Add MSNet datasets#31
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Sequence DiagramsequenceDiagram
participant User as User
participant Info as Information View
participant Table as MSNetShow Component
participant API as API Layer
participant Data as Data/Endpoints
User->>Info: Open MSNet tab
Info->>API: getMSNet()
API->>Data: GET /data/MSNet.json
Data-->>API: return catalog
API-->>Info: catalog
Info->>Table: pass modelValue (datasets)
Table->>User: render table
User->>Table: expand row
Table->>Table: determine accession type
alt PXD prefix
Table->>API: getPrideDatasetDetails(path)
else other accession
Table->>API: getMSNetDatasetDetails(path)
end
API->>Data: fetch dataset endpoint
Data-->>API: dataset details
API-->>Table: details
Table->>Table: cache details
Table->>User: display detail panel
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~25 minutes Poem
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Actionable comments posted: 6
🧹 Nitpick comments (3)
src/views/information/index.vue (1)
50-52:@update:modelValuehandler is unused.The
MSNetTablecomponent doesn't emit anupdate:modelValueevent - themodelValueprop is treated as read-only. The handlertableDataMSNet = $eventwill never be triggered.This is consistent with the existing
Tablecomponent bindings, but if the intent is two-way binding,MSNetTablewould need to emit the event. If not needed, the handler could be removed for clarity.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@src/views/information/index.vue` around lines 50 - 52, The `@update`:modelValue handler on the MSNetTable binding is dead code because MSNetTable does not emit update:modelValue; remove the unused handler " `@update`:modelValue='tableDataMSNet = $event' " from the MSNetTable element (or alternatively implement emitting in MSNetTable if two-way binding is intended). Locate the MSNetTable usage that binds :modelValue="filterMSNetTable" and either delete the update handler to match the read-only prop or add an emit('update:modelValue', value) in the MSNetTable component where model changes occur to enable two-way binding with tableDataMSNet.src/components/MSNetShow/index.vue (2)
100-113: Accession link renders with emptyhrefwhen path is empty.When
scope.row.accession.pathis empty (which occurs for many entries inMSNet.json), theel-linkrenders with an emptyhref, creating a non-functional link that may confuse users.Consider conditionally rendering as plain text when no path exists:
Proposed fix
<el-table-column label="Accession" width="110"> <template `#default`="scope"> <div class="d-flex align-center"> - <el-link + <el-link + v-if="scope.row.accession.path" :href="scope.row.accession.path" type="primary" class="accession-link" > {{ scope.row.accession.id }} </el-link> + <span v-else class="accession-text">{{ scope.row.accession.id }}</span> </div> </template> </el-table-column>🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@src/components/MSNetShow/index.vue` around lines 100 - 113, The Accession column in the MSNetShow component currently always renders an el-link with :href="scope.row.accession.path", resulting in an empty/non-functional link when scope.row.accession.path is falsy; update the template inside the el-table-column so it conditionally renders the clickable el-link only when scope.row.accession.path is a non-empty string and otherwise renders plain text (scope.row.accession.id) or a visually identical span, using a v-if/v-else (or equivalent conditional) around the el-link and the fallback, keeping the existing class "accession-link" for styling consistency.
268-271: EmptyonMountedhook serves no purpose.The
onMountedhook contains only a comment and no actual logic. It can be removed.-// Lifecycle hooks -onMounted(() => { - // Initialize component -});🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@src/components/MSNetShow/index.vue` around lines 268 - 271, Remove the empty onMounted hook in MSNetShow (the onMounted(() => { /* Initialize component */ }); block) since it has no logic; delete the entire block and then remove the onMounted import from the component's script setup if it is no longer used elsewhere to avoid an unused import.
