - Commit: %(commit)s - %(message)s"
 
-if not os.path.isabs(config_values.LOG_LOCATION):
-    raise ValueError(f"Log location is not an absolute path: {config_values.LOG_LOCATION}")
+    if not os.path.isabs(config_values.LOG_LOCATION):
+        raise ValueError(f"Log location is not an absolute path: {config_values.LOG_LOCATION}")
 
-if os.path.exists(config_values.LOG_LOCATION) and not os.path.isdir(config_values.LOG_LOCATION):
-    raise ValueError(f"Log Location exists but is not a directory: {config_values.LOG_LOCATION}")
+    if os.path.exists(config_values.LOG_LOCATION) and not os.path.isdir(config_values.LOG_LOCATION):
+        raise ValueError(f"Log Location exists but is not a directory: {config_values.LOG_LOCATION}")
 
-log_file = os.path.join(config_values.LOG_LOCATION, "DailyRead.log")
+    log_file = os.path.join(config_values.LOG_LOCATION, "DailyRead.log")
 
-rotating_file_handler = logging.handlers.RotatingFileHandler(
-    log_file, maxBytes=1024 * 1024 * 100, backupCount=5
-)  # 5 files of 100MB
-rotating_file_handler.addFilter(daily_read.utils.ContextFilter())
+    rotating_file_handler = logging.handlers.RotatingFileHandler(
+        log_file, maxBytes=1024 * 1024 * 100, backupCount=5
+    )  # 5 files of 100MB
+    rotating_file_handler.addFilter(daily_read.utils.ContextFilter())
 
+    logging.basicConfig(
+        level="INFO",
+        format=LOG_FORMAT,
+        handlers=[rich_handler, rotating_file_handler],
+    )
 
-logging.basicConfig(
-    level="INFO",
-    format=LOG_FORMAT,
-    handlers=[rich_handler, rotating_file_handler],
-)
 
 log = logging.getLogger(__name__)
 
 
-@click.group(context_settings=dict(help_option_names=["-h", "--help"]))
-def daily_read_cli():
-    pass
-
-
 ### GENERATE ###
 @daily_read_cli.group()
-def generate():
+@click.pass_context
+def generate(ctx):
     """Generate reports and save in a local git repository"""
     pass
 
 
 @generate.command(name="all")
 @click.option("-u", "--upload", is_flag=True, help="Trigger upload of reports.")
 @click.option("--develop", is_flag=True, help="Only generate max 5 reports, for dev purposes.")
-def generate_all(upload=False, develop=False):
+@click.pass_context
+def generate_all(ctx, upload=False, develop=False):
     # Fetch data from all sources (configurable)
+    config_values = ctx.obj["config_values"]
     projects_data = daily_read.ngi_data.ProjectDataMaster(config_values)
 
     log.info(f"Fetching data for {projects_data.source_names}")
@@ -137,7 +142,9 @@ def generate_all(upload=False, develop=False):
     help="Include projects that are older than 6 months.",
     is_flag=True,
 )
-def generate_single(project, include_older=False):
+@click.pass_context
+def generate_single(ctx, project, include_older=False):
+    config_values = ctx.obj["config_values"]
     projects_data = daily_read.ngi_data.ProjectDataMaster(config_values)
     # Fetch all projects so that the report will look the same
     log.info("Fetching data from NGI sources")

diff --git a/daily_read/config.py b/daily_read/config.py
@@ -4,8 +4,8 @@
 
 
 class Config(object):
-    def __init__(self):
-        dotenv.load_dotenv()
+    def __init__(self, env_file_path):
+        dotenv.load_dotenv(dotenv_path=env_file_path)
         self.ORDER_PORTAL_URL = os.getenv("DAILY_READ_ORDER_PORTAL_URL")
         self.ORDER_PORTAL_API_KEY = os.getenv("DAILY_READ_ORDER_PORTAL_API_KEY")
         self.REPORTS_LOCATION = os.getenv("DAILY_READ_REPORTS_LOCATION")

