psdi-data-conversion 0.0.23__py3-none-any.whl

psdi_data_conversion/static/javascript/format.js

@@ -0,0 +1,611 @@
+/*
+  format.js
+  Version 1.0, 27th November 2024
+
+  This is the JavaScript which makes the Format and Converter Selection gui work.
+*/
+
+import {
+    getInputFormats, getOutputFormats, getOutputFormatsForInputFormat,
+    getInputFormatsForOutputFormat, getConverters, getConverterByName, getLevelChemInfo
+} from "./data.js";
+import { loadProductionMode } from "./common.js";
+
+var fromList = new Array(),
+    toList = new Array(),
+    qualityCriteriaCount = 0,
+    qualityMeasureSum = 0;
+
+$(document).ready(function () {
+
+    // Populates the "Convert from" selection list
+    getInputFormats().then((formats) => {
+        populateList(formats, "from");
+    });
+
+    // Populates the "Convert to" selection list
+    getOutputFormats().then((formats) => {
+        populateList(formats, "to");
+    });
+
+    sessionStorage.setItem("token", token);
+    sessionStorage.setItem("max_file_size", max_file_size);
+    sessionStorage.setItem("service_mode", service_mode);
+    sessionStorage.setItem("production_mode", production_mode);
+    sessionStorage.setItem("in_str", "");
+    sessionStorage.setItem("out_str", "");
+    sessionStorage.setItem("success", "");
+
+    // Set the production mode variable for this page so that only appropriate elements are shown
+    loadProductionMode();
+
+    $("#fromList").click(populateConversionSuccess);
+    $("#toList").click(populateConversionSuccess);
+    $("#searchTo").keyup(filterOptions);
+    $("#searchFrom").keyup(filterOptions);
+    $("#yesButton").click(goToConversionPage);
+    $("#success").click(showConverterDetails);
+    $("#resetButton").click(resetAll);
+    $("#showButton").click(showQualityDetails);
+});
+
+/**
+ * Gets the input and output extensions and their notes from what's currently selected in the search boxes.
+ * @returns {Array<str>} Input extension, Input note, Output extension, Output note
+ */
+function getExtAndNotes() {
+    const in_str = $("#searchFrom").val(), // e.g. "ins: ShelX"
+        in_str_array = in_str.split(": "),
+        in_ext = in_str_array[0],           // e.g. "ins"
+        in_note = in_str_array[1];          // e.g. "ShelX"
+
+    const out_str = $("#searchTo").val(),
+        out_str_array = out_str.split(": "),
+        out_ext = out_str_array[0],
+        out_note = out_str_array[1];
+
+    return [in_ext, in_note, out_ext, out_note];
+}
+
+// Selects a file format; populates the "Conversion success" selection list given input and output IDs;
+// filters the output format list when an input format is selected, and vice versa (formats not convertible
+// to/from the selected format are removed); and removes converter details and text input (if showing)
+function populateConversionSuccess(event) {
+    const selectedText = getSelectedText(this);
+    let filterQuery = ``;
+
+    if (this.id == "fromList") {
+        $("#searchFrom").val(selectedText);
+    }
+    else {
+        $("#searchTo").val(selectedText);
+    }
+
+    const from_text = $("#searchFrom").val(),
+        to_text = $("#searchTo").val();
+
+    sessionStorage.setItem("in_str", from_text);
+    sessionStorage.setItem("out_str", to_text);
+
+    this.selectionStart = -1;
+    this.selectionEnd = -1;
+    this.blur();
+
+    emptySuccess();
+    hideConverterDetails();
+    hideOffer();
+
+    try {
+        const [in_ext, in_note, out_ext, out_note] = getExtAndNotes();
+
+        if (this.id == "fromList") {
+            toList = [];
+            $("#toList").children().remove();
+            getOutputFormatsForInputFormat(in_ext, in_note).then(formats => populateList(formats, "to"));
+        }
+        else if (this.id == "toList") {
+            fromList = [];
+            $("#fromList").children().remove();
+            getInputFormatsForOutputFormat(out_ext, out_note).then(formats => populateList(formats, "from"));
+        }
+
+        getConverters(in_ext, in_note, out_ext, out_note).then((converters) => {
+            populateList(converters, "success");
+        });
+    }
+    catch (e) {
+        // Can do without an error message if the 'Conversion options' box remains empty;
+        // however, consider a greyed-out message inside the box (using some of the commented out code below).
