Merge pull request #4 from cdisc-org/add-cosmos-endpoints

Add COSMoS endpoints to the CDISC library client

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# VSCode
+.vscode/

README.md

@@ -1,19 +1,42 @@
 # cdisc-library-client
+
 Python client for accessing the CDISC library. Deployed to PYPI
 
-# operations
+## operations
+
 ```
 get_sdtm - get an sdtm standard
 get_adam - get an adam or adamig standard
 get_cdash - get a cdash standard
 get_sdtmig - gets sdtmig standard
 get_sendig - gets sendig standard
 get_cdashig - gets cdashig standard
+
 get_terminology_package - get a ct package given the version
 get_codelist_terms - returns an array of all terms in a codelist
 get_codelist_term - returns the library representation of a codelist term
+
 get_rule_catalogs - returns a list of links to all rule catalogs in the CDISC Library
 get_rules_catalog - returns all rules in a single rules catalog.
 get_rule - gets a rule definition given standard, version, and rule id
+
+get_bc_packages - get biomedical concept package list
+get_bc_package_biomedicalconcepts - get biomedical concept list in a package 
+get_bc_package_biomedicalconcept - get biomedical concept in a package
+get_bc_latest_biomedicalconcepts - get biomedical concept list (latest versions)
+get_bc_latest_biomedicalconcept - get biomedical concept (latest version)
+get_bc_categories - get biomedical concept categories list
+get_bc_latest_biomedicalconcepts_category - get biomedical concepts for a given category (latest version)
+
+get_sdtm_packages - get sdtm dataset specialization package list
+get_sdtm_package_datasetspecializations - get sdtm dataset specialization list in a package
+get_sdtm_package_datasetspecialization - get sdtm dataset specialization in a package
+get_sdtm_latest_sdtm_datasetspecializations - get sdtm dataset specialization list (latest versions)
+get_sdtm_latest_sdtm_datasetspecialization - get sdtm dataset specialization (latest version)
+get_sdtm_domains - get sdtm dataset specialization domain list
+get_sdtm_latest_sdtm_datasetspecializations_domain - get a list of sdtm dataset specializations for a given domain (latest version)
+
+get_biomedicalconcept_latest_datasetspecializations - get a list of dataset specializations that specialize a biomedical concept (latest versions)
 ```
-More info on CDISC Library API endpoints can be found here: https://www.cdisc.org/cdisc-library/api-documentation
+
+More info on CDISC Library API endpoints can be found at the [CDISC Library API Portal](https://api.developer.library.cdisc.org/).

cdisc_library_client/library_client.py

@@ -31,19 +31,19 @@ def get_api_json(self, uri):
             raise ResourceNotFoundException(f"Resource {self.base_api_url+uri} is not found.")
         else:
             raise Exception(f"Request to {self.base_api_url+uri} returned unsuccessful {raw_data.status_code} response")
-    
+
     def get_raw_response(self, uri):
         headers = {
             'Accept': 'application/json',
             'api-key': self.api_key,
             "User-Agent": "pipeline"
         }
         return self._session.get(self.base_api_url+uri, headers=headers)
-    
+
     def get_products(self):
         href = "/mdr/products"
         return self.get_api_json(href)
-    
+
     def get_sdtm(self, version):
         href = f"/mdr/sdtm/{version}"
         return self.get_api_json(href)
@@ -59,19 +59,19 @@ def get_sendig(self, version):
     def get_adam(self, version):
         href = f"/mdr/adam/{version}"
         return self.get_api_json(href)
-    
+
     def get_cdash(self, version):
         href = f"/mdr/cdash/{version}"
         return self.get_api_json(href)
-        
+
     def get_cdashig(self, version):
         href = f"/mdr/cdashig/{version}"
         return self.get_api_json(href)
 
