Merge branch 'release_23.2' into dev

client/src/components/History/CurrentHistory/HistoryOperations/SelectionOperations.vue

@@ -91,6 +91,7 @@
             id="change-dbkey-of-selected-content"
             title="Change Database/Build?"
             title-tag="h2"
+            body-class="modal-with-selector"
             @ok="changeDbkeyOfSelected">
             <p v-localize>Select a new Database/Build for {{ numSelected }} items:</p>
             <DbKeyProvider v-slot="{ item: dbkeys, loading: loadingDbKeys }">
@@ -99,14 +100,14 @@
                     :loading="loadingDbKeys"
                     :items="dbkeys"
                     :current-item-id="selectedDbKey"
-                    class="mb-5 pb-5"
                     @update:selected-item="onSelectedDbKey" />
             </DbKeyProvider>
         </b-modal>
         <b-modal
             id="change-datatype-of-selected-content"
             title="Change data type?"
             title-tag="h2"
+            body-class="modal-with-selector"
             :ok-disabled="selectedDatatype == null"
             @ok="changeDatatypeOfSelected">
             <p v-localize>Select a new data type for {{ numSelected }} items:</p>
@@ -116,7 +117,6 @@
                     :loading="loadingDatatypes"
                     :items="datatypes"
                     :current-item-id="selectedDatatype"
-                    class="mb-5 pb-5"
                     @update:selected-item="onSelectedDatatype" />
             </DatatypesProvider>
         </b-modal>
@@ -347,3 +347,9 @@ export default {
     },
 };
 </script>
+
+<style>
+.modal-with-selector {
+    overflow: initial;
+}
+</style>

client/src/components/Panels/utilities.ts

@@ -158,22 +158,13 @@ export function getValidToolsInCurrentView(
     isWorkflowPanel = false,
     excludedSectionIds: string[] = []
 ) {
-    const addedToolTexts: string[] = [];
     const toolEntries = Object.entries(toolsById).filter(([, tool]) => {
-        // filter out duplicate tools (different ids, same exact name+description)
-        // related ticket: https://github.com/galaxyproject/galaxy/issues/16145
-        const toolText = tool.name + tool.description;
-        if (addedToolTexts.includes(toolText)) {
-            return false;
-        } else {
-            addedToolTexts.push(toolText);
-        }
         // filter on non-hidden, non-disabled, and workflow compatibile (based on props.workflow)
         return (
             !tool.hidden &&
             tool.disabled !== true &&
             !(isWorkflowPanel && !tool.is_workflow_compatible) &&
-            !excludedSectionIds.includes(tool.panel_section_id || "")
+            !excludedSectionIds.includes(tool.panel_section_id)
         );
     });
     return Object.fromEntries(toolEntries);

client/src/components/Upload/UploadModal.vue

@@ -101,6 +101,6 @@ defineExpose({
 
 .upload-dialog-body {
     height: 500px;
-    overflow: hidden;
+    overflow: initial;
 }
 </style>

client/src/components/WorkflowInvocationState/WorkflowInvocationSummary.vue

@@ -2,11 +2,19 @@
     <div class="mb-3 workflow-invocation-state-component">
         <div v-if="invocationAndJobTerminal">
             <span>
-                <b-button v-b-tooltip.hover size="sm" class="invocation-report-link" :href="invocationLink">
+                <b-button
+                    v-b-tooltip.hover
+                    :title="invocationStateSuccess ? reportTooltip : disabledReportTooltip"
+                    :disabled="!invocationStateSuccess"
+                    size="sm"
+                    class="invocation-report-link"
+                    :href="invocationLink">
                     View Report
                 </b-button>
                 <b-button
                     v-b-tooltip.hover
+                    :title="invocationStateSuccess ? generatePdfTooltip : disabledReportTooltip"
+                    :disabled="!invocationStateSuccess"
                     size="sm"
                     class="invocation-pdf-link"
                     :href="invocationPdfLink"
@@ -109,6 +117,8 @@ export default {
         return {
             stepStatesInterval: null,
             jobStatesInterval: null,
+            reportTooltip: "View report for this workflow invocation",
+            generatePdfTooltip: "Generate PDF report for this workflow invocation",
         };
     },
     computed: {
@@ -126,6 +136,28 @@ export default {
         invocationState: function () {
             return this.invocation?.state || "new";
         },
+        invocationStateSuccess: function () {
+            return this.invocationState == "scheduled" && this.runningCount === 0 && this.invocationAndJobTerminal;
+        },
+        disabledReportTooltip: function () {
+            const state = this.invocationState;
+            const runCount = this.runningCount;
+            if (this.invocationState != "scheduled") {
+                return (
+                    "This workflow is not currently scheduled. The current state is ",
+                    state,
+                    ". Once the workflow is fully scheduled and jobs have complete this option will become available."
+                );
+            } else if (runCount != 0) {
+                return (
+                    "The workflow invocation still contains ",
+                    runCount,
+                    " running job(s). Once these jobs have completed this option will become available. "
+                );
+            } else {
+                return "Steps for this workflow are still running. A report will be available once complete.";
+            }
+        },
         stepCount: function () {
             return this.invocation?.steps.length;
         },