+    }
+}
+
+// Shows how the conversion quality was determined for the selected conversion/converter combination
+function showQualityDetails(event) {
+    const [in_ext, in_note, out_ext, out_note] = getExtAndNotes();
+    const converter = sessionStorage.getItem("success").split(": ")[0]
+
+    getLevelChemInfo(in_ext, in_note, out_ext, out_note).then(entries => displayLevelChemInfo(entries));
+}
+
+/**
+ * Compiles details on quality issues for a conversion between two formats
+ * @param {*} entries 
+ * @param {bool} format 
+ * @returns {Array<str>} A long description of quality issues, the percent rating of the conversion, a short description
+ *                       of the quality
+ */
+function getQualityDetails(entries, format = false) {
+    var composition_in = entries[0].composition,
+        composition_out = entries[1].composition,
+        connections_in = entries[0].connections,
+        connections_out = entries[1].connections,
+        two_dim_in = entries[0].two_dim,
+        two_dim_out = entries[1].two_dim,
+        three_dim_in = entries[0].three_dim,
+        three_dim_out = entries[1].three_dim;
+
+    qualityCriteriaCount = 0;
+    qualityMeasureSum = 0;
+
+    var quality = qualityDetail(composition_in, composition_out, 'Composition') +
+        qualityDetail(connections_in, connections_out, 'Connections') +
+        qualityDetail(two_dim_in, two_dim_out, '2D coordinates') +
+        qualityDetail(three_dim_in, three_dim_out, '3D coordinates');
+    let percent, qualityText;
+
+    if (qualityCriteriaCount == 0) {
+        quality = 'Conversion quality details not available for this converter/conversion combination.';
+        percent = "N/A";
+        qualityText = "N/A";
+    }
+    else {
+        qualityText = 'very poor';
+        percent = qualityMeasureSum * 20 / qualityCriteriaCount;
+
+        percent = (Math.round(percent * 100) / 100);
+
+        if (percent >= 80.0) {
+            qualityText = 'very good';
+        }
+        else if (percent >= 60.0) {
+            qualityText = 'good';
+        }
+        else if (percent >= 40.0) {
+            qualityText = 'okay';
+        }
+        else if (percent >= 20.0) {
+            qualityText = 'poor';
+        }
+
+        if (quality != '') {
+            quality = "<strong>WARNING:</strong> Potential data loss or extrapolation in conversion due to a " +
+                "mismatch in representation between input and output formats:\n<ul>" + quality + "</ul>";
+        }
+    }
+
+    // Strip the HTML formatting from the output if it isn't desired
+    if (!format) {
+        quality = quality.replaceAll(/<.*?>/g, "");
+    }
+
+    return [quality, percent, qualityText];
+}
+
+// Assemble quality information based on level of chemical information and display it.
+function displayLevelChemInfo(entries) {
+    var [quality, percent, qualityText] = getQualityDetails(entries);
+
+    if (percent != "N/A") {
+
+        quality += '-----------------------------\n' +
+            'Total score: ' + percent + '%\n' +
+            'Conversion quality: ' + qualityText + '\n' +
+            '-----------------------------\n';
+
+    }
+
+    alert(quality);
+}
+
+// Determine a statement of quality based on level of chemical information and populate the converter select box.
