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- update according to biodata changes - improve tiering params for tiering wrapper analysis - fix sonnar issues
…by using the configuration file, and adding JUnit tests, #TASK-7983
…nit tests, #TASK-7983
…sorders, #TASK-7983
…prove rd interpretation analysis by adding name, description and primary/secondary interpretation support, #TASK-7983
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| for (String panelId : panelIds) { | ||
| OpenCGAResult<Panel> panelResult = catalogManager.getPanelManager().get(study, panelId, QueryOptions.empty(), token); | ||
| if (panelResult.getNumResults() == 0) { | ||
| logger.warn("Panel '{}' not found. Skipping it.", panelId); |
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Code scanning / SonarCloud
Logging should not be vulnerable to injection attacks Low
…ation file, #TASK-7983
| StopWatch stopWatch = StopWatch.createStarted(); | ||
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| for (String panelAppId : panelAppIds) { | ||
| URL url = new URL("https://panelapp.genomicsengland.co.uk/api/v1/panels/" + panelAppId + "?format=json"); |
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Could this URL be moved to the configuration file?
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You had already the
String host = configuration.getPanel().getHost();Why hardcoding the URL, and deprecating the "panel" section from configuration.yml ?
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That host configuration was useful to know where all our pre-parsed Panels could be located but always following some specific convention and mainly because that url could easily change. We are no longer doing things that way and we are now downloading, parsing and registering panels directly. Panels from panel app have been stored in that url for years. I don't think we are storing clinvar ncbi url in the configuration either, are we?
…d name, version and commit, #TASk-7983
6 participants
Fix the clinical interpretation analysis tool