Oncotree migration #318
Oncotree migration #318
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web/src/main/go/package-lock.json
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We should delete this file
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Delete the file or gitignore?
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Looks like this is generated automatically by the annotations you added to the files in server/main.go. Could you add documentation on how to regenerate? Also, will regenerating recreate the json and yaml versions as well?
NIT: Maybe we can put the generated files in swagger/generated. That way, it's obvious these are the swagger docs and that it's generated so people don't mess with the files.
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Can we add the dependencies in the go.mod at the root of the go directory?
web/src/main/go/cmd/server/main.go
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| gin.DefaultErrorWriter = log.WriterLevel(logrus.ErrorLevel) | ||
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| // TODO: can we configure the static folder location? | ||
| router.Static("/assets", "../resources/static/assets") |
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router.Static("/", "../resources/static") doesn't work. It doesn't read /assets
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| flattened := flattenTumorTypes(tree) |
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Probably no need to flatten the tree first. Can't we just search the tumor types in a BFS?
| Visible bool `json:"visible"` | ||
| } | ||
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| func getHardcodedVersions() []Version { |
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I'm fine with hardcoding the identifiers, but we probably shouldn't hardcode the release date. Since they change, we would need to update the code once we change them. We should set up the system to use the most recent tree as latest stable, and we need to find a way to denote candidate.
Need to make sure to communicate this change with Ritika
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Implemented.
- The version identifier remains consistent, but the release date is refreshed to reflect the most recent release.
- Whenever a new input version is detected, the system resolves and validates it by locating the latest file and updating the version reference accordingly.
web/src/main/go/cmd/server/utils.go
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| func isValidVersion(version string) bool { | ||
| treeDir := "../../../../trees" | ||
| versions, err := GetAvailableVersionIdentifiers(treeDir) |
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It would probably be better practice to just look for the file we are interested in instead of getting all available versions
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Sounds good, changed
web/src/main/go/cmd/server/utils.go
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| return node.Code | ||
| case "name": | ||
| return node.Name | ||
| case "maintype": |
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Looks like the current API uses mainType with capital T
| for _, lvlStr := range strings.Split(levelsStr, ",") { | ||
| lvlStr = strings.TrimSpace(lvlStr) | ||
| lvl, err := strconv.ParseUint(lvlStr, 10, 32) | ||
| if err == nil && lvl != 0 { |
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Can we handle error by returning BadRequest instead of skipping over them?
web/src/main/go/cmd/server/utils.go
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| return max | ||
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| func writeTSVRows(node internal.TreeNode, levels []string, sb *strings.Builder) { |
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Could you just get the sorted nodes (you could figure out the max level during this process) and then write the rows in a for loop. The recursive logic where you pass in an empty string array as well as the string builder is a bit confusing
* add tsv parsing step * add precursors automatically from ampping * populate precursors and revocations from last available tree with no mapping * add tree generation to git workflow
* fix docker build and add tree files * remove test trees * remove print statements * remove static files from source control
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