From b53b6eb07a81c8181f9545a637261acfc0def221 Mon Sep 17 00:00:00 2001 From: Victor Baham <83256374+MasterPastures@users.noreply.github.com> Date: Tue, 1 Oct 2024 13:10:04 -0400 Subject: [PATCH 1/5] Update generate-current-manifests.yml I have written an action that generates a PR using the corresponding action on the GitHub Actions marketplace. Notable parts: * This creates a branch called 'update-manifests' which will contains the changes to the manifests * This is automatically generated and is a different branch from the one which the PR is generated * It is set to delete so that a branch with the same name can be safely created with each workflow run --- .../workflows/generate-current-manifests.yml | 24 +++++++++++++------ 1 file changed, 17 insertions(+), 7 deletions(-) diff --git a/.github/workflows/generate-current-manifests.yml b/.github/workflows/generate-current-manifests.yml index fd02165..ff58d2b 100644 --- a/.github/workflows/generate-current-manifests.yml +++ b/.github/workflows/generate-current-manifests.yml @@ -38,10 +38,20 @@ jobs: working-directory: tests run: ./generate_all_templates.sh - - name: Commit and push changes - run: | - git config --local user.name "$GITHUB_ACTOR" - git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" - git add --all - git commit -m "GitHub Action: generate latest manifests" || echo "No changes to commit" - git push + - name: Create Pull Request + uses: peter-evans/create-pull-request@v5 + with: + token: ${{ secrets.GITHUB_TOKEN }} + commit-message: "GitHub Action: generate latest manifests" + title: "Update manifests" + body: | + This PR updates the manifests based on the latest changes. + Please review and merge if everything looks correct. + branch: update-manifests + base: main + labels: | + automated pr + manifest update + reviewers: $$ {github.actor }} + draft: false + delete-branch: true From a9b31d55e736048bdbaf037f8a346428dce0abde Mon Sep 17 00:00:00 2001 From: Victor Baham <83256374+MasterPastures@users.noreply.github.com> Date: Tue, 1 Oct 2024 13:11:15 -0400 Subject: [PATCH 2/5] Removed trivial "DELETEME" test value from study.csv File is back to as it was before that commit --- modules/ADKP/study.csv | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/ADKP/study.csv b/modules/ADKP/study.csv index aa1b5a1..0cd0506 100644 --- a/modules/ADKP/study.csv +++ b/modules/ADKP/study.csv @@ -1,5 +1,5 @@ Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module -study,Study,"3Dchromatin, ABC-DS, Abeta_microglia, ACOM, ACT, AD_ADRD_Exposome, AD-BXD, ADAMTS7, ADAtlas_Archive, ADMC_ADNI_BakerLipidomics, ADMC_ADNI_Biocrates_MxP_Q500, ADMC_ADNI_NightingaleNMR, ADMC_ADNI_UHawaiiGutMetabolites, ADMC_ADNI1, ADMC_ADNI2-GO, ADMC_UPenn, Aging-PheWAS, AMP-AD_DiverseCohorts, APOE-TR, APOE4_Myelination, APOEPSC, Banner, BCM-DMAS, BipSeq, BLSA, BPSD_AD_AnimalStudy_NU, BrainGVEX, BroadAstrom109, BroadiPSC, BroadMDMi, CHDWB, CMC, CMC_HBCC, CMC-PEC, CNON, DELETEME, DiCAD, diseasePseudotime, DukeAD_PTSD, ELPSCRNA, Emory_ADRC, EmoryDrosophilaTau, EpiGABA, EpiMap, eQTLmetaAnalysis, FreshMicro, HBI_scRNAseq, HBTRC, HDAC1-cKOBrain, HumanFC, IL10_APPmouse, iNiAstshRNA, IntegrativePathwayAnalysis, iPSC, iPSC-HiC, iPSCAstrocytes, iPSCMicroglia, Jax.IU.Pitt_APOE4.Trem2.R47H, Jax.IU.Pitt_APP.PS1, Jax.IU.Pitt_Levetiracetam-5XFAD, Jax.IU.Pitt_LOAD2.PrimaryScreen, Jax.IU.Pitt_MicrobiomePilot, Jax.IU.Pitt_PrimaryScreen, Jax.IU.Pitt_StrainValidation, Jax.IU.Pitt_Verubecestat_5XFAD, Jax.IU.Pitt.Proteomics_Metabolomics_Pilot, LBP, LillyMicroglia, LLFS, lncRNA Pilot, MARS WISCONSIN, MayoeGWAS, MayoHippocampus, MayoLOADGWAS, MayoPilotRNAseq, MayoRNAseq, MC_snRNA, MC-BrAD, MC-CAA, MCMPS, MEF2_Resilience, MindPhenomeKB, miR155, MIT_ROSMAP_Multiomics, MOA-PAD, MODEL-AD_5XFAD, MODEL-AD_Abca7_APOE4_Trem2, MODEL-AD_APOE4_KI, MODEL-AD_APOE4_Trem2, MODEL-AD_Ceacam_KO_APOE4_Trem2, MODEL-AD_hAbeta_KI, MODEL-AD_Harmonization, MODEL-AD_hCR1_KI_on_APOE4_Trem2, MODEL-AD_hTau_Trem2, MODEL-AD_Il1rapKO_APOE4_Trem2_exon2KO, MODEL-AD_Mthfr_APOE4_Trem2, MODEL-AD_Rat_F344, MODEL-AD_Trem2_R47H, MouseHAL, MRGWAS, MSBB, MSBB_ArrayTissuePanel, MSDM, MSMM, MSSMiPSC, mtDNA_AD, NAPS, NHP-Chimpanzee, NHP-Macaque, NPS-AD, OFMM, omicsADDS, Organoid_scRNAseq, Plxnb1_KO, RADEL, RNAseq_Harmonization, rnaSeqReprocessing, rnaSeqSampleSwap, ROSMAP, ROSMAP_bsSeq, ROSMAP_CellTypeSpecificHA, ROSMAP_CognitiveResilience, ROSMAP_Lipidomics_Emory, ROSMAP_MammillaryBody, ROSMAP_nucleus_hashing, ROSMAP-IA, ROSMAP-IN, RR_APOE4, scRNAseq_microglia_wild_ADmice, SEA-AD, SMIB-AD, snRNAseqAD_TREM2, StJude_BannerSun, SUNYStrokeModel, SuperAgerEpiMap, SV_xQTL, SWS, SY5Y_Emory, SY5Y_REST, TASTPM, TAUAPPms, TauD35, Trisomy21iN, TS-RNAseq, TWAS, TyrobpKO, TyrobpKO_AppPs1, U1-70_PrimaryCellCulture, UAB_ADRC, UCI_3xTg-AD, UCI_ABCA7, UCI_Apoe-Ch, UCI_BIN1, UCI_CCLines, UCI_Microbiome, UCI_Multiomics, UCI_PrimaryScreen, UCI_StrainValidation, UCI_Trem2_Cuprizone, UCI_Trem2-R47H_NSS, UCLA-ASD, UCSF_MAC, UFLOR_ABI3_GNGT2, UPenn, VirusResilience_Banner, VirusResilience_iPSC, VirusResilience_LCL, VirusResilience_Mayo.MSBB.ROSMAP, VMC, WallOfTargets, WGBS Pilot, WGS_Harmonization, Yale-ASD",,,TRUE,ManifestColumn,,sage.annotations-neuro.study-0.0.57,,string,ADKP +study,Study,"3Dchromatin, ABC-DS, Abeta_microglia, ACOM, ACT, AD_ADRD_Exposome, AD-BXD, ADAMTS7, ADAtlas_Archive, ADMC_ADNI_BakerLipidomics, ADMC_ADNI_Biocrates_MxP_Q500, ADMC_ADNI_NightingaleNMR, ADMC_ADNI_UHawaiiGutMetabolites, ADMC_ADNI1, ADMC_ADNI2-GO, ADMC_UPenn, Aging-PheWAS, AMP-AD_DiverseCohorts, APOE-TR, APOE4_Myelination, APOEPSC, Banner, BCM-DMAS, BipSeq, BLSA, BPSD_AD_AnimalStudy_NU, BrainGVEX, BroadAstrom109, BroadiPSC, BroadMDMi, CHDWB, CMC, CMC_HBCC, CMC-PEC, CNON, DiCAD, diseasePseudotime, DukeAD_PTSD, ELPSCRNA, Emory_ADRC, EmoryDrosophilaTau, EpiGABA, EpiMap, eQTLmetaAnalysis, FreshMicro, HBI_scRNAseq, HBTRC, HDAC1-cKOBrain, HumanFC, IL10_APPmouse, iNiAstshRNA, IntegrativePathwayAnalysis, iPSC, iPSC-HiC, iPSCAstrocytes, iPSCMicroglia, Jax.IU.Pitt_APOE4.Trem2.R47H, Jax.IU.Pitt_APP.PS1, Jax.IU.Pitt_Levetiracetam-5XFAD, Jax.IU.Pitt_LOAD2.PrimaryScreen, Jax.IU.Pitt_MicrobiomePilot, Jax.IU.Pitt_PrimaryScreen, Jax.IU.Pitt_StrainValidation, Jax.IU.Pitt_Verubecestat_5XFAD, Jax.IU.Pitt.Proteomics_Metabolomics_Pilot, LBP, LillyMicroglia, LLFS, lncRNA Pilot, MARS WISCONSIN, MayoeGWAS, MayoHippocampus, MayoLOADGWAS, MayoPilotRNAseq, MayoRNAseq, MC_snRNA, MC-BrAD, MC-CAA, MCMPS, MEF2_Resilience, MindPhenomeKB, miR155, MIT_ROSMAP_Multiomics, MOA-PAD, MODEL-AD_5XFAD, MODEL-AD_Abca7_APOE4_Trem2, MODEL-AD_APOE4_KI, MODEL-AD_APOE4_Trem2, MODEL-AD_Ceacam_KO_APOE4_Trem2, MODEL-AD_hAbeta_KI, MODEL-AD_Harmonization, MODEL-AD_hCR1_KI_on_APOE4_Trem2, MODEL-AD_hTau_Trem2, MODEL-AD_Il1rapKO_APOE4_Trem2_exon2KO, MODEL-AD_Mthfr_APOE4_Trem2, MODEL-AD_Rat_F344, MODEL-AD_Trem2_R47H, MouseHAL, MRGWAS, MSBB, MSBB_ArrayTissuePanel, MSDM, MSMM, MSSMiPSC, mtDNA_AD, NAPS, NHP-Chimpanzee, NHP-Macaque, NPS-AD, OFMM, omicsADDS, Organoid_scRNAseq, Plxnb1_KO, RADEL, RNAseq_Harmonization, rnaSeqReprocessing, rnaSeqSampleSwap, ROSMAP, ROSMAP_bsSeq, ROSMAP_CellTypeSpecificHA, ROSMAP_CognitiveResilience, ROSMAP_Lipidomics_Emory, ROSMAP_MammillaryBody, ROSMAP_nucleus_hashing, ROSMAP-IA, ROSMAP-IN, RR_APOE4, scRNAseq_microglia_wild_ADmice, SEA-AD, SMIB-AD, snRNAseqAD_TREM2, StJude_BannerSun, SUNYStrokeModel, SuperAgerEpiMap, SV_xQTL, SWS, SY5Y_Emory, SY5Y_REST, TASTPM, TAUAPPms, TauD35, Trisomy21iN, TS-RNAseq, TWAS, TyrobpKO, TyrobpKO_AppPs1, U1-70_PrimaryCellCulture, UAB_ADRC, UCI_3xTg-AD, UCI_ABCA7, UCI_Apoe-Ch, UCI_BIN1, UCI_CCLines, UCI_Microbiome, UCI_Multiomics, UCI_PrimaryScreen, UCI_StrainValidation, UCI_Trem2_Cuprizone, UCI_Trem2-R47H_NSS, UCLA-ASD, UCSF_MAC, UFLOR_ABI3_GNGT2, UPenn, VirusResilience_Banner, VirusResilience_iPSC, VirusResilience_LCL, VirusResilience_Mayo.MSBB.ROSMAP, VMC, WallOfTargets, WGBS Pilot, WGS_Harmonization, Yale-ASD",,,TRUE,ManifestColumn,,sage.annotations-neuro.study-0.0.57,,string,ADKP 3Dchromatin,The neuronal and glial 3D chromatin architecture study,,,,,study,,https://www.synapse.org/#!Synapse:syn21754060,,string,ADKP ABC-DS,The Alzheimer's Biomarkers Consortium - Down Syndrome (ABC-DS) Study,,,,,study,,https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn38190930,,string,ADKP Abeta_microglia,The differential