diff --git a/.github/workflows/ci_docs_publish.yml b/.github/workflows/ci_docs_publish.yml new file mode 100644 index 0000000..dcda564 --- /dev/null +++ b/.github/workflows/ci_docs_publish.yml @@ -0,0 +1,38 @@ +name: Publish Documentation + +on: + push: + branches: main + +permissions: + contents: write + +jobs: + deploy: + runs-on: ubuntu-24.04 + steps: + - uses: actions/checkout@v4 + + - name: Configure Git Credentials + run: | + git config user.name github-actions[bot] + git config user.email 41898282+github-actions[bot]@users.noreply.github.com + + - name: Install extra dependencies for a python install + run: | + sudo apt-get update + sudo apt -y install --no-install-recommends liblzma-dev libbz2-dev libreadline-dev + + - name: Install asdf cli + uses: asdf-vm/actions/setup@b7bcd026f18772e44fe1026d729e1611cc435d47 + + - name: Install software through asdf + uses: asdf-vm/actions/install@b7bcd026f18772e44fe1026d729e1611cc435d47 + + - name: reshim asdf + run: asdf reshim + + - name: ensure poetry using desired python version + run: poetry env use $(asdf which python) + + - run: mkdocs gh-deploy --force diff --git a/.github/workflows/ci_linting.yml b/.github/workflows/ci_linting.yml index f1b8982..fc9d2bf 100644 --- a/.github/workflows/ci_linting.yml +++ b/.github/workflows/ci_linting.yml @@ -3,8 +3,6 @@ name: CI Formatting & Linting on: pull_request: types: [opened, reopened, synchronize] - branches: - - main jobs: @@ -19,10 +17,10 @@ jobs: sudo apt -y install --no-install-recommends liblzma-dev libbz2-dev libreadline-dev - name: Install asdf cli - uses: asdf-vm/actions/setup@v4 + uses: asdf-vm/actions/setup@b7bcd026f18772e44fe1026d729e1611cc435d47 - name: Install software through asdf - uses: asdf-vm/actions/install@v4 + uses: asdf-vm/actions/install@b7bcd026f18772e44fe1026d729e1611cc435d47 - name: reshim asdf run: asdf reshim @@ -30,17 +28,9 @@ jobs: - name: ensure poetry using desired python version run: poetry env use $(asdf which python) - - name: Cache Poetry virtualenv - uses: actions/cache@v4 - with: - path: ~/.cache/pypoetry - key: ${{ runner.os }}-poetry-${{ hashFiles('**/poetry.lock') }} - restore-keys: | - ${{ runner.os }}-poetry- - - name: Install lint dependencies run: | - make install + poetry install --sync --no-interaction --with lint - name: Run black run: poetry run black src diff --git a/.github/workflows/ci_testing.yml b/.github/workflows/ci_testing.yml index 5f9bc95..ac25451 100644 --- a/.github/workflows/ci_testing.yml +++ b/.github/workflows/ci_testing.yml @@ -20,28 +20,20 @@ jobs: sudo apt -y install --no-install-recommends liblzma-dev libbz2-dev libreadline-dev libxml2-utils - name: Install asdf cli - uses: asdf-vm/actions/setup@v4 + uses: asdf-vm/actions/setup@b7bcd026f18772e44fe1026d729e1611cc435d47 - name: Install software through asdf - uses: asdf-vm/actions/install@v4 + uses: asdf-vm/actions/install@b7bcd026f18772e44fe1026d729e1611cc435d47 - name: reshim asdf run: asdf reshim - name: ensure poetry using desired python version run: poetry env use $(asdf which python) - - - name: Cache Poetry virtualenv - uses: actions/cache@v4 - with: - path: ~/.cache/pypoetry - key: ${{ runner.os }}-poetry-${{ hashFiles('**/poetry.lock') }} - restore-keys: | - ${{ runner.os }}-poetry- - name: Install test dependencies run: | - make install + poetry install --sync --no-interaction --with test - name: Run pytest and coverage run: | diff --git a/.gitignore b/.gitignore index d84f5cb..46856a4 100644 --- a/.gitignore +++ b/.gitignore @@ -32,7 +32,6 @@ share/python-wheels/ .installed.cfg *.egg MANIFEST -poetry.lock # PyInstaller # Usually these files are written by a python script from a template diff --git a/docs/advanced_guidance/backends.md b/docs/advanced_guidance/backends.md new file mode 100644 index 0000000..e69de29 diff --git a/docs/advanced_guidance/code_docs/core_engine.md b/docs/advanced_guidance/code_docs/core_engine.md new file mode 100644 index 0000000..703c398 --- /dev/null +++ b/docs/advanced_guidance/code_docs/core_engine.md @@ -0,0 +1,5 @@ +::: dve.core_engine.engine.CoreEngine + handler: python + options: + show_root_heading: false + show_source: true diff --git a/docs/assets/images/favicon.ico b/docs/assets/images/favicon.ico new file mode 100644 index 0000000..aff7490 Binary files /dev/null and b/docs/assets/images/favicon.ico differ diff --git a/docs/assets/images/favicon.svg b/docs/assets/images/favicon.svg new file mode 100644 index 0000000..cd21739 --- /dev/null +++ b/docs/assets/images/favicon.svg @@ -0,0 +1,4 @@ + + + + diff --git a/docs/assets/images/nhsuk-icon-180.png b/docs/assets/images/nhsuk-icon-180.png new file mode 100644 index 0000000..4881d5e Binary files /dev/null and b/docs/assets/images/nhsuk-icon-180.png differ diff --git a/docs/assets/images/nhsuk-icon-192.png b/docs/assets/images/nhsuk-icon-192.png new file mode 100644 index 0000000..459248f Binary files /dev/null and b/docs/assets/images/nhsuk-icon-192.png differ diff --git a/docs/assets/images/nhsuk-icon-512.png b/docs/assets/images/nhsuk-icon-512.png new file mode 100644 index 0000000..a2697f4 Binary files /dev/null and b/docs/assets/images/nhsuk-icon-512.png differ diff --git a/docs/assets/images/nhsuk-icon-mask.svg b/docs/assets/images/nhsuk-icon-mask.svg new file mode 100644 index 0000000..970859e --- /dev/null +++ b/docs/assets/images/nhsuk-icon-mask.svg @@ -0,0 +1,3 @@ + + + diff --git a/docs/assets/images/nhsuk-opengraph-image.png