phactor 0.2.0__tar.gz

phactor-0.2.0/.gitignore

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+.venv/
+__pycache__/
+*.pyc
+*.egg-info/
+dist/
+build/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.codex
+.env

phactor-0.2.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to the Phactor Python SDK are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+While the SDK is pre-1.0 (`0.x`), breaking changes may accompany a minor version bump.
+
+## [0.2.0] - 2026-07-04
+
+### Breaking
+
+- **`ConditionInput.value` (a single `str`) is now `ConditionInput.values` (a
+  `list[str]`).** This matches the current Query API schema;
+  the previous singular field produced GraphQL-invalid queries against any
+  environment running that schema. Wrap each code in a list:
+
+  ```python
+  # Before (0.1.x)
+  {"conditions": {"values": [{"type": "ICD10", "value": "E11"}]}}
+
+  # After (0.2.0)
+  {"conditions": {"values": [{"type": "ICD10", "values": ["E11"]}]}}
+  ```
+
+  A single condition input can now carry multiple codes:
+  `{"type": "ICD10", "values": ["E11", "E10"]}`.
+
+- **`LabValueInput` and `ClinicalMeasurementInput` now validate cross-field and
+  raise on under-specified criteria.** Previously the connector silently skipped
+  a lab/measurement criterion that carried neither a numeric comparison nor an
+  interpretation, inflating cohort counts. The SDK now fails fast at construction
+  time:
+  - `LabValueInput` requires **either** a complete numeric comparison (`operator`
+    **and** `value` **and** `unit`) **or** a non-empty `interpretation`, and at
+    least one of `test_code` / `test_name`.
+  - `ClinicalMeasurementInput` requires **either** a numeric comparison
+    (`operator` **and** `value`) **or** a non-empty `interpretation`. Note the
+    asymmetry: `unit` is **not** part of the measurement numeric pair.
+
+  To support categorical-only queries, `operator` / `value` / `unit` on
+  `LabValueInput` and `operator` / `value` on `ClinicalMeasurementInput` are now
+  optional. Existing fully-specified numeric criteria are unaffected.
+
+### Changed
+
+- **The request timeout now defaults to 600 seconds (previously 30).** The
+  default sits deliberately above the platform's own deadlines (connector
+  `statement_timeout` 420s < query-api fan-out 540s), so a slow cohort returns a
+  server error naming the provider rather than a client-side `TimeoutError` that
+  is then retried. `PhactorClient(timeout=...)` and `AsyncPhactorClient(timeout=...)`
+  take `float | None` instead of `float`; passing `None` (the new default) resolves
+  the value from `PHACTOR_TIMEOUT`, then falls back to 600. Set either to fail faster.
+
+### Added
+
+- Typed inputs for procedures, allergies, and immunizations — previously
+  raw-dict passthrough, now first-class validated models: `ProcedureInput` /
+  `ProceduresInput`, `AllergyInput` / `AllergiesInput`, `ImmunizationInput` /
+  `ImmunizationsInput`, wired into `PropositionInput.procedures` / `.allergies` /
+  `.immunizations`. The wrapper models omit the internal `criteriaErrors`
+  forwarding field.
+- Clinical qualifier filters on existing criteria: `ConditionInput.status` /
+  `.severity` / `.stage` (with a new `ConditionStageInput`),
+  `MedicationInput.status`, and `.interpretation` on both `LabValueInput` and
+  `ClinicalMeasurementInput`.
+- Nine new enums mirroring the query-api schema: `ConditionClinicalStatus`,
+  `ConditionSeverity`, `MedicationStatus`, `ProcedureTypeEnum`,
+  `ProcedureOutcome`, `AllergyTypeEnum`, `AllergyCriticality`,
+  `ImmunizationTypeEnum`, and `InterpretationCode`.
+- The full criteria-building surface (enums and input models) is now exported
+  from `phactor` and `phactor.cohorts`, backfilling previously unexported input
+  models alongside the new ones.
+
+## [0.1.0] - 2026-03-11
+
+- Initial release: authenticated GraphQL client (`PhactorClient` /
+  `AsyncPhactorClient`), typed cohort-analysis models, the fluent
+  `CohortBuilder`, and pandas result helpers.
+

