From 52167a78471a14cf4bb01af52d433604eeb52e78 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 14 Apr 2022 16:11:07 +0200
Subject: [PATCH 1/9] Fix collection `populated_state` error check

The backend returns `failed` and not `error` as `populated_state`
---
 client/src/mvc/history/job-states-model.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/src/mvc/history/job-states-model.js b/client/src/mvc/history/job-states-model.js
index 167650dd339..f6d52f16f87 100644
--- a/client/src/mvc/history/job-states-model.js
+++ b/client/src/mvc/history/job-states-model.js
@@ -7,6 +7,7 @@ var UPDATE_DELAY = 2000;
 var NON_TERMINAL_STATES = ["new", "queued", "running", "waiting"];
 var ERROR_STATES = ["error", "deleted"];
 var TERMINAL_STATES = ["ok"].concat(ERROR_STATES);
+const POPULATED_STATE_FAILED = "failed";
 /** Fetch state on add or just wait for polling to start. */
 var FETCH_STATE_ON_ADD = false;
 var BATCH_FETCH_STATE = true;
@@ -27,7 +28,7 @@ var JobStatesSummary = Backbone.Model.extend({
     },
 
     errored: function () {
-        return this.get("populated_state") === "error" || this.anyWithStates(ERROR_STATES);
+        return this.get("populated_state") === POPULATED_STATE_FAILED || this.anyWithStates(ERROR_STATES);
     },
 
     states: function () {

From f5d96e8aa69df9279453758e9b3cf511257a8b54 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 14 Apr 2022 16:55:31 +0200
Subject: [PATCH 2/9] Fix collection error message rendering

- Display `populated_state_message` as description when the populated_state is `failed`
---
 client/src/components/JobStates/CollectionJobStates.vue | 5 ++++-
 client/src/components/JobStates/mixin.js                | 3 +++
 client/src/mvc/history/job-states-model.js              | 6 +++++-
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/client/src/components/JobStates/CollectionJobStates.vue b/client/src/components/JobStates/CollectionJobStates.vue
index cf001d77e4f..c1b211148ca 100644
--- a/client/src/components/JobStates/CollectionJobStates.vue
+++ b/client/src/components/JobStates/CollectionJobStates.vue
@@ -1,5 +1,5 @@
 <template>
-    <div v-if="!jobSourceType || jobSourceType == 'Job' || isTerminal">
+    <div v-if="!jobSourceType || jobSourceType == 'Job' || (isTerminal && !isErrored)">
         {{ simpleDescription }}
     </div>
     <div v-else-if="!jobStatesSummary || !jobStatesSummary.hasDetails()">
@@ -52,6 +52,9 @@ export default {
             return DC_VIEW.collectionDescription(this.collection);
         },
         errorDescription() {
+            if (this.isPopulationFailed) {
+                return `${this.collection.get("populated_state_message")}`;
+            }
             var jobCount = this.jobCount;
             var errorCount = this.jobStatesSummary.numInError();
             return `a ${this.collectionTypeDescription} with ${errorCount} / ${jobCount} jobs in error`;
diff --git a/client/src/components/JobStates/mixin.js b/client/src/components/JobStates/mixin.js
index 320d08e08ca..8495912e582 100644
--- a/client/src/components/JobStates/mixin.js
+++ b/client/src/components/JobStates/mixin.js
@@ -7,6 +7,9 @@ export default {
         isErrored() {
             return this.jobStatesSummary && this.jobStatesSummary.errored();
         },
+        isPopulationFailed() {
+            return this.jobStatesSummary && this.jobStatesSummary.populationFailed();
+        },
         isTerminal() {
             return this.jobStatesSummary && this.jobStatesSummary.terminal();
         },
diff --git a/client/src/mvc/history/job-states-model.js b/client/src/mvc/history/job-states-model.js
index f6d52f16f87..c330962eed6 100644
--- a/client/src/mvc/history/job-states-model.js
+++ b/client/src/mvc/history/job-states-model.js
@@ -27,8 +27,12 @@ var JobStatesSummary = Backbone.Model.extend({
         return !this.hasDetails() || this.get("populated_state") == "new";
     },
 
+    populationFailed: function () {
+        return this.get("populated_state") === POPULATED_STATE_FAILED;
+    },
+
     errored: function () {
-        return this.get("populated_state") === POPULATED_STATE_FAILED || this.anyWithStates(ERROR_STATES);
+        return this.populationFailed() || this.anyWithStates(ERROR_STATES);
     },
 
     states: function () {

From 1b36d16f058df31a2b5afede4c39e9794827fe9f Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 14 Apr 2022 20:08:32 +0200
Subject: [PATCH 3/9] Display population error in collection panel