client/src/stores/toolStore.ts

@@ -27,7 +27,7 @@ export interface Tool {
     link: string;
     min_width: number;
     target: string;
-    panel_section_id: string | null;
+    panel_section_id: string;
     panel_section_name: string | null;
     form_style: string;
     disabled?: boolean;

lib/galaxy/job_metrics/instrumenters/cgroup.py

@@ -1,4 +1,5 @@
 """The module describes the ``cgroup`` job metrics plugin."""
+import decimal
 import logging
 import numbers
 from collections import namedtuple
@@ -17,7 +18,27 @@
 
 log = logging.getLogger(__name__)
 
+VALID_VERSIONS = ("auto", "1", "2")
+DEFAULT_PARAMS = (
+    # cgroupsv1 - this is probably more params than are useful to collect, but don't remove any for legacy reasons
+    "memory.memsw.max_usage_in_bytes",
+    "memory.max_usage_in_bytes",
+    "memory.limit_in_bytes",
+    "memory.memsw.limit_in_bytes",
+    "memory.soft_limit_in_bytes",
+    "memory.failcnt",
+    "memory.oom_control.oom_kill_disable",
+    "memory.oom_control.under_oom",
+    "cpuacct.usage",
+    # cgroupsv2
+    "memory.events.oom_kill",
+    "memory.peak",
+    "cpu.stat.system_usec",
+    "cpu.stat.usage_usec",
+    "cpu.stat.user_usec",
+)
 TITLES = {
+    # cgroupsv1
     "memory.memsw.max_usage_in_bytes": "Max memory usage (MEM+SWP)",
     "memory.max_usage_in_bytes": "Max memory usage (MEM)",
     "memory.limit_in_bytes": "Memory limit on cgroup (MEM)",
@@ -27,14 +48,35 @@
     "memory.oom_control.oom_kill_disable": "OOM Control enabled",
     "memory.oom_control.under_oom": "Was OOM Killer active?",
     "cpuacct.usage": "CPU Time",
+    # cgroupsv2
+    "memory.events.low": "Number of times the cgroup was reclaimed due to high memory pressure even though its usage is under the low "
+    "boundary",
+    "memory.events.high": "Number of times processes of the cgroup were throttled and routed to perform direct memory reclaim because "
+    "the high memory boundary was exceeded",
+    "memory.events.max": "Number of times the cgroup's memory usage was about to go over the max boundary",
+    "memory.events.oom": "Number of time the cgroup's memory usage reached the limit and allocation was about to fail",
+    "memory.events.oom_kill": "Number of processes belonging to this cgroup killed by any kind of OOM killer",
+    "memory.events.oom_group_kill": "Number of times a group OOM has occurred",
+    "memory.high": "Memory usage throttle limit",
+    "memory.low": "Best-effort memory protection",
+    "memory.max": "Memory usage hard limit",
+    "memory.min": "Hard memory protection",
+    "memory.peak": "Max memory usage recorded",
+    "cpu.stat.system_usec": "CPU system time",
+    "cpu.stat.usage_usec": "CPU usage time",
+    "cpu.stat.user_usec": "CPU user time",
 }
 CONVERSION = {
     "memory.oom_control.oom_kill_disable": lambda x: "No" if x == 1 else "Yes",
     "memory.oom_control.under_oom": lambda x: "Yes" if x == 1 else "No",
+    "memory.peak": lambda x: nice_size(x),
     "cpuacct.usage": lambda x: formatting.seconds_to_str(x / 10**9),  # convert nanoseconds
+    "cpu.stat.system_usec": lambda x: formatting.seconds_to_str(x / 10**6),  # convert microseconds
+    "cpu.stat.usage_usec": lambda x: formatting.seconds_to_str(x / 10**6),  # convert microseconds
+    "cpu.stat.user_usec": lambda x: formatting.seconds_to_str(x / 10**6),  # convert microseconds
 }
-CPU_USAGE_TEMPLATE = r"""
-if [ -e "/proc/$$/cgroup" -a -d "{cgroup_mount}" ]; then
+CGROUPSV1_TEMPLATE = r"""
+if [ -e "/proc/$$/cgroup" -a -d "{cgroup_mount}" -a ! -f "{cgroup_mount}/cgroup.controllers" ]; then
     cgroup_path=$(cat "/proc/$$/cgroup" | awk -F':' '($2=="cpuacct,cpu") || ($2=="cpu,cpuacct") {{print $3}}');
     if [ ! -e "{cgroup_mount}/cpu$cgroup_path/cpuacct.usage" ]; then
         cgroup_path="";
@@ -44,12 +86,6 @@
             echo "__$(basename $f)__" >> {metrics}; cat "$f" >> {metrics} 2>/dev/null;
         fi;
     done;
-fi
-""".replace(
-    "\n", " "
-).strip()
-MEMORY_USAGE_TEMPLATE = """
-if [ -e "/proc/$$/cgroup" -a -d "{cgroup_mount}" ]; then
     cgroup_path=$(cat "/proc/$$/cgroup" | awk -F':' '$2=="memory"{{print $3}}');
     if [ ! -e "{cgroup_mount}/memory$cgroup_path/memory.max_usage_in_bytes" ]; then
         cgroup_path="";
@@ -61,6 +97,16 @@
 """.replace(
     "\n", " "
 ).strip()
+CGROUPSV2_TEMPLATE = r"""
+if [ -e "/proc/$$/cgroup" -a -f "{cgroup_mount}/cgroup.controllers" ]; then
+    cgroup_path=$(cat "/proc/$$/cgroup" | awk -F':' '($1=="0") {{print $3}}');
+    for f in {cgroup_mount}/${{cgroup_path}}/{{cpu,memory}}.*; do
+        echo "__$(basename $f)__" >> {metrics}; cat "$f" >> {metrics} 2>/dev/null;
+    done;
+fi
+""".replace(
+    "\n", " "
+).strip()
 