+function getQuality(entries, rows) {
+    var composition_in = entries[0].composition,
+        composition_out = entries[1].composition,
+        connections_in = entries[0].connections,
+        connections_out = entries[1].connections,
+        two_dim_in = entries[0].two_dim,
+        two_dim_out = entries[1].two_dim,
+        three_dim_in = entries[0].three_dim,
+        three_dim_out = entries[1].three_dim,
+        qualityText = ' Conversion quality is very poor.';
+
+    qualityCriteriaCount = 0;
+    qualityMeasureSum = 0;
+
+    qualityDetail(composition_in, composition_out, 'Composition') +
+        qualityDetail(connections_in, connections_out, 'Connections') +
+        qualityDetail(two_dim_in, two_dim_out, '2D coordinates') +
+        qualityDetail(three_dim_in, three_dim_out, '3D coordinates');
+
+    if (qualityCriteriaCount == 0) {
+        qualityText = ' Conversion quality not tested.';
+    }
+    else {
+        var percent = qualityMeasureSum * 20 / qualityCriteriaCount;
+
+        percent = (Math.round(percent * 100) / 100);
+
+        if (percent >= 80.0) {
+            qualityText = ' Conversion quality is very good.';
+        }
+        else if (percent >= 60.0) {
+            qualityText = ' Conversion quality is good.';
+        }
+        else if (percent >= 40.0) {
+            qualityText = ' Conversion quality is okay.';
+        }
+        else if (percent >= 20.0) {
+            qualityText = ' Conversion quality is poor.';
+        }
+    }
+
+    rows.sort(function (a, b) {
+        return a.toLowerCase().localeCompare(b.toLowerCase());
+    });
+
+    for (var i = 0; i < rows.length; i++) {
+        const support = rows[i].substring(0, 10) == "Open Babel" ||
+            rows[i].substring(0, 6) == "Atomsk" ||
+            rows[i].substring(0, 3) == "c2x" ? " supported on this site." : " not supported on this site." //" (supported)" : " (unsupported)";
+
+        $("#success").append($('<option>', { text: rows[i] + support + qualityText }));
+    }
+}
+
+// Returns 'true' if textbox text is exactly the same as a select box option
+function isOption(str, boxId) {
+    var isOption = false;
+
+    $("#" + boxId + " > option").each(function () {
+        if (str == this.text) {
+            isOption = true;
+        }
+    });
+
+    return isOption;
+}
+
+// Retrieve selected text from the "Conversion success" textarea
+// $$$$$$$$$$ Can delete this PROVIDED the mobile 'phone select box issue can be solved without it? BUT NEED TO DO IT ANOTHER WAY!! $$$$$$$$$$
+function getSelectedText(el) {
+    const text = el.value,
+        before = text.substring(0, el.selectionStart),
+        after = text.substring(el.selectionEnd, text.length);
+
+    el.selectionStart = before.lastIndexOf("\n") >= 0 ? before.lastIndexOf("\n") + 1 : 0;
+    el.selectionEnd = after.indexOf("\n") >= 0 ? el.selectionEnd + after.indexOf("\n") : text.length;
+
+    return el.value.substring(el.selectionStart, el.selectionEnd);
+}
+
+// Hides converter details
+function hideConverterDetails() {
+    $("#converter").css({ display: "none" });
+    $("h3").css({ display: "none" });
+}
+
+// Show conversion offer
+function showOffer() {
+
+    const [in_ext, in_note, out_ext, out_note] = getExtAndNotes();
+
+    const quest = " like to convert a file from '" + in_ext + "' to '" + out_ext + "' on this site";
+
+    if ($("#name").html() == "Open Babel" || $("#name").html() == "Atomsk" || $("#name").html() == "c2x") {
+        $("#info").html("");
+        $("#visit").html("visit website");
+        $("#question").html("Would you" + quest + " using " + $("#name").html() + "?");
+        $("#yesButton").css({ display: "inline" });
+
+        // Check for any warnings about this conversion
+        getLevelChemInfo(in_ext, in_note, out_ext, out_note).then(function (entries) {
+            const [quality, _percent, _qualityText] = getQualityDetails(entries, true);
+            if (quality != "") {
+                $("#formatWarning").html(quality);
+                $("#formatWarning").css({ display: "block" });
+            }
+        });
+
+    }
+    else {
+        $("#info").html("This converter is not supported on our website; however, you can find out how to use it at");
+        $("#visit").html("this website.");
+        $("#question").html("As an alternative, if you would" + quest + ", please select a supported converter above (if available).");
+        $("#yesButton").css({ display: "none" });
+    }
+
+    $("#question").css({ display: "inline" });
+    $("#offer").css({ display: "inline" });
+}
+
+// Hide conversion offer
+function hideOffer() {
+    $("#converter").css({ display: "none" });
+    $("#question").css({ display: "none" });
+    $("#offer").css({ display: "none" });
+    $("#formatWarning").css({ display: "none" });
+}
+
+// Displays converter details given its name
+function showConverterDetails(event) {
+    var selectedText = getSelectedText(this);
+
+    if (selectedText != "") {
+        sessionStorage.setItem("success", selectedText);
+
