plexora 0.0.1__py3-none-any.whl

plexora/plugins/gating/static/gating.css

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+/* ------------------------------------------------------------------------
+   Moved out of core's viewer.css.
+
+   These style ids that only this plugin's templates render (panel.html,
+   legacy.html), so core was carrying a plugin's appearance: a core-only build
+   shipped ~150 lines of CSS for a tool it does not have, and gating alone got
+   a look it never had to ship. No plugin written by anyone else would be
+   styled by core, which made gating privileged in a way the plugin API is
+   meant to rule out.
+   Kept at the top of this file because viewer.css loaded first; the cascade
+   these rules take part in is therefore unchanged.
+   Custom properties (--surface-2 and friends) still resolve -- core's :root
+   defines them for the whole document, and core is always present.
+   ------------------------------------------------------------------------ */
+
+#gate_marker_section {
+    border-color: var(--accent-gate-soft);
+    position: relative;
+}
+
+#gate_marker_section .section-heading h2 {
+    color: #ffe5da;
+}
+
+#gate_auto_button {
+    background: #4a5160;
+    color: #f1f4f8;
+}
+
+/* Was two rules in viewer.css: a shared one with #channel_list_wrapper, then
+   an override. Merged here -- the override's top wins, as it did before. */
+#csv_channel_list_wrapper {
+    background-color: rgba(0, 0, 0, 0);
+    left: 0;
+    position: absolute;
+    top: 120px;
+    width: 360px;
+    z-index: 1;
+}
+
+#boxHeading3 {
+    color: rgba(255, 255, 255, 1);
+    font-size: 16px;
+    position: relative;
+}
+
+#download-gating-header-div {
+    color: rgba(255, 255, 255, 1);
+}
+
+#gating_upload_icon, #gating_download_icon {
+    cursor: pointer;
+}
+
+#gating_download_panel {
+    background: var(--surface-2);
+    border: 1px solid var(--border-strong);
+    border-radius: var(--radius-md);
+    box-shadow: var(--shadow-md);
+    color: #eef3f8;
+    left: 0;
+    margin: 0;
+    padding: 28px 10px 12px;
+    position: absolute;
+    right: 0;
+    top: 42px;
+    visibility: hidden;
+    width: auto;
+    z-index: 105;
+}
+
+#gating_download_panel #gating_exit {
+    color: var(--text-secondary);
+    cursor: pointer;
+    font-size: 14px;
+    position: absolute;
+    right: 9px;
+    top: 5px;
+    transition: color var(--duration-fast) var(--ease-standard);
+}
+
+#gating_download_panel #gating_exit:hover {
+    color: #ffffff;
+}
+
+#gating_download_panel label {
+    color: var(--text-secondary);
+    font-size: 12px;
+    margin-bottom: 8px;
+    width: 100%;
+}
+
+#gating_download_panel .download_flex {
+    display: flex;
+    gap: 7px;
+    margin-top: 4px;
+    width: 100%;
+}
+
+#gating_download_panel .download_flex input[type=text] {
+    background: var(--surface-1);
+    border: 1px solid var(--border-strong);
+    border-radius: 4px;
+    color: #eef3f8;
+    font-size: 11px;
+    min-width: 0;
+    padding: 5px;
+    width: 100%;
+}
+
+#gating_download_panel .download_button {
+    color: var(--accent-gate);
+    cursor: pointer;
+    font-size: 18px;
+    line-height: 1;
+    transition: transform var(--duration-fast) var(--ease-standard);
+}
+
+#gating_download_panel .download_button:hover {
+    transform: scale(1.1);
+}
+
+#gating_save_anndata_panel {
+    background: var(--surface-2);
+    border: 1px solid var(--border-strong);
+    border-radius: var(--radius-md);
+    box-shadow: var(--shadow-md);
+    color: #eef3f8;