---
 client/src/mvc/collection/collection-view.js | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/client/src/mvc/collection/collection-view.js b/client/src/mvc/collection/collection-view.js
index 07467adf885..13b10d5e0c1 100644
--- a/client/src/mvc/collection/collection-view.js
+++ b/client/src/mvc/collection/collection-view.js
@@ -62,11 +62,16 @@ var CollectionView = _super.extend(
         },
 
         handleWarning: function ($newRender) {
+            var $warns = $newRender.find(".elements-warning");
+            if (this.model.get("populated_state") === "failed") {
+                var error = _l(`${this.model.get("populated_state_message")}`);
+                $warns.html(`<div class="errormessagesmall">${error}</div>`);
+                return;
+            }
             var viewLength = this.views.length;
             var elementCount = this.model.get("element_count");
             if (elementCount && elementCount !== viewLength) {
                 var warning = _l(`displaying only ${viewLength} of ${elementCount} items`);
-                var $warns = $newRender.find(".elements-warning");
                 $warns.html(`<div class="warningmessagesmall">${warning}</div>`);
             }
         },

From d33b563463250e6508dba7ae0f7a37331505726f Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 14 Apr 2022 20:10:37 +0200
Subject: [PATCH 4/9] Simulate errored datasets when collection population
 fails

This is a temporal hack for the legacy history panel. It needs to be correctly handled in the new history.
---
 client/src/mvc/collection/collection-model.js | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/client/src/mvc/collection/collection-model.js b/client/src/mvc/collection/collection-model.js
index 56135897264..8c70bf2ce79 100644
--- a/client/src/mvc/collection/collection-model.js
+++ b/client/src/mvc/collection/collection-model.js
@@ -252,6 +252,15 @@ var DatasetCollection = Backbone.Model.extend(BASE_MVC.LoggableMixin)
                     _.extend(element, {
                         parent_hdca_id: parentHdcaId,
                     });
+
+                    // Warning: MEGA-hack ahead...
+                    if (!element.element_type && !element.object) {
+                        // The DCE has to be in error state... so we simulate it
+                        _.extend(element, {
+                            element_type: "hda",
+                            object: { state: "error" },
+                        });
+                    }
                 });
                 this.elements = new collectionClass(elements);
                 //this.debug( 'collectionClass:', this.collectionClass + '', this.elements );

From b621f83d0e2d8aec633b00bd838dc0b6ba1c80bd Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 19 Apr 2022 11:38:44 -0400
Subject: [PATCH 5/9] Update python-irodsclient

---
 lib/galaxy/dependencies/conditional-requirements.txt | 2 +-
 lib/galaxy/dependencies/dev-requirements.txt         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index f54da1cda7a..3015911d40b 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -8,7 +8,7 @@ drmaa
 statsd
 docker
 azure-storage==0.32.0
-python-irodsclient==1.0.0
+python-irodsclient==1.1.3
 python-ldap==3.4.0
 python-pam
 galaxycloudrunner
diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index e809b654c97..6d5ed71b927 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -152,7 +152,7 @@ pytest-pythonpath==0.7.3
 pytest-shard==0.1.2; python_version >= "3.6"
 pytest==6.2.5; python_version >= "3.6"
 python-dateutil==2.8.2; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.3.0"
-python-irodsclient==1.1.0
+python-irodsclient==1.1.3
 python-jose==3.3.0
 python-multipart==0.0.5
 python3-openid==3.2.0; python_version >= "3.0"

From e83a691293324b93363d9686a24622686a97d760 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 19 Apr 2022 11:38:44 -0400
Subject: [PATCH 6/9] Update python-irodsclient

---
 lib/galaxy/dependencies/conditional-requirements.txt | 2 +-
 lib/galaxy/dependencies/dev-requirements.txt         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index f54da1cda7a..3015911d40b 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/lib/galaxy/dependencies/conditional-requirements.txt
@@ -8,7 +8,7 @@ drmaa
 statsd
 docker
 azure-storage==0.32.0
-python-irodsclient==1.0.0
+python-irodsclient==1.1.3
 python-ldap==3.4.0
 python-pam
 galaxycloudrunner
diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 30a5ce95516..36425698bf4 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -158,7 +158,7 @@ pytest-pythonpath==0.7.3
 pytest-shard==0.1.2; python_version >= "3.6"
 pytest==6.2.5; python_version >= "3.6"
 python-dateutil==2.8.2; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.3.0"
-python-irodsclient==1.1.0
+python-irodsclient==1.1.3
 python-jose==3.3.0
 python-multipart==0.0.5
 python3-openid==3.2.0; python_version >= "3.0"