+        const str_array = selectedText.split(": ", 1),
+            conv_name = str_array[0];                                     // e.g. "Open Babel"
+
+        getConverterByName(conv_name).then((converter) => {
+            if (converter) {
+                $("#name").html(converter.name);
+                $("#description").html(converter.description);
+                $("#url").html(converter.url);
+                $("#visit").attr("href", converter.url);
+                $("#converter").css({ display: "block" });
+                $("h3").css({ display: "block" });
+            }
+
+            const el = this;
+
+            // Search textarea for "Open Babel"     $$$$$ textarea? $$$$$
+            const text = el.value;
+
+            el.selectionStart = 0;
+            el.selectionEnd = 0;
+
+            while (el.selectionStart < text.length) {
+                const selectedText = getSelectedText(el),
+                    name = selectedText.split(": ")[0];
+
+                showOffer();
+
+                el.selectionEnd += 1;
+                el.selectionStart = el.selectionEnd;
+            }
+
+            el.selectionStart = -1;
+            el.selectionEnd = -1;
+            el.blur();
+        });
+    }
+}
+
+// Create content for conversion quality details based on level of chemical information
+function qualityDetail(input, output, type) {
+
+    let label;
+    if (type.includes("2D")) {
+        label = "2D atomic coordinates are"
+    } else if (type.includes("3D")) {
+        label = "3D atomic coordinates are"
+    } else if (type.includes("Composition")) {
+        label = "Atomic composition is"
+    } else if (type.includes("Connections")) {
+        label = "Atomic connections are"
+    } else {
+        label = "The '" + type + "' property is"
+    }
+
+    if (input == true && output == true) {
+        qualityCriteriaCount += 1;
+        qualityMeasureSum += 5;
+        return '';
+    }
+    else if (input == true && output == false) {
+        return '<li><strong>Potential data loss:</strong> ' + label +
+            ' represented in the input format but not the output format.</li>\n';
+    }
+    else if (input == false && output == true) {
+        // We penalize the quality if the output format contains information that the input doesn't, as this might
+        // result in info being extrapolated
+        qualityCriteriaCount += 1;
+        return '<li><strong>Potential data extrapolation:</strong> ' + label +
+            ' represented in the output format but not the input format.</li>\n';
+    }
+    else {
+        return '';
+    }
+}
+
+// Only options having user filter input as a substring (case insensitive) are included in the selection list $$$$$$$$$$ REVISE $$$$$$$$$$
+function filterOptions(event) {
+    const str = event.target.value.toLowerCase();
+    var box, list,
+        count = 0,
+        text = "";
+
+    if (event.target.id == "searchFrom") {
+        toList = [];
+        $("#toList").children().remove();
+        getOutputFormats().then(formats => populateList(formats, "to"));
+        box = $("#fromList");
+        list = fromList;
+    }
+    else {
+        fromList = [];
+        $("#fromList").children().remove();
+        getInputFormats().then(formats => populateList(formats, "from"));
+        box = $("#toList");
+        list = toList;
+    }
+
+    box.children().remove();
+
+    for (var i = 0; i < list.length; i++) {
+        if (list[i].toLowerCase().includes(str)) {
+            box.append($('<option>', { text: list[i] }));
+            count += 1;
+        }
+    }
+
+    if (event.target.id == "searchFrom") {
+        $("#fromLabel").html("Select format to convert from (" + count + "):");
+    }
+    else {
+        $("#toLabel").html("Select format to convert to (" + count + "):");
+    }
+
+    emptySuccess();
+    hideConverterDetails();
+    hideOffer();
+}
+
+// Only options having user filter input as a substring (case insensitive) are included in the slection list
+function filter(id) {
+    try {
+        const str = $("#" + id).val().toLowerCase();
+        var box, list,
+            count = 0,
+            text = "";
+
+        if (id == "searchFrom") {
+            box = $("#fromList");
+            list = fromList;
+        }
+        else {
+            box = $("#toList");
+            list = toList;
+        }
+
+        box.children().remove();
+
+        for (var i = 0; i < list.length; i++) {
+            if (list[i].toLowerCase().includes(str)) {
+                box.append($('<option>', { text: list[i] }));
+                count += 1;
+            }
+        }
+
+        if (id == "searchFrom") {
+            $("#fromLabel").html("Select format to convert from (" + count + "):");
+        }
+        else {
+            $("#toLabel").html("Select format to convert to (" + count + "):");
+        }
+
+        emptySuccess();
+        hideConverterDetails();
+        hideOffer();
+    }
+    catch (e) {
+        // No need for an error message here. No need to filter if text box is empty.
