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Merge pull request #25 from medizininformatik-initiative/add-activity…
…-definition-query Add activity definition query
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,216 @@ | ||
| from prettytable import PrettyTable | ||
| import requests | ||
| import logging | ||
| import csv | ||
|
|
||
| process_name_to_plugin_map = { | ||
| "Report Autostart": "mii-process-report", | ||
| "Report Send": "mii-process-report", | ||
| "Report Receive": "mii-process-report", | ||
| "FeasibilityRequest": "mii-process-feasibility", | ||
| "ExecuteFeasibility": "mii-process-feasibility", | ||
| "dataSend": "mii-process-data-transfer", | ||
| "dataReceive": "mii-process-data-transfer", | ||
| "Ping": "dsf-process-ping-pong", | ||
| "Pong": "dsf-process-ping-pong", | ||
| "PingAutostart": "dsf-process-ping-pong", | ||
| "DownloadAllowList": "dsf-process-allowlist", | ||
| "UpdateAllowList": "dsf-process-allowlist", | ||
| } | ||
|
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||
|
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| def get_next_link(link_elem): | ||
| for elem in link_elem: | ||
| if elem["relation"] == "next": | ||
| return elem["url"] | ||
|
|
||
| return None | ||
|
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|
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| def page_through_results_and_collect(resp, dsf_cert_path, dsf_key_path): | ||
|
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| result_entry = [] | ||
|
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| if resp.status_code != 200: | ||
| return result_entry | ||
|
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| next_link = get_next_link(resp.json()["link"]) | ||
| if "entry" not in resp.json().keys(): | ||
| return result_entry | ||
| if len(resp.json()["entry"]) > 0: | ||
| result_entry = result_entry + resp.json()["entry"] | ||
|
|
||
| if next_link: | ||
| logging.debug(f"Getting next page {next_link}") | ||
| resp = requests.get(next_link, cert=(dsf_cert_path, dsf_key_path)) | ||
| if "entry" not in resp.json().keys(): | ||
| return result_entry | ||
|
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||
| return result_entry + page_through_results_and_collect(resp, dsf_cert_path, dsf_key_path) | ||
|
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| return result_entry | ||
|
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|
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| def convert_process_info_to_process_name(process): | ||
| return f"{process['plugin']}|{process['name']}|{process['version']}" | ||
|
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| def create_results_table(activity_information): | ||
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| process_list = [] | ||
|
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| for site_ident in activity_information.keys(): | ||
| site_info = activity_information[site_ident] | ||
|
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| for process in site_info["installedProcesses"]: | ||
|
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| process_name_version = convert_process_info_to_process_name(process) | ||
|
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| if process_name_version not in process_list: | ||
| process_list.append(process_name_version) | ||
|
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| process_list_overall = [0] * len(process_list) | ||
| site_process_lists = [] | ||
|
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| process_list = sorted(process_list) | ||
|
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| for site_ident in activity_information.keys(): | ||
| site_info = activity_information[site_ident] | ||
| site_process_list = [0] * len(process_list) | ||
|
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| for process_index in range(0, len(process_list)): | ||
|
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| process = process_list[process_index] | ||
| for installed_process in site_info["installedProcesses"]: | ||
|
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| process_name_version = convert_process_info_to_process_name(installed_process) | ||
|
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| if process == process_name_version: | ||
| site_process_list[process_index] = 1 | ||
| process_list_overall[process_index] = process_list_overall[process_index] + 1 | ||
| break | ||
|
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| site_process_lists.append([site_ident] + site_process_list) | ||
|
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| table = [] | ||
|
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| table.append(["Site Identifier"] + process_list) | ||
| table.append(["Overall"] + process_list_overall) | ||
|
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| for site_process_list in site_process_lists: | ||
| table.append(site_process_list) | ||
|
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| return table | ||
|
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|
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| def map_process_name_to_plugin(process_name): | ||
|
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| if process_name not in process_name_to_plugin_map: | ||
| return "unknown-process" | ||
| else: | ||
| return process_name_to_plugin_map[process_name] | ||
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|
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| def create_activity_list_and_add_to_org( | ||
| organization_list, organization, endpoint, activity_definitions | ||
| ): | ||
| activity_definition_list = [] | ||
|
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| for activity_definition in activity_definitions: | ||
|
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| activity_definition = activity_definition["resource"] | ||
|
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| if "url" not in activity_definition: | ||
| logging.error(f"ERROR - broken activity defnition in endpoint {endpoint}") | ||
| continue | ||
|
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| activity_definition_list.append( | ||
| { | ||
| "url": activity_definition["url"], | ||
| "name": activity_definition["name"], | ||
| "plugin": map_process_name_to_plugin(activity_definition["name"]), | ||
| "version": activity_definition["version"], | ||
| "status": activity_definition["status"], | ||
| } | ||
| ) | ||
|
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| organization_list[organization["resource"]["identifier"][0]["value"]] = { | ||
| "endpoint": endpoint, | ||
| "installedProcesses": activity_definition_list, | ||
| } | ||
|
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|