From 99025c770b5d71a4d37176dd0889a768b2d7950f Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Tue, 12 Apr 2022 13:24:55 +0200
Subject: [PATCH 7/9] Fix mypy error

---
 lib/galaxy/util/bool_expressions.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/util/bool_expressions.py b/lib/galaxy/util/bool_expressions.py
index 488e8687849..14fb641225b 100644
--- a/lib/galaxy/util/bool_expressions.py
+++ b/lib/galaxy/util/bool_expressions.py
@@ -14,7 +14,6 @@ from typing import (
 from pyparsing import (
     alphanums,
     CaselessKeyword,
-    Forward,
     infixNotation,
     Keyword,
     opAssoc,
@@ -132,7 +131,7 @@ class BooleanExpressionEvaluator:
         action.evaluator = evaluator
         boolOperand = TRUE | FALSE | Word(token_format or DEFAULT_TOKEN_FORMAT)
         boolOperand.setParseAction(action)
-        self.boolExpr: Forward = infixNotation(
+        self.boolExpr = infixNotation(
             boolOperand,
             [
                 (NOT_OP, 1, opAssoc.RIGHT, BoolNot),

From 5e8eea67593e33e903e49e58d35566d0478b5e2c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20L=C3=B3pez?=
 <46503462+davelopez@users.noreply.github.com>
Date: Tue, 12 Apr 2022 13:42:57 +0200
Subject: [PATCH 8/9] Add type hint suggestion

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 lib/galaxy/util/bool_expressions.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/util/bool_expressions.py b/lib/galaxy/util/bool_expressions.py
index 14fb641225b..162ca0f8562 100644
--- a/lib/galaxy/util/bool_expressions.py
+++ b/lib/galaxy/util/bool_expressions.py
@@ -131,7 +131,7 @@ class BooleanExpressionEvaluator:
         action.evaluator = evaluator
         boolOperand = TRUE | FALSE | Word(token_format or DEFAULT_TOKEN_FORMAT)
         boolOperand.setParseAction(action)
-        self.boolExpr = infixNotation(
+        self.boolExpr: ParserElement = infixNotation(
             boolOperand,
             [
                 (NOT_OP, 1, opAssoc.RIGHT, BoolNot),

From 5dcb129490befd8a479e7af996ecb52b90c56d60 Mon Sep 17 00:00:00 2001
From: Kaivan Kamali <kxk302@psu.edu>
Date: Tue, 19 Apr 2022 14:50:59 -0400
Subject: [PATCH 9/9] Added exist_ok flag so creating an directory that already
 exists does not error out

---
 lib/galaxy/objectstore/irods.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/objectstore/irods.py b/lib/galaxy/objectstore/irods.py
index 57cf93c082f..8b03563aff4 100644
--- a/lib/galaxy/objectstore/irods.py
+++ b/lib/galaxy/objectstore/irods.py
@@ -336,7 +336,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         # Ensure the cache directory structure exists (e.g., dataset_#_files/)
         rel_path_dir = os.path.dirname(rel_path)
         if not os.path.exists(self._get_cache_path(rel_path_dir)):
-            os.makedirs(self._get_cache_path(rel_path_dir))
+            os.makedirs(self._get_cache_path(rel_path_dir), exist_ok=True)
         # Now pull in the file
         file_ok = self._download(rel_path)
         self._fix_permissions(self._get_cache_path(rel_path_dir))
@@ -461,7 +461,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
         if dir_only and base_dir:
             # for JOB_WORK directory
             if not os.path.exists(rel_path):
-                os.makedirs(rel_path)
+                os.makedirs(rel_path, exist_ok=True)
             log.debug("irods_pt _exists: %s", ipt_timer)
             return True
         log.debug("irods_pt _exists: %s", ipt_timer)
@@ -489,7 +489,7 @@ class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
             # Create given directory in cache
             cache_dir = os.path.join(self.staging_path, rel_path)
             if not os.path.exists(cache_dir):
-                os.makedirs(cache_dir)
+                os.makedirs(cache_dir, exist_ok=True)
 
             if not dir_only:
                 rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")