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Merged
merged 6 commits into from
Jul 10, 2025
Merged

Updates & debugs #20

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28e4d5b
feat: add compatability for new structuree
CodyCBakerPhD Jul 10, 2025
526395c
feat: update base branch
CodyCBakerPhD Jul 10, 2025
06aa4b8
feat: add pre-commit
CodyCBakerPhD Jul 10, 2025
0be4ba5
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 10, 2025
a2c3951
feat: add pre-commit
CodyCBakerPhD Jul 10, 2025
540e2e6
Merge branch 'new' of https://github.com/dandi/access-page into new
CodyCBakerPhD Jul 10, 2025
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2 changes: 1 addition & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
# PyCharm
.idea/*
.idea/*
25 changes: 25 additions & 0 deletions .pre-commit-config.yaml
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@@ -0,0 +1,25 @@
default_install_hook_types:
- pre-commit
- commit-msg

repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v5.0.0
hooks:
- id: check-yaml
- id: end-of-file-fixer
- id: trailing-whitespace

- repo: https://github.com/codespell-project/codespell
rev: v2.4.1
hooks:
- id: codespell
additional_dependencies:
- tomli

- repo: https://github.com/compilerla/conventional-pre-commit
rev: v4.2.0
hooks:
- id: conventional-pre-commit
stages: [commit-msg]
args: [--verbose]
1 change: 1 addition & 0 deletions index.html
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Expand Up @@ -6,6 +6,7 @@

<title>Dandiset Access Summaries</title>

<script src="https://cdn.jsdelivr.net/npm/js-yaml@4.1.0/dist/js-yaml.min.js"></script>
<script src="https://cdn.plot.ly/plotly-3.0.1.min.js" charset="utf-8"></script>
<script src="errors.js" defer></script>
<script src="plots.js" defer></script>
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92 changes: 47 additions & 45 deletions plots.js
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Expand Up @@ -6,8 +6,8 @@ const BASE_URL = "https://raw.githubusercontent.com/dandi/access-summaries/main"
const BASE_TSV_URL = `${BASE_URL}/content/summaries`;

const ARCHIVE_TOTALS_URL = `${BASE_URL}/content/archive_totals.json`;
const ALL_DANDISET_TOTALS_URL = `${BASE_URL}/content/all_dandiset_totals.json`;
const REGION_CODES_TO_LATITUDE_LONGITUDE_URL = `${BASE_URL}/content/region_codes_to_coordinates.json`;
const ALL_DANDISET_TOTALS_URL = `${BASE_URL}/content/totals.json`;
const REGION_CODES_TO_LATITUDE_LONGITUDE_URL = `${BASE_URL}/content/region_codes_to_coordinates.yaml`;

let REGION_CODES_TO_LATITUDE_LONGITUDE = {};
let ALL_DANDISET_TOTALS = {};
Expand All @@ -28,11 +28,11 @@ window.addEventListener("load", () => {
if (logScaleCheckbox) {
logScaleCheckbox.addEventListener("change", function() {
USE_LOG_SCALE = this.checked;

// Get the current dandiset ID
const dandiset_selector = document.getElementById("dandiset_selector");
const selected_dandiset = dandiset_selector.value;

// Reload plots with the current dandiset ID
load_over_time_plot(selected_dandiset);
load_per_asset_histogram(selected_dandiset);
Expand Down Expand Up @@ -112,15 +112,15 @@ function resizePlots() {
fetch(REGION_CODES_TO_LATITUDE_LONGITUDE_URL)
.then((response) => {
if (!response.ok) {
throw new Error(`Failed to fetch JSON file: ${response.statusText}`);
throw new Error(`Failed to fetch YAML file: ${response.statusText}`);
}
return response.json();
return response.text();
})
.then((data) => {
REGION_CODES_TO_LATITUDE_LONGITUDE = data;
REGION_CODES_TO_LATITUDE_LONGITUDE = jsyaml.load(data);
})
.catch((error) => {
console.error("Error loading JSON file:", error);
console.error("Error loading YAML file:", error);
});

fetch(ARCHIVE_TOTALS_URL)
Expand Down Expand Up @@ -153,7 +153,20 @@ fetch(ALL_DANDISET_TOTALS_URL)
})
.then((all_dandiset_totals_text) => {
Object.assign(ALL_DANDISET_TOTALS, JSON.parse(all_dandiset_totals_text));
const dandiset_ids = Object.keys(ALL_DANDISET_TOTALS);
let dandiset_ids = Object.keys(ALL_DANDISET_TOTALS);
dandiset_ids.sort((a, b) => {
if (a === "archive") return -1;
if (b === "archive") return 1;
// Compare as numbers if both are numeric
const aNum = Number(a);
const bNum = Number(b);
if (!isNaN(aNum) && !isNaN(bNum)) {
return aNum - bNum;
}
// Fallback to string comparison
return a.localeCompare(b);
});

const selector = document.getElementById("dandiset_selector");

if (!selector) {
Expand Down Expand Up @@ -208,7 +221,7 @@ function update_totals(dandiset_id) {
const footnote = document.createElement("div");
footnote.style.fontSize = "0.5em";
footnote.style.marginTop = "7px";
footnote.innerHTML = "<sup>*</sup> These values are only estimates for publically released datasets and are subject to change as additional information becomes available.";
footnote.innerHTML = "<sup>*</sup> These values are only estimates for publicly released datasets and are subject to change as additional information becomes available.";
totals_element.appendChild(footnote);
} catch (error) {
console.error("Error:", error);
Expand All @@ -221,13 +234,7 @@ function update_totals(dandiset_id) {
// Function to fetch and render the over time for a given Dandiset ID
function load_over_time_plot(dandiset_id) {
const plot_element_id = "over_time_plot";
let by_day_summary_tsv_url;