b/docs/assets/images/nhsuk-opengraph-image.png new file mode 100644 index 0000000..434b2d9 Binary files /dev/null and b/docs/assets/images/nhsuk-opengraph-image.png differ diff --git a/docs/assets/stylesheets/extra.css b/docs/assets/stylesheets/extra.css new file mode 100644 index 0000000..70c9435 --- /dev/null +++ b/docs/assets/stylesheets/extra.css @@ -0,0 +1,42 @@ +:root { + --nhs-blue: #005EB8 +} + +.md-footer-meta { + background-color: transparent !important; + box-shadow: none; +} + +.md-footer-meta::before { + content: ""; + display: block; + height: 3px; + background-color: var(--nhs-blue); +} + +.md-footer-meta.md-typeset a svg { + transition: transform 0.2s ease, filter 0.2s ease; +} + +.md-footer-meta.md-typeset a:hover svg { + transform: scale(1.12); + filter: brightness(1.2) drop-shadow(0 0 6px rgba(30, 136, 229, 0.7)); +} + +/* Light mode */ +[data-md-color-scheme="default"] { + --md-primary-fg-color: var(--nhs-blue); + --md-footer-bg-color: var(--md-default-bg-color); + --md-footer-fg-color: #000000; + --md-footer-fg-color--light: #333333; + --md-footer-fg-color--lighter: #555555; +} + +/* Dark mode */ +[data-md-color-scheme="slate"] { + --md-primary-fg-color:var(--nhs-blue); + --md-footer-bg-color: var(--md-default-bg-color); + --md-footer-fg-color: #e0e0e0; + --md-footer-fg-color--light: #bdbdbd; + --md-footer-fg-color--lighter: #9e9e9e; +} diff --git a/docs/detailed_guidance/feedback_messages.md b/docs/detailed_guidance/feedback_messages.md deleted file mode 100644 index 56ac983..0000000 --- a/docs/detailed_guidance/feedback_messages.md +++ /dev/null @@ -1 +0,0 @@ -WIP - it's a class in [DVE/core_engine/message.py](../../src/core_engine/message.py). \ No newline at end of file diff --git a/docs/README.md b/docs/index.md similarity index 79% rename from docs/README.md rename to docs/index.md index 7ab5d92..7c8c5c9 100644 --- a/docs/README.md +++ b/docs/index.md @@ -1,16 +1,24 @@ +--- +title: Data Validation Engine +tags: + - Home +--- + +# Data Validation Engine + The Data Validation Engine (DVE) is a configuration driven data validation library. There are 3 core steps within the DVE: -1. [File transformation](./detailed_guidance/file_transformation.md) - Parsing files from their submitted format into a common format. -2. [Data contract](./detailed_guidance/data_contract.md) - Validating the types that have been submitted and casting them. -3. [Business rules](./detailed_guidance/business_rules.md) - Performing more complex validations such as comparisons between fields and tables. +1. [File transformation](user_guidance/file_transformation.md){ data-preview } - Parsing files from their submitted format into a common format. +2. [Data contract](user_guidance/data_contract.md){ data-preview } - Validating the types that have been submitted and casting them. +3. [Business rules](user_guidance/business_rules.md){ data-preview } - Performing more complex validations such as comparisons between fields and tables. with a 4th step being important but more variable depending on platform and users: -4. [Error reports](./detailed_guidance/feedback_messages.md) - Compiles the errors generated from the previous stages and presents them within an Excel report. However, this could be reconfigured to meet the needs of your users. +4. [Error reports](user_guidance/feedback_messages.md){ data-preview } - Compiles the errors generated from the previous stages and presents them within an Excel report. However, this could be reconfigured to meet the needs of your users. -Each of these steps produce a list of [Feedback message](details/Feedback%20message.md) objects which can be reported back to the user for them to fix any issues. +Each of these steps produce a list of [Feedback message](user_guidance/feedback_messages.md){ data-preview } objects which can be reported back to the user for them to fix any issues. DVE configuration can be instantiated from a json (dischema) file which might be structured like this: @@ -83,7 +91,7 @@ DVE configuration can be instantiated from a json (dischema) file which might be } } ``` -"Contract" is where [Data Contract](./detailed_guidance/data_contract.md) and [File Transformation](./detailed_guidance/file_transformation.md) (in the reader configs) are configured, and (due to legacy naming) transformations are where [Business rules](./detailed_guidance/business_rules.md) are configured. +"Contract" is where [Data Contract](user_guidance/data_contract.md) and [File Transformation](user_guidance/file_transformation.md) (in the reader configs) are configured, and (due to legacy naming) transformations are where [Business rules](user_guidance/business_rules.md) are configured. ## Quick start In the code example shared above we have a json file named `cwt_example.dischema.json` and an xml file with the following structure: @@ -103,7 +111,7 @@ We can see in `config.contract.datasets` that there is a `CWTHeader` entity decl `version` is declared to be a `constr` which is the constrained string type from the Pydantic library. Therefore, any keyword arguments `constr` can be passed as `constraints` here. In this case we are constraining it to a regex 1-2 digits, followed by a literal period followed by 1-2 digits. This should match an `max n2` data type. -`periodStartDate` on the other hand is a `conformatteddate`, this type is one that's defined in the DVE library as a `domain_type` see [Domain types](./detailed_guidance/domain_types.md). The