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refactor: ♻️ update issue dashboard template for CWL section #54

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merged 1 commit into from
Aug 12, 2024
Merged

refactor: ♻️ update issue dashboard template for CWL section #54

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106 changes: 47 additions & 59 deletions bot/utils/renderer/index.js
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Original file line number Diff line number Diff line change
Expand Up @@ -276,9 +276,35 @@ export async function applyCWLTemplate(
const existingCWL = await cwlCollection.findOne({
repositoryId: repository.id,
});
const overallSection = `\n\n## Language Specific Standards\n\nTo make your software FAIR is it important to follow language specific standards and best practices, as recommended in the [FAIR-BioRS guidelines](https://fair-biors.org/). Codefair will check below that your code complies with applicable standards,`;

if (subjects.cwl.removed_files.length > 0) {
// Remove the files from the database
const existingCWL = await cwlCollection.findOne({
repositoryId: repository.id,
});

if (existingCWL) {
const newFiles = existingCWL.files.filter((file) => {
return !subjects.cwl.removed_files.includes(file.path);
});

await cwlCollection.updateOne(
{ repositoryId: repository.id },
{
$set: {
contains_cwl_files: newFiles.length > 0,
files: newFiles,
updated_at: Date.now(),
},
},
);
}
}

// If no CWL files are found in the list of files
if (subjects.cwl.files.length === 0) {
let overallStatus = "";
let tableContent = "";
if (!existingCWL) {
// Entry does not exist in the db, create a new one
Expand All @@ -289,7 +315,7 @@ export async function applyCWLTemplate(
created_at: newDate,
files: [],
identifier,
overall_status: "",
overall_status: overallStatus,
owner,
repo: repository.name,
repositoryId: repository.id,
Expand All @@ -303,7 +329,8 @@ export async function applyCWLTemplate(
{ $set: { updated_at: Date.now() } },
);

// TODO: Create a table of the cwl files that were validated
overallStatus = existingCWL.overall_status;

for (const file of existingCWL.files) {
tableContent += `| ${file.path} | ${file.validation_status === "valid" ? "✔️" : "❌"} |\n`;
}
Expand All @@ -315,9 +342,11 @@ export async function applyCWLTemplate(
return baseTemplate;
}

const validOverall = overallStatus === "valid";

// No new CWL files were found in the repository but some were validated already
const cwlBadge = `[![CWL](https://img.shields.io/badge/View_CWL_Report-0ea5e9.svg)](${url})`;
baseTemplate += `\n\n## CWL Validations\n\nNo new CWL files were found in the repository but ***${existingCWL.files.length}/${existingCWL.files.length}*** that were validated already are considered valid by the [cwltool validator](https://cwltool.readthedocs.io/en/latest/).\n\n<details>\n<summary>Summary of the validation report</summary>\n\n| File | Status |\n| :---- | :----: |\n${tableContent}</details>\n\nTo view the full report of each CWL file or rerun the validation, click the "View CWL Report" button below.\n\n${cwlBadge}`;
baseTemplate += `${overallSection}\n\n### CWL Validations ${validOverall ? "✔️" : "❗"}\n\nCodefair has detected that you are following the Common Workflow Language (CWL) standard to describe your command line tool. Codefair ran the [cwltool validator](https://cwltool.readthedocs.io/en/latest/) and ${validOverall ? `all ***${subjects.cwl.files.length}*** CWL file(s) in your repository are valid.` : `***${subjects.cwl.files.length - failedCount}/${subjects.cwl.files.length}*** CWL file(s) in your repository are not valid.`}\n\n<details>\n<summary>Summary of the validation report</summary>\n\n| File | Validation result |\n| :---- | :----: |\n${tableContent}</details>\n\nTo view the full report of each CWL file or to rerun the validation, click the "View CWL Report" button below.\n\n${cwlBadge}`;
} else {
const cwlFiles = [];
let validOverall = true;
Expand Down Expand Up @@ -390,7 +419,15 @@ export async function applyCWLTemplate(
});
} else {
// An entry exists in the db, thus possible old files exist (merge both lists)
const newFiles = [...existingCWL.files, ...cwlFiles];
const newFiles = [
...existingCWL.files,
...cwlFiles.filter(
(file) =>
!existingCWL.files.some(
(existingFile) => existingFile.path === file.path,
),
),
];
await cwlCollection.updateOne(
{ repositoryId: repository.id },
{
Expand All @@ -404,7 +441,9 @@ export async function applyCWLTemplate(
);
url = `${CODEFAIR_DOMAIN}/view/cwl-validation/${existingCWL.identifier}`;