     def get_terminology_package(self, version):
         href = f"/mdr/ct/packages/{version}"
         return self.get_api_json(href)
-    
+
     def get_codelist_terms(self, version, codelist):
         terms = []
         try:
@@ -94,7 +94,7 @@ def get_codelist_term(self, version, codelist, term):
     def get_qrs_instrument(self, instrument, version):
         href = f"/mdr/qrs/instruments/{instrument}/versions/{version}"
         return self.get_api_json(href)
-    
+
     def get_rule_catalogs(self):
         """
         Returns an object containing a mapping of catalog titles to links to the catalogs of the form:
@@ -109,7 +109,7 @@ def get_rule_catalogs(self):
         href = f"/mdr/rules"
         response = self.get_api_json(href)
         return response.get("_links", {}).get("catalogs", {})
-    
+
     def get_rules_catalog(self, standard: str, version: str):
         """
         Returns an object containing a mapping of rule id to rule definitions
@@ -124,3 +124,74 @@ def get_rule(self, standard: str, version: str, rule_id: str):
         """
         href = f"/mdr/rules/{standard}/{version}/rule/{rule_id}"
         return self.get_api_json(href)
+
+    def get_bc_packages(self, version: str):
+        href = f"/cosmos/{version}/mdr/bc/packages"
+        response = self.get_api_json(href)
+        return response.get("_links", {}).get("packages", [])
+
+    def get_bc_package_biomedicalconcepts(self, version: str, package: str):
+        href = f"/cosmos/{version}/mdr/bc/packages/{package}/biomedicalconcepts"
+        response = self.get_api_json(href)
+        return response.get("_links", {}).get("biomedicalConcepts", [])
+
+    def get_bc_package_biomedicalconcept(self, version: str, package: str, biomedicalconcept: str):
+        href = f"/cosmos/{version}/mdr/bc/packages/{package}/biomedicalconcepts/{biomedicalconcept}"
+        return self.get_api_json(href)
+
+    def get_bc_latest_biomedicalconcepts(self, version: str):
+        href = f"/cosmos/{version}/mdr/bc/biomedicalconcepts"
+        response = self.get_api_json(href)
+        return response.get("_links", {}).get("biomedicalConcepts", [])
+
+    def get_bc_latest_biomedicalconcept(self, version: str, biomedicalconcept: str):
+        href = f"/cosmos/{version}/mdr/bc/biomedicalconcepts/{biomedicalconcept}"
+        return self.get_api_json(href)
+
+    def get_bc_categories(self, version: str):
+        href = f"/cosmos/{version}/mdr/bc/categories"
+        response = self.get_api_json(href)
+        return response.get("_links", {}).get("categories", [])
+
+    def get_bc_latest_biomedicalconcepts_category(self, version: str, category: str):
+        href = f"/cosmos/{version}/mdr/bc/biomedicalconcepts?category={category}"
+        response = self.get_api_json(href)
+        return response.get("_links", {}).get("biomedicalConcepts", [])
+
+    def get_sdtm_packages(self, version: str):
+        href = f"/cosmos/{version}/mdr/specializations/sdtm/packages"
+        response = self.get_api_json(href)
+        return response.get("_links", {}).get("packages", [])
+
+    def get_sdtm_package_datasetspecializations(self, version: str, package: str):
+        href = f"/cosmos/{version}/mdr/specializations/sdtm/packages/{package}/datasetspecializations"
+        response = self.get_api_json(href)
+        return response.get("_links", {}).get("datasetSpecializations", [])
+
+    def get_sdtm_package_datasetspecialization(self, version: str, package: str, datasetspecialization: str):
+        href = f"/cosmos/{version}/mdr/specializations/sdtm/packages/{package}/datasetspecializations/{datasetspecialization}"
+        return self.get_api_json(href)
+
+    def get_sdtm_latest_sdtm_datasetspecializations(self, version: str):
+        href = f"/cosmos/{version}/mdr/specializations/sdtm/datasetspecializations"
+        response = self.get_api_json(href)
+        return response.get("_links", {}).get("datasetSpecializations", [])
+
+    def get_sdtm_latest_sdtm_datasetspecialization(self, version: str, datasetspecialization: str):
+        href = f"/cosmos/{version}/mdr/specializations/sdtm/datasetspecializations/{datasetspecialization}"
+        return self.get_api_json(href)
+
+    def get_sdtm_domains(self, version: str):
+        href = f"/cosmos/{version}/mdr/specializations/sdtm/domains"
+        response = self.get_api_json(href)
+        return response.get("domains", [])
+
+    def get_sdtm_latest_sdtm_datasetspecializations_domain(self, version: str, domain: str):
+        href = f"/cosmos/{version}/mdr/specializations/sdtm/datasetspecializations?domain={domain}"
+        response = self.get_api_json(href)
+        return response.get("_links", {}).get("datasetSpecializations", [])
+
+    def get_biomedicalconcept_latest_datasetspecializations(self, version: str, biomedicalconcept: str):
+        href = f"/cosmos/{version}/mdr/specializations/datasetspecializations?biomedicalconcept={biomedicalconcept}"
+        response = self.get_api_json(href)
+        return response.get("_links", {}).get("datasetSpecializations", [])