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@public/data/MSNet.json`:
- Around line 10-13: The JSON has empty accession.path values which cause
getMSNetDatasetDetails(row.accession.path) in MSNetShow/index.vue (inside
handleExpandChange) to request an invalid URL; either populate valid paths in
the MSNet.json entries (replace "" with the correct dataset path string for
accession id like "HuiYan-Bat") or add a guard in MSNetShow/index.vue: before
calling getMSNetDatasetDetails, check if row.accession.path is a non-empty
string and if not, skip the fetch and set the row state to display "No details
available" (or return early from handleExpandChange), ensuring no network call
is made for empty paths.
- Around line 1305-1324: Update the reanalysis "path" values that currently
start with "XD014877-..." to include the missing leading "P" so they read
"PXD014877-..."; specifically edit the objects under the "reanalysis" arrays
where accession id "PXD014877" is used (look for the "path" key in those
reanalysis entries) and change "XD014877-Gossypium", "XD014877-Roseburia", and
"XD014877-Akkermansia_muciniphilia" to "PXD014877-Gossypium",
"PXD014877-Roseburia", and "PXD014877-Akkermansia_muciniphilia" respectively so
the URLs match the accession ID pattern.
In `@src/components/MSNetShow/index.vue`:
- Around line 29-44: The template is checking a non-existent
props.row.title.pubmedId; replace that check and the publication link loop to
pull pubmed IDs from the actual data path (e.g., props.row.reanalysis array or
datasetDetails[props.row.accession.id].references) — update the v-if from
props.row.title.pubmedId to something real like props.row.reanalysis &&
props.row.reanalysis.length and change the v-for to iterate the correct
collection (e.g., v-for="pub in props.row.reanalysis" or v-for="pub in
datasetDetails[props.row.accession.id].references") and use the correct field
name (pub.pubmedId or pub.pubmedID) when generating the link and key so the
publication-links section renders.
- Around line 303-336: The handler handleExpandChange should guard against empty
accession.path before calling getMSNetDatasetDetails: if row.accession.id does
not startWith('PXD') and row.accession.path is falsy/empty, avoid calling
getMSNetDatasetDetails, set a sensible placeholder in
datasetDetails.value[row.accession.id] (e.g., title/description set to empty
strings or "Unavailable") and skip the network request (still clear
loading.value in finally or immediately), otherwise proceed with the API call as
before; update references to getMSNetDatasetDetails, datasetDetails, and
row.accession.path in the function to implement this guard and ensure no invalid
requests are made.
- Around line 344-353: The onSortChange handler must handle order === null
(clear sort) instead of treating it as descending; update the onSortChange
function to check if order is null and, if so, restore sortedData to the
original unsorted array (e.g., use a preserved copy like originalData or the
incoming props data via originalData.value.slice()) and return early; otherwise
compute sortOrder as before and perform the sort using sortedData.value.sort
with the existing comparator using prop and order.
- Around line 321-329: The non-PXD branch that calls getMSNetDatasetDetails
builds a details object with labHead/submitter but the template expects labPIs,
submitters, keywords, references, submissionDate, publicationDate, and doi;
update the non-PXD mapping in the block that constructs details so it populates
those template fields (e.g., map response.data.principal_investigator -> labPIs
as an array, response.data.submitter -> submitters, and set
keywords/references/submissionDate/publicationDate/doi from available response
fields or null/empty defaults), and/or add conditional rendering in the template
around the sections that reference
labPIs/submitters/keywords/references/submissionDate/publicationDate/doi so
missing fields don’t break rendering; locate the construction in the else branch
that calls getMSNetDatasetDetails and the template references of
labPIs/submitters/keywords/references/submissionDate/publicationDate/doi to
implement either mapping or conditionals.
---
Nitpick comments:
In `@src/components/MSNetShow/index.vue`:
- Around line 100-113: The Accession column in the MSNetShow component currently
always renders an el-link with :href="scope.row.accession.path", resulting in an
empty/non-functional link when scope.row.accession.path is falsy; update the
template inside the el-table-column so it conditionally renders the clickable
el-link only when scope.row.accession.path is a non-empty string and otherwise
renders plain text (scope.row.accession.id) or a visually identical span, using
a v-if/v-else (or equivalent conditional) around the el-link and the fallback,
keeping the existing class "accession-link" for styling consistency.