diff --git a/daily_read/templates/daily_report.html.j2 b/daily_read/templates/daily_report.html.j2
@@ -1,6 +1,8 @@
 <!DOCTYPE html>
 <html lang="en">
-<iframe id="ngi_progress_report" srcdoc='
+  <iframe
+    id="ngi_progress_report"
+    srcdoc='
   <head>
     <meta charset="utf-8" />
     <meta http-equiv="X-UA-Compatible" content="IE=edge" />
@@ -153,69 +155,73 @@
     {% else %}
       <div id="projects_list">
         {% for date_prio, date_type in priority | dictsort %}
-          {% if date_type != "None"%}
-          <div class="row p-3">
-            <div
-              class="col-sm border-end border-primary me-3 d-flex align-items-center"
-              style="--bs-border-width: 15px;"
-            >
-              <div class="fs-1">
-                {{ date_type }}
-              </div>
-              <div class="fs-5">
-              <i class="bi bi-patch-question px-1" data-bs-toggle="tooltip" data-bs-title="{{status_desc[date_type]}}"></i>
+          {% if date_type != "None" %}
+            <div class="row p-3">
+              <div
+                class="col-sm border-end border-primary me-3 d-flex align-items-center"
+                style="--bs-border-width: 15px;"
+              >
+                <div class="fs-1">
+                  {{ date_type }}
+                </div>
+                <div class="fs-5">
+                  <i
+                    class="bi bi-patch-question px-1"
+                    data-bs-toggle="tooltip"
+                    data-bs-title="{{ status_desc[date_type] }}"
+                  ></i>
+                </div>
               </div>
-            </div>
-            <div class="col-sm projects-accordions">
-              {% for project in data["projects"][date_type] %}
-                <div class="accordion mb-1">
-                  <div class="accordion-item">
-                    <h2 class="accordion-header">
-                      <button
-                        class="accordion-button collapsed"
-                        type="button"
-                        data-bs-toggle="collapse"
-                        data-bs-target="#panel_project_{{ project.project_id }}"
-                        aria-expanded="false"
-                        aria-controls="panel_project_{{ project.project_id }}"
-                      >
-                        <h4 class="mb-0">{{ project.internal_name }}</h4>
-                      </button>
-                    </h2>
-                    <div id="panel_project_{{ project.project_id }}" class="accordion-collapse collapse">
-                      <div class="accordion-body pb-0">
-                        <p>
-                          Order Portal:
-                          <a target="_parent" href="{{ portal_url }}/order/{{ project.project_id }}">
-                            {{ project.project_id }}
-                          </a>
-                        </p>
-                        {% for date, statuses in project.project_dates | dictsort %}
-                          {% if project.project_dates[date] and project.project_dates[date] != "XXXX-XX-XX" %}
-                            <dl class="row ml-3">
-                              <dt class="list-group-item col-4">{{ date }}</dt>
-                              <dd class="list-group-item col-8">
-                                {% for status in statuses %}
-                                  <i class="bi bi-{{ icons[status] }}"></i>
-                                  <span style="padding-left: 0.5rem">{{ status }}</span>
-                                  <i
-                                    class="bi bi-patch-question px-1"
-                                    data-bs-toggle="tooltip"
-                                    data-bs-title="{{ status_desc[status] }}"
-                                  ></i
-                                  ><br />
-                                {% endfor %}
-                              </dd>
-                            </dl>
-                          {% endif %}
-                        {% endfor %}
+              <div class="col-sm projects-accordions">
+                {% for project in data["projects"][date_type] %}
+                  <div class="accordion mb-1">
+                    <div class="accordion-item">
+                      <h2 class="accordion-header">
+                        <button
+                          class="accordion-button collapsed"
+                          type="button"
+                          data-bs-toggle="collapse"
+                          data-bs-target="#panel_project_{{ project.project_id }}"
+                          aria-expanded="false"
+                          aria-controls="panel_project_{{ project.project_id }}"
+                        >
+                          <h4 class="mb-0">{{ project.internal_name }}</h4>
+                        </button>
+                      </h2>
+                      <div id="panel_project_{{ project.project_id }}" class="accordion-collapse collapse">
+                        <div class="accordion-body pb-0">
+                          <p>
+                            Order Portal:
+                            <a target="_parent" href="{{ portal_url }}/order/{{ project.project_id }}">
+                              {{ project.project_id }}
+                            </a>
+                          </p>
+                          {% for date, statuses in project.project_dates | dictsort %}
+                            {% if project.project_dates[date] and project.project_dates[date] != "XXXX-XX-XX" %}
+                              <dl class="row ml-3">
+                                <dt class="list-group-item col-4">{{ date }}</dt>
+                                <dd class="list-group-item col-8">
+                                  {% for status in statuses %}
+                                    <i class="bi bi-{{ icons[status] }}"></i>
+                                    <span style="padding-left: 0.5rem">{{ status }}</span>
+                                    <i
+                                      class="bi bi-patch-question px-1"
+                                      data-bs-toggle="tooltip"
+                                      data-bs-title="{{ status_desc[status] }}"
+                                    ></i
+                                    ><br />
+                                  {% endfor %}
+                                </dd>
+                              </dl>
+                            {% endif %}
+                          {% endfor %}
+                        </div>
                       </div>
                     </div>
                   </div>
-                </div>
-              {% endfor %}
+                {% endfor %}
+              </div>
             </div>
-          </div>
           {% endif %}
         {% endfor %}
       </div>
@@ -235,6 +241,10 @@
       const tooltipList = [...tooltipTriggerList].map(tooltipTriggerEl => new bootstrap.Tooltip(tooltipTriggerEl));
     </script>
   </body>
-    ' width="120%" height="2000" frameborder="0" sandbox="allow-scripts allow-top-navigation"></iframe>
-
-</html>
+    '
+    width="120%"
+    height="2000"
+    frameborder="0"
+    sandbox="allow-scripts allow-top-navigation"
+  ></iframe>
+</html>
diff --git a/setup.py b/setup.py
@@ -1,6 +1,6 @@
 from setuptools import setup, find_packages
 