if (dandiset_id === "archive") {
by_day_summary_tsv_url = `${BASE_TSV_URL}/archive_summary_by_day.tsv`;
} else {
by_day_summary_tsv_url = `${BASE_TSV_URL}/${dandiset_id}/dandiset_summary_by_day.tsv`;
}
let by_day_summary_tsv_url = `${BASE_TSV_URL}/${dandiset_id}/by_day.tsv`;

fetch(by_day_summary_tsv_url)
.then((response) => {
Expand Down Expand Up @@ -261,8 +268,9 @@ function load_over_time_plot(dandiset_id) {

const plot_info = [
{
type: "scatter",
mode: "lines+markers",
//type: "scatter",
//mode: "lines+markers",
type: "bar",
x: dates, // Use raw dates for proper alignment
y: plot_data,
text: dates.map((date, index) => `${date}<br>${human_readable_bytes_sent[index]}`),
Expand Down Expand Up @@ -310,7 +318,7 @@ function load_over_time_plot(dandiset_id) {
// Function to fetch and render histogram over asset IDs
function load_per_asset_histogram(dandiset_id) {
const plot_element_id = "per_asset_histogram";
let by_day_summary_tsv_url = "";
let by_asset_summary_tsv_url = "";

// Suppress div element content if 'archive' is selected
if (dandiset_id === "archive") {
Expand All @@ -320,10 +328,10 @@ function load_per_asset_histogram(dandiset_id) {
}
return "";
} else {
by_day_summary_tsv_url = `${BASE_TSV_URL}/${dandiset_id}/dandiset_summary_by_asset.tsv`;
by_asset_summary_tsv_url = `${BASE_TSV_URL}/${dandiset_id}/by_asset.tsv`;
}

fetch(by_day_summary_tsv_url)
fetch(by_asset_summary_tsv_url)
.then((response) => {
if (!response.ok) {
throw new Error(`Failed to fetch TSV file: ${response.statusText}`);
Expand All @@ -346,23 +354,25 @@ function load_per_asset_histogram(dandiset_id) {
throw new Error("Currently only supports NWB files.");
}

// TODO: this was a heuristic idea for shortening the asset names
// const subject_and_session = filename.split("_");
// const subject = subject_and_session.at(0).split("-").slice(1).join("-");
// const session = subject_and_sessions.slice(1).split("-").slice(1).join("-");
// return `${subject} ${session}`;

return filename;
});
const bytes_sent = data.map((row) => parseInt(row[1], 10));
const human_readable_bytes_sent = bytes_sent.map((bytes) => format_bytes(bytes));

// Sort asset_names and bytes_sent in descending order by bytes_sent
const combined = asset_names.map((name, idx) => ({ name, bytes: bytes_sent[idx] }));
combined.sort((a, b) => b.bytes - a.bytes);

const sorted_asset_names = combined.map(item => item.name);
const sorted_bytes_sent = combined.map(item => item.bytes);
const human_readable_bytes_sent = sorted_bytes_sent.map((bytes) => format_bytes(bytes));

// Use sorted arrays in the plot
const plot_data = [
{
type: "bar",
x: asset_names,
y: bytes_sent,
text: asset_names.map((name, index) => `${name}<br>${human_readable_bytes_sent[index]}`),
x: sorted_asset_names,
y: sorted_bytes_sent,
text: sorted_asset_names.map((name, index) => `${name}<br>${human_readable_bytes_sent[index]}`),
textposition: "none",
hoverinfo: "text",
}
Expand All @@ -375,14 +385,10 @@ function load_per_asset_histogram(dandiset_id) {
},
xaxis: {
title: {
text: "Asset Name",
text: "(hover over an entry for asset names)",
font: { size: 16 }
},
showticklabels: false,
// TODO: ticks are currently too long to fit since heuristic is not working well
// tickangle: -45,
// tickfont: { size: 10 },
// automargin: true,
},
yaxis: {
title: {
Expand All @@ -403,21 +409,17 @@ function load_per_asset_histogram(dandiset_id) {
console.error("Error:", error);
const plot_element = document.getElementById(plot_element_id);
if (plot_element) {
plot_element.innerText = "Failed to load data for per asset (current supports NWB datasets only).";
while (plot_element.firstChild) {
plot_element.removeChild(plot_element.firstChild);
}
}
});
}

// Function to fetch and render heatmap over geography
function load_geographic_heatmap(dandiset_id) {
const plot_element_id = "geography_heatmap";
let by_region_summary_tsv_url;

if (dandiset_id === "archive") {
by_region_summary_tsv_url = `${BASE_TSV_URL}/archive_summary_by_region.tsv`;
} else {
by_region_summary_tsv_url = `${BASE_TSV_URL}/${dandiset_id}/dandiset_summary_by_region.tsv`;
}
let by_region_summary_tsv_url = `${BASE_TSV_URL}/${dandiset_id}/by_region.tsv`;

if (!REGION_CODES_TO_LATITUDE_LONGITUDE) {
console.error("Error:", error);
Expand Down