replace all biospecdb -> biodb

Signed-off-by: James Noss <[email protected]>

.coveragerc

@@ -5,7 +5,7 @@ omit =
     */migrations/*
     manage.py
     _version.py
-    biospecdb/apps/dash/*
-    biospecdb/asgi.py
-    biospecdb/wsgi.py
-    biospecdb/settings/*
+    biodb/apps/dash/*
+    biodb/asgi.py
+    biodb/wsgi.py
+    biodb/settings/*

CITATION.cff

@@ -16,6 +16,6 @@ authors:
 - family-names: "Mitschang"
   given-names: "Arik"
   orcid: "https://orcid.org/0000-0001-9239-012X"
-title: "BioSpecDB"
+title: "biodb"
 doi: "10048241"
-url: "https://github.com/rispadd/biospecdb"
+url: "https://github.com/rispadd/biodb"

Dockerfile

@@ -11,7 +11,7 @@ COPY requirements/prd.txt /app/requirements.txt
 RUN pip3 install -r requirements.txt
 
 COPY manage.py /app/
-COPY biospecdb/ /app/biospecdb/
+COPY biodb/ /app/biodb/
 COPY config/ /app/config/
 
 CMD ["python", "manage.py", "runserver", "0.0.0.0:8000"]

README.md

@@ -1,9 +1,9 @@
-# SSEC-JHU BioSpecDB
+# SSEC-JHU biodb
 
-[![CI](https://github.com/rispadd/biospecdb/actions/workflows/ci.yml/badge.svg)](https://github.com/rispadd/biospecdb/actions/workflows/ci.yml)
-[![Documentation Status](https://readthedocs.org/projects/biospecdb/badge/?version=latest)](https://biospecdb.readthedocs.io/en/latest/?badge=latest)
-[![codecov](https://codecov.io/gh/RISPaDD/biospecdb/graph/badge.svg?token=Ld95EDCYNZ)](https://codecov.io/gh/RISPaDD/biospecdb)
-[![Security](https://github.com/rispadd/biospecdb/actions/workflows/security.yml/badge.svg)](https://github.com/rispadd/biospecdb/actions/workflows/security.yml)
+[![CI](https://github.com/rispadd/biodb/actions/workflows/ci.yml/badge.svg)](https://github.com/rispadd/biodb/actions/workflows/ci.yml)
+[![Documentation Status](https://readthedocs.org/projects/biodb/badge/?version=latest)](https://biodb.readthedocs.io/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/RISPaDD/biodb/graph/badge.svg?token=Ld95EDCYNZ)](https://codecov.io/gh/RISPaDD/biodb)
+[![Security](https://github.com/rispadd/biodb/actions/workflows/security.yml/badge.svg)](https://github.com/rispadd/biodb/actions/workflows/security.yml)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10048241.svg)](https://doi.org/10.5281/zenodo.10048241)
 
 ![SSEC-JHU Logo](docs/_static/SSEC_logo_horiz_blue_1152x263.png)
@@ -62,7 +62,7 @@ For additional cmds see the [Conda cheat-sheet](https://docs.conda.io/projects/c
   #### with Python ecosystem (for development):
   * Follow the above [Build with Python ecosystem instructions](#with-python-ecosystem).
   * For a completely fresh start and rebuild of the database: ``./scripts/dev/rebuild_sqlite.sh``.
-  * Run ``DJANGO_SETTINGS_MODULE=biospecdb.settings.dev python manage.py runserver 0.0.0.0:8000``
+  * Run ``DJANGO_SETTINGS_MODULE=biodb.settings.dev python manage.py runserver 0.0.0.0:8000``
   * The site can then be accessed using any browser from ``http://localhost:8000``
 
   ### Self signed SSL certificates:
@@ -117,8 +117,8 @@ When the models are changed only the following migration commands are required:
 * ``python manage.py makemigrations user``
 * ``python manage.py makemigrations uploader``
 * ``python manage.py makemigrations catalog``
-* ``git add biospecdb/apps/uploader/migrations``
-* ``git add biospecdb/apps/user/migrations``
+* ``git add biodb/apps/uploader/migrations``
+* ``git add biodb/apps/user/migrations``
 * ``git commit -asm"Update model migrations"``
 * ``python manage.py migrate``
 * ``python manage.py migrate --database=bsr``
@@ -157,7 +157,7 @@ _NOTE: These commands must be run from the ``/app/`` directory on the server.
 
