Merge pull request #405 from AllenNeuralDynamics/release-v0.23.0

Release v0.23.0

Author: helen-m-lin

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+    -   id: flake8
+-   repo: https://github.com/psf/black
+    rev: 24.2.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort 

CODE_OF_CONDUCT.md

@@ -0,0 +1,133 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+ScientificComputing@AllenInstitute.onmicrosoft.com.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+[https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available
+at [https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.0]: https://www.contributor-covenant.org/version/2/0/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

README.md

@@ -130,33 +130,56 @@ docker run -it -p 58350:58350 -p 5000:5000 --env-file=.env aind-metadata-service
 
 There are several libraries used to run linters, check documentation, and run tests.
 
-- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
+The following checks are enforced through GitHub Actions CI:
+- **flake8** to check that code is up to standards (no unused imports, etc.)
+- **interrogate** to check documentation coverage
+- **coverage** for 100% test coverage requirement
 
-```
+Checks should ideally be run locally before pushing to github:
+
+Test your changes using the **coverage** library, which will run the tests and log a coverage report:
+```bash
 coverage run -m unittest discover && coverage report
 ```
 
-- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
-
-```
-interrogate .
+Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
+```bash
+interrogate --verbose .
 ```
 
-- Use **flake8** to check that code is up to standards (no unused imports, etc.):
-```
+Use **flake8** to check that code is up to standards (no unused imports, etc.):
+```bash
 flake8 .
 ```
 
-- Use **black** to automatically format the code into PEP standards:
-```
+Additional recommended but optional tools:
+
+Use **black** to automatically format the code into PEP standards:
+```bash
 black .
 ```
 
-- Use **isort** to automatically sort import statements:
-```
+Use **isort** to automatically sort import statements:
+```bash
 isort .
 ```
 
+#### Optional: Pre-commit Hooks
+
+To automatically run style checks before each commit (recommended but optional):
+
+```bash
+# Install pre-commit (already included in dev dependencies)
+pre-commit install
+```
+
+The hooks will run automatically on each commit, but can be bypassed with `git commit --no-verify` if needed.
+
+Code style specifications:
+- Line length: 79 characters
+- Python version: 3.10+
+- Style guide: PEP 8 (enforced by flake8)
+
 ### Pull requests
 
 For internal members, please create a branch. For external members, please fork the repo and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
@@ -178,7 +201,7 @@ where scope (optional) describes the packages affected by the code changes and t
 ### Documentation
 To generate the rst files source files for documentation, run
 ```
-sphinx-apidoc -o doc_template/source/ src 
+sphinx-apidoc -o doc_template/source/ src
 ```
 Then to create the documentation html files, run
 ```
@@ -188,7 +211,7 @@ More info on sphinx installation can be found here: https://www.sphinx-doc.org/e
 
 ### API Response Codes
 There are 6 possible status code responses for aind-metadata-service:
-- **200**: successfully retrieved valid data without any problems. 
+- **200**: successfully retrieved valid data without any problems.
 - **406**: successfully retrieved some data, but failed to validate against pydantic models.
 - **404**: found no data that matches query.
 - **300**: queried the server, but more items were returned than expected.

pyproject.toml

@@ -34,6 +34,7 @@ dev = [
     'interrogate',
     'isort',
     'Sphinx',
+    'pre-commit',
 ]
 
 server = [

src/aind_metadata_service/__init__.py

@@ -1,3 +1,3 @@
 """REST service to retrieve metadata from databases."""
 
-__version__ = "0.22.0"
+__version__ = "0.23.0"

src/aind_metadata_service/server.py

@@ -304,6 +304,32 @@ async def retrieve_slims_water_restriction(
     return response
 