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| def generate_activity_list_for_orgs( | ||
| organization_list, organizations, dsf_base_url, dsf_cert_path, dsf_key_path | ||
| ): | ||
| for organization in organizations: | ||
|
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| org_ident = organization["resource"]["identifier"][0]["value"] | ||
|
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| if "endpoint" not in organization["resource"]: | ||
| continue | ||
|
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| endpoint = requests.get( | ||
| f'{dsf_base_url}/{organization["resource"]["endpoint"][0]["reference"]}?_format=json', | ||
| cert=(dsf_cert_path, dsf_key_path), | ||
| ).json()["address"] | ||
|
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| logging.info(f"Querying endpoint: {endpoint} for org: {org_ident}") | ||
|
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| try: | ||
| activity_def_req_res = requests.get( | ||
| f"{endpoint}/ActivityDefinition?_format=json", | ||
| cert=(dsf_cert_path, dsf_key_path), | ||
| timeout=10, | ||
| ) | ||
| activity_definitions = page_through_results_and_collect( | ||
| activity_def_req_res, dsf_cert_path, dsf_key_path | ||
| ) | ||
|
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||
| except requests.exceptions.RequestException: | ||
| logging.debug(f"Could not connect to endpoint {endpoint}") | ||
| organization_list[org_ident] = { | ||
| "endpoint": endpoint, | ||
| "installedProcesses": [], | ||
| "errors": [ | ||
| { | ||
| "code": "connection-error", | ||
| "display": "Could not connect to endpoint", | ||
| } | ||
| ], | ||
| } | ||
|
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| continue | ||
|
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| create_activity_list_and_add_to_org( | ||
| organization_list, organization, endpoint, activity_definitions | ||
| ) | ||
|
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|
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| def save_results_to_disk(table): | ||
|
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| with open("reports/dsf_installed_plugins.csv", "w", newline="") as csvfile: | ||
| writer = csv.writer(csvfile, delimiter=";", quotechar='"', quoting=csv.QUOTE_MINIMAL) | ||
|
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| for row in table: | ||
| writer.writerow(row) | ||
|
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|
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| def execute_collect_activity_definitions(dsf_base_url, dsf_cert_path, dsf_key_path): | ||
|
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| organization_list = {} | ||
| organizations_req_res = requests.get( | ||
| f"{dsf_base_url}/Organization?_format=json", | ||
| cert=(dsf_cert_path, dsf_key_path), | ||
| timeout=20, | ||
| ) | ||
| organizations = page_through_results_and_collect( | ||
| organizations_req_res, dsf_cert_path, dsf_key_path | ||
| ) | ||
|
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||
| generate_activity_list_for_orgs( | ||
| organization_list, organizations, dsf_base_url, dsf_cert_path, dsf_key_path | ||
| ) | ||
| sorted_orgs_list = dict(sorted(organization_list.items())) | ||
| table = create_results_table(sorted_orgs_list) | ||
| save_results_to_disk(table) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
| from prettytable import PrettyTable | ||
| import requests | ||
| import logging | ||
| import csv | ||
| import json | ||
|
|
||
|
|
||
| def get_next_link(link_elem): | ||
| for elem in link_elem: | ||
| if elem["relation"] == "next": | ||
| return elem["url"] | ||
|
|
||
| return None | ||
|
|
||
|
|
||
| def page_through_results_and_collect(resp, dsf_cert_path, dsf_key_path): | ||
|
|
||
| result_entry = [] | ||
|
|
||
| if resp.status_code != 200: | ||
| return result_entry | ||
|
|
||
| next_link = get_next_link(resp.json()["link"]) | ||
| if "entry" not in resp.json().keys(): | ||
| return result_entry | ||
| if len(resp.json()["entry"]) > 0: | ||
| result_entry = result_entry + resp.json()["entry"] | ||
|
|
||
| if next_link: | ||
| logging.debug(f"Getting next page {next_link}") | ||
| resp = requests.get(next_link, cert=(dsf_cert_path, dsf_key_path)) | ||
| if "entry" not in resp.json().keys(): | ||
| return result_entry | ||
|
|
||
| return result_entry + page_through_results_and_collect(resp, dsf_cert_path, dsf_key_path) | ||
|
|
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| return result_entry | ||
|
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|
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| def create_results_table(reports): | ||
|
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| table = [] | ||
|
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| table.append(["Site Identifier", "Last Report"]) | ||
|
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| for site_ident in reports.keys(): | ||
| table.append([site_ident, reports[site_ident]]) | ||
|
|
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| return table | ||
|
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|
|
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| def save_results_to_disk(table): | ||
|
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| with open("reports/last_kds_reports.csv", "w", newline="") as csvfile: | ||
| writer = csv.writer(csvfile, delimiter=";", quotechar='"', quoting=csv.QUOTE_MINIMAL) | ||
|
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| for row in table: | ||
| writer.writerow(row) | ||
|
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|
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| def execute_collect_report_overview(dsf_base_url, dsf_cert_path, dsf_key_path): | ||
|
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| report_list = {} | ||
| report_req_res = requests.get( | ||
| f"{dsf_base_url}/Bundle?_format=json&_profile=http://medizininformatik-initiative.de/fhir/Bundle/search-bundle-response-report|1.0", | ||
| cert=(dsf_cert_path, dsf_key_path), | ||
| timeout=20, | ||
| ) | ||
|
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| print(report_req_res.status_code) | ||
|
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| reports = page_through_results_and_collect( | ||
| report_req_res, dsf_cert_path, dsf_key_path | ||
| ) | ||
|
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| for report in reports: | ||
| report_list[report['resource']['identifier']['value']] = report['resource']['meta']['lastUpdated'][0:10] | ||
|
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| results_table = create_results_table(report_list) | ||
| save_results_to_disk(results_table) | ||
|
|
||
| print(json.dumps(report_list)) |
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