Merge pull request #142 from AllenNeuralDynamics/release-v0.17.1

Release v0.17.1

Author: helen-m-lin

.env.template

@@ -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
+[email protected].
+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

CODE_OF_CONDUCT.md

@@ -10,12 +10,12 @@ AIND metadata for data assets is stored in various places and must be
 kept in sync:
 
 1. **S3 buckets** store raw metadata files, including the ``metadata.nd.json``.
-2. A **document database (DocDB)** contains unstructured json
+2. A **document database (DocDB)** contains unstructured JSON
    documents describing the ``metadata.nd.json`` for a data asset.
-3. **Code Ocean**: data assets are mounted as CodeOcean data assets.
+3. **Code Ocean**: data assets are mounted as Code Ocean data assets.
    Processed results are also stored in an internal Code Ocean bucket.
 
-We have automated jobs to keep changes in DocDB and S3 in sync.
+We have automated jobs to keep changes in DocDB, S3 and Code Ocean in sync.
 This repository contains the code for these index jobs.
 
 More information including a user guide and contributor guidelines can be found at [readthedocs](https://aind-data-asset-indexer.readthedocs.io).

README.md

@@ -32,7 +32,7 @@ For development,
    off of ``main``
 
 Consult the `Branches and Pull Requests <#branches-and-pull-requests>`__
-and `Release Cycles <#release-cycles>`__ for more details.
+and `Release Cycles <#release-cycles>`__ sections for more details.
 
 From the root directory, run:
 
@@ -47,14 +47,13 @@ to install the relevant code for development.
 Running indexer jobs locally
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-
 The jobs are intended to be run as scheduled AWS ECS tasks.
 The job settings are stored in AWS Parameter Store.
 
 If you wish to run the jobs locally, follow these steps:
 
 1. Ensure the correct ``AWS_PROFILE`` is exported. This profile will be used to
-   read/write from S3 bucketsand DocumentDB (through the API Gateway).
+   read/write from S3 buckets and DocumentDB (through the API Gateway).
 
 2. For the `IndexAindBucketsJob`, you will need to set the ``PARAM_STORE_NAME``.
    Then, run the following:
@@ -206,7 +205,7 @@ Hotfixes
 ~~~~~~~~
 
 -  A ``hotfix`` branch is created off of ``main``
--  A Pull Request into is ``main`` is opened, reviewed, and merged into
+-  A Pull Request into ``main`` is opened, reviewed, and merged into
    ``main``
 -  A new ``tag`` with a patch bump is created, and a new ``release`` is
    deployed
@@ -235,7 +234,7 @@ Pre-release checklist
 ~~~~~~~~~~~~~~~~~~~~~
 
 -  ☐ Increment ``__version__`` in
-   ``aind_data_asset-indexer/__init__.py`` file
+   ``aind_data_asset_indexer/__init__.py`` file
 -  ☐ Run linters, unit tests, and integration tests
 -  ☐ Verify code is deployed and tested in test environment
 -  ☐ Update examples

docs/source/Contributing.rst

@@ -20,35 +20,34 @@ kept in sync:
       all core schema fields.
    -  ``original_metadata/{core_schema}.json``: a copy of each
       core schema file as it was originally uploaded to S3.
-2. A **document database (DocDB)** contains unstructured json
+2. A **document database (DocDB)** contains unstructured JSON
    documents describing the ``metadata.nd.json`` for a data asset.
-3. **Code Ocean**: data assets are mounted as CodeOcean data asssets.
+3. **Code Ocean**: data assets are mounted as Code Ocean data assets.
    Processed results are also stored in an internal Code Ocean bucket.
 
 Once the data is initially uploaded, the DocDB is assumed to be the
 source of truth for metadata. All updates to existing metadata should
 be made in the DocDB.
 
-We have automated jobs to keep changes in DocDB and S3 in sync.
+We have automated jobs to keep changes in DocDB, S3, and Code Ocean in sync.
 This repository contains the code for these index jobs:
 
 1. `AindIndexBucketJob <#aindindexbucketjob>`__: Syncs changes in S3 and DocDB.
-2. `CodeOceanIndexBucketJob <#codeoceanindexbucketjob>`__: Syncs changes in CodeOcean and DocDB.
+2. `CodeOceanIndexBucketJob <#codeoceanindexbucketjob>`__: Syncs changes in Code Ocean and DocDB.
 
 
 AindIndexBucketJob
 ------------------
 
 The `AindIndexBucketJob` handles syncing changes from DocDB to S3 for a
-particular S3 bucket. There is a `IndexAindBucketsJob` wrapper job that
+particular S3 bucket. There is an `IndexAindBucketsJob` wrapper job that
 runs the `AindIndexBucketJob` for a list of buckets.
 
-
 The workflow is generally as follows:
 
 1. Paginate DocDB to get records for a particular bucket.
 
-   -  Typically we filter for records that have been updated in the last
+   -  Typically, we filter for records that have been updated in the last
       14 days.
 2. For each DocDB record, process by syncing any changes in DocDB to S3.
 
@@ -66,7 +65,7 @@ The workflow is generally as follows:
    -  If the metadata record exists in S3 but not in DocDB, copy it
       to DocDB.
    -  If the metadata record does not exist in S3, create it and save
-      it to S3. Assume a lambda function will move it over to DocDB.
+      it to S3. Assume a Lambda function will move it over to DocDB.
    -  In both cases above, ensure the original metadata folder and core
       files are in sync with the metadata.nd.json file.
 
@@ -77,16 +76,16 @@ CodeOceanIndexBucketJob
 -----------------------
 
 The `CodeOceanIndexBucketJob` updates the external links for DocDB records
-with their CO data asset ids and indexes Code Ocean (CO) processed results.
+with their Code Ocean (CO) data asset IDs and indexes CO processed results.
 
 The workflow is generally as follows:
 
 1. For records in AIND buckets, update the external links with CO data
-   asset ids if needed.
+   asset IDs if needed.
 
-   -  Retrieve a list of CO data asset ids and locations
-   -  Paginate through docdb records where the location does not match
-      internal CO bucket
+   -  Retrieve a list of CO data asset IDs and locations.
+   -  Paginate through DocDB records where the location does not match
+      the internal CO bucket.
    -  Add or remove the external links from the DocDB record as needed.
 2. Index CO processed results from the CO internal bucket.
 

docs/source/UserGuide.rst

@@ -1,3 +1,3 @@
 """Package"""
 
-__version__ = "0.17.0"
+__version__ = "0.17.1"