 
+@app.get("/slims/viral_injections")
+async def retrieve_slims_injections(
+    subject_id: Optional[str] = Query(None, alias="subject_id"),
+    start_date_gte: Optional[str] = Query(
+        None,
+        alias="start_date_gte",
+        description="Experiment run created on or after. (ISO format)",
+    ),
+    end_date_lte: Optional[str] = Query(
+        None,
+        alias="end_date_lte",
+        description="Experiment run created on or before. (ISO format)",
+    ),
+):
+    """
+    Retrieves Viral Injection data from SLIMS server
+    """
+    response = await run_in_threadpool(
+        slims_client.get_slims_viral_injection_response,
+        subject_id=subject_id,
+        start_date=start_date_gte,
+        end_date=end_date_lte,
+    )
+    return response
+
+
 @app.get("/subject/{subject_id}")
 async def retrieve_subject(subject_id):
     """

src/aind_metadata_service/slims/client.py

@@ -28,6 +28,12 @@
 from aind_metadata_service.slims.histology.mapping import SlimsHistologyMapper
 from aind_metadata_service.slims.imaging.handler import SlimsImagingHandler
 from aind_metadata_service.slims.imaging.mapping import SlimsSpimMapper
+from aind_metadata_service.slims.viral_injection.handler import (
+    SlimsViralInjectionHandler,
+)
+from aind_metadata_service.slims.viral_injection.mapping import (
+    SlimsViralInjectionMapper,
+)
 from aind_metadata_service.slims.water_restriction.handler import (
     SlimsWaterRestrictionHandler,
 )
@@ -500,3 +506,66 @@ def get_water_restriction_procedures_model_response(
         except Exception as e:
             logging.exception(e)
             return ModelResponse.internal_server_error_response()
+
+    def get_slims_viral_injection_response(
+        self,
+        subject_id: str,
+        start_date: Optional[str],
+        end_date: Optional[str],
+    ) -> JSONResponse:
+        """
+
+        Parameters
+        ----------
+        subject_id : str | None
+        start_date : str | None
+          Optional ISO Format datetime string
+        end_date :  str | None
+          Optional ISO Format datetime string
+        Returns
+        -------
+        JSONResponse
+        """
+        if subject_id is not None and subject_id == "":
+            return ModelResponse.bad_request_error_response(
+                message="subject_id cannot be an empty string!"
+            ).map_to_json_response()
+        parsed_start_date = self._parse_date(start_date)
+        if isinstance(parsed_start_date, ModelResponse):
+            return parsed_start_date.map_to_json_response()
+        parsed_end_date = self._parse_date(end_date)
+        if isinstance(parsed_end_date, ModelResponse):
+            return parsed_end_date.map_to_json_response()
+        try:
+            slims_vm_handler = SlimsViralInjectionHandler(
+                client=self.client.db
+            )
+            slims_vm_data = (
+                slims_vm_handler.get_viral_injection_info_from_slims(
+                    subject_id=subject_id,
+                    start_date_greater_than_or_equal=parsed_start_date,
+                    end_date_less_than_or_equal=parsed_end_date,
+                )
+            )
+            vm_data = SlimsViralInjectionMapper(
+                slims_vm_data=slims_vm_data
+            ).map_info_from_slims()
+            if len(vm_data) == 0:
+                m = ModelResponse.no_data_found_error_response()
+                return m.map_to_json_response()
+            response = JSONResponse(
+                status_code=StatusCodes.VALID_DATA.value,
+                content=(
+                    {
+                        "message": "Data from SLIMS",
+                        "data": [
+                            json.loads(m.model_dump_json()) for m in vm_data
+                        ],
+                    }
+                ),
+            )
+            return response
+        except Exception as e:
+            logging.exception(e)
+            m = ModelResponse.internal_server_error_response()
+            return m.map_to_json_response()

src/aind_metadata_service/slims/ecephys/mapping.py

@@ -2,6 +2,7 @@
 Module to handle mapping data from SLIMS
 """
 
+import html
 from datetime import datetime
 from decimal import Decimal
 from typing import List, Optional
@@ -52,8 +53,8 @@ class StreamModule(BaseModel):
     )
     def parse_micrometer_unit(cls, v):
         """Parse HTML entity for micrometer"""
-        if isinstance(v, str) and v.strip() == "μm":
-            return "um"
+        if isinstance(v, str):
+            v = html.unescape(v)
         return v
 
 

src/aind_metadata_service/slims/histology/handler.py

@@ -153,7 +153,7 @@ def _get_specimen_data(
         specimen_id = None
         subject_id = None
         for record in records:
-            n_subject_id = get_attr_or_none(record, "cntn_cf_parentBarcode")
+            n_subject_id = get_attr_or_none(record, "cntn_id")
             if n_subject_id is not None:
                 subject_id = n_subject_id
             n_specimen_id = get_attr_or_none(record, "cntn_barCode")