+    }
+}
+
+// Empties the "Conversion success" textarea     $$$$$ textarea? $$$$$
+function emptySuccess() {
+    $("#success").html("");
+}
+
+// Retrieves a file format from a string (e.g. "ins: ShelX") from a selection list
+function getFormat(str) {
+    const str_array = str.split(": ");
+    return str_array[0];               // e.g. "ins"
+}
+
+// Stores chosen formats and switches to the Conversion page
+function goToConversionPage(event) {
+    var path = ``;
+
+    if ($("#name").html() == "Open Babel") {
+        path = `static/content/convert.htm`;
+    }
+    else if ($("#name").html() == "Atomsk") {
+        path = `static/content/convertato.htm`;
+    }
+    else if ($("#name").html() == "c2x") {
+        path = `static/content/convertc2x.htm`;
+    }
+
+    const a = $("<a>")
+        .attr("href", path)
+        .appendTo("body");
+
+    a[0].click();
+    a.remove();
+}
+
+// Populates a selection list
+function populateList(entries, sel) {
+    const [in_ext, in_note, out_ext, out_note] = getExtAndNotes();
+
+    let rows;
+
+    if ((sel === "from") || (sel === "to")) {
+
+        rows = entries.map(entry => `${entry.extension}: ${entry.note}`);
+
+    } else if (sel === "success") {
+
+        rows = entries.map(entry => `${entry.name}:`);
+
+        if (in_ext != "" && out_ext != "") {
+            const quality = getLevelChemInfo(in_ext, in_note, out_ext, out_note).then(formats => getQuality(formats, rows));
+        }
+    }
+
+    if (sel !== "success") {
+        rows.sort(function (a, b) {
+            return a.toLowerCase().localeCompare(b.toLowerCase());
+        });
+
+        for (var i = 0; i < rows.length; i++) {
+            const support = rows[i].substring(0, 10) == "Open Babel" || rows[i].substring(0, 6) == "Atomsk" ? " (supported)" : " (unsupported)";
+
+            if (sel == "from") {
+                $("#fromList").append($('<option>', { value: rows[i], text: rows[i] }));
+                fromList[i] = rows[i] + "\n";
+            }
+            else if (sel == "to") {
+                $("#toList").append($('<option>', { value: rows[i], text: rows[i] }));
+                toList[i] = rows[i] + "\n";
+            }
+        }
+    }
+
+    const in_str = in_ext + ": " + in_note;
+    const out_str = out_ext + ": " + out_note;
+    if (sel == "from" && !isOption(in_str, "toList")) {
+        filter("searchFrom");
+    }
+    else if (sel == "to" && !isOption(out_str, "fromList")) {
+        filter("searchTo");
+    }
+
+    if (sel == "from") {
+        $("#fromLabel").html("Select format to convert from (" + $("#fromList").children('option').length + "):");
+        $("#fromList option[value='" + in_str + "']").prop('selected', 'selected');
+        $("#fromList").hide().show();
+    }
+    else if (sel == "to") {
+        $("#toLabel").html("Select format to convert to (" + $("#toList").children('option').length + "):");
+        $("#toList option[value='" + out_str + "']").prop('selected', 'selected');
+        $("#toList").hide().show();
+    }
+}
+
+// Resets the filtering, format list and converter list boxes
+function resetAll() {
+    $("#fromList").children().remove();
+    $("#toList").children().remove();
+
+    $("#searchFrom").val("");
+    $("#searchTo").val("");
+
+    // Populates the "Convert from" selection list
+    getInputFormats().then(formats => populateList(formats, "from"));
+
+    // Populates the "Convert to" selection list