-version = "0.0.1"
+from daily_read import __version__
 
 with open("README.md") as f:
     readme = f.read()
@@ -10,7 +10,7 @@
 
 setup(
     name="Daily Read",
-    version=version,
+    version=__version__,
     description="A utility to generate and upload automatic progress reports for NGI Sweden.",
     long_description=readme,
     long_description_content_type="text/markdown",

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -323,7 +323,7 @@ def data_repo_full(
 @pytest.fixture
 def mock_project_data_record():
     def _method(status):
-        config_values = config.Config()
+        config_values = config.Config(env_file_path=".test.env")
         if status == "open":
             mock_record = ngi_data.ProjectDataRecord(
                 "NGIS/2023/NGI123456.json",
@@ -441,3 +441,10 @@ def mocked_statusdb_conn_rows():
         },
     )
     return [row1, row2, row3]
+
+
+@pytest.fixture(autouse=True)
+def get_env_file_path():
+    """returns the test env file path"""
+
+    return ".test.env"
diff --git a/tests/test_daily_report.py b/tests/test_daily_report.py
@@ -6,11 +6,11 @@
 from daily_read import daily_report, config, ngi_data, order_portal
 
 
-def test_write_report_to_out_dir(data_repo_full, mock_project_data_record, create_report_path):
+def test_write_report_to_out_dir(data_repo_full, mock_project_data_record, create_report_path, get_env_file_path):
     """Test existence of html report when provided with out_dir"""
     orderer = "[email protected]"
     order_id = "NGI123456"
-    config_values = config.Config()
+    config_values = config.Config(env_file_path=get_env_file_path)
     daily_rep = daily_report.DailyReport()
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)