- Around line 268-271: Remove the empty onMounted hook in MSNetShow (the
onMounted(() => { /* Initialize component */ }); block) since it has no logic;
delete the entire block and then remove the onMounted import from the
component's script setup if it is no longer used elsewhere to avoid an unused
import.
In `@src/views/information/index.vue`:
- Around line 50-52: The `@update`:modelValue handler on the MSNetTable binding is
dead code because MSNetTable does not emit update:modelValue; remove the unused
handler " `@update`:modelValue='tableDataMSNet = $event' " from the MSNetTable
element (or alternatively implement emitting in MSNetTable if two-way binding is
intended). Locate the MSNetTable usage that binds :modelValue="filterMSNetTable"
and either delete the update handler to match the read-only prop or add an
emit('update:modelValue', value) in the MSNetTable component where model changes
occur to enable two-way binding with tableDataMSNet.
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📒 Files selected for processing (4)
public/data/MSNet.jsonsrc/api/getTable.jssrc/components/MSNetShow/index.vuesrc/views/information/index.vue
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Actionable comments posted: 4
♻️ Duplicate comments (5)
src/components/MSNetShow/index.vue (4)
344-353:⚠️ Potential issue | 🟡 MinorRestore original order when Element Plus clears sorting.
When
orderbecomesnull, this code currently falls through the descending branch and keeps mutatingsortedData. Clear-sort should reset to the unsortedprops.modelValueorder instead.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@src/components/MSNetShow/index.vue` around lines 344 - 353, The onSortChange handler currently treats any non-"ascending" order as descending and continues mutating sortedData; modify onSortChange so when order is null it restores the original sequence from props.modelValue (e.g., set sortedData.value = [...props.modelValue] or otherwise reassign the original array) and return early; otherwise keep the existing sort logic that computes sortOrder and sorts sortedData.value by prop. Ensure you reference onSortChange, sortedData, and props.modelValue when making the change.
321-322:⚠️ Potential issue | 🟠 MajorGuard empty non-PXD paths before calling
getMSNetDatasetDetails().
public/data/MSNet.jsonstill includes rows likeHuiYan-BatandHuiYan-E480withaccession.path: "". Expanding those rows will call the API helper with an empty URL instead of showing a "no details" state.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@src/components/MSNetShow/index.vue` around lines 321 - 322, The code calls getMSNetDatasetDetails(row.accession.path) even when row.accession.path is an empty string; add a guard around the expansion logic (where the else branch runs) to check row.accession?.path (or Boolean(row.accession.path)) and only call getMSNetDatasetDetails when it is non-empty, otherwise set the component's detail state to the "no details" state (e.g., null or a dedicated flag) so empty non-PXD rows like HuiYan-Bat / HuiYan-E480 do not trigger an API call.
323-328:⚠️ Potential issue | 🟠 MajorMap non-PXD detail responses to the template's object shape.
Here
labPIsandsubmittersare assigned raw strings, while the template treats them as arrays of person objects and also expectskeywords,references,submissionDate,publicationDate, anddoi. Those panels won't render correctly for non-PXD rows.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@src/components/MSNetShow/index.vue` around lines 323 - 328, The details object assignment is populating labPIs and submitters as raw strings and omitting expected fields (keywords, references, submissionDate, publicationDate, doi), causing the template (which expects arrays of person objects and those fields) to break; update the mapping where details is built (the details = { ... } block) to convert response.data.principal_investigator and response.data.submitter into arrays of person objects (e.g., [{ name: ... }]) when they are strings, and provide safe defaults for keywords (empty array), references (empty array), submissionDate/publicationDate (null or formatted date), and doi (empty string) so the template panels can render for non-PXD rows. Ensure you perform type checks on response.data.* before mapping to avoid runtime errors and keep the property names exactly as used by the template (labPIs, submitters, keywords, references, submissionDate, publicationDate, doi).
