added ctkp and removed outdated KPs and ARAs

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:

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',
 ]

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

tr_sys/tr_ara_ncats/ncats_app.py → 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

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'

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',

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)),