Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: relax requirements on minimum information model components for … #264

Merged
merged 4 commits into from
Oct 3, 2023
Merged

feat: relax requirements on minimum information model components for … #264

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
72b0814
feat: relax requirements on minimum information model components for …
katiestahl Sep 6, 2023
eefc195
feat: relaxing requirements on minimum information model components
katiestahl Sep 14, 2023
bd9dbbb
feat: relaxing requirements on minimum information model for nomencla…
katiestahl Sep 25, 2023
8f98f1d
Merge branch 'staging' of https://github.com/cancervariants/fusion-cu…
katiestahl Sep 25, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
81 changes: 0 additions & 81 deletions client/src/components/Pages/Summary/Invalid/Invalid.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -98,63 +98,6 @@ export const Invalid: React.FC<Props> = ({
</ListItemText>
);

const noEventError = (
<ListItemText>
The causative event is not specified.{" "}
<Link href="#" onClick={() => setVisibleTab(2)}>
Declare the event type
</Link>{" "}
to resolve.
</ListItemText>
);

const noAssayError = (
<ListItemText>
No assay metadata is provided. You must{" "}
<Link href="#" onClick={() => setVisibleTab(3)}>
identify the assay, detection method, and methodology that was used to
uncover the fusion
</Link>{" "}
in order to resolve.
</ListItemText>
);

const assayIdCurieError = (
<ListItemText>
The provided assay ID is not a valid{" "}
<Link
href="https://www.w3.org/TR/2010/NOTE-curie-20101216/"
target="_blank"
rel="noopener noreferrer"
>
W3 CURIE
</Link>
.{" "}
<Link href="#" onClick={() => setVisibleTab(3)}>
Update the assay ID
</Link>{" "}
to resolve.
</ListItemText>
);

const assayMethodUriCurieError = (
<ListItemText>
The provided assay method URI is not a valid{" "}
<Link
href="https://www.w3.org/TR/2010/NOTE-curie-20101216/"
target="_blank"
rel="noopener noreferrer"
>
W3 CURIE
</Link>
.{" "}
<Link href="#" onClick={() => setVisibleTab(3)}>
Update the method URI
</Link>{" "}
to resolve.
</ListItemText>
);

const unknownError = (
<>
<ListItemText>
Expand All @@ -164,8 +107,6 @@ export const Invalid: React.FC<Props> = ({
</>
);

const CURIE_PATTERN = /^\w[^:]*:.+$/;

const geneElements = fusion.structural_elements.filter(el => el.type === "GeneElement").map(el => { return el.nomenclature })
const findDuplicates = arr => arr.filter((item, index) => arr.indexOf(item) !== index)
const duplicateGenes = findDuplicates(geneElements)
Expand Down Expand Up @@ -193,28 +134,6 @@ export const Invalid: React.FC<Props> = ({
if (duplicateGenes.length > 0) {
errorElements.push(duplicateGeneError(duplicateGenes))
}
if (fusion.type == "AssayedFusion") {
if (
!(
fusion.assay &&
fusion.assay.assay_name &&
fusion.assay.assay_id &&
fusion.assay.method_uri
)
) {
errorElements.push(noAssayError);
} else {
if (!fusion.assay.assay_id.match(CURIE_PATTERN)) {
errorElements.push(assayIdCurieError);
}
if (!fusion.assay.method_uri.match(CURIE_PATTERN)) {
errorElements.push(assayMethodUriCurieError);
}
}
if (!fusion.causative_event) {
errorElements.push(noEventError);
}
}
if (errorElements.length == 0) {
errorElements.push(
<>
Expand Down
7 changes: 5 additions & 2 deletions client/src/components/Pages/Summary/Readable/Readable.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,9 @@ export const Readable: React.FC<Props> = ({ validatedFusion }) => {
);
}, [validatedFusion]);

const assayName = fusion.assay?.assay_name ? fusion.assay.assay_name : ""
const assayId = fusion.assay?.assay_id ? `(${fusion.assay.assay_id})` : ""

/**
* Render rows specific to assayed fusion fields
* @returns React component containing table rows
Expand All @@ -43,7 +46,7 @@ export const Readable: React.FC<Props> = ({ validatedFusion }) => {
</TableCell>
<TableCell align="right">
<Typography>
{eventDisplayMap[fusion.causative_event.event_type] || ""}
{eventDisplayMap[fusion.causative_event?.event_type] || ""}
</Typography>
</TableCell>
</TableRow>
Expand All @@ -52,7 +55,7 @@ export const Readable: React.FC<Props> = ({ validatedFusion }) => {
<Typography className="row-name">Assay</Typography>
</TableCell>
<TableCell align="right">
<Typography>{`${fusion.assay.assay_name} (${fusion.assay.assay_id})`}</Typography>
<Typography>{fusion.assay ? `${assayName} ${assayId}` : ""}</Typography>
</TableCell>
</TableRow>
</>
Expand Down
2 changes: 1 addition & 1 deletion requirements.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ decorator==5.1.1
executing==1.2.0
fake-useragent==1.1.3
fastapi==0.100.0
fusor==0.0.28.dev0
fusor==0.0.30.dev1
ga4gh.vrs==0.8.4
ga4gh.vrsatile.pydantic==0.0.13
gene-normalizer==0.1.39
Expand Down
2 changes: 1 addition & 1 deletion server/setup.cfg
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ install_requires =
fastapi >= 0.72.0
aiofiles
asyncpg
fusor ~= 0.0.28-dev0
fusor ~= 0.0.30-dev1
sqlparse >= 0.4.2
urllib3 >= 1.26.5
click
Expand Down