phactor-0.2.0/LICENSE

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phactor-0.2.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: phactor
+Version: 0.2.0
+Summary: Python SDK for the Phactor clinical trial feasibility platform
+Project-URL: Homepage, https://phactor.ai
+Project-URL: Documentation, https://docs.phactor.ai
+Author: Janeiro Digital
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: clinical-trials,cohort,feasibility,graphql,healthcare,real-world-data,sdk
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: httpx<1,>=0.27
+Requires-Dist: pydantic<3,>=2.0
+Requires-Dist: pyjwt<3,>=2.0
+Provides-Extra: dev
+Requires-Dist: mypy>=1.10; extra == 'dev'
+Requires-Dist: pandas-stubs>=2.0; extra == 'dev'
+Requires-Dist: pandas>=1.5; extra == 'dev'
+Requires-Dist: pytest-asyncio>=0.24; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: respx>=0.22; extra == 'dev'
+Requires-Dist: ruff>=0.8; extra == 'dev'
+Provides-Extra: pandas
+Requires-Dist: pandas>=1.5; extra == 'pandas'
+Description-Content-Type: text/markdown
+
+# Phactor Python SDK
+
+Python SDK for the Phactor clinical trial feasibility platform. Authenticate via OAuth2 client credentials and run cohort feasibility queries programmatically.
+
+## Installation
+
+```bash
+pip install phactor
+```
+
+## Quick Start
+
+### Async
+
+```python
+import asyncio
+
+from phactor import AsyncPhactorClient
+
+
+async def main() -> None:
+    async with AsyncPhactorClient(verify="/etc/ssl/certs/zscaler-ca.pem") as client:
+        result = await client.cohorts.analyze(
+            providers=["provider-uuid"],
+            cohort_groups=[
+                {
+                    "inclusionGroupOperator": "AND",
+                    "inclusionGroups": [
+                        {
+                            "name": "Adults",
+                            "operator": "AND",
+                            "propositions": [{"age": {"from": 18, "to": 65}}],
+                        }
+                    ],
+                }
+            ],
+            include_impact_analysis=True,
+        )
+
+        for analysis in result.analyses:
+            print(f"{analysis.provider.name}: {analysis.total_patients} patients")
+
+
+asyncio.run(main())
+```
+
+### Sync
+
+```python
+from phactor import PhactorClient
+
+with PhactorClient(verify="/etc/ssl/certs/zscaler-ca.pem") as client:
+    result = client.cohorts.analyze(
+        providers=["provider-uuid"],
+        cohort_groups=[
+            {
+                "inclusionGroupOperator": "AND",
+                "inclusionGroups": [
+                    {
+                        "name": "Adults",
+                        "operator": "AND",
+                        "propositions": [{"age": {"from": 18, "to": 65}}],
+                    }
+                ],
+            }
+        ],
+    )
+
+    for analysis in result.analyses:
+        print(f"{analysis.provider.name}: {analysis.total_patients} patients")
+```
+
+## Configuration
+
+Pass credentials directly or use environment variables:
+
+| Parameter | Environment Variable |
+|-----------|---------------------|
+| `client_id` | `PHACTOR_CLIENT_ID` |
+| `client_secret` | `PHACTOR_CLIENT_SECRET` |
+| `entity_id` | `PHACTOR_ENTITY_ID` |
+| `fusionauth_url` | `PHACTOR_FUSIONAUTH_URL` |
+| `gateway_url` | `PHACTOR_GATEWAY_URL` |
+| `verify` | `PHACTOR_CA_BUNDLE` |
+| `timeout` | `PHACTOR_TIMEOUT` |
+
+```bash
+export PHACTOR_CLIENT_ID="your-client-id"
+export PHACTOR_CLIENT_SECRET="your-client-secret"
+export PHACTOR_ENTITY_ID="your-entity-id"
+export PHACTOR_FUSIONAUTH_URL="https://auth.phactor.ai"
+export PHACTOR_GATEWAY_URL="https://federated-gateway.phactor.ai/graphql"
+export PHACTOR_CA_BUNDLE="/etc/ssl/certs/zscaler-ca.pem"
+export PHACTOR_TIMEOUT="600"   # seconds; optional, this is the default
+```
+
