diff --git a/config/config.yaml b/config/config.yaml index 9ae667f8..0f441a41 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -14,29 +14,15 @@ httpclients: # https://aragorn.renci.org/1.2 endpoint: asyncquery params: - # MW says aragorn_exp_app is experimental. If so, we don't need a second official infores key. - # https://aragorn.renci.org/query - infores:aragorn-ranker-exp: - method: query - params: infores:arax: endpoint: asyncquery params: infores:biothings-explorer: endpoint: asyncquery params: - infores:explanatory-agent: - endpoint: query - params: - infores:explanatory-agent-creative-mode: - endpoint: asyncquery - params: infores:improving-agent: endpoint: query params: - infores:example: - endpoint: query - params: infores:unsecret-agent: endpoint: query params: @@ -58,14 +44,17 @@ httpclients: infores:genetics-data-provider: endpoint: query params: + infores:multiomics-clinicaltrials: + endpoint: query + params: infores:molepro: endpoint: query params: infores:openpredict: endpoint: query params: - infores:automat-text-mining-provider: - endpoint: query + infores:text-mining-provider-targeted: + endpoint: query params: inactive_clients: diff --git a/config/tr_sys_settings.py b/config/tr_sys_settings.py index ed518323..dca5f4c7 100755 --- a/config/tr_sys_settings.py +++ b/config/tr_sys_settings.py @@ -47,19 +47,17 @@ 'tr_ara_aragorn.aragorn_app.AppConfig', 'tr_ara_arax.arax_app.AppConfig', 'tr_ara_bte.bte_app.AppConfig', - 'tr_ara_explanatory.explanatory_app.AppConfig', - 'tr_ara_explanatory_exp.explanatory_exp_app.AppConfig', 'tr_ara_improving.improving_app.AppConfig', - 'tr_ara_ncats.ncats_app.AppConfig', 'tr_ara_unsecret.unsecret_app.AppConfig', 'tr_ara_wfr.wfr_app.AppConfig', 'tr_kp_genetics.genetics_app.AppConfig', + 'tr_kp_clinical.clinical_app.AppConfig', 'tr_kp_molecular.molecular_app.AppConfig', 'tr_kp_cam.cam_app.AppConfig', 'tr_kp_textmining.textmining_app.AppConfig', 'tr_kp_openpredict.openpredict_app.AppConfig', - 'tr_ara_aragorn_exp.aragorn_exp_app.AppConfig', 'tr_kp_chp.chp_app.AppConfig', + 'tr_kp_cohd.cohd_app.AppConfig', 'django_celery_results', 'markdownify', ] diff --git a/config/url-config-legacy.yaml b/config/url-config-legacy.yaml index a6800dfa..ca12b97d 100644 --- a/config/url-config-legacy.yaml +++ b/config/url-config-legacy.yaml @@ -7,22 +7,18 @@ # url-config-legacy.yaml is not a way for the ARS to avoid a successful request to smart-api.info in order # to be ready to serve requests. -infores:aragorn: https://aragorn.renci.org/1.2 -# MW says aragorn_exp_app is experimental. If so, we don't need a second official infores key. -infores:aragorn-ranker-exp: https://aragorn.renci.org -infores:arax: https://arax.ncats.io/api/arax/v1.2 -infores:biothings-explorer: https://api.bte.ncats.io/v1 -infores:explanatory-agent: https://explanatory-agent.azurewebsites.net/v1.2 -infores:explanatory-agent-creative-mode: https://explanatory-agent-creative.azurewebsites.net/ARA/v1.3 -infores:improving-agent: https://ia.ci.transltr.io/api/v1.3 -infores:example: http://transltr.io:7073 +infores:aragorn: https://aragorn.ci.transltr.io/aragorn +infores:arax: https://arax.ci.transltr.io/api/arax/v1.4 +infores:biothings-explorer: https://bte.ci.transltr.io/v1 +infores:improving-agent: https://ia.ci.transltr.io/api/v1.5/ infores:unsecret-agent: https://medikanren-trapi.ci.transltr.io -infores:workflow-runner: https://translator-workflow-runner.renci.org -infores:cqs: https://cqs-dev.apps.renci.org/v0.2/asyncquery -infores:automat-cam-kp: https://automat.ci.transltr.io/cam-kp/1.4 -infores:connections-hypothesis: http://chp.thayer.dartmouth.edu -infores:cohd: https://cohd.io/api -infores:genetics-data-provider: https://translator.broadinstitute.org/genetics_provider/trapi/v1.1 -infores:molepro: https://translator.broadinstitute.org/molepro/trapi/v1.2 -infores:openpredict: https://openpredict.semanticscience.org -infores:automat-text-mining-provider: https://api.bte.ncats.io/v1/smartapi/978fe380a147a8641caf72320862697b +infores:workflow-runner: https://translator-workflow-runner.ci.transltr.io +infores:cqs: https://cqs.ci.transltr.io +infores:automat-cam-kp: https://automat.ci.transltr.io/cam-kp +infores:connections-hypothesis: https://chp-api.ci.transltr.io +infores:cohd: https://cohd-api.ci.transltr.io/api +infores:genetics-data-provider: https://genetics-kp.ci.transltr.io/genetics_provider/trapi/v1.5 +infores:multiomics-clinicaltrials: https://multiomics.ci.transltr.io/ctkp +infores:molepro: https://molepro-trapi.ci.transltr.io/molepro/trapi/v1.5 +infores:openpredict: https://openpredict.ci.transltr.io +infores:text-mining-provider-targeted: https://biothings.ci.transltr.io/text_mining_targeted_association diff --git a/tr_sys/tr_ara_aragorn_exp/aragorn_exp_app.py b/tr_sys/tr_ara_aragorn_exp/aragorn_exp_app.py deleted file mode 100644 index 7302e0f6..00000000 --- a/tr_sys/tr_ara_aragorn_exp/aragorn_exp_app.py +++ /dev/null @@ -1,24 +0,0 @@ -from tr_ars.default_ars_app.ars_app import AppConfig as ARSAppConfig -from django.urls import path, include -from tr_ars.default_ars_app.api import * - -class AppConfig(ARSAppConfig): - name = 'tr_ara_aragorn_exp.aragorn_exp_app' # must be dot path for module - actors = [make_actorconf('infores:aragorn-ranker-exp', # !!! fictitious inforesid - 'runquery', ['general'], - 'query')] # tuple of remote, name, channel - app_path = 'ara-aragorn-exp' - regex_path = '^' + app_path + '/' - -### code below this line is required, but doesn't require updating in most cases - -apipatterns = [path(r'', init_api_index(AppConfig.actors, AppConfig.app_path), name=AppConfig.app_path + '-api')] -for actor in AppConfig.actors: - query_path = actor.name() - query_name = AppConfig.app_path + '-' + query_path - apipatterns.append(path(query_path, init_api_fn(actor), name=query_name)) - -urlpatterns = [ - path(r'', init_redirect(AppConfig.app_path), name=AppConfig.app_path + '-base'), - path(r'api/', include(apipatterns)), -] diff --git a/tr_sys/tr_ara_explanatory/explanatory_app.py b/tr_sys/tr_ara_explanatory/explanatory_app.py deleted file mode 100644 index a252e4f6..00000000 --- a/tr_sys/tr_ara_explanatory/explanatory_app.py +++ /dev/null @@ -1,26 +0,0 @@ -from tr_ars.default_ars_app.ars_app import AppConfig as ARSAppConfig -from django.urls import path, include -from tr_ars.default_ars_app.api import * - -class AppConfig(ARSAppConfig): - name = 'tr_ara_explanatory.explanatory_app' # must be dot path for module - actors = [make_actorconf('infores:explanatory-agent', - 'runquery', ['general'], - 'query')] # tuple of remote, name, channel - app_path = 'ara-explanatory' - regex_path = '^' + app_path + '/' - -### code below this line is required, but doesn't require updating in most cases - -apipatterns = [path(r'', init_api_index(AppConfig.actors, AppConfig.app_path), name=AppConfig.app_path + '-api')] -for actor in AppConfig.actors: - query_path = actor.name() - query_name = AppConfig.app_path + '-' + query_path - apipatterns.append(path(query_path, init_api_fn(actor), name=query_name)) - -urlpatterns = [ - path(r'', init_redirect(AppConfig.app_path), name=AppConfig.app_path + '-base'), - path(r'api/', include(apipatterns)), -] - - diff --git a/tr_sys/tr_ara_explanatory_exp/explanatory_exp_app.py b/tr_sys/tr_ara_explanatory_exp/explanatory_exp_app.py deleted file mode 100644 index 0b44ed37..00000000 --- a/tr_sys/tr_ara_explanatory_exp/explanatory_exp_app.py +++ /dev/null @@ -1,26 +0,0 @@ -from tr_ars.default_ars_app.ars_app import AppConfig as ARSAppConfig -from django.urls import path, include -from tr_ars.default_ars_app.api import * - -class AppConfig(ARSAppConfig): - name = 'tr_ara_explanatory_exp.explanatory_exp_app' # must be dot path for module - actors = [make_actorconf('infores:explanatory-agent-creative-mode', - 'runquery', ['general'], - 'asyncquery')] # tuple of remote, name, channel - app_path = 'ara-explanatory-exp' - regex_path = '^' + app_path + '/' - -### code below this line is required, but doesn't require updating in most cases - -apipatterns = [path(r'', init_api_index(AppConfig.actors, AppConfig.app_path), name=AppConfig.app_path + '-api')] -for actor in AppConfig.actors: - query_path = actor.name() - query_name = AppConfig.app_path + '-' + query_path - apipatterns.append(path(query_path, init_api_fn(actor), name=query_name)) - -urlpatterns = [ - path(r'', init_redirect(AppConfig.app_path), name=AppConfig.app_path + '-base'), - path(r'api/', include(apipatterns)), -] - - diff --git a/tr_sys/tr_ara_ncats/ncats_app.py b/tr_sys/tr_kp_clinical/clinical_app.py similarity index 71% rename from tr_sys/tr_ara_ncats/ncats_app.py rename to tr_sys/tr_kp_clinical/clinical_app.py index 785fb105..13d45fad 100644 --- a/tr_sys/tr_ara_ncats/ncats_app.py +++ b/tr_sys/tr_kp_clinical/clinical_app.py @@ -3,11 +3,11 @@ from tr_ars.default_ars_app.api import * class AppConfig(ARSAppConfig): - name = 'tr_ara_ncats.ncats_app' # must be dot path for module - actors = [make_actorconf('infores:example', # !!! fictitious inforesid - 'runquery', ['general'], - 'query')] # tuple of remote, name, channel - app_path = 'ara-ncats' + name = 'tr_kp_clinical.clinical_app' # must be dot path for module + actors = [make_actorconf('infores:multiomics-clinicaltrials', + 'runquery', ['general'], + 'query')] # tuple of remote, name, channel + app_path = 'kp-clinical' regex_path = '^' + app_path + '/' ### code below this line is required, but doesn't require updating in most cases diff --git a/tr_sys/tr_kp_textmining/textmining_app.py b/tr_sys/tr_kp_textmining/textmining_app.py index c970272d..9d6f5efb 100644 --- a/tr_sys/tr_kp_textmining/textmining_app.py +++ b/tr_sys/tr_kp_textmining/textmining_app.py @@ -4,7 +4,7 @@ class AppConfig(ARSAppConfig): name = 'tr_kp_textmining.textmining_app' # must be dot path for module - actors = [make_actorconf('infores:automat-text-mining-provider', + actors = [make_actorconf('infores:text-mining-provider-targeted', 'runquery', ['general'], 'query')] # tuple of remote, name, channel app_path = 'kp-textmining' diff --git a/tr_sys/tr_sys/settings.py b/tr_sys/tr_sys/settings.py index 1d800c9c..4c3cb6e2 100644 --- a/tr_sys/tr_sys/settings.py +++ b/tr_sys/tr_sys/settings.py @@ -46,20 +46,17 @@ 'tr_ara_aragorn.aragorn_app.AppConfig', 'tr_ara_arax.arax_app.AppConfig', 'tr_ara_bte.bte_app.AppConfig', - 'tr_ara_explanatory.explanatory_app.AppConfig', - 'tr_ara_explanatory_exp.explanatory_exp_app.AppConfig', 'tr_ara_improving.improving_app.AppConfig', - 'tr_ara_ncats.ncats_app.AppConfig', 'tr_ara_unsecret.unsecret_app.AppConfig', 'tr_ara_wfr.wfr_app.AppConfig', 'tr_ara_cqs.cqs_app.AppConfig', 'tr_kp_genetics.genetics_app.AppConfig', + 'tr_kp_clinical.clinical_app.AppConfig', 'tr_kp_molecular.molecular_app.AppConfig', 'tr_kp_cam.cam_app.AppConfig', 'tr_kp_textmining.textmining_app.AppConfig', 'tr_kp_openpredict.openpredict_app.AppConfig', 'tr_kp_cohd.cohd_app.AppConfig', - 'tr_ara_aragorn_exp.aragorn_exp_app.AppConfig', 'tr_kp_chp.chp_app.AppConfig', 'django_celery_results', 'markdownify', diff --git a/tr_sys/tr_sys/urls.py b/tr_sys/tr_sys/urls.py index 527f450e..3860088f 100644 --- a/tr_sys/tr_sys/urls.py +++ b/tr_sys/tr_sys/urls.py @@ -25,15 +25,12 @@ from tr_ara_aragorn.aragorn_app import AppConfig as AragornApp from tr_ara_arax.arax_app import AppConfig as ARAXApp from tr_ara_bte.bte_app import AppConfig as BTEApp -from tr_ara_explanatory.explanatory_app import AppConfig as ExplanatoryApp from tr_ara_improving.improving_app import AppConfig as ImprovingApp -from tr_ara_ncats.ncats_app import AppConfig as NCATSApp -from tr_ara_aragorn_exp.aragorn_exp_app import AppConfig as AragornExpApp from tr_ara_unsecret.unsecret_app import AppConfig as UnsecretApp from tr_ara_wfr.wfr_app import AppConfig as WfrApp -from tr_ara_explanatory_exp.explanatory_exp_app import AppConfig as ExplanatoryExpApp from tr_ara_cqs.cqs_app import AppConfig as CqsApp from tr_kp_genetics.genetics_app import AppConfig as GeneticsApp +from tr_kp_clinical.clinical_app import AppConfig as ClinicalApp from tr_kp_molecular.molecular_app import AppConfig as MolecularApp from tr_kp_cam.cam_app import AppConfig as CamApp from tr_kp_textmining.textmining_app import AppConfig as TextMiningApp @@ -51,15 +48,12 @@ re_path(AragornApp.regex_path, include(AragornApp.name)), re_path(ARAXApp.regex_path, include(ARAXApp.name)), re_path(BTEApp.regex_path, include(BTEApp.name)), - re_path(ExplanatoryApp.regex_path,include(ExplanatoryApp.name)), - re_path(ExplanatoryExpApp.regex_path, include(ExplanatoryExpApp.name)), re_path(ImprovingApp.regex_path, include(ImprovingApp.name)), - re_path(NCATSApp.regex_path, include(NCATSApp.name)), - re_path(AragornExpApp.regex_path, include(AragornExpApp.name)), re_path(WfrApp.regex_path, include(WfrApp.name)), re_path(CqsApp.regex_path, include(CqsApp.name)), re_path(UnsecretApp.regex_path, include(UnsecretApp.name)), re_path(GeneticsApp.regex_path, include(GeneticsApp.name)), + re_path(ClinicalApp.regex_path, include(ClinicalApp.name)), re_path(MolecularApp.regex_path, include(MolecularApp.name)), re_path(CamApp.regex_path, include(CamApp.name)), re_path(TextMiningApp.regex_path, include(TextMiningApp.name)),