From acc038116f2e88d3fbc136e73547e70031e1846d Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 21 Jul 2026 20:25:22 -0700 Subject: [PATCH] NEXT_TASKS: record magnetite-redox causal curation (#246) + Edison fix (#245) Add CommunityMech:000268 (Rhodopseudomonas-Geobacter magnetite battery) to the causal "done" list (~60/304), point Next at ORNL trophic model 000176, and replace the Edison env-shadowing workaround note with the runner fix (#245): load_api_key() now treats the repo .env FILE as source of truth, so a plain `just research-community-causal ` works with no `env -u`. Co-Authored-By: Claude Opus 4.8 (1M context) --- NEXT_TASKS.md | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/NEXT_TASKS.md b/NEXT_TASKS.md index a789c387..a133869c 100644 --- a/NEXT_TASKS.md +++ b/NEXT_TASKS.md @@ -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 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 ` -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 ` 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)