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🧹 Nitpick comments (1)
content/FLASHTnT/FLASHTnTViewer.py (1)
163-163: Consider updating initialization of per_scan_contentsWhile the key changes are effective, the initialization of
per_scan_contentsdictionary still uses the old'sequence_view'key which is no longer used in the code.-per_scan_contents = {'spectrum_view': False, 'sequence_view': False} +per_scan_contents = {'spectrum_view': False, 'fragment_ions': False}
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js-component/dist/assets/index-7a358364.jsis excluded by!**/dist/**js-component/dist/assets/index-d20033af.cssis excluded by!**/dist/**js-component/dist/index.htmlis excluded by!**/dist/**
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content/FLASHTnT/FLASHTnTViewer.py(2 hunks)openms-streamlit-vue-component(1 hunks)
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content/FLASHTnT/FLASHTnTViewer.py (1)
src/components.py (1)
SequenceView(90-92)
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🔇 Additional comments (5)
openms-streamlit-vue-component (1)
1-1:Details
❓ Verification inconclusive
Confirm submodule update commit
Please verify that the referenced commit00232c916e41a7c7ad7a1610dbfde7312107606fin theopenms-streamlit-vue-componentsubmodule exists upstream and contains the necessary support for the renamed'fragment_ions'key and the new download functionality in standalone mode.Run this script to validate the commit reference:
🏁 Script executed:
#!/bin/bash # Verify the commit exists in the submodule remote git ls-remote https://github.com/OpenMS/openms-streamlit-vue-component.git 00232c916e41a7c7ad7a1610dbfde7312107606fLength of output: 239
🏁 Script executed:
#!/bin/bash # Display .gitmodules to confirm the submodule URL echo "### .gitmodules ###" if [ -f .gitmodules ]; then cat .gitmodules else echo ".gitmodules not found" fi # Search codebase for any references to the submodule echo "### grep for openms-streamlit-vue-component references ###" grep -R "openms-streamlit-vue-component" -n .Length of output: 1839
🏁 Script executed:
#!/bin/bash # Verify the commit exists in the submodule remote at the correct URL(s) echo "### Checking HTTPS remote ###" git ls-remote https://github.com/t0mdavid-m/openms-streamlit-vue-component.git 00232c916e41a7c7ad7a1610dbfde7312107606f echo "" echo "### Checking SSH remote ###" git ls-remote git@github.com:t0mdavid-m/openms-streamlit-vue-component.git 00232c916e41a7c7ad7a1610dbfde7312107606fLength of output: 455
Submodule commit not found upstream
The commit00232c916e41a7c7ad7a1610dbfde7312107606fdoes not appear in thet0mdavid-m/openms-streamlit-vue-componentrepository (using both HTTPS and SSH remotes).• Please confirm that this commit SHA is correct and has been pushed to the submodule’s upstream branch.
• If it’s from a fork or private repo, ensure the URL in.gitmodulespoints to the correct remote containing this commit.content/FLASHTnT/FLASHTnTViewer.py (4)
181-181: Improved semantic namingThe change from
per_scan_contents['sequence_view']toper_scan_contents['fragment_ions']better represents the actual data that needs to be loaded rather than the component that uses it. This makes the code more intuitive and easier to maintain.
184-185: Key fix for fragment data loading in standalone modeThis addition directly addresses the issue where fragment data wasn't being loaded when the internal fragment map was used without the sequence view component. By setting the
'fragment_ions'flag toTruefor both components, the code ensures consistent data loading regardless of which component is present.
206-206: Consistent condition check for data loadingThis change completes the fix by updating the condition to check for the new
'fragment_ions'key instead of'sequence_view', ensuring the appropriate data frames are loaded when either component is present in the layout.
1-302:Details
❓ Verification inconclusive
Verify download feature mentioned in PR description
The PR objectives mention adding a download option for the fragment map, but this isn't evident in the provided code changes. This functionality is likely handled by the frontend component that's updated in the subproject reference (
openms-streamlit-vue-component).
🏁 Script executed:
#!/bin/bash # Check the commits in the subproject reference to verify implementation of download functionality git ls-tree -r HEAD | grep "openms-streamlit-vue-component" | awk '{print $3}' | xargs git showLength of output: 267
I’ll search for the grid component implementation and any “download” hooks in our codebase to confirm if the download feature is present.
🏁 Script executed:
#!/bin/bash # Locate the flash_viewer_grid_component definition rg -n "def flash_viewer_grid_component" --color never # Look for any references to "download" in our Python and configuration files rg -n "download" --color neverLength of output: 69021
I’ll inspect the download handling in
content/FLASHTnT/FLASHTnTDownload.pyto confirm if the fragment‐map download button is implemented:
🏁 Script executed:
#!/bin/bash # Show the download logic in FLASHTnTDownload.py sed -n '1,200p' content/FLASHTnT/FLASHTnTDownload.pyLength of output: 3114
Confirm fragment‐map download integration
The PR description notes adding a “Download” option for the fragment map in FLASHViewer, but:
- No download button or handler was added in
content/FLASHTnT/FLASHTnTViewer.pyor in theFlashViewerComponent.- The existing download page (
FLASHTnTDownload.py) zips experiment outputs (TSVs, mzMLs, JSONs) but does not include the fragment‐map visualization.- We found no references to an
openms-streamlit-vue-componentsubproject in this repo.Please verify:
- Has the front‑end component (e.g.
openms-streamlit-vue-component) been updated to emit a fragment‑map ZIP download?- Should the Streamlit viewer code include a download button or API call to expose that functionality?
🧰 Tools
🪛 Ruff (0.8.2)
53-53: Loop control variable
inot used within loop body(B007)
59-59: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
65-65: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
154-154: Ambiguous variable name:
l(E741)
195-195: Multiple statements on one line (colon)
(E701)
284-284: Loop control variable
exp_layoutnot used within loop bodyRename unused
exp_layoutto_exp_layout(B007)
285-285: Multiple statements on one line (colon)
(E701)
1 participant
This PR fixes an issue were fragment data was not loaded if the internal fragment map was operated standalone and adds a download option.
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