diff --git a/data/testResults/README.md b/data/testResults/README.md index 6ed6d67d..83c6daac 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -21,11 +21,11 @@ own files. The pull request in each row is the one whose run last wrote those fi | Result file(s) | Produced by | Last updated by | | --- | --- | --- | -| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1061** (model QC checks) | -| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1061** (model QC checks) | -| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1061** (model QC checks) | -| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1061** (MACAW and balance) | -| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1061** (MEMOTE) | +| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1030** (model QC checks) | +| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1030** (model QC checks) | +| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1030** (model QC checks) | +| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1030** (MACAW and balance) | +| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1030** (MEMOTE) | | `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1027** (gene essentiality) | ## 2. What each check means diff --git a/data/testResults/model_qc_summary.md b/data/testResults/model_qc_summary.md index fdac8f39..19635a38 100644 --- a/data/testResults/model_qc_summary.md +++ b/data/testResults/model_qc_summary.md @@ -1,59 +1,59 @@ ## Model quality report -:warning: **6 pre-existing finding(s), no regressions vs `main`.** Non-blocking. +:warning: **6 pre-existing finding(s), no regressions vs `develop`.** Non-blocking. -_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md)._ +_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md)._ ### Model checks _Duplicate keys (model unloadable) and no growth block the merge; every other row is a non-blocking report._ -| Check | Result | Δ vs `main` | | +| Check | Result | Δ vs `develop` | | | --- | ---: | ---: | :---: | -| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#duplicate-omap-keys) | 0 | new | :white_check_mark: | -| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#growth-biomass-producible) | 125 | new | :white_check_mark: | -| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-with-no-metabolites) | 0 | new | :white_check_mark: | -| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | new | :white_check_mark: | -| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | new | :white_check_mark: | -| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-formula) | 0 | new | :white_check_mark: | -| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-charge) | 0 | new | :white_check_mark: | -| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | new | :white_check_mark: | -| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | new | :white_check_mark: | -| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-metabolites) | 0 | new | :white_check_mark: | -| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-genes) | 0 | new | :white_check_mark: | -| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#malformed-cross-references) | 0 | new | :white_check_mark: | -| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_annotation_issues.csv) | new | :warning: | +| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#duplicate-omap-keys) | 0 | 0 | :white_check_mark: | +| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#growth-biomass-producible) | 125 | 0 | :white_check_mark: | +| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#reactions-with-no-metabolites) | 0 | 0 | :white_check_mark: | +| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | 0 | :white_check_mark: | +| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | 0 | :white_check_mark: | +| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#metabolites-missing-formula) | 0 | 0 | :white_check_mark: | +| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#metabolites-missing-charge) | 0 | 0 | :white_check_mark: | +| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | 0 | :white_check_mark: | +| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | 0 | :white_check_mark: | +| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#unused-metabolites) | 0 | 0 | :white_check_mark: | +| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#unused-genes) | 0 | 0 | :white_check_mark: | +| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#malformed-cross-references) | 0 | 0 | :white_check_mark: | +| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/qc_annotation_issues.csv) | 0 | :warning: | ### MACAW and mass/charge balance -| Check | Result | Δ vs `main` | | +| Check | Result | Δ vs `develop` | | | --- | ---: | ---: | :---: | -| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -703 | :warning: | -| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -2 | :warning: | -| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: | -| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: | -| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_structure_consistency.csv) | new | :warning: | +| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/macaw_results.csv) | 0 | :warning: | +| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/macaw_results.csv) | 0 | :warning: | +| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/balance_results.csv) | 0 | :warning: | +| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/balance_results.csv) | 0 | :warning: | +| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/qc_structure_consistency.csv) | 0 | :warning: | ### Model file and metabolic tasks | Check | Result | | | --- | ---: | :---: | -| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: | -| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: | -| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: | -| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: | -| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: | +| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: | +| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: | +| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: | +| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: | +| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: | -### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#memote) +### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#memote) -**Total score: 63.2%** (core subset)   +**Total score: 63.2%** (core subset)   0 | Section | Score | Δ vs base | | --- | ---: | ---: | -| consistency | 42.4% | | -| annotation_met | 73.0% | | -| annotation_rxn | 72.7% | | -| annotation_gene | 46.7% | | -| annotation_sbo | 81.7% | | +| consistency | 42.4% | 0 | +| annotation_met | 73.0% | 0 | +| annotation_rxn | 72.7% | 0 | +| annotation_gene | 46.7% | 0 | +| annotation_sbo | 81.7% | 0 |
Per-test scores @@ -89,11 +89,11 @@ _Duplicate keys (model unloadable) and no growth block the merge; every other ro
-**Full suite: 64.2%**   · _from the last_ `/run memote`. +**Full suite: 64.2%**   0 · _from the last_ `/run memote`. _The score above is the fast core subset. Comment_ `/run memote` _to run the full suite on this pull request; the score updates here when it finishes._ -### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#gene-essentiality-hart-2015) +### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#gene-essentiality-hart-2015) _Not run automatically (it takes hours). Comment_ `/run gene-essentiality` _to run it on this pull request; the result posts as its own comment._ diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 5dc46667..73e88181 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -75717,7 +75717,7 @@ - MAM02877c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000038274 or ENSG00000151224 or ENSG00000168906" + - gene_reaction_rule: "ENSG00000151224 or ENSG00000168906" - rxnFrom: "HMRdatabase" - eccodes: "2.5.1.6" - references: "PMID:7213623" @@ -77128,7 +77128,7 @@ - MAM02891c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000038274 or ENSG00000151224 or ENSG00000168906" + - gene_reaction_rule: "ENSG00000151224 or ENSG00000168906" - rxnFrom: "HMRdatabase" - eccodes: "2.5.1.6" - subsystem: "Metabolism of other amino acids" @@ -252374,9 +252374,6 @@ - !!omap - id: "ENSG00000038210" - name: "PI4K2B" - - !!omap - - id: "ENSG00000038274" - - name: "MAT2B" - !!omap - id: "ENSG00000039123" - name: "MTREX" diff --git a/model/genes.tsv b/model/genes.tsv index 797c979d..1fa2bc38 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -121,7 +121,6 @@ "ENSG00000037897" "ENST00000324871;ENST00000257848;ENST00000547653;ENST00000548504;ENST00000551117;ENST00000553125;ENST00000548681;ENST00000549773" "ENSP00000314441;ENSP00000257848;ENSP00000447838;ENSP00000449397;ENSP00000447988;ENSP00000448342" "Q9UBP6" "METTL1" "4234" "methyltransferase like 1" "C12orf1;TRM8;TRMT8" "Nucleus" "SwissProt;CellAtlas" "ENSG00000038002" "ENST00000264595;ENST00000502310;ENST00000506853;ENST00000510635;ENST00000510955;ENST00000511231" "ENSP00000264595;ENSP00000423798;ENSP00000421471" "P20933" "AGA" "175" "aspartylglucosaminidase" "ASRG" "Lysosome" "SwissProt" "ENSG00000038210" "ENST00000512921;ENST00000264864" "ENSP00000423373;ENSP00000264864" "Q8TCG2" "PI4K2B" "55300" "phosphatidylinositol 4-kinase type 2 beta" "FLJ11105;PI4KIIB;PIK42B" "Endoplasmic reticulum;Golgi apparatus;Cytosol" "SwissProt;CellAtlas" -"ENSG00000038274" "ENST00000280969;ENST00000519719;ENST00000321757;ENST00000421814;ENST00000518095;ENST00000523606;ENST00000520449;ENST00000521838" "ENSP00000280969;ENSP00000325425;ENSP00000397371;ENSP00000428046;ENSP00000431071" "Q9NZL9" "MAT2B" "27430" "methionine adenosyltransferase 2B" "MATIIbeta;SDR23E1" "Cytosol" "DeepLoc2" "ENSG00000039123" "ENST00000230640;ENST00000504388;ENST00000506750;ENST00000503165;ENST00000504997;ENST00000505565;ENST00000502953;ENST00000518955;ENST00000508716" "ENSP00000230640;ENSP00000425042;ENSP00000422125;ENSP00000426641" "P42285" "MTREX" "23517" "Mtr4 exosome RNA helicase" "Dob1;fSAP118;KIAA0052;Mtr4;SKIV2L2" "Nucleus" "SwissProt;CellAtlas" "ENSG00000039650" "ENST00000596624;ENST00000636840;ENST00000595081;ENST00000601816;ENST00000594661;ENST00000627232;ENST00000593946;ENST00000600910;ENST00000322344;ENST00000599454;ENST00000631020;ENST00000596014;ENST00000600573;ENST00000597965;ENST00000640501;ENST00000625216;ENST00000593706;ENST00000627317;ENST00000629179;ENST00000637325;ENST00000636214;ENST00000599543;ENST00000596726;ENST00000625299;ENST00000598020;ENST00000637897;ENST00000626274;ENST00000629088;ENST00000595792;ENST00000636994;ENST00000638016" "ENSP00000490737;ENSP00000486037;ENSP00000468896;ENSP00000473137;ENSP00000323511;ENSP00000486707;ENSP00000472300;ENSP00000469826;ENSP00000471097;ENSP00000491347;ENSP00000486898;ENSP00000486500;ENSP00000489983;ENSP00000469848;ENSP00000470887;ENSP00000470346;ENSP00000490539;ENSP00000490791;ENSP00000489771" "Q96T60" "PNKP" "11284" "polynucleotide kinase 3'-phosphatase" "PNK" "Nucleus" "SwissProt;CellAtlas" "ENSG00000040933" "ENST00000409016;ENST00000409851;ENST00000409463;ENST00000409540;ENST00000463367;ENST00000523221;ENST00000468638;ENST00000467042;ENST00000498026;ENST00000074304" "ENSP00000386704;ENSP00000386777;ENSP00000386329;ENSP00000387294;ENSP00000427722;ENSP00000074304" "Q96PE3" "INPP4A" "3631" "inositol polyphosphate-4-phosphatase type I A" "INPP4" "Nucleus;Cytosol" "SwissProt;CellAtlas"