+    margin-top: 8px;
+    /* Top padding leaves room for the absolutely-positioned close button,
+       matching #gating_download_panel above. */
+    padding: 28px 10px 12px;
+    position: relative;
+    width: 100%;
+}
+
+#gating_save_anndata_panel #save_anndata_exit {
+    color: var(--text-secondary);
+    font-size: 14px;
+    position: absolute;
+    right: 6px;
+    top: 4px;
+}
+
+#gating_save_anndata_panel #save_anndata_exit:hover {
+    color: #ffffff;
+}
+
+#gating_save_anndata_panel label {
+    color: var(--text-secondary);
+    display: block;
+    font-size: 12px;
+    margin-bottom: 8px;
+    width: 100%;
+}
+
+#gating_save_anndata_panel input[type=text] {
+    background: var(--surface-1);
+    border: 1px solid var(--border-strong);
+    border-radius: 4px;
+    color: #eef3f8;
+    font-size: 11px;
+    margin-top: 4px;
+    padding: 5px;
+    width: 100%;
+}
+
+#gating_save_anndata_panel .save-anndata-actions {
+    display: flex;
+    gap: 8px;
+    margin-top: 4px;
+}
+
+#gating_save_anndata_panel .save-anndata-actions .sidebar-action {
+    flex: 1;
+}
+
+#gating_save_anndata_panel #save_anndata_status {
+    font-size: 11px;
+    margin-top: 8px;
+    word-break: break-word;
+}
+
+#gating_save_anndata_panel #save_anndata_status.error {
+    color: #ff6b6b;
+}
+
+#gating_save_anndata_panel #save_anndata_status.success {
+    color: #2bd46f;
+}
+
+/* --- this plugin's own stylesheet, as it already was -------------------- */
+
+/* viewer.css also had `#channel_list, #csv_gating_list { ... }`. Every one of
+   its declarations is repeated identically below, so it was dropped on the way
+   out rather than moved. */
+#csv_gating_list {
+    width: 100%;
+    height: 80vh;
+    font-size: 10pt;
+    overflow-y: auto;
+    overflow-x: hidden;
+    box-shadow: 0 4px 8px 0 rgba(0, 0, 0, 0.2), 0 6px 20px 0 rgba(0, 0, 0, 0.19);
+
+}
+
+#csv_gating_list .list-group-item {
+    padding: .20rem 0.5rem;
+    border: 0;
+}
+
+#csv_gating_list .active {
+    background-color: rgba(0, 0, 0, 0.75);
+    border-top: 1px solid rgba(255, 255, 255, 0.5);
+    border-right: none;
+    border-bottom: 1px solid rgba(255, 255, 255, 0.5);
+    border-left: none;
+    height: 90px;
+}
+
+#csv_gating_list .list-group {
+    border-radius: 0rem;
+}
+
+#csv_gating_list_loader {
+    margin-left: 33px;
+}
+
+.auto-btn {
+    float: right;
+    padding-top: 0;
+    padding-bottom: 0;
+    border: 1px;
+}
+
+.distribution_line {
+    stroke: rgba(130, 130, 130, 0.5);
+    stroke-width: 4px;
+    fill: none;
+}
+
+.gmm_line {
+    stroke-width: 1px;
+    stroke-opacity: 0.75;
+    fill: none;
+}
+
+line.track {
+    stroke-width: 4px !important;
+}
+
+
+#drag-and-drop-text {
+    font-size: 30pt;
+    text-align: center;
+}
+
+#drag-and-drop-info {
+    display: none;
+}
+
+.dz-preview, .dz-file-preview {
+    display: none;
+}
+
+#arrow-upload-form, #arrow-upload-form * {
+    display: none
+}
+
+.viewer-sidebar #gating_download_panel {
+    background: #101721;
+    border: 1px solid rgba(255, 255, 255, 0.14);
+    border-radius: 8px;
+    box-shadow: 0 10px 28px rgba(0, 0, 0, 0.35);
+    color: #eef3f8;
+    left: 0;
+    margin: 0;
+    padding: 28px 10px 12px;
+    position: absolute;
+    right: 0;
+    top: auto;
+    visibility: hidden;
+    width: auto;
+    z-index: 105;
+}
+
+.viewer-sidebar #gate_marker_section #gating_download_panel {
+    top: 42px;
+}

plexora/plugins/gating/static/gatingApi.js

@@ -0,0 +1,221 @@
+/**
+ * GatingApi - this plugin's own HTTP client.
