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WalkthroughUI in FLASHDeconv and FLASHTnT adds per-row rename/edit, moves to workspace-level cache paths, and switches dropdowns to display-name mappings. Download ZIP creation now excludes archives and uses display names. FileManager gains helpers for listing, display names, renaming, existence checks, and storage. Large example-data configurations and generated files are removed. Changes
Sequence Diagram(s)sequenceDiagram
autonumber
actor U as User
participant UI as Download Page
participant FM as FileManager
Note over UI: Per-row edit
U->>UI: Click "Edit"
UI->>UI: Toggle edit_mode[experiment]=True
U->>UI: Enter new_name + Save
UI->>UI: Validate (non-empty, <=100 chars)
UI->>FM: rename_dataset(experiment, new_name)
FM-->>UI: success/failure
UI->>UI: Exit edit_mode, rerun on success
sequenceDiagram
autonumber
actor U as User
participant UI as Download Page
participant FM as FileManager
Note over UI: Prepare ZIP using display name
U->>UI: Click "Prepare Download"
UI->>FM: get_display_name(experiment)
FM-->>UI: current_name
UI->>FM: get_all_files_except(experiment, ['download_archive'])
FM-->>UI: files (paths)
UI->>FM: store_file(experiment,'download_archive', zip_stream, current_name+".zip")
FM-->>UI: stored
UI-->>U: Download button: current_name.zip
sequenceDiagram
autonumber
actor U as User
participant V as Viewer (Deconv/FTnT)
participant FM as FileManager
V->>FM: get_results_list([...])
FM-->>V: experiments (IDs)
V->>FM: get_display_name(id) * N
FM-->>V: display_names
U->>V: Select display name
V->>V: Map to id via display_name_to_id
V->>V: Validate index via display_name_to_index
Note over V: Use id for downstream rendering
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~25 minutes Possibly related PRs
Poem
Pre-merge checks and finishing touches❌ Failed checks (1 warning, 1 inconclusive)
✅ Passed checks (1 passed)
✨ Finishing touches
🧪 Generate unit tests (beta)
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📒 Files selected for processing (53)
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- example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250525-204033/toppic_ms2.feature
- example-data/workspaces/workshop/flashtnt/cache/files/example_fd_20250823-151911/toppic_ms2.feature
- example-data/workspaces/workshop/flashdeconv/cache/files/example_fd_20250823-152120/FD_parameters.json
- example-data/workspaces/workshop/flashtnt/cache/files/example_spectrum_antibody_20250525-204021/toppic_ms2.feature
🧰 Additional context used
🧬 Code graph analysis (4)
content/FLASHDeconv/FLASHDeconvViewer.py (2)
content/FLASHTnT/FLASHTnTViewer.py (1)
validate_selected_index(27-39)src/workflow/FileManager.py (2)
get_results_list(392-430)get_display_name(563-595)
content/FLASHTnT/FLASHTnTViewer.py (3)
content/FLASHDeconv/FLASHDeconvViewer.py (2)
validate_selected_index(21-31)select_experiment(12-19)src/workflow/FileManager.py (2)
get_results_list(392-430)get_display_name(563-595)src/render/render.py (1)
render_grid(54-105)
content/FLASHTnT/FLASHTnTDownload.py (1)
src/workflow/FileManager.py (3)
get_display_name(563-595)rename_dataset(597-633)get_all_files_except(484-510)
content/FLASHDeconv/FLASHDeconvDownload.py (1)
src/workflow/FileManager.py (3)
get_display_name(563-595)rename_dataset(597-633)get_all_files_except(484-510)
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- GitHub Check: build-full-app
- GitHub Check: build-openms
Comment on lines
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| # Create display names and mappings | ||
| display_names = [file_manager.get_display_name(exp_id) for exp_id in results] | ||
| display_name_to_id = {file_manager.get_display_name(exp_id): exp_id for exp_id in results} | ||
| display_name_to_index = {n : i for i, n in enumerate(display_names)} | ||
| # Keep backward compatibility mapping for experiment IDs |
Contributor
There was a problem hiding this comment.
Duplicate display names hijack viewer selections.
Here too we key both display_name_to_id and display_name_to_index by the human-friendly label. If two runs share the same name (perfectly possible after renaming), the later entry clobbers the earlier one. The dropdown then always resolves to the last dataset with that label, so the wrong experiment loads and previously stored selections jump indices. Please keep the dataset ID as the canonical option value—e.g. pass results to the selectbox and supply a format_func that renders file_manager.get_display_name(exp_id)—or otherwise guarantee uniqueness when building the mapping.
🤖 Prompt for AI Agents
In content/FLASHDeconv/FLASHDeconvViewer.py around lines 70-74, the mappings use
human-friendly display names as keys which allows duplicate names to clobber
earlier entries; change the select/options to use the canonical experiment ID as
the option value (i.e. use results list/IDs as the selectbox values) and render
the label with a format_func that calls file_manager.get_display_name(exp_id),
or alternatively build maps keyed by exp_id (display_name_to_id =>
id->display_name and display_name_to_index => id->index) so every option is
unique and selections reliably map back to the correct experiment ID.
Comment on lines
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| # Create display names and mappings | ||
| display_names = [file_manager.get_display_name(exp_id) for exp_id in results] | ||
| display_name_to_id = {file_manager.get_display_name(exp_id): exp_id for exp_id in results} | ||
| display_name_to_index = {n : i for i, n in enumerate(display_names)} | ||
| # Keep backward compatibility mapping for experiment IDs | ||
| name_to_index = {n : i for i, n in enumerate(results)} | ||
|
|
||
| if len(layout) == 2 and side_by_side: |
Contributor
There was a problem hiding this comment.
Display-name collisions break experiment selection.
display_name_to_id / display_name_to_index use the display name as the dictionary key. After renaming, two experiments can legitimately share the same display name. In that case the later entry overwrites the former, so selecting the “other” duplicate in the dropdown resolves to the wrong dataset (and its index lookup also points to the last duplicate). We need the widget to keep the unique dataset ID as the underlying value—e.g. feed the selectbox with the results list and use format_func (or an expanded tuple) to render the display name—so every selection keeps its own ID while still showing friendly text. That avoids collisions without forcing unique display names.
🤖 Prompt for AI Agents
In content/FLASHTnT/FLASHTnTViewer.py around lines 67 to 74, display_name_to_id
and display_name_to_index use display names as keys which allows collisions to
overwrite entries; change the select widget to use the unique experiment IDs
(the entries from results) as the underlying values and render friendly text via
format_func or by passing (id, display_name) tuples so selections always map to
the correct dataset ID; replace the display-name-keyed dicts with mappings keyed
by experiment ID (e.g., id -> display_name and id -> index) and feed the
selectbox the results list (or id tuples) while using format_func to show
file_manager.get_display_name(id).
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Shares files between TnT and Deconv. Also allows users to rename files.
Summary by CodeRabbit
New Features
Refactor
Chores