output of a `conformatteddate` is a date type. +`periodStartDate` on the other hand is a `conformatteddate`, this type is one that's defined in the DVE library as a `domain_type` see [Domain types](user_guidance/domain_types.md). The output of a `conformatteddate` is a date type. This means that after the data contract step the resulting data will have the types: `version::string` and `periodStartDate::date`. @@ -155,8 +163,8 @@ readers = {"XMLStreamReader": SparkXMLStreamReader} # File transformation step here entities = {} for entity in data_contract_config.schemas: - # get config based on file type you're parsing - ext_config = reader_configs[entity][".xml"] + # get config based on file type you're parsing + ext_config = reader_configs[entity][".xml"] reader = readers[ext_config.reader](**ext_config.parameters) df = reader.read_to_dataframe( "cwt_example.xml", entity, stringify_model(data_contract_config.schemas[entity]) @@ -187,6 +195,7 @@ from the top down we **data contract** - instatiate the SparkDataContract class with a spark session - apply the data contract to the dict of entities returning the entities in the correct types. any validation messages and a success bool + ### Business rules Now we have typed entities we can apply business rules to them. We need a step implementation. we'll import that from the spark rules backend. @@ -200,10 +209,10 @@ business_rule_config = config.get_rule_metadata() messages = business_rules.apply_rules(entities, business_rule_config) ``` -There we go. Messages is a list of [Feedback message](./detailed_guidance/feedback_messages.md) for every failed rule. +There we go. Messages is a list of [Feedback message](user_guidance/feedback_messages.md) for every failed rule. ### Utilising the Pipeline objects to run the DVE -Within the DVE package, we have also created the ability to build pipeline objects to help orchestrate the running of the DVE from start to finish. We currently have an implementation for `Spark` and `DuckDB`. These pipeline objects abstract some of the complexity described above and only requires you to supply a few objects to run the DVE from start (file transformation) to finish (error reports). These can be read in further detail [here](../src/pipeline/) and we have tests [here](../tests/test_pipeline/) to ensure they are working as expected. Furthermore, if you have a situation where maybe you only want to run the Data Contract, then you can utilise the pipeline objects in a way that only runs the specific stages that you want. Below will showcase an example where the full e2e pipeline is run and how you can trigger the stages that you want. +Within the DVE package, we have also created the ability to build pipeline objects to help orchestrate the running of the DVE from start to finish. We currently have an implementation for `Spark` and `DuckDB`. These pipeline objects abstract some of the complexity described above and only requires you to supply a few objects to run the DVE from start (file transformation) to finish (error reports). These can be read in further detail [here](https://github.com/NHSDigital/data-validation-engine/tree/main/src/dve/pipeline) and we have tests [here](https://github.com/NHSDigital/data-validation-engine/tree/main/tests/test_pipeline) to ensure they are working as expected. Furthermore, if you have a situation where maybe you only want to run the Data Contract, then you can utilise the pipeline objects in a way that only runs the specific stages that you want. Below will showcase an example where the full e2e pipeline is run and how you can trigger the stages that you want. > **note in the version that comes from gitlab, the dve library is spread across a number of modules. We are looking to put this in a top level `dve` module** @@ -272,7 +281,7 @@ If you'd rather not rely on needing a `metadata.json` associated with your submi ### Mixing backends -The examples shown above are using the Spark Backend. DVE also has a DuckDB backend found at [core_engine.backends.implementations.duckdb](../src/core_engine/backends/implementations/duckdb/). In order to mix the two you will need to convert from one type of entity to the other. For example from a spark `Dataframe` to DuckDB `relation`. The easiest way to do this is to use the `write_parquet` method from one backend and use `read_parquet` from another backend. +The examples shown above are using the Spark Backend. DVE also has a DuckDB backend found at [core_engine.backends.implementations.duckdb](https://github.com/NHSDigital/data-validation-engine/tree/main/src/dve/core_engine/backends/implementations/duckdb). In order to mix the two you will need to convert from one type of entity to the other. For example from a spark `Dataframe` to DuckDB `relation`. The easiest way to do this is to use the `write_parquet` method from one backend and use `read_parquet` from another backend. Currently the configuration isn't backend agnostic for applying business rules. So if you want to swap between spark and duckdb, the business rules need to be written using only features that are common to both backends. For example, a regex check in spark would be something along the lines of... ```sql @@ -285,20 +294,20 @@ regexp_matches(nhsnumber, '^\d{10}$') Failures in parsing the expressions lead to failure messages such as ```python FeedbackMessage( - entity=None, - record=None, - failure_type='integrity', - is_informational=False, - error_type=None, - error_location=None, - error_message="Unexpected