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magnuleiclaude
magnulei
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claude
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Upgrade itables to 2.9.1 with Scroller, ColReorder, and layout fixes
- Bump itables 2.7.3 -> 2.9.1; enable Scroller (virtual scrolling), deferRender, and ColReorder on the Projects/Samples/Sequencing tables - Fix white table background and residual page scrollbar introduced by itables' dark-mode CSS and the desktop zoom scale hack; dynamically fit table height to the viewport instead of a fixed vh value - Switch column filters to table headers, fix the resulting blank column-visibility labels, and rename Search Builder to Filter Builder - Reorganize the toolbar (move Select All/Deselect Filtered Rows and Export into the Filter section) and enable the SearchBuilder rename via language.searchBuilder - Truncate long text columns (NIRD Filename, Reagent Label, Comment, Billing Description, Experiment Name, Species) with a hover tooltip for the full value instead of letting the column stretch unbounded - Add feature/itables-2.9.1 to the deploy workflow's push trigger to update the test Posit instance; deploy_mode.txt stays on test Refs #78, #3 Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
1 parent 38ce68d commit 6defdfd

9 files changed

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‎.github/workflows/deploy.yml‎

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@@ -8,7 +8,7 @@ on:
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push:
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branches:
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- main # Trigger when pushing to main
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- feature/run-to-samples-filter
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- feature/itables-2.9.1
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jobs:
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update-branches:
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env:

‎deploy_mode.txt‎

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@@ -1 +1 @@
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prod
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test

‎pyproject.toml‎

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@@ -10,7 +10,7 @@ readme = "README.md"
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requires-python = ">=3.11.5"
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dependencies = [
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"faicons==0.2.2",
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"itables==2.7.3",
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"itables==2.9.1",
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"pandas==2.2.2",
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"pins==0.8.5",
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"psycopg[binary]>=3.3.3,<4",

‎src/shinylims/assets/styles.css‎

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@@ -17,6 +17,13 @@
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--text-muted: rgba(9, 26, 62, 0.76);
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--shadow-soft: 0 4px 12px rgba(9, 26, 62, 0.05);
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--shadow-hover: 0 10px 24px rgba(28, 79, 185, 0.12);
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/* itables >=2.9 paints its widget/table container with this instead of
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leaving it transparent; match the app background so it doesn't show
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as a white block against --surface-page. itables injects its own
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:root/:host rule for this variable via an inline <style> tag added
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to <head> after this stylesheet loads, so !important is required to
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win the cascade regardless of load order. */
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--dt-html-background: var(--surface-page) !important;
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}
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html,
@@ -107,7 +114,10 @@ table.dataTable td.left-column {
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/* Modal Backdrop Fix for Scaled UI */
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/* ─────────────────────────────────────────────────────────────── */
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/* Ensures modal backdrop covers entire viewport even after scaling */
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/* Ensures modal backdrop covers entire viewport even after scaling. The
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backdrop is a child of body, so it's shrunk by body's own `zoom` just
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like everything else; scale it back up by zoom's inverse so it still
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spans the true viewport instead of only 80% of it. */
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.modal-backdrop {
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position: fixed !important;
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top: 0 !important;
@@ -1358,13 +1368,14 @@ div.dt-button-collection:has(.dtsb-searchBuilder) {
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/* ─────────────────────────────────────────────────────────────── */
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@media (min-width: 992px) {
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/* Scale entire app to 80% while compensating the width and height */
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/* Shrink the entire app to 80% on desktop widths. `zoom` (unlike
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`transform: scale`) resizes the actual layout box rather than just the
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painted output, so body's real height/width already match what's
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visible on screen -- no width/height/position compensation hack needed,
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and no artificially inflated scrollHeight causing a residual outer
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scrollbar. */
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body {
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transform: scale(0.8);
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transform-origin: top left;
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width: 125%;
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height: 125%;
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position: absolute;
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zoom: 0.8;
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}
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/* Expand wrapper and table elements fully */

‎src/shinylims/features/projects.py‎

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@@ -9,7 +9,9 @@
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import pandas as pd
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from shinylims.ui_helpers.table_controls import (
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COLVIS_COLUMN_TEXT,
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DATE_VALUE_RENDERER,
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FILTER_BUILDER_LANGUAGE,
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build_filter_status_bar,
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clear_all_filters_script,
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deselect_all_columns_button,
@@ -68,14 +70,18 @@ def projects_table():
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return ITable(
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dat,
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select=True,
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layout={"topStart": "buttons", "topEnd": "search"},
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column_filters="footer",
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layout={"topStart": "buttons", "topEnd": "search", "bottomEnd": None},
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column_filters="header",
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search={"smart": True, "regex": True, "caseInsensitive": True},
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lengthMenu=[[200, 500, 1000, 2000, -1], [200, 500, 1000, 2000, "All"]],
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classes="compact hover order-column cell-border",
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scrollY="84vh",
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scrollX=True,
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paging=True,
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scroller=True,
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deferRender=True,
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colReorder=True,
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language=FILTER_BUILDER_LANGUAGE,
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maxBytes=0,
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allow_html=True,
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autoWidth=True,
@@ -86,6 +92,7 @@ def projects_table():
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"extend": "colvis",
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"text": "Selection",
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"collectionLayout": "two-column",
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"columnText": COLVIS_COLUMN_TEXT,
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},
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{
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"extend": "collection",
@@ -95,8 +102,8 @@ def projects_table():
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deselect_all_columns_button(),
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],
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},
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{"extend": "spacer", "style": "bar", "text": "Rows"},
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"pageLength",
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{"extend": "spacer", "style": "bar", "text": "Filter"},
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{"extend": "searchBuilder"},
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{"extend": "spacer", "style": "bar", "text": "Export"},
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{
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"extend": "collection",
@@ -121,8 +128,6 @@ def projects_table():
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},
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],
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},
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{"extend": "spacer", "style": "bar", "text": "Filter"},
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{"extend": "searchBuilder"},
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{"extend": "spacer", "style": "bar"},
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],
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order=[[order_column_index, "desc"]],

