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Merge pull request #15594 from mvdbeek/dev

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Merge 23.0 into dev
This commit is contained in:
Marius van den Beek
2023-02-16 14:53:01 +01:00
committed by GitHub
parent 0742d6e277 91f0ac8a88
commit a8e1362725
3 changed files with 127 additions and 116 deletions
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client/src/components/History/CurrentHistory/HistoryPanel.vue
+22 -15
View File
@@ -367,21 +367,28 @@ export default {
},
onDrop(evt) {
this.showDropZone = false;
const data = JSON.parse(evt.dataTransfer.getData("text"))[0];
const dataSource = data.history_content_type === "dataset" ? "hda" : "hdca";
if (data.history_id != this.historyId) {
copyDataset(data.id, this.historyId, data.history_content_type, dataSource)
.then(() => {
if (data.history_content_type === "dataset") {
Toast.info("Dataset copied to history");
} else {
Toast.info("Collection copied to history");
}
this.loadHistoryById(this.historyId);
})
.catch((error) => {
this.onError(error);
});
let data;
try {
data = JSON.parse(evt.dataTransfer.getData("text"))[0];
} catch (error) {
// this was not a valid object for this dropzone, ignore
}
if (data) {
const dataSource = data.history_content_type === "dataset" ? "hda" : "hdca";
if (data.history_id != this.historyId) {
copyDataset(data.id, this.historyId, data.history_content_type, dataSource)
.then(() => {
if (data.history_content_type === "dataset") {
Toast.info("Dataset copied to history");
} else {
Toast.info("Collection copied to history");
}
this.loadHistoryById(this.historyId);
})
.catch((error) => {
this.onError(error);
});
}
}
},
onError(error) {
client/src/composables/fileDrop.ts
+88 -96
View File
@@ -1,6 +1,5 @@
import { ref, unref, type Ref } from "vue";
import { computed, ref, unref, type Ref } from "vue";
import { useEventListener, type MaybeComputedRef } from "@vueuse/core";
import { wait } from "@/utils/wait";
export type FileDropHandler = (event: DragEvent) => void;
@@ -9,114 +8,108 @@ export type FileDropHandler = (event: DragEvent) => void;
* @param dropZone Element which files should be dropped on
* @param onDrop callback function called when drop occurs
* @param solo when true, only reacts if no modal is open
* @param idleTime how long to wait until state resets
*/
export function useFileDrop(
dropZone: MaybeComputedRef<EventTarget | null | undefined>,
onDrop: Ref<FileDropHandler> | FileDropHandler,
solo: MaybeComputedRef<boolean>
solo: MaybeComputedRef<boolean>,
idleTime = 800
) {
const isFileOverDocument = ref(false);
const isFileOverDropZone = ref(false);
// blocks drag events in this composable, to avoid drag events in unwanted situations
let dragBlocked = false;
// keeps track if the drag has exited, to avoid premature drag canceling
let hasExited = true;
// Don't react to page-internal drag events
useEventListener(
document.body,
"dragstart",
() => {
dragBlocked = true;
},
true
);
useEventListener(
document.body,
"dragover",
(event) => {
if (!dragBlocked) {
// prevent the browser from opening the file
event.preventDefault();
hasExited = false;
}
},
true
);
useEventListener(
document.body,
"drop",
(event) => {
if (!dragBlocked) {
// prevent the browser from opening the file
event.preventDefault();
if (isFileOverDropZone.value && isFileOverDocument.value) {
const dropHandler = unref(onDrop);
dropHandler(event as DragEvent);
}
}
isFileOverDocument.value = false;
dragBlocked = false;
hasExited = true;
},
true
);
/** Reset all variables */
const reset = () => {
isFileOverDocument.value = false;
isFileOverDropZone.value = false;
dragBlocked = false;
hasExited = true;
};
useEventListener(document.body, "dragend", reset, true);
useEventListener(document.body, "dragleave", async () => {
hasExited = true;
// This event may have been triggered by components
// which have not been properly childed to the body yet.
