CLI reports.h5: sedmlDataSetShapes per job, and Y curves labelled ::X
Maintainers usually reply within 1 day
Nobody has claimed this yet.
Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 55/100
Research direction
Start in vcell-cli/src/main/java/org/vcell/cli/run/results/NonSpatialResultsConverter.java around line 170, where one shapes list is shared across data sets and each job's flat size is appended. Then check the label format strings in ResultsConverter.java at lines 84 and 93, and the comment above add2DPlotsAsReports in prepareNonSpatialDataForHdf5. Done means one comma-joined shape per data set, curve data sets labelled without the ::X suffix, and the comment matching the BioSimulators-mode condition. Confirm the output still matches the legacy writer's expected reports.h5 on the UnifiedDataModel branch, since the issue asks for both changes to be deliberate.
Written by the indexing model from the issue text.
Description
Summary
Two places where the CLI's reports.h5 deviates from the BioSimulators conventions. Both are intentionally reproduced, for now, by the new data system on the UnifiedDataModel branch so its output can be checked byte-for-byte against the legacy writer. Fix them deliberately, in both places.
1. sedmlDataSetShapes has one entry per data set per job. NonSpatialResultsConverter.java:170 shares one shapes list across all data sets and appends each job's flat size to it. A 3-data-set report over a 3-value scan gets 9 entries such as "21", where the convention is one comma-joined shape per data set.
2. Plots reported as reports label every curve data set <plot>.<curve>::X. That includes the Y data generators: ResultsConverter.java:84 and line 93 use the same format string.
Related, minor: the comment above add2DPlotsAsReports in prepareNonSpatialDataForHdf5 says plots are added when not in BioSimulators mode, but the code adds them only in BioSimulators mode.
- Dominant language
- Java
- Stars
- 140
- Forks
- 35
- Avg merge
- 17h 39m
- Merged PRs (30d)
- 19
Getting set up
- Ships a Dockerfile or Docker Compose file
- No pull request template
- Read the contributing guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
More from virtualcell/vcell
-
Difficulty 2/5 1-3 hours Newbie friendliness 72/100
virtualcell/vcell#2193 · 1 comment ·
Maintainers usually reply within 1 day
-
Accessibility Requirement Java-based User Interface
Difficulty 2/5 1-3 hours Newbie friendliness 74/100
virtualcell/vcell#2138 ·
Maintainers usually reply within 1 day
-
Accessibility Requirement Java-based
Difficulty 2/5 1-3 hours Newbie friendliness 80/100
virtualcell/vcell#2137 ·
Maintainers usually reply within 1 day
-
Accessibility Requirement User Interface
Difficulty 2/5 1-3 hours Newbie friendliness 88/100
virtualcell/vcell#2135 ·
Maintainers usually reply within 1 day
-
Accessibility Requirement Java-based User Interface
Difficulty 2/5 1-3 hours Newbie friendliness 84/100
virtualcell/vcell#2134 ·
Maintainers usually reply within 1 day
All issues in virtualcell/vcell
Similar issues
-
Type: Bug
Difficulty 2/5 1-3 hours Newbie friendliness 76/100
Maintainers usually reply within 1 day
-
javaoperatorsdk.client.oauth-token has no effect on the Kubernetes clientPossibly taken @RaphaelFakhri claimed this today. Open
Difficulty 2/5 1-3 hours Newbie friendliness 82/100
-
MCP add-on: JSON responses with non-ASCII characters are truncated (wrong Content-Length)Possibly taken @dhanushbs10 claimed this today. Openadd-on bug in:mcp
Difficulty 2/5 1-3 hours Newbie friendliness 78/100
Maintainers usually reply within 1 day
-
Map.Coordinate does not implement proper equalsPossibly taken A pull request linked to this issue is open or already merged. Openvaadin-map
Difficulty 2/5 1-3 hours Newbie friendliness 70/100
vaadin/flow-components#10586 ·
Maintainers usually reply within 1 day
-
WeReadInstaller writes the launcher database on the main thread at handover (Activity pause timeout)Openbug good first issue
Difficulty 2/5 1-3 hours Newbie friendliness 70/100