‎src/shinylims/features/samples.py‎

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@@ -9,13 +9,16 @@
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import pandas as pd
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import io
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from shinylims.ui_helpers.table_controls import (
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COLVIS_COLUMN_TEXT,
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DATE_VALUE_RENDERER,
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FILTER_BUILDER_LANGUAGE,
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batch_filter_button,
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build_filter_status_bar,
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clear_all_filters_script,
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deselect_all_columns_button,
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filter_state_draw_callback,
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select_all_columns_button,
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truncated_text_renderer,
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visibility_preset_button,
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)
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import re
@@ -440,17 +443,27 @@ def data_samples():
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column_index = 0
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date_column_index = -1
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# Indices for columns whose content is truncated with a hover tooltip
447+
nird_filename_index = dat.columns.get_loc("NIRD Filename") if "NIRD Filename" in dat.columns else -1
448+
experiment_name_index = dat.columns.get_loc("Experiment Name") if "Experiment Name" in dat.columns else -1
449+
billing_description_index = dat.columns.get_loc("Billing Description") if "Billing Description" in dat.columns else -1
450+
reagent_label_index = dat.columns.get_loc("Reagent Label") if "Reagent Label" in dat.columns else -1
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443452
return ITable(
444453
dat,
445454
select=True,
446-
layout={"topStart": "buttons", "topEnd": "search"},
455+
layout={"topStart": "buttons", "topEnd": "search", "bottomEnd": None},
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lengthMenu=[[200, 500, 1000, 2000, -1], [200, 500, 1000, 2000, "All"]],
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column_filters="footer",
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column_filters="header",
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search={"smart": True},
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classes="nowrap compact hover order-column cell-border",
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scrollY="84vh",
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scrollX=True,
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paging=True,
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scroller=True,
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deferRender=True,
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colReorder=True,
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language=FILTER_BUILDER_LANGUAGE,
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autoWidth=True,
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maxBytes=0,
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allow_html=True,
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"extend": "colvis",
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"text": "Selection",
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"collectionLayout": "two-column",
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"columnText": COLVIS_COLUMN_TEXT,
467481
},
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{
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"extend": "collection",
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visibility_preset_button([2, 3, 4, 5, 9, 10, 21]),
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]
476490
},
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# ── Row settings ──────────────────────────────────────────
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{'extend': "spacer",
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'style': 'bar',
480-
'text': 'Rows'},
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"pageLength",
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'text': 'Filter'},
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batch_filter_button(),
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{"extend": "searchBuilder"},
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{
483497
"text": "☑️ Select All Filtered Rows",
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"action": JavascriptFunction("""
@@ -497,29 +511,25 @@ def data_samples():
497511
}
498512
""")
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},
500-
# ── Export ────────────────────────────────────────────────
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{'extend': "spacer",
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'style': 'bar',
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'text': 'Export'},
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{
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"extend": "collection",
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"text": "📤 Export",
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"buttons": [
508-
# Export to CSV — selected rows, visible columns
509521
{
510522
"extend": "csvHtml5",
511523
"exportOptions": {"columns": ":visible"},
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"text": "📄 Export to CSV",
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"title": "Sample Data Export"
514526
},
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# Export to Excel — selected rows, visible columns
516527
{
517528
"extend": "excelHtml5",
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"exportOptions": {"columns": ":visible"},
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"text": "📊 Export to Excel",
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"title": "Sample Data Export"
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},
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# Send selected rows to SAGA via FTP — triggers Shiny server logic
523533
{
524534
"text": "🖥️ Send to SAGA for ATLAS",
525535
"action": JavascriptFunction("""
@@ -537,11 +547,6 @@ def data_samples():
537547
},
538548
]
539549
},
540-
{'extend': "spacer",
541-
'style': 'bar',
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'text': 'Filter'},
543-
batch_filter_button(),
544-
{"extend": "searchBuilder"},
545550
{'extend': "spacer",
546551
'style': 'bar'},
547552
],
@@ -554,7 +559,31 @@ def data_samples():
554559
"targets": date_column_index,
555560
"type": "date",
556561
"render": DATE_VALUE_RENDERER
557-
}
562+
},
563+
{
564+
"targets": nird_filename_index,
565+
"className": "left-column",
566+
"width": "805px",
567+
"render": truncated_text_renderer(max_chars=172, max_width_px=805),
568+
} if nird_filename_index != -1 else {},
569+
{
570+
"targets": experiment_name_index,
571+
"className": "left-column",
572+
"width": "260px",
573+
"render": truncated_text_renderer(max_chars=60, max_width_px=260),
574+
} if experiment_name_index != -1 else {},
575+
{
576+
"targets": billing_description_index,
577+
"className": "left-column",
578+
"width": "320px",
579+
"render": truncated_text_renderer(max_chars=100, max_width_px=320),
580+
} if billing_description_index != -1 else {},
581+
{
582+
"targets": reagent_label_index,
583+
"className": "left-column",
584+
"width": "690px",
585+
"render": truncated_text_renderer(max_chars=156, max_width_px=690),
586+
} if reagent_label_index != -1 else {},
558587
]
559588
)
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