 
 Metric = namedtuple("Metric", ("key", "subkey", "value"))
@@ -76,7 +122,7 @@ def format(self, key, value):
                 return title, nice_size(value)
             except ValueError:
                 pass
-        elif isinstance(value, (numbers.Integral, numbers.Real)) and value == int(value):
+        elif isinstance(value, (decimal.Decimal, numbers.Integral, numbers.Real)) and value == int(value):
             value = int(value)
         return title, value
 
@@ -90,33 +136,36 @@ class CgroupPlugin(InstrumentPlugin):
     def __init__(self, **kwargs):
         self.verbose = asbool(kwargs.get("verbose", False))
         self.cgroup_mount = kwargs.get("cgroup_mount", "/sys/fs/cgroup")
+        self.version = str(kwargs.get("version", "auto"))
+        assert self.version in VALID_VERSIONS, f"cgroup metric version option must be one of {VALID_VERSIONS}"
         params_str = kwargs.get("params", None)
         if isinstance(params_str, list):
             params = params_str
         elif params_str:
             params = [v.strip() for v in params_str.split(",")]
         else:
-            params = list(TITLES.keys())
+            params = list(DEFAULT_PARAMS)
         self.params = params
 
     def post_execute_instrument(self, job_directory: str) -> List[str]:
         commands: List[str] = []
-        commands.append(self.__record_cgroup_cpu_usage(job_directory))
-        commands.append(self.__record_cgroup_memory_usage(job_directory))
+        if self.version in ("auto", "1"):
+            commands.append(self.__record_cgroup_v1_usage(job_directory))
+        if self.version in ("auto", "2"):
+            commands.append(self.__record_cgroup_v2_usage(job_directory))
         return commands
 
     def job_properties(self, job_id, job_directory: str) -> Dict[str, Any]:
         metrics = self.__read_metrics(self.__cgroup_metrics_file(job_directory))
         return metrics
 
-    def __record_cgroup_cpu_usage(self, job_directory: str) -> str:
-        # comounted cgroups (which cpu and cpuacct are on the supported Linux distros) can appear in any order (cpu,cpuacct or cpuacct,cpu)
-        return CPU_USAGE_TEMPLATE.format(
+    def __record_cgroup_v1_usage(self, job_directory: str) -> str:
+        return CGROUPSV1_TEMPLATE.format(
             metrics=self.__cgroup_metrics_file(job_directory), cgroup_mount=self.cgroup_mount
         )
 
-    def __record_cgroup_memory_usage(self, job_directory: str) -> str:
-        return MEMORY_USAGE_TEMPLATE.format(
+    def __record_cgroup_v2_usage(self, job_directory: str) -> str:
+        return CGROUPSV2_TEMPLATE.format(
             metrics=self.__cgroup_metrics_file(job_directory), cgroup_mount=self.cgroup_mount
         )