27-39:⚠️ Potential issue | 🟠 MajorUse the actual publication data source here.
props.rowhas no top-leveltitle.pubmedIdfield inpublic/data/MSNet.json; this dereference cannot resolve valid publication links and can error once the expand panel renders.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@src/components/MSNetShow/index.vue` around lines 27 - 39, The template is referencing a non-existent field props.row.title.pubmedId; open public/data/MSNet.json to determine the actual publications array (for example it may be props.row.publications or props.row.title.publications) and update the v-if, v-for and :key/:href bindings in the MSNetShow component to use that real field (replace props.row.title.pubmedId everywhere), and add a safe presence check (optional chaining or check length) before rendering to prevent runtime errors.public/data/MSNet.json (1)
1538-1540:⚠️ Potential issue | 🟡 MinorFix the remaining
XD014877path typos.These two reanalysis URLs still drop the leading
P, so they no longer match accessionPXD014877and will point users at the wrong directory.Suggested fix
- "path": "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-collections/msnet/XD014877-Roseburia/" + "path": "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-collections/msnet/PXD014877-Roseburia/" ... - "path": "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-collections/msnet/XD014877-Akkermansia_muciniphilia/" + "path": "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-collections/msnet/PXD014877-Akkermansia_muciniphilia/"Also applies to: 1727-1729
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@public/data/MSNet.json` around lines 1538 - 1540, The JSON entries for the PXD014877 reanalysis still have paths missing the leading "P" (e.g., the "path" value containing ".../msnet/XD014877-Roseburia/"); update those "path" strings to include the correct accession prefix "P" (change "XD014877-..." to "PXD014877-...") for the object with "id": 1 and "title": "PXD014877" and apply the same fix to the other affected entries referenced around lines 1727-1729 so the URLs point to the correct directories.
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@public/data/MSNet.json`:
- Around line 52-55: The accession.path entries in public/data/MSNet.json are
using plain http and cause mixed-content failures when getMSNetDatasetDetails()
in src/components/MSNetShow/index.vue fetches them from the browser; update
those accession.path URLs to use https (or point them to your server-side proxy
endpoint) for every IPX entry (e.g., the objects with "accession": { "id":
"...", "path": "http://..." }) so the client fetches via HTTPS (or the proxy)
and avoid mixed-content blocking.
- Around line 1819-1823: The Superkingdom metadata for the entry with "Species":
"Riftia pachyptila" is incorrect (currently "Superkingdom": "Prokaryote");
update that value to the correct taxonomic kingdom "Eukaryote" so the record is
grouped properly (look for the JSON object containing the "Species": "Riftia
pachyptila" key and change its "Superkingdom" field to "Eukaryote").
- Around line 1874-1877: The HSV entry in public/data/MSNet.json (object with
"id": 1 and "title": "PXD019483") incorrectly reuses the VSV reanalysis path
("PXD019483_VSV/"); update the HSV object's "path" value to the correct HSV
reanalysis path (or remove the duplicate HSV object if it should not exist) so
it does not point to "PXD019483_VSV/"; locate the HSV record by searching for
the "Species": "HSV" entry near the object with "title": "PXD019483" and change
its "path" field to the proper HSV-specific directory name (or delete the
duplicate object) and ensure no two entries share the same accession/path.
In `@src/components/MSNetShow/index.vue`:
- Around line 101-110: The accession links in MSNetShow bind directly to
scope.row.accession.path which is empty for many PXD rows; change the template
to bind :href to a helper (e.g., getAccessionHref(scope.row.accession)) and
implement getAccessionHref(accession) in the MSNetShow component to return
accession.path when present, otherwise build a sensible fallback using
accession.id (for example an internal dataset route or the external PRIDE URL
for PXD IDs) so links point to a browsable dataset page instead of a dead/JSON
response.
