Skip to content

NEXT_TASKS: record magnetite-redox causal curation (#246) + Edison fix (#245) #248

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

Merged
realmarcin merged 1 commit into from
Jul 22, 2026
Merged

NEXT_TASKS: record magnetite-redox causal curation (#246) + Edison fix (#245) #248

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
20 changes: 12 additions & 8 deletions NEXT_TASKS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -343,18 +343,22 @@ in #228), `Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy` (#229),
`ANME_SRB_Marine_Methane_Seep_Consortium` (#230),
`Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture` (#243; CommunityMech:000190,
syntrophic loop 1→2→3→1 + negative product-inhibition edge from the Edison graph on
PMID:30038609). ~59/304 records now carry `downstream` causal edges. **Next:** continue
on high-value syntrophies; always use the RECORD's canonical taxon ids (Edison
PMID:30038609), `Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture` (#246;
CommunityMech:000268, reversible magnetite-"battery" loop 2⇄3 + both half-reactions →
battery, PMID:25814583). ~60/304 records now carry `downstream` causal edges. **Next:**
continue on high-value syntrophies (e.g. `ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model`
000176, 4 nodes/0 downstream); always use the RECORD's canonical taxon ids (Edison
Comment on lines +349 to +350
groundings have had errors, e.g. sulfite → CHEBI:16731 *(E)-cinnamaldehyde* instead of
CHEBI:17359).

**Edison auth (resolved 2026-07-21):** the key was refreshed in `.env`
(`EDISON_API_KEY`) and now authenticates (HTTP 200). **Gotcha:** the shell profile
exports a stale `EDISON_PLATFORM_API_KEY` that the runner prefers over `.env`
(`load_dotenv` does not override an already-exported var), and it still 403s — so run
causal jobs with `env -u EDISON_PLATFORM_API_KEY just research-community-causal <id>`
until that profile export is updated/removed, or add the good key to `.env` as
`EDISON_PLATFORM_API_KEY=`.
(`EDISON_API_KEY`) and authenticates (HTTP 200). The stale-key shadowing footgun is
**fixed in the runner** (#245): `load_api_key()` now treats the repo `.env` FILE as the
source of truth (via `dotenv_values`), preferring it over any ambient/inherited
`EDISON_PLATFORM_API_KEY`. So a plain `just research-community-causal <id>` now works —
**no `env -u` workaround needed** (000268 was curated this way). See
[[edison-auth-env-shadowing]]. NB: `.bash_profile`'s export was already commented out;
the stale value was only inherited into the launching terminal session.

## Space-regolith community curation (curatable subset DONE, 9/16)

Expand Down