error (AnalysisException: Undefined function: 'regexp_matches'. This function is neither a registered temporary function nor a permanent function registered in the database 'default'.; line 1 pos 5) in transformations (rule: root; step: 0; id: None)", - error_code=None, - reporting_field=None, - reporting_field_name=None, - value=None, - category=None + entity=None, + record=None, + failure_type='integrity', + is_informational=False, + error_type=None, + error_location=None, + error_message="Unexpected error (AnalysisException: Undefined function: 'regexp_matches'. This function is neither a registered temporary function nor a permanent function registered in the database 'default'.; line 1 pos 5) in transformations (rule: root; step: 0; id: None)", + error_code=None, + reporting_field=None, + reporting_field_name=None, + value=None, + category=None ) ``` # Extra information -Thanks for reading the documentation and looking into utilising the DVE. If you need more information on any of the steps you can find the following guidance below. If you need additional support, please raise an issue ([see guidance here](../CONTRIBUTE.md)) and we will try and respond to you as quickly as possible. +Thanks for reading the documentation and looking into utilising the DVE. If you need more information on any of the steps you can find the following guidance below. If you need additional support, please raise an issue ([see guidance here](https://github.com/NHSDigital/data-validation-engine/blob/main/CONTRIBUTE.md)) and we will try and respond to you as quickly as possible. diff --git a/docs/json_schemas/README.md b/docs/json_schemas/jsonschemas.md similarity index 79% rename from docs/json_schemas/README.md rename to docs/json_schemas/jsonschemas.md index 10d96e1..c8ff5fa 100644 --- a/docs/json_schemas/README.md +++ b/docs/json_schemas/jsonschemas.md @@ -28,3 +28,6 @@ For autocomplete support in VS Code, alter `settings.json` and add new entries t Data Ingest JSON schemas (when saved with file_name `dataset.dischema.json`) should then have autocomplete support. + +# Components +[https://github.com/NHSDigital/data-validation-engine/tree/main/docs/json_schemas](https://github.com/NHSDigital/data-validation-engine/tree/main/docs/json_schemas) diff --git a/docs/tags.md b/docs/tags.md new file mode 100644 index 0000000..ab72389 --- /dev/null +++ b/docs/tags.md @@ -0,0 +1,5 @@ +# Tags + +Following is a list of relevant tags: + + diff --git a/docs/detailed_guidance/business_rules.md b/docs/user_guidance/business_rules.md similarity index 96% rename from docs/detailed_guidance/business_rules.md rename to docs/user_guidance/business_rules.md index adb4e37..7b08f85 100644 --- a/docs/detailed_guidance/business_rules.md +++ b/docs/user_guidance/business_rules.md @@ -1,5 +1,5 @@ # Business Rules -Business rules are defined in the `transformations` section of the config. There are 6 keys within the json document that we will discuss in more detail throughout this document. +Business rules are defined within the `transformations` section of the config. There are 6 keys within the json document that we will discuss in more detail throughout this document. ## Keys | Key | Purpose | @@ -15,19 +15,20 @@ Business rules are defined in the `transformations` section of the config. There These are the most simple of the business rules. These are defined as a json object with the following structure: ```json { -"entity": "APCActivity", -"name": "EpiNo_is_valid", -"expression": "EpiNo IS NULL OR EpiNo RLIKE '^(0[1-9]|[1-7][0-9]|8[0-7]|9[89])$'", -"failure_type": "submission", -"failure_message": "is invalid", -"error_code": "1203", -"reporting_field": "EpiNo", -"is_informational" : false, -"category": "Bad value" + "entity": "APCActivity", + "name": "EpiNo_is_valid", + "expression": "EpiNo IS NULL OR EpiNo RLIKE '^(0[1-9]|[1-7][0-9]|8[0-7]|9[89])$'", + "failure_type": "submission", + "failure_message": "is invalid", + "error_code": "1203", + "reporting_field": "EpiNo", + "is_informational" : false, + "category": "Bad value" } ``` This rule checks that EpiNo must be present and that the value is 01-87 or 98 or 99. If EpiNo is missing this rule doesnt fire (to prevent double dinging a missing value). Any EpiNo that are present but not one of the values expected will raise a 1203 error with the message "is invalid". Lets break it down: + | Key | Purpose | | --- | ------- | | `entity` | This is the name of the entity to perform the filter on. In this Case the `APCActivity` dataframe | @@ -220,7 +221,7 @@ We've covered adding filters to complex rules, but we can add rules to them aswe - used for things like checking submitting all dates in a file match the header - one_to_one_join - join to another entity expecting no change in the number of rows. integrity check can be toggled off -> see [json_schemas/transformations](../json_schemas/transformations/) for expected fields for each operation +> see [json_schemas/transformations](../json_schemas/jsonschemas.md) for expected fields for each operation Rules are executed in the order they are put into the array. So a join then select should be implemented in that order. diff --git a/docs/detailed_guidance/data_contract.md b/docs/user_guidance/data_contract.md similarity index 97% rename from docs/detailed_guidance/data_contract.md rename to docs/user_guidance/data_contract.md index 5be63d3..cb5e9f1 