pysof 0.1.47__tar.gz → 0.2.1__tar.gz

{pysof-0.1.47 → pysof-0.2.1}/Cargo.toml

@@ -16,14 +16,17 @@ name = "pysof"
 crate-type = ["cdylib"]
 
 [dependencies]
-pyo3 = { version = ">=0.27", features = ["extension-module", "generate-import-lib"] }
-helios-sof = { path = "../sof", version = "0.1.47" }
-helios-fhir = { path = "../fhir", version = "0.1.47" }
+pyo3 = { version = ">=0.29", features = ["extension-module", "generate-import-lib"] }
+helios-sof = { path = "../sof", version = "0.2.1", default-features = false }
+helios-fhir = { path = "../fhir", version = "0.2.1", default-features = false }
 serde = { workspace = true }
 serde_json = { workspace = true }
 chrono = { version = "0.4", features = ["serde"] }
-pythonize = "0.27"
+pythonize = "0.29"
 csv = "1.3"
+# Drives helios-sof's async remote-resolve functions from the synchronous
+# PyO3 entry points via a current-thread runtime.
+tokio = { version = "1", default-features = false, features = ["rt", "net", "time"] }
 
 [features]
 default = ["R4"]
@@ -37,4 +40,4 @@ R6 = ["helios-sof/R6", "helios-fhir/R6"]
 openssl = { version = "0.10", features = ["vendored"] }
 
 [build-dependencies]
-pyo3-build-config = "0.27"
+pyo3-build-config = "0.29"

{pysof-0.1.47 → pysof-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysof
-Version: 0.1.47
+Version: 0.2.1
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -176,6 +176,44 @@ result = pysof.run_view_definition_with_options(
 )
 ```
 
+### Remote `resolve()` (Trusted Servers)
+
+`resolve()` dereferences references against the input bundle by default. You can
+optionally let it fetch references that point at **explicitly trusted** FHIR
+servers and fold them into the resolution pool before rows are generated. This is
+**off by default** and gated by a strict allowlist (matching scheme + host + port
++ path-prefix; private/loopback addresses are blocked unless opted in).
+
+```python
+import pysof
+
+config = pysof.RemoteResolveConfig(
+    ["https://fhir.example.org/r4"],   # trusted base URLs (allowlist)
+    max_fetches=256,                    # per-run/-stream fetch cap
+    max_depth=1,                        # chained-reference rounds
+    allow_private_addresses=False,      # allow internal LBs (e.g. Traefik) by hostname
+    bearer_tokens={"fhir.example.org": "TOKEN"},  # optional per-host auth
+)
+
+# Or build it from SOF_RESOLVE_* environment variables:
+# config = pysof.RemoteResolveConfig.from_env()
+
+result = pysof.run_view_definition_remote(
+    view_definition, bundle, "json", config, fhir_version="R4"
+)
+
+# Streaming NDJSON with remote resolve() (one shared cache across chunks):
+stats = pysof.process_ndjson_to_file_remote(
+    view_definition, "input.ndjson", "output.json", "ndjson", config, chunk_size=1000
+)
+```
+
+When `config.is_active()` is `False` (disabled or empty allowlist) these behave
+exactly like their non-remote counterparts. Enabling remote resolution makes
+output depend on remote server state at run time. See the
+[SQL-on-FHIR guide](../../book/src/ch06-sql-on-fhir.md) for the full security
+model and configuration reference.
+
 ### Utility Functions
 
 ```python

{pysof-0.1.47 → pysof-0.2.1}/README.md

@@ -147,6 +147,44 @@ result = pysof.run_view_definition_with_options(
 )
 ```
 
+### Remote `resolve()` (Trusted Servers)
+
+`resolve()` dereferences references against the input bundle by default. You can
+optionally let it fetch references that point at **explicitly trusted** FHIR
+servers and fold them into the resolution pool before rows are generated. This is
+**off by default** and gated by a strict allowlist (matching scheme + host + port
++ path-prefix; private/loopback addresses are blocked unless opted in).
+
+```python
+import pysof
+
+config = pysof.RemoteResolveConfig(
+    ["https://fhir.example.org/r4"],   # trusted base URLs (allowlist)
+    max_fetches=256,                    # per-run/-stream fetch cap
+    max_depth=1,                        # chained-reference rounds
+    allow_private_addresses=False,      # allow internal LBs (e.g. Traefik) by hostname
+    bearer_tokens={"fhir.example.org": "TOKEN"},  # optional per-host auth
+)
+
+# Or build it from SOF_RESOLVE_* environment variables:
+# config = pysof.RemoteResolveConfig.from_env()
+
+result = pysof.run_view_definition_remote(
+    view_definition, bundle, "json", config, fhir_version="R4"
+)
+
+# Streaming NDJSON with remote resolve() (one shared cache across chunks):
+stats = pysof.process_ndjson_to_file_remote(
+    view_definition, "input.ndjson", "output.json", "ndjson", config, chunk_size=1000
+)
+```
+
+When `config.is_active()` is `False` (disabled or empty allowlist) these behave
+exactly like their non-remote counterparts. Enabling remote resolution makes
+output depend on remote server state at run time. See the
+[SQL-on-FHIR guide](../../book/src/ch06-sql-on-fhir.md) for the full security
+model and configuration reference.
+
 ### Utility Functions
 
 ```python

{pysof-0.1.47 → pysof-0.2.1}/crates/fhir/Cargo.toml

@@ -24,13 +24,17 @@ xml = ["helios-serde-support/xml"]
 serde = { workspace = true }
 serde_json = { workspace = true, features = ["raw_value"] }
 clap = { version = "4.0", features = ["derive"] }
-helios-fhir-macro = { path = "../fhir-macro", version = "0.1.47" }
-helios-serde-support = { path = "../serde-support", version = "0.1.47" }
-helios-fhirpath-support = { path = "../fhirpath-support", version = "0.1.47" }
+helios-fhir-macro = { path = "../fhir-macro", version = "0.2.1" }
+helios-serde-support = { path = "../serde-support", version = "0.2.1" }
+helios-fhirpath-support = { path = "../fhirpath-support", version = "0.2.1" }
 time = "0.3"
 chrono = { workspace = true }
 # Re-add serde-with-arbitrary-precision, keep macros
 rust_decimal = { version = "1.0", features = ["serde-with-arbitrary-precision", "macros"] }
+# SearchParameter registry/loader (moved from helios-persistence so helios-sof
+# can do compartment-aware filtering without a circular dep).
+regex = "1"
+tracing = "0.1"
 
 [dev-dependencies]
 rust_decimal_macros = "1.0"

pysof-0.2.1/crates/fhir/src/compartment_expressions/mod.rs

@@ -0,0 +1,20 @@
+//! Compartment search-param FHIRPath expression tables for each FHIR version.
+//!
+//! For each `(compartment, resource_type)` pair from a FHIR
+//! `CompartmentDefinition`, exposes the `(search-param-name,
+//! FHIRPath-expression)` pairs that link the resource to the
+//! compartment. Used by `helios_sof::compartment` to drive `$viewdefinition-run`'s
+//! patient/group filter against raw resource JSON without any runtime
+//! data-file dependency — the tables are compiled in.
+//!
+//! Submodules are generated by `cargo run -p helios-fhir-gen --bin
+//! compartment-expressions`; do not edit by hand.
+
+#[cfg(feature = "R4")]
+pub mod r4;
+#[cfg(feature = "R4B")]
+pub mod r4b;
+#[cfg(feature = "R5")]
+pub mod r5;
+#[cfg(feature = "R6")]
+pub mod r6;