Merge pull request #28 from paulsaxe/main

Protected against corrupt job_data.json files.

Makefile

@@ -57,28 +57,28 @@ format: ## reformat with black
 	black --extend-exclude '_version.py' $(MODULE)
 
 typing: ## check typing
-	pytype seamm_datastore
+	pytype $(MODULE)
 
 test: ## run tests quickly with the default Python
-	pytest -rP seamm_datastore/tests
+	pytest -rP $(MODULE)/tests
 
 test-all: ## run tests on every Python version with tox
 	tox
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source seamm_datastore -m pytest
+	coverage run --source $(MODULE) -m pytest
 	coverage report -m
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
 docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/seamm_datastore.rst
+	rm -f docs/$(MODULE).rst
 	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ seamm_datastore
+	sphinx-apidoc -o docs/ $(MODULE)
 	$(MAKE) -C docs clean
 	$(MAKE) -C docs html
 	$(BROWSER) docs/_build/html/index.html
-	rm -f docs/seamm_datastore.rst
+	rm -f docs/$(MODULE).rst
 	rm -f docs/modules.rst
 
 servedocs: docs ## compile the docs watching for changes
@@ -93,12 +93,10 @@ check-release: clean ## check the release for errors
 	python -m twine check dist/*
 
 dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
-	ls -l dist
+	python -m build
 
 install: uninstall ## install the package to the active Python's site-packages
-	python setup.py install
+	pip install .
 
 uninstall: clean ## uninstall the package
-	pip uninstall --yes seamm_datastore
+	pip uninstall --yes $(MODULE)

seamm_datastore/connect.py

@@ -81,7 +81,6 @@ def __init__(
         datastore_location: str = None,
         default_project: str = "default",
     ):
-
         if database_uri.lower() == "sqlite:///:memory:":
             initialize = True
 
@@ -212,7 +211,6 @@ def add_job(
         parameters=None,
         status="submitted",
     ):
-
         warn(
             "Deprecation warning: This method will no longer be available",
             " in the next version of the seamm datastore.",
@@ -223,7 +221,6 @@ def add_job(
             parameters = {"cmdline": []}
 
         with session_scope(self.Session) as session:
-
             job = self.Job.create(
                 id,
                 flowchart_filename,

seamm_datastore/database/build.py

@@ -130,40 +130,42 @@ def import_datastore(session, location, as_json=True):
                 potential_job = os.path.join(potential_project, potential_job)
 
                 if os.path.isdir(potential_job):
-
                     # Check for job_data.json - has to have this to be job
                     check_path = os.path.join(potential_job, "job_data.json")
                     if os.path.exists(check_path):
-                        job_data = Job.parse_job_data(check_path)
-
-                        if "command line" in job_data:
-                            parameters = {"cmdline": job_data["command line"]}
-                        else:
-                            parameters = {"cmdline": []}
-
                         try:
-                            job = Job.create(
-                                job_data["id"],
-                                potential_job + "/flowchart.flow",
-                                project_names=job_data["project_names"],
-                                path=potential_job,
-                                title=job_data["title"],
-                                description=job_data.get("description", ""),
-                                submitted=job_data.get("submitted", None),
-                                started=job_data.get("started", None),
-                                finished=job_data.get("finished", None),
-                                status=job_data["status"],
-                                parameters=parameters,
-                            )
-                        except Exception:
-                            print(
-                                f"Job {job_data['id']} not imported because it is "
-                                "already in the database."
-                            )
+                            job_data = Job.parse_job_data(check_path)
+                        except Exception as e:
+                            print(f"Could not read the job data {check_path}: {str(e)}")
                         else:
-                            session.add(job)
-                            session.commit()
-                            jobs.append(job)
+                            if "command line" in job_data:
+                                parameters = {"cmdline": job_data["command line"]}
+                            else:
+                                parameters = {"cmdline": []}
+
+                            try:
+                                job = Job.create(
+                                    job_data["id"],
+                                    potential_job + "/flowchart.flow",
+                                    project_names=job_data["project_names"],
+                                    path=potential_job,
+                                    title=job_data["title"],
+                                    description=job_data.get("description", ""),
+                                    submitted=job_data.get("submitted", None),
+                                    started=job_data.get("started", None),
+                                    finished=job_data.get("finished", None),
+                                    status=job_data["status"],
+                                    parameters=parameters,
+                                )
+                            except Exception:
+                                print(
+                                    f"Job {job_data['id']} not imported because it is "
+                                    "already in the database."
+                                )
+                            else:
+                                session.add(job)
+                                session.commit()
+                                jobs.append(job)
 
     session.commit()
 

seamm_datastore/database/models.py

@@ -321,7 +321,6 @@ class Flowchart(Base, Resource):
 