 The above management commands (and others) can be run in production from an EC2 instance correctly configured. To
 aid in shell setup, the following script can be executed:
- * ``source repo/biospecdb/scripts/prd/ec2_init.sh``
+ * ``source repo/biodb/scripts/prd/ec2_init.sh``
 
 _NOTE: ``scripts/prd/ec2_init.sh`` will export all AWS secrets as shell environment variables. 
 
@@ -180,7 +180,7 @@ Entries in the ``SpectralData`` table can be annotated by running ``QCAnnotators
 stored as an ``ACAnnotation`` associated with the ``SpectralData`` entry. The ``SpectralData`` table contains the actual
 spectral data file containing the wavelength and intensity values. It may be desirable to annotate this data with
 certain quality control metrics that can later be used to filter the data. Such quality control functions are to be
-implemented as a subclass of ``Biospecdb.app.uploader.qc.qcfilter.QcFilter``.
+implemented as a subclass of ``biodb.app.uploader.qc.qcfilter.QcFilter``.
 They can then be added to the database belonging to the ``QCAnnotator``
 table. Annotations of this annotators can then either be manually associated with a ``SpectralData`` entry manually via
 the admin form, or by "default" if the ``QCAnnotator.default = True``. They can also be run by using the
@@ -189,7 +189,7 @@ population of the ``QCAnnotation`` table is configurable and is described below.
 
 #### Settings:
 
-The following QC annotator settings are available in ``biospecdb.settings.base``:
+The following QC annotator settings are available in ``biodb.settings.base``:
 
  * ``AUTO_ANNOTATE``: If ``True`` and if default annotators exist in the DB, they will be automatically run upon
                       adding/updating ``SpectralData`` entries. _(Default: True)_
@@ -220,7 +220,7 @@ Facilitates in testing typos, syntax, style, and other simple code analysis test
 ### Security Checks:
 Facilitates in checking for security concerns using [Bandit](https://bandit.readthedocs.io/en/latest/index.html).
  * ``cd`` into repo dir.
- * ``bandit -c pyproject.toml --severity-level=medium -r biospecdb``
+ * ``bandit -c pyproject.toml --severity-level=medium -r biodb``
 
 ### Unit Tests:
 Facilitates in testing core package functionality at a modular level.
@@ -248,7 +248,7 @@ Facilitates in building, testing & viewing the docs.
 
 # The DB Model:
 
-![BioSpecDB Model.jpg](..%2F..%2F..%2FDownloads%2FBioSpecDB%20Model.jpg)
+![biodb Model.jpg](..%2F..%2F..%2FDownloads%2Fbiodb%20Model.jpg)
 
 ## Column Names:
 

apprunner.yaml

@@ -10,7 +10,7 @@ build:
       - pipenv run make -C docs html
   env:
     - name: DJANGO_SETTINGS_MODULE
-      value: "biospecdb.settings.aws"
+      value: "biodb.settings.aws"
 run:
   runtime-version: 3.11
   pre-run:
@@ -24,7 +24,7 @@ run:
     - name: DB_VENDOR
       value: "postgresql"
     - name: DJANGO_SETTINGS_MODULE
-      value: "biospecdb.settings.aws"
+      value: "biodb.settings.aws"
   secrets:
     - name: EMAIL_USE_TLS
       value-from: "arn:aws:secretsmanager:eu-west-2:339712857727:secret:EMAIL_USE_TLS-KbwnER"

biodb/__init__.py

@@ -1,4 +1,4 @@
-__project__ = "biospecdb"
+__project__ = "biodb"
 
 try:
     from ._version import __version__

biodb/apps/catalog/models.py

@@ -14,7 +14,7 @@
 from django.utils.module_loading import import_string
 from django.utils.translation import gettext_lazy as _
 
-from biospecdb import __version__
+from biodb import __version__
 from explorer.models import Query
 from uploader.base_models import DatedModel
 

biodb/apps/catalog/tests/test_datasets.py

@@ -5,7 +5,7 @@
 
 import pytest
 
-from biospecdb import __version__
+from biodb import __version__
 from catalog.models import Dataset
 from explorer.models import Query
 from uploader.models import SpectralData

biodb/apps/uploader/admin.py

@@ -10,7 +10,7 @@
 from django import forms
 from nested_admin import NestedStackedInline, NestedTabularInline, NestedModelAdmin
 