+ *
+ * These nine methods lived on core's DataLayer, which meant core shipped the
+ * URLs of a plugin's routes: `plugins/gating/save_gating_list` and friends were
+ * written into plexora/client/src/js/services/dataLayer.js. A core-only build
+ * carried them for a tool it did not have, and no third-party plugin could ever
+ * be given the same treatment -- it would have to bring its own client. Gating
+ * was privileged in exactly the way the plugin API exists to rule out.
+ *
+ * Nothing about the requests changed in the move. Only the two globals they
+ * reached for did: `plexoraUrl(...)` and the bare `datasource` are now
+ * `ctx.url(...)` and `ctx.datasource`, which is what makes these calls resolve
+ * correctly under a mounted deployment (PLEXORA_BASE_URL, e.g. Jupyter's proxy)
+ * instead of depending on core's script-scope names.
+ *
+ * Each method swallows its own errors, as it did on DataLayer. That is what hid
+ * `saveGatingList` failing outright for every call after `lassos` stopped being
+ * a parameter but stayed in the payload; tests/js/datalayer_globals_probe.mjs
+ * exists to catch a repeat, and points here.
+ */
+class GatingApi {
+
+    constructor(ctx) {
+        this.url = ctx.url;
+        this.datasource = ctx.datasource;
+    }
+
+    async getUploadedGatingCsvValues() {
+        try {
+            let response = await fetch(this.url('plugins/gating/get_uploaded_gating_csv_values') + '?' + new URLSearchParams({
+                datasource: this.datasource
+            }))
+            let response_data = await response.json();
+            return response_data;
+        } catch (e) {
+            console.log("Error Getting Uploaded Gates", e);
+        }
+    }
+
+    async getSavedGatingList() {
+        try {
+            let response = await fetch(this.url('plugins/gating/get_saved_gating_list') + '?' + new URLSearchParams({
+                datasource: this.datasource
+            }))
+            let response_data = await response.json();
+            return response_data;
+        } catch (e) {
+            console.log("Error Getting Saved Gating List", e);
+        }
+    }
+
+    downloadGatingCSV(channels, selections, selection_ids, fullCsv = false) {
+        let form = document.createElement("form");
+        form.action = this.url("plugins/gating/download_gating_csv");
+
+        form.method = "post";
+
+        let filename = '';
+        if (!fullCsv) {
+            filename = document.getElementById('download_input1').value;
+        }else{
+            filename = document.getElementById('download_input2').value;
+        }
+        let fileNameElemment = document.createElement("input");
+        fileNameElemment.type = "hidden";
+        fileNameElemment.value = _.toString(filename);
+        fileNameElemment.name = "filename";
+        form.appendChild(fileNameElemment);
+
+        let fullCsvElemment = document.createElement("input");
+        fullCsvElemment.type = "hidden";
+        fullCsvElemment.value = _.toString(fullCsv);
+        fullCsvElemment.name = "fullCsv";
+        form.appendChild(fullCsvElemment);
+
+        let encoding = document.getElementById('encoding').value;
+        let encodingElement = document.createElement("input");
+        encodingElement.type = "hidden";
+        encodingElement.value = _.toString(encoding);
+        encodingElement.name = "encoding";
+        form.appendChild(encodingElement);
+
+        let selectionsElement = document.createElement("input");
+        selectionsElement.type = "hidden";
+        selectionsElement.value = JSON.stringify(selections);
+        selectionsElement.name = "filter";
+        form.appendChild(selectionsElement);
+
+        let channelsElement = document.createElement("input");
+        channelsElement.type = "hidden";
+        channelsElement.value = JSON.stringify(channels);
+        channelsElement.name = "channels";
+        form.appendChild(channelsElement);
+
+
+        let idsElement = document.createElement("input");
+        idsElement.type = "hidden";
+        idsElement.value = JSON.stringify(selection_ids);
+        idsElement.name = "selection_ids";
+        form.appendChild(idsElement);
