File size: 4,528 Bytes
71174bc | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 | import { runWorker } from "@/Core/WebWorkers/RunWorker";
import { QueueParent } from "@/Queue/QueueParent";
import { IJobInfo } from "@/Queue/QueueTypes";
import { messagesApi } from "@/Api/Messages";
/**
* A convert-with-openbabel queue.
*/
export class OpenBabelQueue extends QueueParent {
/**
* Run a batch of jobs.
*
* @param {IJobInfo[]} inputBatch The input batch.
* @param {number} procs The number of processors to use.
* @returns {Promise<IJobInfo[]>} The output batch.
*/
public runJobBatch(
inputBatch: IJobInfo[],
procs: number
): Promise<IJobInfo[]> {
const inputs = inputBatch.map((jobInfo) => jobInfo.input);
// Remove any tree node (to avoid serialization issues).
for (let i = 0; i < inputs.length; i++) {
if (inputs[i].inputFile.treeNode !== undefined) {
inputs[i].inputFile.treeNode = undefined;
}
}
return runWorker(
new Worker(new URL("./OpenBabel.worker.ts", import.meta.url)),
inputs,
true // auto terminate the worker.
)
.then((outputBatch: any[]) => {
const errorMessages: string[] = [];
for (let i = 0; i < outputBatch.length; i++) {
const output = outputBatch[i];
const input = inputs[i];
if (
output.stdErr &&
output.stdErr.toLowerCase().includes("error")
) {
if (input.surpressMsgs) {
continue;
}
const stdErr = output.stdErr;
let errorMessage: string;
if (
stdErr.includes("Cannot enlarge memory") ||
stdErr.includes("(OOM)")
) {
errorMessage = `The molecule '${input.inputFile.name}' is too large to process due to memory limitations.`;
} else {
let details = stdErr.replace("Open Babel ", "");
details = details.replace(/^=+$/gm, "");
details = details.replace(/^\*{1,10}/gm, "");
details = details.trim();
details = details.replace(/([^.!?])$/gm, "$1.");
details = details.replace(/\s{2,}/g, " ");
details = details.trim();
details = details.replace(/\n/g, " ");
errorMessage = `Could not process '${input.inputFile.name}'. The structure may be too large or the format incorrect. Technical details: ${details}`;
}
errorMessages.push(errorMessage);
}
}
if (errorMessages.length > 0) {
let finalMessage = "";
if (errorMessages.length === 1) {
finalMessage = errorMessages[0];
} else {
finalMessage =
"<p>Multiple errors occurred during processing:</p><ul><li>" +
errorMessages.join("</li><li>") +
"</li></ul>";
}
messagesApi.popupError(finalMessage);
}
// If any of the files have {ERROR} in them, let user know and
// remove from outputBatch.
for (let i = 0; i < outputBatch.length; i++) {
if (outputBatch[i].outputFiles) {
outputBatch[i].outputFiles = outputBatch[
i
].outputFiles.filter(
(file: string | undefined) =>
file !== "{ERROR}" && file !== undefined
);
} else {
outputBatch[i].outputFiles = [];
}
}
// Update .output value of each jobInfo.
for (let i = 0; i < inputBatch.length; i++) {
inputBatch[i].output = outputBatch[i];
}
return inputBatch;
})
.catch((err) => {
throw err;
});
}
}
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