-from biospecdb.util import to_bool
+from biodb.util import to_bool
 from .models import BioSample, Observable, Instrument, Patient, SpectralData, Observation, UploadedFile, Visit,\
     QCAnnotator, QCAnnotation, Center, get_center, BioSampleType, SpectraMeasurementType
 from uploader.forms import ModelForm

biodb/apps/uploader/base_models.py

@@ -5,7 +5,7 @@
 from django.db import connection, models, transaction
 from django.utils.module_loading import import_string
 
-import biospecdb.util
+import biodb.util
 from uploader.sql import drop_view, update_view
 
 
@@ -131,7 +131,7 @@ def cast(self, value):
             return
 
         if self.name == "BOOL":
-            return biospecdb.util.to_bool(value)
+            return biodb.util.to_bool(value)
         elif self.name == "STR":
             return str(value)
         elif self.name == "INT":
@@ -217,4 +217,4 @@ def save(self, *args, update_view=True, **kwargs):
                 sql_view.update_view()
 
     def asave(self, *args, **kwargs):
-        raise NotImplementedError("See https://github.com/rispadd/biospecdb/issues/66")
+        raise NotImplementedError("See https://github.com/rispadd/biodb/issues/66")

biodb/apps/uploader/charts.py

@@ -8,7 +8,7 @@
 
 import uploader.io
 from uploader.models import Observable, Patient, SpectralData
-from biospecdb.util import to_uuid
+from biodb.util import to_uuid
 
 logger = logging.getLogger(__name__)
 

biodb/apps/uploader/fixtures/qcannotators.json

@@ -4,7 +4,7 @@
     "pk": 1,
     "fields": {
       "name": "sum",
-      "fully_qualified_class_name": "biospecdb.qc.qcfilter.QcSum",
+      "fully_qualified_class_name": "biodb.qc.qcfilter.QcSum",
       "description": "Sum of the spectral data (total flux)",
       "default": true,
       "value_type": "FLOAT",

biodb/apps/uploader/io.py

@@ -13,7 +13,7 @@
 import pandas as pd
 from pandas._libs.parsers import STR_NA_VALUES
 
-from biospecdb.util import StrEnum, to_uuid
+from biodb.util import StrEnum, to_uuid
 
 # TODO: move to settings
 DEFAULT_PATIENT_ID_STR = "patient_id"
@@ -109,7 +109,7 @@ def _read_raw_data(file, ext=None):
     # ‘NULL’, ‘NaN’, ‘None’, ‘n/a’, ‘nan’, ‘null’.
 
     # NOTE: When the file size is > 2.5M Django will chunk and this will need to be handled. See
-    # https://github.com/rispadd/biospecdb/issues/38
+    # https://github.com/rispadd/biodb/issues/38
     if ext == FileFormats.CSV:
         data = pd.read_csv(file, **kwargs)
     elif ext == FileFormats.XLSX:

biodb/apps/uploader/loaddata.py

@@ -6,7 +6,7 @@
 from django.db import transaction
 from django.db.models import Q
 
-from biospecdb.util import get_object_or_raise_validation
+from biodb.util import get_object_or_raise_validation
 import uploader.io
 
 
@@ -107,7 +107,7 @@ def save_data_to_db(meta_data, spectral_data, center=None, joined_data=None, dry
                         continue
 
                     # TODO: Should the following logic belong to Observation.__init__()?
-                    #  See https://github.com/rispadd/biospecdb/issues/42
+                    #  See https://github.com/rispadd/biodb/issues/42
                     observation_value = Observable.Types(observable.value_class).cast(observation_value)
                     observation = Observation(observable=observable,
                                               visit=visit,

biodb/apps/uploader/management/commands/send_test_email.py

@@ -36,7 +36,7 @@ def handle(self, *args, **options):
                 form.save(**opts)
             else:
                 email_from = settings.EMAIL_FROM
-                send_mail("BiospecDB test email", "This is just a test.", email_from, [email_address],
+                send_mail("biodb test email", "This is just a test.", email_from, [email_address],
                           fail_silently=False)
             self.stdout.write(self.style.SUCCESS(f"Test email sent to {email_address}, check inbox for verification."))
         except CommandError:

biodb/apps/uploader/models.py

@@ -15,8 +15,8 @@
 from django.utils.translation import gettext_lazy as _
 import pandas as pd
 