100644 --- a/docs/detailed_guidance/data_contract.md +++ b/docs/user_guidance/data_contract.md @@ -1,4 +1,4 @@ -Lets look at the data contract configuration from [Introduction to DVE](../README.md) more closely, with a few more fields added: +Lets look at the data contract configuration from [Introduction to DVE](https://github.com/NHSDigital/data-validation-engine/blob/main/README.md) more closely, with a few more fields added: ```json { @@ -246,7 +246,7 @@ Schemas can have `mandatory_fields` but don't require reader configurations. ### Field types -Fields can have a type defined as a string, either a base type like `date`, `str`, a [Domain type](Domain%20types.md), or a defined [type](#types): +Fields can have a type defined as a string, either a base type like `date`, `str`, a [Domain type](./domain_types.md), or a defined [type](#types): ```json { @@ -291,7 +291,7 @@ It can be a model type defined in [schemas](#schemas), which can be also be an a } ``` -Finally callables. These are functions that return a type. Like `constr` from pydantic or `conformatteddate` in DVE [Domain types](Domain%20types.md). Any keyword arguments that go to these callables are passed in as `constraints`. +Finally callables. These are functions that return a type. Like `constr` from pydantic or `conformatteddate` in DVE [Domain types](./domain_types.md). Any keyword arguments that go to these callables are passed in as `constraints`. ```json { diff --git a/docs/detailed_guidance/domain_types.md b/docs/user_guidance/domain_types.md similarity index 99% rename from docs/detailed_guidance/domain_types.md rename to docs/user_guidance/domain_types.md index 62279b1..74cc219 100644 --- a/docs/detailed_guidance/domain_types.md +++ b/docs/user_guidance/domain_types.md @@ -4,6 +4,7 @@ Domain types are custom defined pydantic types that solve common problems with u This might include Postcodes, NHS Numbers, dates with specific formats etc. Below is a list of defined types, their output type and any contraints. Nested beneath them are any constraints that area allowed and their default values if there are any. + | Defined Type | Output Type | Contraints & Defaults | Supported Implementations | | ------------ | ----------- | --------------------- | ------------------------- | | NHSNumber | str | | Spark, DuckDB | @@ -18,6 +19,7 @@ Below is a list of defined types, their output type and any contraints. Nested b | identifier | str |
  • min_digits : NonNegativeInt = 1
  • max_digits: PositiveInt = 1
    • | Spark, DuckDB | **Other types that are allowed include:** + - str - int - date diff --git a/docs/user_guidance/feedback_messages.md b/docs/user_guidance/feedback_messages.md new file mode 100644 index 0000000..4230c42 --- /dev/null +++ b/docs/user_guidance/feedback_messages.md @@ -0,0 +1 @@ +WIP - it's a class in [DVE/core_engine/message.py](https://github.com/NHSDigital/data-validation-engine/blob/main/src/dve/core_engine/message.py). diff --git a/docs/detailed_guidance/file_transformation.md b/docs/user_guidance/file_transformation.md similarity index 100% rename from docs/detailed_guidance/file_transformation.md rename to docs/user_guidance/file_transformation.md diff --git a/docs/user_guidance/implementations/duckdb.md b/docs/user_guidance/implementations/duckdb.md new file mode 100644 index 0000000..d8b4c6e --- /dev/null +++ b/docs/user_guidance/implementations/duckdb.md @@ -0,0 +1 @@ +todo - wip diff --git a/docs/user_guidance/implementations/spark.md b/docs/user_guidance/implementations/spark.md new file mode 100644 index 0000000..d8b4c6e --- /dev/null +++ b/docs/user_guidance/implementations/spark.md @@ -0,0 +1 @@ +todo - wip diff --git a/docs/user_guidance/install.md b/docs/user_guidance/install.md new file mode 100644 index 0000000..d8b4c6e --- /dev/null +++ b/docs/user_guidance/install.md @@ -0,0 +1 @@ +todo - wip diff --git a/docs/user_guidance/pipelines/duckdb_pipeline.md b/docs/user_guidance/pipelines/duckdb_pipeline.md new file mode 100644 index 0000000..e69de29 diff --git a/docs/user_guidance/pipelines/palantir_foundry_pipeline.md b/docs/user_guidance/pipelines/palantir_foundry_pipeline.md new file mode 100644 index 0000000..d8b4c6e --- /dev/null +++ b/docs/user_guidance/pipelines/palantir_foundry_pipeline.md @@ -0,0 +1 @@ +todo - wip diff --git a/docs/user_guidance/pipelines/spark_pipeline.md b/docs/user_guidance/pipelines/spark_pipeline.md new file mode 100644 index 0000000..d8b4c6e --- /dev/null +++ b/docs/user_guidance/pipelines/spark_pipeline.md @@ -0,0 +1 @@ +todo - wip diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..516c883 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,154 @@ +site_name: Data Validation Engine +repo_url: https://github.com/NHSDigital/data-validation-engine +repo_name: Data Validation Engine +edit_uri: edit/main/docs/ + +plugins: + - search + - tags + # - git-revision-date-localized: # todo - requires 3rd party dependency mkdocs-git-revision-date-localized-plugin + # enable_creation_date: true + # - git-committers: # todo - requires 3rd party dependency mkdocs-git-committers-plugin-2 + # repository: squidfunk/mkdocs-material + # branch: main + # - git-authors # todo - requires 3rd party depedency mkdocs-git-authors-plugin and alt to git-commiters + - mkdocstrings: + locale: en + +extra_css: + - assets/stylesheets/extra.css + +theme: + name: material + palette: + # Palette toggle for automatic mode + - media: "(prefers-color-scheme)" + toggle: + icon: material/brightness-auto + name: Switch to light mode + + # Palette toggle for light mode + - media: "(prefers-color-scheme: light)" + scheme: default + toggle: + icon: material/brightness-7 + name: Switch to dark mode + + # Palette toggle for dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + toggle: + icon: material/brightness-4 + name: Switch to system preference + font: + text: Arial + language: en + logo: assets/images/favicon.svg + favicon: assets/images/favicon.ico + features: + # navigations https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/ + - navigation.instant + - navigation.instant.progress + # - navigation.tracking # TODO - not convinced I understand the benefit of this yet + - navigation.tabs + # - navigation.tabs.sticky # TODO - possibly activate later if useful + - navigation.sections + - navigation.expand + - navigation.path # ! Requirement/Recommended by NHS, so will keep active + - navigation.indexes + - toc.follow + - toc.integrate + - navigation.top + # Searching https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/ + - search.share + # Site Analytics https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-analytics/ + # Tags https://squidfunk.github.io/mkdocs-material/setup/setting-up-tags/ + # Git interactions https://squidfunk.github.io/mkdocs-material/setup/adding-a-git-repository/ + - content.action.edit + - content.code.copy + - content.code.select + - content.code.annotate + icon: + repo: fontawesome/brands/github + custom_dir: overrides + +markdown_extensions: + - attr_list + - pymdownx.emoji: + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg + - material.extensions.preview: + configurations: + - targets: + include: + - CHANGELOG.md + # TODO - not entirely sure how material.extensions.preview is working + - pymdownx.highlight: + anchor_linenums: true + line_spans: __span + pygments_lang_class: true + - pymdownx.inlinehilite + - pymdownx.snippets + - pymdownx.superfences + - toc: + permalink: true + +nav: + - User Guidance: + - index.md + - Installation: user_guidance/install.md + - Writing a rules config (dischema creation): + - File Transformation: user_guidance/file_transformation.md + - Data Contract: + - Writing a Data Contract: user_guidance/data_contract.md + - Domain Types: user_guidance/domain_types.md + - Business Rules: user_guidance/business_rules.md + - Feedback Messages: user_guidance/feedback_messages.md + - Backend Implementations: + - DuckDB: user_guidance/implementations/duckdb.md + - Spark: user_guidance/implementations/spark.md + - Choosing a Pipeline: + - DuckDB: user_guidance/pipelines/duckdb_pipeline.md + - Spark: user_guidance/pipelines/spark_pipeline.md + - Platform specific: + - Palantir Foundry Pipeline: user_guidance/pipelines/palantir_foundry_pipeline.md + - Advanced User Guidance: + - DVE Package Documentation: + - advanced_guidance/code_docs/core_engine.md + - Implementing a new backend: advanced_guidance/backends.md + - json_schemas/jsonschemas.md + - Tags: tags.md + +copyright: > +
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    Copyright © 2026 Crown Copyright (NHS England)

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    All content is available under the + Open Government Licence v3.0, + except where otherwise stated. + +

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    + +extra: + consent: + title: Cookie consent + description: >- + We use cookies to recognize your repeated visits and preferences, as well + as to measure the effectiveness of our documentation and whether users + find what they're searching for. With your consent, you're helping us to + make our documentation better. + generator: false + social: + - icon: nhseng + link: https://www.england.nhs.uk/ + - icon: fontawesome/brands/github + link: https://github.com/NHSDigital + tags: + : + # TODO - set versioning up later and associate with releases on github + # TODO - https://squidfunk.github.io/mkdocs-material/setup/setting-up-versioning/ + # version: + # provider: mike + # default: stable diff --git a/overrides/.icons/nhseng.svg b/overrides/.icons/nhseng.svg new file mode 100644 index 0000000..cd21739 --- /dev/null +++ b/overrides/.icons/nhseng.svg @@ -0,0 +1,4 @@ + + + + diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..bf4e1db --- /dev/null +++ b/poetry.lock @@ -0,0 +1,3505 @@ +# This file is automatically @generated by Poetry 2.2.0 and should not be changed by hand. + +[[package]] +name = "argcomplete" +version = "3.6.3" +description = "Bash tab completion for argparse" +optional = false 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(>=2.2)"] +test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] + +[metadata] +lock-version = "2.1" +python-versions = ">=3.10,<3.12" +content-hash = "2872cced0ecd01f9c19fa38d170e51d4a34dc45f3d77dcd93bf5659c47268dd0" diff --git a/pyproject.toml b/pyproject.toml index ca0c98f..96f3240 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,29 +18,19 @@ classifiers = [ [tool.poetry.dependencies] python = ">=3.10,<3.12" -boto3 = "1.34.162" -botocore = "1.34.162" -delta-spark = "2.4.0" -duckdb = "1.1.0" # mitigates security vuln in < 1.1.0 -formulas = "1.2.4" -idna = "3.7" # Downstream dep of requests but has security vuln < 3.7 -Jinja2 = "3.1.6" # mitigates security vuln in < 3.1.6 -lxml = "4.9.1" -openpyxl = "3.1.0" -pandas = "2.2.2" -polars = "0.20.14" -pyarrow = "17.0.0" -pydantic = "1.10.15" # Mitigates security vuln in < 1.10.13 -pymongo = "4.6.3" -pyspark = "3.4.4" -pytz = 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xlsx2csv = "0.8.2" @@ -89,6 +78,14 @@ types-setuptools = "68.2.0.0" types-urllib3 = "1.26.25.14" types-xmltodict = "0.13.0.3" +[tool.poetry.group.docs] +optional = true + +[tool.poetry.group.docs.dependencies] +mkdocs-material = "^9.7.1" +click = "8.2.1" +mkdocstrings = { version = "^1.0.3", extras = ["python"] } + [tool.ruff] line-length = 100 @@ -98,10 +95,9 @@ ignore = ["B028", "D213", "D203", "D205", "D107", "D105"] [tool.mypy] plugins = ["pydantic.mypy"] -enable_recursive_aliases = true [[tool.mypy.overrides]] -module = "polars" +module = "polars.