+If you prefer explicit configuration, pass the same values into `PhactorClient(...)` or `AsyncPhactorClient(...)`.
+
+If `verify` is not passed explicitly, the SDK will use `PHACTOR_CA_BUNDLE` when present and otherwise default to standard TLS verification. The same setting is used for both FusionAuth token requests and Phactor gateway API requests.
+
+```python
+from phactor import PhactorClient
+
+client = PhactorClient(
+    client_id="your-client-id",
+    client_secret="your-client-secret",
+    fusionauth_url="https://auth.phactor.ai",
+    gateway_url="https://federated-gateway.phactor.ai/graphql",
+    verify="/etc/ssl/certs/zscaler-ca.pem",
+)
+```
+
+## Reliability Notes
+
+- The SDK caches OAuth tokens and refreshes them automatically when needed.
+- API requests retry on transient failures such as `429`, `502`, `503`, `504`, timeouts, and temporary connection errors.
+- The request timeout defaults to **600 seconds**, deliberately above the platform's own deadlines (connector 420s < query fan-out 540s), so a slow cohort returns a server error naming the provider rather than a client-side `TimeoutError` that is then retried three times. Lower it with `PHACTOR_TIMEOUT` or `timeout=` if you want to fail faster.
+- If an API request returns `401`, the SDK invalidates the cached token, fetches a fresh token, and retries once before raising `AuthenticationError`.
+- `AsyncPhactorClient` should be used through `async with` or closed explicitly with `await client.close()`. Once closed, further use raises `PhactorError`.
+
+## Fluent Cohort Builder
+
+```python
+from phactor.cohorts import CohortBuilder, Proposition
+
+cohort = (
+    CohortBuilder(inclusion_operator="OR")
+    .include("Core criteria", operator="AND")
+    .add(Proposition(age={"from": 18}))
+    .add(
+        Proposition(
+            conditions={
+                "values": [
+                    {"type": "ICD10", "values": ["E11"]}  # Type 2 Diabetes
+                ]
+            }
+        )
+    )
+    .done()
+    .exclude("Recent CV events", operator="OR")
+    .add(
+        Proposition(
+            conditions={
+                "values": [
+                    {
+                        "type": "ICD10",
+                        "values": ["I21"],  # myocardial infarction
+                        "timing": {
+                            "operator": "LESS_THAN_OR_EQUALS",
+                            "value": 180,
+                            "unit": "DAYS",
+                            "reference": "SCREENING",
+                        },
+                    }
+                ]
+            }
+        )
+    )
+    .done()
+    .build()
+)
+
+async with AsyncPhactorClient() as client:
+    result = await client.cohorts.analyze(
+        providers=["provider-1"],
+        cohort_groups=[cohort],
+        include_impact_analysis=True,
+    )
+```
+
+You can also pass typed models directly instead of raw dictionaries:
+
+```python
+from phactor import CohortGroupInput, CriteriaGroupInput, PropositionInput
+
+cohort = CohortGroupInput(
+    inclusion_group_operator="AND",
+    inclusion_groups=[
+        CriteriaGroupInput(
+            name="Adults",
+            operator="AND",
+            propositions=[PropositionInput(age={"from": 18, "to": 65})],
+        )
+    ],
+)
+```
+
+There are three independent operator levels:
+
+- `cohort_group_operator` combines complete pathways when a request intentionally
+  contains more than one `CohortGroupInput`.
+- `inclusion_group_operator` combines the inclusion groups inside one pathway.
+- `CriteriaGroupInput.operator` (`AND`, `OR`, or `SOME`) combines propositions
+  inside one named criteria group.
+
+Exclusion groups are always unioned and subtracted from the pathway's combined
+inclusion result. For example, an `OR` pathway with inclusion groups `A` and `B`
+and exclusion group `E` evaluates as `(A OR B) EXCEPT E`.