---
Duplicate comments:
In `@public/data/MSNet.json`:
- Around line 1538-1540: The JSON entries for the PXD014877 reanalysis still
have paths missing the leading "P" (e.g., the "path" value containing
".../msnet/XD014877-Roseburia/"); update those "path" strings to include the
correct accession prefix "P" (change "XD014877-..." to "PXD014877-...") for the
object with "id": 1 and "title": "PXD014877" and apply the same fix to the other
affected entries referenced around lines 1727-1729 so the URLs point to the
correct directories.
In `@src/components/MSNetShow/index.vue`:
- Around line 344-353: The onSortChange handler currently treats any
non-"ascending" order as descending and continues mutating sortedData; modify
onSortChange so when order is null it restores the original sequence from
props.modelValue (e.g., set sortedData.value = [...props.modelValue] or
otherwise reassign the original array) and return early; otherwise keep the
existing sort logic that computes sortOrder and sorts sortedData.value by prop.
Ensure you reference onSortChange, sortedData, and props.modelValue when making
the change.
- Around line 321-322: The code calls getMSNetDatasetDetails(row.accession.path)
even when row.accession.path is an empty string; add a guard around the
expansion logic (where the else branch runs) to check row.accession?.path (or
Boolean(row.accession.path)) and only call getMSNetDatasetDetails when it is
non-empty, otherwise set the component's detail state to the "no details" state
(e.g., null or a dedicated flag) so empty non-PXD rows like HuiYan-Bat /
HuiYan-E480 do not trigger an API call.
- Around line 323-328: The details object assignment is populating labPIs and
submitters as raw strings and omitting expected fields (keywords, references,
submissionDate, publicationDate, doi), causing the template (which expects
arrays of person objects and those fields) to break; update the mapping where
details is built (the details = { ... } block) to convert
response.data.principal_investigator and response.data.submitter into arrays of
person objects (e.g., [{ name: ... }]) when they are strings, and provide safe
defaults for keywords (empty array), references (empty array),
submissionDate/publicationDate (null or formatted date), and doi (empty string)
so the template panels can render for non-PXD rows. Ensure you perform type
checks on response.data.* before mapping to avoid runtime errors and keep the
property names exactly as used by the template (labPIs, submitters, keywords,
references, submissionDate, publicationDate, doi).
- Around line 27-39: The template is referencing a non-existent field
props.row.title.pubmedId; open public/data/MSNet.json to determine the actual
publications array (for example it may be props.row.publications or
props.row.title.publications) and update the v-if, v-for and :key/:href bindings
in the MSNetShow component to use that real field (replace
props.row.title.pubmedId everywhere), and add a safe presence check (optional
chaining or check length) before rendering to prevent runtime errors.
ℹ️ Review info
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Review profile: CHILL
Plan: Pro
Run ID: 20f72177-f325-4103-8448-63b306e6ffc5
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public/data/MSNet.jsonsrc/components/MSNetShow/index.vue
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Actionable comments posted: 2
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@public/data/MSNet.json`:
- Line 1591: Fix the misspelled Superkingdom value "Archea" to "Archaea"
wherever it occurs in the JSON entries; specifically update the "Superkingdom"
field for the records with "Species": "Halobacterium sp" and "Species":
"Sulfolobus solfataricus" (and any other entries that use "Archea") so
grouping/filtering by Superkingdom is consistent.
- Line 1790: Fix the typos in the species entries: remove the trailing space in
the "Phaeodactylum tricornutum " string (make it "Phaeodactylum tricornutum"),
correct "Vitris vinifera" to "Vitis vinifera", and correct "Saccharomyces
cerevisia" to "Saccharomyces cerevisiae"; update the exact JSON string values
shown in the file so quotes and JSON formatting remain valid and no extra
whitespace is left.
ypriverol
approved these changes
Mar 11, 2026
This was referenced Apr 10, 2026
Merged
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Summary by CodeRabbit
New Features
New Data