     @classmethod
     def create(cls, **flowchart_info):
-
         try:
             flowchart = cls.query.filter_by(
                 sha256_strict=flowchart_info["sha256_strict"]
@@ -709,7 +708,6 @@ def update(
 
     @classmethod
     def create_from_file(cls, job_data_file):
-
         job_data = cls.parse_job_data(job_data_file)
 
         job = Job.create(job_data)

seamm_datastore/flask_authorize_patch.py

@@ -43,7 +43,6 @@
 def generate_association_table(
     entity_name, resource_name, entity_tablename=None, resource_tablename=None
 ):
-
     # Make them plural by adding 's' :)
     if not entity_tablename:
         entity_tablename = entity_name.lower() + "s"
@@ -183,7 +182,6 @@ def allowed(self, *args, **kwargs):  # pragma: no cover
     # must have authorization to proceed.
     operation = set(self.permission)
     for arg in args:
-
         if not isinstance(arg.__class__, six.class_types):
             continue
 

seamm_datastore/tests/conftest.py

@@ -48,7 +48,6 @@ def admin_connection(connection):
 
 @pytest.fixture(scope="function")
 def filled_db(connection):
-
     # The lazy way to do this for now
     import os
 

seamm_datastore/tests/test_build.py

@@ -6,7 +6,6 @@
 
 
 def test_build(connection):
-
     from seamm_datastore.database.models import Flowchart
 
     loc = os.path.abspath(os.path.dirname(__file__))

seamm_datastore/tests/test_create.py

@@ -21,13 +21,11 @@ def test_project_create(connection):
 
 
 def test_project_exists(connection):
-
     with pytest.raises(ValueError):
         connection.Project.create(name="default")
 
 
 def test_project_no_user(connection):
-
     with pytest.raises(ValueError):
         connection.logout()
         connection.Project.create(name="test")
@@ -43,7 +41,6 @@ def test_project_create_group(connection):
 
 
 def test_flowchart_parse(connection):
-
     this_file = os.path.dirname(os.path.abspath(__file__))
     filepath = os.path.join(this_file, "..", "data", "sample_flowchart_v2.flow")
 
@@ -59,7 +56,6 @@ def test_flowchart_parse(connection):
 
 
 def test_flowchart_from_file(connection):
-
     this_file = os.path.dirname(os.path.abspath(__file__))
     filepath = os.path.join(this_file, "..", "data", "sample_flowchart_v2.flow")
 
@@ -72,7 +68,6 @@ def test_flowchart_from_file(connection):
 
 
 def test_create_user(connection):
-
     user = connection.User.create(username="test", password="test")
 
     assert user.username == "test"

seamm_datastore/tests/test_methods.py

@@ -112,15 +112,13 @@ def test_get_queries(
 
 
 def test_job_update_error(filled_db):
-
     from seamm_datastore.database.models import Job
 
     with pytest.raises(ValueError):
         Job.update(1, description="This is a new description.")
 
 
 def test_job_update(filled_db):
-
     from seamm_datastore.database.models import Job
 
     job = Job.update(92, description="This is a new description.")

versioneer.py

@@ -339,9 +339,9 @@ def get_config_from_root(root):
     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
     # the top of versioneer.py for instructions on writing your setup.cfg .
     setup_cfg = os.path.join(root, "setup.cfg")
-    parser = configparser.SafeConfigParser()
+    parser = configparser.ConfigParser()
     with open(setup_cfg, "r") as f:
-        parser.readfp(f)
+        parser.read_file(f)
     VCS = parser.get("versioneer", "VCS")  # mandatory
 
     def get(parser, name):