-from biospecdb.util import get_field_value, get_object_or_raise_validation, is_valid_uuid, lower, to_uuid
-from biospecdb.qc.qcfilter import QcFilter
+from biodb.util import get_field_value, get_object_or_raise_validation, is_valid_uuid, lower, to_uuid
+from biodb.qc.qcfilter import QcFilter
 import uploader.io
 from uploader.loaddata import save_data_to_db
 from uploader.sql import secure_name
@@ -26,7 +26,7 @@
 # Changes here need to be migrated, committed, and activated.
 # See https://docs.djangoproject.com/en/4.2/intro/tutorial02/#activating-models
 # python manage.py makemigrations uploader
-# git add biospecdb/apps/uploader/migrations
+# git add biodb/apps/uploader/migrations
 # git commit -asm"Update uploader model(s)"
 # python manage.py migrate --database=bsr
 
@@ -898,11 +898,11 @@ def clean(self):
             self.data = cleaned_file
 
     #@transaction.atomic(using="bsr")  # Really? Not sure if this even can be if run in background...
-    # See https://github.com/rispadd/biospecdb/issues/77
+    # See https://github.com/rispadd/biodb/issues/77
     def annotate(self, annotator=None, force=False) -> list:
         """ Run the quality control annotation on the spectral data. """
         # TODO: This needs to return early and run in the background.
-        # See https://github.com/rispadd/biospecdb/issues/77
+        # See https://github.com/rispadd/biodb/issues/77
 
         existing_annotators = self.get_annotators()
 
@@ -939,7 +939,7 @@ def save(self, *args, **kwargs):
         # such that new data is complete such that it has associated QC metrics.
         if settings.AUTO_ANNOTATE:
             # TODO: This should return early and runs async in the background.
-            # See https://github.com/rispadd/biospecdb/issues/77
+            # See https://github.com/rispadd/biodb/issues/77
             self.annotate()
 
     def asave(self, *args, **kwargs):
@@ -1204,7 +1204,7 @@ def get_value(self):
             return self.annotator.cast(self.value)
 
     def run(self, save=True):
-        # NOTE: This waits. See https://github.com/rispadd/biospecdb/issues/77
+        # NOTE: This waits. See https://github.com/rispadd/biodb/issues/77
         value = self.annotator.run(self.spectral_data)
         self.value = value
 

biodb/apps/uploader/tests/conftest.py

@@ -13,7 +13,7 @@
 import pytest
 
 
-from biospecdb.util import find_package_location
+from biodb.util import find_package_location
 from uploader.models import SpectralData, UploadedFile, Center
 from user.models import Center as UserCenter
 

biodb/apps/uploader/tests/test_models.py

@@ -16,7 +16,7 @@
 from uploader.loaddata import save_data_to_db
 from user.models import Center as UserCenter
 from uploader.models import Center as UploaderCenter
-import biospecdb.util
+import biodb.util
 from uploader.tests.conftest import bulk_upload, DATA_PATH
 
 
@@ -342,7 +342,7 @@ def test_files_added(self, mock_data_from_files):
 
     def test_no_file_validation(self, db):
         """ Test that a validation error is raised rather than any other python exception which would indicate a bug.
-            See https://github.com/rispadd/biospecdb/pull/181
+            See https://github.com/rispadd/biodb/pull/181
         """
         data = SpectralData()
         with pytest.raises(ValidationError):
@@ -366,7 +366,7 @@ def test_no_duplicate_data_files(self, mock_data_from_files):
 
     @pytest.mark.skip("Unimplemented See #141")
     def test_all_files_deleted_upon_transaction_failure(self):
-        # I'm not sure how to mock this... See https://github.com/rispadd/biospecdb/issues/141
+        # I'm not sure how to mock this... See https://github.com/rispadd/biodb/issues/141
         ...
 
     @pytest.mark.parametrize("ext", uploader.io.FileFormats.list())
@@ -487,7 +487,7 @@ def test_patient_ids(self, mock_data_from_files, file_ext):
     def test_index_match_validation(self, db, observables, instruments, file_ext, tmp_path):
         meta_data_path = (DATA_PATH / "meta_data").with_suffix(file_ext)
 
-        biospecdb.util.mock_bulk_spectral_data(path=tmp_path)
+        biodb.util.mock_bulk_spectral_data(path=tmp_path)
         spectral_file_path = tmp_path / "spectral_data.csv"
         with meta_data_path.open(mode="rb") as meta_data, spectral_file_path.open(mode="rb") as spectral_data:
             data_upload = UploadedFile(meta_data_file=django.core.files.File(meta_data,