+
+        let datasourceElement = document.createElement("input");
+        datasourceElement.type = "hidden";
+        datasourceElement.value = this.datasource;
+        datasourceElement.name = "datasource";
+        form.appendChild(datasourceElement);
+
+        document.body.appendChild(form);
+        form.submit()
+    }
+
+    async saveGatingList(channels, selections) {
+        try {
+            let response = await fetch(this.url('plugins/gating/save_gating_list'), {
+                method: 'POST',
+                headers: {
+                    'Accept': 'application/json',
+                    'Content-Type': 'application/json'
+                },
+                body: JSON.stringify(
+                    {
+                        datasource: this.datasource,
+                        filter: selections,
+                        channels: channels
+                    }
+                )
+            });
+            let response_data = await response.json();
+            return response_data;
+        } catch (e) {
+            console.log("Error Saving Gating List", e);
+        }
+    }
+
+    async saveGatesToAnndata(tableName) {
+        let response = await fetch(this.url('plugins/gating/save_gates_to_anndata'), {
+            method: 'POST',
+            headers: {
+                'Accept': 'application/json',
+                'Content-Type': 'application/json'
+            },
+            body: JSON.stringify(
+                {
+                    datasource: this.datasource,
+                    table_name: tableName
+                }
+            )
+        });
+        let response_data = await response.json();
+        if (!response.ok || !response_data.success) {
+            throw new Error(response_data.error || 'Failed to save gates to AnnData');
+        }
+        return response_data;
+    }
+
+    async getGatesFromAnndata(tableName = "gates") {
+        try {
+            let response = await fetch(this.url('plugins/gating/get_gates_from_anndata') + '?' + new URLSearchParams({
+                datasource: this.datasource,
+                table_name: tableName
+            }));
+            let response_data = await response.json();
+            return response_data.success ? response_data.gates : {};
+        } catch (e) {
+            console.log("Error Getting Gates From AnnData", e);
+            return {};
+        }
+    }
+
+    async submitGatingUpload(formData) {
+        try {
+            formData.append('datasource', this.datasource);
+            let response = await fetch(this.url('plugins/gating/upload_gates'), {
+                method: "POST",
+                body: formData
+            })
+            let cell = await response.json();
+            return cell;
+        } catch (e) {
+            console.log("Error Getting Submitting Form Upload", e);
+        }
+    }
+
+    async getGatedCellIds(filter, start_keys) {
+        try {
+            let response = await fetch(this.url('plugins/gating/get_gated_cell_ids') + '?' + new URLSearchParams({
+                filter: JSON.stringify(filter),
+                start_keys: start_keys,
+                datasource: this.datasource
+            }))
+            let cellIds = await response.json();
+            return cellIds;
+        } catch (e) {
+            console.log("Error Getting Gated Cell Ids", e);
+        }
+    }
+
+    async getGatingGMM(channel, selection_ids) {
+        try {
+            let response = await fetch(this.url('plugins/gating/get_gating_gmm'), {
+                method: 'POST',
+                headers: {
+                    'Accept': 'application/json',
+                    'Content-Type': 'application/json'
+                },
+                body: JSON.stringify(
+                    {
+                        channel: channel,
+                        datasource: this.datasource,
+                        selection_ids: selection_ids
+                    }
+                )
+            });
+            let packet_gmm = await response.json();
+            return packet_gmm;
+        } catch (e) {
+            console.log("Error Getting Gating GMM", e);
+        }
+    }
+}