examples/get_cosmos_data.py

@@ -0,0 +1,109 @@
+import os
+from cdisc_library_client import CDISCLibraryClient
+
+if __name__ == "__main__":
+    api_key = os.environ.get("CDISC_LIBRARY_API_KEY")
+    client = CDISCLibraryClient(api_key=api_key)
+
+    # Get BC packages
+    bc_packages = client.get_bc_packages("v2")
+    print(f"There are {len(bc_packages)} Biomedical Concept packages")
+
+    # Get BCs in package
+    for package in bc_packages:
+      title = package['title']
+      href = package['href']
+      package = href.split("/")[-2]
+      biomedicalconcepts = client.get_bc_package_biomedicalconcepts("v2", package)
+      print(f"{title} has {len(biomedicalconcepts)} Biomedical Concepts")
+
+    # Get a specific BC in a package
+    bc = client.get_bc_package_biomedicalconcept("v2", "2023-12-12", "C25298")
+    package = bc['_links']['parentPackage']['title']
+    title = bc['shortName']
+    print(f"{title} in {package} has {len(bc['dataElementConcepts'])} Data Element Concepts")
+
+    # Get latest BCs
+    biomedicalconcepts = client.get_bc_latest_biomedicalconcepts("v2")
+    print(f"There are {len(biomedicalconcepts)} Biomedical Concepts in the CDISC Library")
+
+    # Get the latest version of a specific BC
+    bc = client.get_bc_latest_biomedicalconcept("v2", "C25298")
+    package = bc['_links']['parentPackage']['title']
+    title = bc['shortName']
+    print(f"{title} in {package} has {len(bc['dataElementConcepts'])} Data Element Concepts")
+
+    # Get BC categories
+    categories = client.get_bc_categories("v2")
+    print(f"There are {len(categories)} Biomedical Concept categories")
+
+    # Get latest BCs in a category
+    biomedicalconcepts = client.get_bc_latest_biomedicalconcepts_category("v2", "RECIST 1.1")
+    print(f"There are {len(biomedicalconcepts)} Biomedical Concepts in the RECIST 1.1 category in the CDISC Library")
+
+    # Get latest BCs in a category
+    biomedicalconcepts = client.get_bc_latest_biomedicalconcepts_category("v2", "")
+    print(f"There are {len(biomedicalconcepts)} Biomedical Concepts in the CDISC Library")
+
+    # Get SDTM Dataset Specialization Packages
+    sdtm_packages = client.get_sdtm_packages("v2")
+    print(f"There are {len(sdtm_packages)} SDTM Dataset Specialization packages")
+
+    # Get Specializations in package
+    for package in sdtm_packages:
+      title = package['title']
+      href = package['href']
+      package = href.split("/")[-2]
+      datasetspecializations = client.get_sdtm_package_datasetspecializations("v2", package)
+      print(f"{title} has {len(datasetspecializations)} SDTM Dataset Specializations")
+
+    # Get a specific SDTM Dataset Specializatio in a package
+    sdtm = client.get_sdtm_package_datasetspecialization("v2", "2023-12-12", "SYSBP")
+    package = sdtm['_links']['parentPackage']['title']
+    title = sdtm['shortName']
+    print(f"{title} in {package} has {len(sdtm['variables'])} Variables")
+
+    # Get SDTM domains
+    domains = client.get_sdtm_domains("v2")
+    print(f"There are {len(domains)} SDTM domains")
+
+    # Get latest SDTM Dataset Specializations
+    specializations = client.get_sdtm_latest_sdtm_datasetspecializations("v2")
+    print(f"There are {len(specializations)} SDTM Dataset Specializations in the CDISC Library")
+
+    # Get the latest version of a specific SDTM Dataset Specialization
+    sdtm = client.get_sdtm_latest_sdtm_datasetspecialization("v2", "SYSBP")
+    package = sdtm['_links']['parentPackage']['title']
+    title = sdtm['shortName']
+    print(f"{title} in {package} has {len(sdtm['variables'])} Variables")
+
+    # Get latest SDTM Dataset Specializations in a domain
+    specializations = client.get_sdtm_latest_sdtm_datasetspecializations_domain("v2", "VS")
+    print(f"There are {len(specializations)} SDTM Dataset Specializations in the VS domain in the CDISC Library")
+
+   # Get latest SDTM Dataset Specializations in a domain
+    specializations = client.get_sdtm_latest_sdtm_datasetspecializations_domain("v2", "")
+    print(f"There are {len(specializations)} SDTM Dataset Specializations in the CDISC Library")
+
+    # Get latest SDTM Dataset Specializations that specialize a Biomedical Concept
+    specializations = client.get_biomedicalconcept_latest_datasetspecializations("v2", "")
+    sdtm_specializations = specializations['sdtm']
+    print(f"There are {len(sdtm_specializations)} SDTM Dataset Specializations in the CDISC Library")
+
+    # Get latest SDTM Dataset Specializations that specialize a Biomedical Concept
+    biomedicalConcept = "C25298"
+    specializations = client.get_biomedicalconcept_latest_datasetspecializations("v2", biomedicalConcept)
+    sdtm_specializations = specializations['sdtm']
+    print(f"There are {len(sdtm_specializations)} SDTM Dataset Specializations in the CDISC Library that specialize {biomedicalConcept}")
+
+    # Get latest SDTM Dataset Specializations that specialize a Biomedical Concept
+    biomedicalConcept = "C105585"
+    specializations = client.get_biomedicalconcept_latest_datasetspecializations("v2", biomedicalConcept)
+    sdtm_specializations = specializations['sdtm']
+    print(f"There are {len(sdtm_specializations)} SDTM Dataset Specializations in the CDISC Library that specialize {biomedicalConcept}")
+
+    # Get latest SDTM Dataset Specializations that specialize a Biomedical Concept
+    biomedicalConcept = "C123456"
+    specializations = client.get_biomedicalconcept_latest_datasetspecializations("v2", biomedicalConcept)
+    sdtm_specializations = specializations['sdtm']
+    print(f"There are {len(sdtm_specializations)} SDTM Dataset Specializations in the CDISC Library that specialize {biomedicalConcept}")

setup.py

@@ -1,4 +1,4 @@
-__version__ = '0.1.4'
+__version__ = '0.1.5'
 
 import setuptools