for (const file of newFiles.files) {
tableContent = "";
failedCount = 0;
for (const file of newFiles) {
tableContent += `| ${file.path} | ${file.validation_status === "valid" ? "✔️" : "❌"} |\n`;
subjects.cwl.files.push(file);

Expand All @@ -416,63 +455,12 @@ export async function applyCWLTemplate(
validOverall = false;
}
}

subjects.cwl.files = newFiles;
}

const cwlBadge = `[![CWL](https://img.shields.io/badge/View_CWL_Report-0ea5e9.svg)](${url})`;
baseTemplate += `\n\n## CWL Validations ${validOverall ? "✔️" : "❗"}\n\nCWL files were found in the repository and ***${subjects.cwl.files.length - failedCount}/${subjects.cwl.files.length}*** are considered valid by the [cwltool validator](https://cwltool.readthedocs.io/en/latest/).\n\n<details>\n<summary>Summary of the validation report</summary>\n\n| File | Status |\n| :---- | :----: |\n${tableContent}</details>\n\nTo view the full report of each CWL file or to rerun the validation, click the "View CWL Report" button below.\n\n${cwlBadge}`;
}

if (subjects.cwl.removed_files.length > 0) {
// Remove the files from the database
const cwlCollection = dbInstance.getDb().collection("cwlValidation");
const existingCWL = await cwlCollection.findOne({
repositoryId: repository.id,
});

if (existingCWL) {
const newFiles = existingCWL.files.filter((file) => {
return !subjects.cwl.removed_files.includes(file.path);
});

await cwlCollection.updateOne(
{ repositoryId: repository.id },
{
$set: {
contains_cwl_files: newFiles.length > 0,
files: newFiles,
updated_at: Date.now(),
},
},
);

const response = await cwlCollection.findOne({
repositoryId: repository.id,
});

const overallStatus = response.overall_status;

const validationString = "\n\n## CWL Validations";
const validEmoji = "✔️";
const invalidEmoji = "❗";

const validationIndex = baseTemplate.indexOf(validationString);
if (validationIndex !== -1) {
const emojiIndex = validationIndex + validationString.length;
if (overallStatus === "valid") {
baseTemplate =
baseTemplate.substring(0, emojiIndex) +
validEmoji +
baseTemplate.substring(emojiIndex + 1);
} else if (overallStatus === "invalid") {
baseTemplate =
baseTemplate.substring(0, emojiIndex) +
invalidEmoji +
baseTemplate.substring(emojiIndex + 1);
}

consola.info("Removed CWL files from the database");
}
}
baseTemplate += `${overallSection}\n\n### CWL Validations ${validOverall ? "✔️" : "❗"}\n\nCodefair has detected that you are following the Common Workflow Language (CWL) standard to describe your command line tool. Codefair ran the [cwltool validator](https://cwltool.readthedocs.io/en/latest/) and ${validOverall ? `all ***${subjects.cwl.files.length}*** CWL file(s) in your repository are valid.` : `***${subjects.cwl.files.length - failedCount}/${subjects.cwl.files.length}*** CWL file(s) in your repository are not valid.`}\n\n<details>\n<summary>Summary of the validation report</summary>\n\n| File | Validation result |\n| :---- | :----: |\n${tableContent}</details>\n\nTo view the full report of each CWL file or to rerun the validation, click the "View CWL Report" button below.\n\n${cwlBadge}`;
}

return baseTemplate;
Expand Down