// Wait a bit, and check if hasExited is still true.
await wait(100);
if (hasExited) {
reset();
}
});
useEventListener(
document.body,
"dragenter",
(event) => {
// init values if drag is possible
if (!dragBlocked && !(unref(solo) && isAnyModalOpen())) {
isFileOverDocument.value = true;
isFileOverDropZone.value = false;
hasExited = false;
event.preventDefault();
}
},
true
);
/** returns if any bootstrap modal is open */
function isAnyModalOpen() {
return document.querySelectorAll(".modal.show").length > 0;
}
type State = "idle" | "blocked" | "fileDragging";
type StateMachine = {
[state in State]: (event: MouseEvent) => State;
};
const currentState: Ref<State> = ref("idle");
let idleTimer: ReturnType<typeof setTimeout> | null = null;
const resetTimer = () => {
if (idleTimer) {
clearTimeout(idleTimer);
}
};
const stateMachine = {
idle(event: MouseEvent): State {
switch (event.type) {
case "dragstart":
return "blocked";
case "dragenter":
if (!(unref(solo) && isAnyModalOpen())) {
return "fileDragging";
}
break;
}
return "idle";
},
blocked(event: MouseEvent): State {
switch (event.type) {
case "drop":
return "idle";
case "dragend":
return "idle";
}
return "blocked";
},
fileDragging(event: MouseEvent): State {
resetTimer();
switch (event.type) {
case "dragover":
event.preventDefault();
idleTimer = setTimeout(() => (currentState.value = "idle"), idleTime);
break;
case "drop":
event.preventDefault();
if (isFileOverDropZone.value) {
const dropHandler = unref(onDrop);
dropHandler(event as DragEvent);
}
return "idle";
case "dragend":
return "idle";
}
return "fileDragging";
},
} as const satisfies StateMachine;
const eventHandler = (event: MouseEvent) => (currentState.value = stateMachine[currentState.value](event));
useEventListener(document.body, "dragstart", eventHandler, true);
useEventListener(document.body, "dragover", eventHandler, true);
useEventListener(document.body, "drop", eventHandler, true);
useEventListener(document.body, "dragend", eventHandler, true);
useEventListener(document.body, "dragenter", eventHandler, true);
const isFileOverDocument = computed({
get() {
return currentState.value === "fileDragging";
},
set(value) {
if (value !== true) {
currentState.value = "idle";
} else {
currentState.value = "fileDragging";
}
},
});
const isFileOverDropZone = ref(false);
useEventListener(
dropZone,
"dragenter",
() => {
isFileOverDropZone.value = true;
hasExited = false;
},
true
);
@@ -126,7 +119,6 @@ export function useFileDrop(
"dragleave",
() => {
isFileOverDropZone.value = false;
hasExited = false;
},
true
);
lib/galaxy/datatypes/converters/uncompressed_to_gz.xml
+17 -5
View File
@@ -1,19 +1,27 @@
<tool id="CONVERTER_uncompressed_to_gz" name="Convert uncompressed file to compressed" hidden="true" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
<macros>
<token name="@TOOL_VERSION@">1.15.1</token>
<token name="@TOOL_VERSION@">1.16</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">htslib</requirement>
<requirement type="package" version="1.0.8">bzip2</requirement>
</requirements>
<command><![CDATA[
cp '$ext_config' galaxy.json &&
bgzip -@ "\${GALAXY_SLOTS:-1}" -c '$input1' > '$output1'
#if $input1.ext.endswith(".bz2"):
bzcat '$input1' | bgzip -@ "\${GALAXY_SLOTS:-1}" -c > '$output1'
#else:
bgzip -@ "\${GALAXY_SLOTS:-1}" -c '$input1' > '$output1'
#end if
]]></command>
<configfiles>
<configfile name="ext_config">{"output1": {
"name": "${input1.name + '.gz' if not $input1.name.endswith('.vcf') else $input1.name + '.bgzip'} compressed",
"ext": "${input1.ext + '.gz' if $input1.ext != 'vcf' else 'vcf_bgzip'}"
<configfile name="ext_config">
#silent ext = $input1.ext[:-4] if $input1.ext.endswith(".bz2") else $input1.ext
#silent ext = ext + '.gz' if ext != 'vcf' else 'vcf_bgzip'
{"output1": {
"name": "${input1.name} compressed",
"ext": "${ext}"
}}</configfile>
</configfiles>
<inputs>
@@ -32,6 +40,10 @@ bgzip -@ "\${GALAXY_SLOTS:-1}" -c '$input1' > '$output1'
<param name="input1" value="1.fasta" ftype="fasta"/>
<output name="output1" file="1.fasta.gz" ftype="fasta.gz" decompress="true"/>
</test>
<test>
<param name="input1" value="1.fastqsanger.bz2" ftype="fastqsanger.bz2"/>
<output name="output1" file="1.fastqsanger.gz" ftype="fastqsanger.gz" decompress="true"/>
</test>
</tests>
<help>
</help>