*" follow_imports = "skip" # ^language server knows what's going on, but mypy can't find attributes on Self? type diff --git a/src/dve/core_engine/backends/base/rules.py b/src/dve/core_engine/backends/base/rules.py index 043f826..ef147b6 100644 --- a/src/dve/core_engine/backends/base/rules.py +++ b/src/dve/core_engine/backends/base/rules.py @@ -360,6 +360,7 @@ def apply_sync_filters( messages: Messages = [] for entity_name, filter_rules in filters_by_entity.items(): + self.logger.info(f"Applying filters to {entity_name}") entity = entities[entity_name] filter_column_names: list[str] = [] @@ -367,6 +368,7 @@ def apply_sync_filters( modified_entities = {entity_name: entity} for rule in filter_rules: + self.logger.info(f"Applying filter {rule.reporting.code}") if rule.reporting.emit == "record_failure": column_name = f"filter_{uuid4().hex}" filter_column_names.append(column_name) @@ -411,7 +413,12 @@ def apply_sync_filters( if not success: return messages, False + self.logger.info(f"Filter {rule.reporting.code} found {len(temp_messages)} issues") + if filter_column_names: + self.logger.info( + f"Filtering records from entity {entity_name} for error code {rule.reporting.code}" # pylint: disable=line-too-long + ) success_condition = " AND ".join( [f"({c_name} IS NOT NULL AND {c_name})" for c_name in filter_column_names] ) @@ -456,6 +463,7 @@ def apply_rules(self, entities: Entities, rule_metadata: RuleMetadata) -> Messag altering the entities in-place. """ + self.logger.info("Applying business rules") rules_and_locals: Iterable[tuple[Rule, TemplateVariables]] if rule_metadata.templating_strategy == "upfront": rules_and_locals = [] @@ -472,6 +480,8 @@ def apply_rules(self, entities: Entities, rule_metadata: RuleMetadata) -> Messag rules_and_locals = rule_metadata messages: Messages = [] + + self.logger.info("Applying pre-sync steps") for rule, local_variables in rules_and_locals: for step in rule.pre_sync_steps: if rule_metadata.templating_strategy == "runtime": @@ -498,6 +508,8 @@ def apply_rules(self, entities: Entities, rule_metadata: RuleMetadata) -> Messag if not success: return messages + self.logger.info("Applying post-sync steps") + for rule, local_variables in rules_and_locals: for step in rule.post_sync_steps: if rule_metadata.templating_strategy == "runtime": diff --git a/src/dve/core_engine/backends/implementations/duckdb/contract.py b/src/dve/core_engine/backends/implementations/duckdb/contract.py index 5113da5..51017a5 100644 --- a/src/dve/core_engine/backends/implementations/duckdb/contract.py +++ b/src/dve/core_engine/backends/implementations/duckdb/contract.py @@ -102,7 +102,6 @@ def apply_data_contract( self, entities: DuckDBEntities, contract_metadata: DataContractMetadata ) -> tuple[DuckDBEntities, Messages, StageSuccessful]: """Apply the data contract to the duckdb relations""" - self.logger.info("Applying data contracts") all_messages: Messages = [] successful = True @@ -131,6 +130,9 @@ def apply_data_contract( coerce_inferred_numpy_array_to_list(relation.df()).apply( application_helper, axis=1 ) # pandas uses eager evaluation so potential memory issue here? + self.logger.info( + f"Data contract found {len(application_helper.errors)} issues in {entity_name}" + ) all_messages.extend(application_helper.errors) casting_statements = [ diff --git a/src/dve/core_engine/backends/implementations/spark/contract.py b/src/dve/core_engine/backends/implementations/spark/contract.py index bbd2d5a..afbd85e 100644 --- a/src/dve/core_engine/backends/implementations/spark/contract.py +++ b/src/dve/core_engine/backends/implementations/spark/contract.py @@ -113,7 +113,10 @@ def apply_data_contract( # .persist(storageLevel=StorageLevel.MEMORY_AND_DISK) ) messages = validated.flatMap(lambda row: row[1]).filter(bool) + messages.cache() + self.logger.info(f"Data contract found {messages.count()} issues in {entity_name}") all_messages.extend(messages.collect()) + messages.unpersist() try: record_df = record_df.select( diff --git a/src/dve/pipeline/duckdb_pipeline.py b/src/dve/pipeline/duckdb_pipeline.py index f04e71c..87e927d 100644 --- a/src/dve/pipeline/duckdb_pipeline.py +++ b/src/dve/pipeline/duckdb_pipeline.py @@ -21,6 +21,7 @@ class DDBDVEPipeline(BaseDVEPipeline): """ Modified Pipeline class for running a DVE Pipeline with Spark """ + # pylint: disable=R0913 def __init__( self, diff --git a/src/dve/pipeline/pipeline.py b/src/dve/pipeline/pipeline.py index 385687b..366b590 100644 --- a/src/dve/pipeline/pipeline.py +++ b/src/dve/pipeline/pipeline.py @@ -190,6 +190,7 @@ def write_file_to_parquet( errors = [] for model_name, model in models.items(): + self._logger.info(f"Transforming {model_name} to stringified parquet") reader: BaseFileReader = load_reader(dataset, model_name, ext) try: if