+    getOutputFormats().then(formats => populateList(formats, "to"));
+}

psdi_data_conversion/static/javascript/load_accessibility.js

@@ -0,0 +1,89 @@
+const r = document.querySelector(':root');
+const s = getComputedStyle(document.documentElement);
+
+function setDefault(default_varname, current_varname) {
+  if (s.getPropertyValue('--' + default_varname) == "") {
+    r.style.setProperty('--' + default_varname, s.getPropertyValue('--' + current_varname))
+  }
+}
+
+setDefault("psdi-default-font", "ifm-font-family-base");
+setDefault("psdi-default-heading-font", "ifm-heading-font-family");
+
+setDefault("psdi-default-font-size", "ifm-font-size-base");
+
+setDefault("psdi-default-font-weight", "ifm-font-weight-base");
+
+setDefault("psdi-default-letter-spacing", "psdi-letter-spacing-base");
+
+setDefault("psdi-default-dark-text-color-body", "psdi-dark-text-color-body");
+setDefault("psdi-default-dark-text-color-heading", "psdi-dark-text-color-heading");
+setDefault("psdi-default-light-text-color-body", "psdi-light-text-color-body");
+setDefault("psdi-default-light-text-color-heading", "psdi-light-text-color-heading");
+
+setDefault("psdi-default-line-height", "ifm-line-height-base");
+
+setDefault("psdi-default-background-color", "ifm-background-color");
+setDefault("psdi-default-color-primary", "ifm-color-primary");
+
+// Load values from session storage
+const font = sessionStorage.getItem("font"),
+  hfont = sessionStorage.getItem("hfont"),
+  size = sessionStorage.getItem("size"),
+  weight = sessionStorage.getItem("weight"),
+  letter = sessionStorage.getItem("letter"),
+  line = sessionStorage.getItem("line"),
+  darkColour = sessionStorage.getItem("darkColour"),
+  lightColour = sessionStorage.getItem("lightColour"),
+  lightBack = sessionStorage.getItem("lightBack"),
+  darkBack = sessionStorage.getItem("darkBack"),
+  mode = sessionStorage.getItem("mode");
+
+function loadProperty(current_varname, value) {
+  if (value != null) {
+    r.style.setProperty('--' + current_varname, value);
+  }
+}
+
+loadProperty("ifm-font-family-base", font);
+loadProperty("ifm-heading-font-family", hfont);
+
+loadProperty("ifm-font-size-base", size);
+
+loadProperty("ifm-font-weight-base", weight);
+
+loadProperty("psdi-letter-spacing-base", letter);
+
+loadProperty("psdi-dark-text-color-body", darkColour);
+loadProperty("psdi-dark-text-color-heading", darkColour);
+loadProperty("psdi-light-text-color-body", lightColour);
+loadProperty("psdi-light-text-color-heading", lightColour);
+
+loadProperty("ifm-line-height-base", line);
+
+loadProperty("ifm-background-color", lightBack);
+loadProperty("ifm-color-primary", darkBack);
+
+if (font != null) {
+
+  r.style.setProperty('--ifm-font-family-base', font);
+  r.style.setProperty('--ifm-heading-font-family', hfont);
+
+  r.style.setProperty('--ifm-font-size-base', size);
+
+  r.style.setProperty('--ifm-font-weight-base', weight);
+
+  r.style.setProperty('--psdi-letter-spacing-base', letter);
+
+  r.style.setProperty('--psdi-dark-text-color-body', darkColour);
+  r.style.setProperty('--psdi-dark-text-color-heading', darkColour);
+  r.style.setProperty('--psdi-light-text-color-body', lightColour);
+  r.style.setProperty('--psdi-light-text-color-heading', lightColour);
+
+  r.style.setProperty('--ifm-line-height-base', line);
+
+  r.style.setProperty('--ifm-background-color', lightBack);
+  r.style.setProperty('--ifm-color-primary', darkBack);
+}
+
+document.documentElement.setAttribute("data-theme", mode);