Merge pull request #285 from slr71/main

CORE-2064: fix an error in the app launch view endpoint.

Author: slr71

project.clj

@@ -23,15 +23,15 @@
                  [metosin/compojure-api "1.1.14"]
                  [org.cyverse/async-tasks-client "0.0.5"]
                  [org.cyverse/authy "3.0.1"]
-                 [org.cyverse/clj-kondo-exports "0.1.0-SNAPSHOT"]
+                 [org.cyverse/clj-kondo-exports "0.1.0"]
                  [org.cyverse/clojure-commons "3.0.11"]
                  [org.cyverse/debug-utils "2.9.0"]
                  [org.cyverse/kameleon "3.0.10"]
                  [org.cyverse/mescal "4.1.0"]
                  [org.cyverse/metadata-client "3.1.2"]
                  [org.cyverse/common-cli "2.8.2"]
                  [org.cyverse/common-cfg "2.8.3"]
-                 [org.cyverse/common-swagger-api "3.4.11-SNAPSHOT"]
+                 [org.cyverse/common-swagger-api "3.4.11"]
                  [org.cyverse/cyverse-groups-client "0.1.9"]
                  [org.cyverse/permissions-client "2.8.4"]
                  [org.cyverse/service-logging "2.8.4"]

skaffold.yaml

@@ -1,14 +1,17 @@
-apiVersion: skaffold/v1
+apiVersion: skaffold/v3
 kind: Config
 metadata:
   name: apps
-deploy:
-  kubectl:
-    manifests:
-    - k8s/apps.yml
 build:
+  artifacts:
+    - image: harbor.cyverse.org/de/apps
   tagPolicy:
     gitCommit: {}
-  artifacts:
-  - image: harbor.cyverse.org/de/apps
   local: {}
+  platforms:
+    - linux/amd64
+manifests:
+  rawYaml:
+    - k8s/apps.yml
+deploy:
+  kubectl: {}

src/apps/metadata/params.clj

@@ -2,6 +2,7 @@
   (:require [apps.metadata.reference-genomes :refer [get-reference-genomes-by-id]]
             [apps.persistence.app-metadata :as persistence]
             [apps.util.conversions :as conv]
+            [honey.sql.helpers :as h]
             [kameleon.uuids :refer [uuidify]]
             [korma.core :as sql]))
 
@@ -69,6 +70,25 @@
       (sql/order [:parent_id :display_order])
       (sql/select)))
 
+(defn hsql-params-base-query
+  []
+  (-> (h/select [:p.description    :description]
+                [:p.id             :id]
+                [:p.name           :name]
+                [:p.label          :label]
+                [:p.is_visible     :is_visible]
+                [:p.required       :required]
+                [:p.omit_if_blank  :omit_if_blank]
+                [:p.ordering       :order]
+                [:p.parameter_type :type]
+                :p.retain
+                :p.is_implicit
+                :p.repeat_option_flag
+                :p.info_type
+                :p.data_format
+                :p.data_source)
+      (h/from [:task_param_listing :p])))
+
 (defn params-base-query
   []
   (-> (sql/select* [:task_param_listing :p])

src/apps/service/apps/de/job_view.clj

@@ -11,9 +11,13 @@
    [apps.service.apps.util :refer [paths-accessible?]]
    [apps.util.service :as service]
    [apps.util.config :as config]
+   [apps.util.db :as db]
    [apps.util.conversions :refer [remove-nil-vals]]
+   [clojure.java.jdbc :as jdbc]
    [clojure-commons.exception-util :as cxu]
-   [korma.core :refer [fields join order select subselect where]]
+   [honey.sql :as sql]
+   [honey.sql.helpers :as h]
+   [korma.core :refer [fields join order select where]]
    [slingshot.slingshot :refer [try+ throw+]]))
 
 (defn- format-step-resource-requirements
@@ -33,28 +37,31 @@
 
 (defn- mapped-input-subselect
   [step-id]
-  (subselect [:workflow_io_maps :wm]
-             (join [:input_output_mapping :iom] {:wm.id :iom.mapping_id})
-             (where {:iom.input      :p.id
-                     :wm.target_step step-id})))
-
-(defn- add-hidden-parameters-clause
-  [query include-hidden-params?]
-  (if-not include-hidden-params?
-    (where query {:p.is_visible true})
-    query))
+  (-> (h/select :*)
+      (h/from [:workflow_io_maps :wm])
+      (h/join [:input_output_mapping :iom] [:= :wm.id :iom.mapping_id])
+      (h/where [:and
+                [:= :iom.input :p.id]
+                [:= :wm.target_step step-id]])))
+
+(defn- get-parameters-query
+  [step-id group-id include-hidden-params?]
+  (-> (mp/hsql-params-base-query)
+      (h/order-by :p.display-order)
+      (h/where [:and
+                [:= :p.parameter_group_id group-id]
+                (when include-hidden-params? :p.is_visible)
+                [:and
+                 [:not [:exists (mapped-input-subselect step-id)]]
+                 [:or
+                  [:= :p.value_type "Input"]
+                  [:not [:coalesce :is_implicit false]]]]])
+      (sql/format)))
 
 (defn- get-parameters
-  [step-id group-id include-hidden-params?]
-  (-> (mp/params-base-query)
-      (order :p.display_order)
-      (where {:p.parameter_group_id group-id})
-      (add-hidden-parameters-clause include-hidden-params?)
-      (where (and [:not [:exists (mapped-input-subselect step-id)]]
-                  (or {:value_type  "Input"}
-                      {:is_implicit nil}
-                      {:is_implicit false})))
-      select))
+  [step-id group-id include-hidden-parameters]
+  (db/with-transaction [tx]
+    (jdbc/query tx (get-parameters-query step-id group-id include-hidden-parameters))))
 
 (defn- get-default-value
   [user type values]