not entity_type: @@ -230,6 +231,7 @@ def audit_received_file_step( self, pool: ThreadPoolExecutor, submitted_files: Iterable[tuple[FileURI, InfoURI]] ) -> tuple[list[SubmissionInfo], list[SubmissionInfo]]: """Set files as being received and mark them for file transformation""" + self._logger.info("Starting audit received file service") audit_received_futures: list[tuple[str, FileURI, Future]] = [] for submission_file in submitted_files: data_uri, metadata_uri = submission_file @@ -291,7 +293,7 @@ def file_transformation( """Transform a file from its original format into a 'stringified' parquet file""" if not self.processed_files_path: raise AttributeError("processed files path not provided") - + self._logger.info(f"Applying file transformation to {submission_info.submission_id}") errors: list[FeedbackMessage] = [] submission_status: SubmissionStatus = SubmissionStatus() submission_file_uri: URI = fh.joinuri( @@ -326,6 +328,7 @@ def file_transformation_step( list[tuple[SubmissionInfo, SubmissionStatus]], list[tuple[SubmissionInfo, SubmissionStatus]] ]: """Step to transform files from their original format into parquet files""" + self._logger.info("Starting file transformation service") file_transform_futures: list[tuple[SubmissionInfo, Future]] = [] for submission_info in submissions_to_process: @@ -397,6 +400,7 @@ def apply_data_contract( self, submission_info: SubmissionInfo, submission_status: Optional[SubmissionStatus] = None ) -> tuple[SubmissionInfo, SubmissionStatus]: """Method for applying the data contract given a submission_info""" + self._logger.info(f"Applying data contract to {submission_info.submission_id}") if not submission_status: submission_status = self.get_submission_status( "contract", submission_info.submission_id @@ -450,6 +454,7 @@ def data_contract_step( list[tuple[SubmissionInfo, SubmissionStatus]], list[tuple[SubmissionInfo, SubmissionStatus]] ]: """Step to validate the types of an untyped (stringly typed) parquet file""" + self._logger.info("Starting data contract service") processed_files: list[tuple[SubmissionInfo, SubmissionStatus]] = [] failed_processing: list[tuple[SubmissionInfo, SubmissionStatus]] = [] dc_futures: list[tuple[SubmissionInfo, SubmissionStatus, Future]] = [] @@ -517,6 +522,7 @@ def apply_business_rules( """Apply the business rules to a given submission, the submission may have failed at the data_contract step so this should be passed in as a bool """ + self._logger.info(f"Applying business rules to {submission_info.submission_id}") if not submission_status: submission_status = self.get_submission_status( "business_rules", submission_info.submission_id @@ -606,6 +612,7 @@ def business_rule_step( list[tuple[SubmissionInfo, SubmissionStatus]], ]: """Step to apply business rules (Step impl) to a typed parquet file""" + self._logger.info("Starting business rules service") future_files: list[tuple[SubmissionInfo, SubmissionStatus, Future]] = [] for submission_info, submission_status in files: @@ -747,7 +754,7 @@ def error_report( SubmissionInfo, SubmissionStatus, Optional[SubmissionStatisticsRecord], Optional[URI] ]: """Creates the error reports given a submission info and submission status""" - + self._logger.info(f"Generating error report for {submission_info.submission_id}") if not submission_status: submission_status = self.get_submission_status( "error_report", submission_info.submission_id @@ -756,6 +763,7 @@ def error_report( if not self.processed_files_path: raise AttributeError("processed files path not provided") + self._logger.info("Reading error dataframes") errors_df, aggregates = self._get_error_dataframes(submission_info.submission_id) if not submission_status.number_of_records: @@ -794,9 +802,11 @@ def error_report( "error_reports", f"{submission_info.file_name}_{submission_info.file_extension.strip('.')}.xlsx", ) + self._logger.info("Writing error report") with fh.open_stream(report_uri, "wb") as stream: stream.write(er.ExcelFormat.convert_to_bytes(workbook)) + self._logger.info("Publishing error aggregates") self._publish_error_aggregates(submission_info.submission_id, aggregates) return submission_info, submission_status, sub_stats, report_uri @@ -812,6 +822,7 @@ def error_report_step( """Step to produce error reports takes processed files and files that failed file transformation """ + self._logger.info("Starting error reports service") futures: list[tuple[SubmissionInfo, SubmissionStatus, Future]] = [] reports: list[ tuple[SubmissionInfo, SubmissionStatus, Union[None, SubmissionStatisticsRecord], URI] diff --git a/src/dve/pipeline/spark_pipeline.py b/src/dve/pipeline/spark_pipeline.py index 4b26163..71fdb32 100644 --- a/src/dve/pipeline/spark_pipeline.py +++ b/src/dve/pipeline/spark_pipeline.py @@ -23,6 +23,7 @@ class SparkDVEPipeline(BaseDVEPipeline): """ Polymorphed Pipeline class for running a DVE Pipeline with Spark """ + # pylint: disable=R0913 def __init__( self, diff --git a/tests/features/steps/steps_audit.py b/tests/features/steps/steps_audit.py index 0694677..6a07fc6 100644 --- a/tests/features/steps/steps_audit.py +++ b/tests/features/steps/steps_audit.py @@ -17,4 +17,4 @@ def check_latest_audit_record_for_submission(context: Context, status: str): proc_status = pipeline._audit_tables.get_current_processing_info( get_submission_info(context).submission_id ) - assert proc_status.processing_status == status + assert proc_status.processing_status == status, proc_status.processing_status