transcriptomic responses of microglia to Ab peptide aggregates (Abeta_microglia) study,,,,,study,,https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn24828089,,string,ADKP @@ -37,7 +37,6 @@ CMC,CommonMind Consortium,,,,,study,,https://www.synapse.org/#!Synapse:syn275979 CMC_HBCC,The CommonMind Consortium Human Brain Collection Core Cohort,,,,,study,,,,string,ADKP CMC-PEC,Data from the CMC cohorts funded through PsychENCODE grants,,,,,study,,https://www.synapse.org/#!Synapse:syn21961394,,string,ADKP CNON,Cultured Neuronal cells derived from Olfactory Neuroepithelium,,,,,study,,https://www.synapse.org/#!Synapse:syn4590897,,string,ADKP -DELETEME, "DELETEME",,,,,study,,https://www.deleteme.edu,,string,ADKP DiCAD,"Interdisciplinary Research to Understand the Interplay of Diabetes, Cerebrovascular disease and Alzheimer's disease",,,,,study,,https://www.synapse.org/#!Synapse:syn9944859,,string,ADKP diseasePseudotime,The diseasePseudotime study,,,,,study,,https://www.synapse.org/#!Synapse:syn22822673,,string,ADKP DukeAD_PTSD,"The Duke Study of Shared Genetic, Epigenetic, and Transcriptomic Profiles Between AD and PTSD study",,,,,study,,https://www.synapse.org/#!Synapse:syn23585917,,string,ADKP From 70f34ffaf666e1b4b8e5e00ab01eae4ee168e3f5 Mon Sep 17 00:00:00 2001 From: MasterPastures Date: Tue, 1 Oct 2024 17:12:22 +0000 Subject: [PATCH 3/5] GitHub Action: assemble *.model.csv from modules directory --- AD.model.csv | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/AD.model.csv b/AD.model.csv index 781d2ce..e6bd71f 100644 --- a/AD.model.csv +++ b/AD.model.csv @@ -984,7 +984,7 @@ specimenIdSource,"The repository or database to which a specimenID maps; or, the spectrometerFrequency,The frequency at which a spectrometer causes hydrogen atoms to resonate (in MHz).,,,,False,ManifestColumn,,sage.annotations-experimentalData.spectrometerFrequency-0.0.2,,number,mass spectrometry stockNumber,Official JAX Mouse stock number,,,,False,ManifestColumn,,sage.annotations-neuro.stockNumber-0.0.1,,string,MODEL-AD strainOfficialNamefficialName,Official JAX Mouse strain nomenclature,,,,False,ManifestColumn,,sage.annotations-neuro.officialName-0.0.1,,string,MODEL-AD -study,Study,"3Dchromatin, ABC-DS, Abeta_microglia, ACOM, ACT, AD_ADRD_Exposome, AD-BXD, ADAMTS7, ADAtlas_Archive, ADMC_ADNI_BakerLipidomics, ADMC_ADNI_Biocrates_MxP_Q500, ADMC_ADNI_NightingaleNMR, ADMC_ADNI_UHawaiiGutMetabolites, ADMC_ADNI1, ADMC_ADNI2-GO, ADMC_UPenn, Aging-PheWAS, AMP-AD_DiverseCohorts, APOE-TR, APOE4_Myelination, APOEPSC, Banner, BCM-DMAS, BipSeq, BLSA, BPSD_AD_AnimalStudy_NU, BrainGVEX, BroadAstrom109, BroadiPSC, BroadMDMi, CHDWB, CMC, CMC_HBCC, CMC-PEC, CNON, DELETEME, DiCAD, diseasePseudotime, DukeAD_PTSD, ELPSCRNA, Emory_ADRC, EmoryDrosophilaTau, EpiGABA, EpiMap, eQTLmetaAnalysis, FreshMicro, HBI_scRNAseq, HBTRC, HDAC1-cKOBrain, HumanFC, IL10_APPmouse, iNiAstshRNA, IntegrativePathwayAnalysis, iPSC, iPSC-HiC, iPSCAstrocytes, iPSCMicroglia, Jax.IU.Pitt_APOE4.Trem2.R47H, Jax.IU.Pitt_APP.PS1, Jax.IU.Pitt_Levetiracetam-5XFAD, Jax.IU.Pitt_LOAD2.PrimaryScreen, Jax.IU.Pitt_MicrobiomePilot, Jax.IU.Pitt_PrimaryScreen, Jax.IU.Pitt_StrainValidation, Jax.IU.Pitt_Verubecestat_5XFAD, Jax.IU.Pitt.Proteomics_Metabolomics_Pilot, LBP, LillyMicroglia, LLFS, lncRNA Pilot, MARS WISCONSIN, MayoeGWAS, MayoHippocampus, MayoLOADGWAS, MayoPilotRNAseq, MayoRNAseq, MC_snRNA, MC-BrAD, MC-CAA, MCMPS, MEF2_Resilience, MindPhenomeKB, miR155, MIT_ROSMAP_Multiomics, MOA-PAD, MODEL-AD_5XFAD, MODEL-AD_Abca7_APOE4_Trem2, MODEL-AD_APOE4_KI, MODEL-AD_APOE4_Trem2, MODEL-AD_Ceacam_KO_APOE4_Trem2, MODEL-AD_hAbeta_KI, MODEL-AD_Harmonization, MODEL-AD_hCR1_KI_on_APOE4_Trem2, MODEL-AD_hTau_Trem2, MODEL-AD_Il1rapKO_APOE4_Trem2_exon2KO, MODEL-AD_Mthfr_APOE4_Trem2, MODEL-AD_Rat_F344, MODEL-AD_Trem2_R47H, MouseHAL, MRGWAS, MSBB, MSBB_ArrayTissuePanel, MSDM, MSMM, MSSMiPSC, mtDNA_AD, NAPS, NHP-Chimpanzee, NHP-Macaque, NPS-AD, OFMM, omicsADDS, Organoid_scRNAseq, Plxnb1_KO, RADEL, RNAseq_Harmonization, rnaSeqReprocessing, rnaSeqSampleSwap, ROSMAP, ROSMAP_bsSeq, ROSMAP_CellTypeSpecificHA, ROSMAP_CognitiveResilience, ROSMAP_Lipidomics_Emory, ROSMAP_MammillaryBody, ROSMAP_nucleus_hashing, ROSMAP-IA, ROSMAP-IN, RR_APOE4, scRNAseq_microglia_wild_ADmice, SEA-AD, SMIB-AD, snRNAseqAD_TREM2, StJude_BannerSun, SUNYStrokeModel, SuperAgerEpiMap, SV_xQTL, SWS, SY5Y_Emory, SY5Y_REST, TASTPM, TAUAPPms, TauD35, Trisomy21iN, TS-RNAseq, TWAS, TyrobpKO, TyrobpKO_AppPs1, U1-70_PrimaryCellCulture, UAB_ADRC, UCI_3xTg-AD, UCI_ABCA7, UCI_Apoe-Ch, UCI_BIN1, UCI_CCLines, UCI_Microbiome, UCI_Multiomics, UCI_PrimaryScreen, UCI_StrainValidation, UCI_Trem2_Cuprizone, UCI_Trem2-R47H_NSS, UCLA-ASD, UCSF_MAC, UFLOR_ABI3_GNGT2, UPenn, VirusResilience_Banner, VirusResilience_iPSC, VirusResilience_LCL, VirusResilience_Mayo.MSBB.ROSMAP, VMC, WallOfTargets, WGBS Pilot, WGS_Harmonization, Yale-ASD",,,True,ManifestColumn,,sage.annotations-neuro.study-0.0.57,,string,ADKP +study,Study,"3Dchromatin, ABC-DS, Abeta_microglia, ACOM, ACT, AD_ADRD_Exposome, AD-BXD, ADAMTS7, ADAtlas_Archive, ADMC_ADNI_BakerLipidomics, ADMC_ADNI_Biocrates_MxP_Q500, ADMC_ADNI_NightingaleNMR, ADMC_ADNI_UHawaiiGutMetabolites, ADMC_ADNI1, ADMC_ADNI2-GO, ADMC_UPenn, Aging-PheWAS, AMP-AD_DiverseCohorts, APOE-TR, APOE4_Myelination, APOEPSC, Banner, BCM-DMAS, BipSeq, BLSA, BPSD_AD_AnimalStudy_NU, BrainGVEX, BroadAstrom109, BroadiPSC, BroadMDMi, CHDWB, CMC, CMC_HBCC, CMC-PEC, CNON, DiCAD, diseasePseudotime, DukeAD_PTSD, ELPSCRNA, Emory_ADRC, EmoryDrosophilaTau, EpiGABA, EpiMap, eQTLmetaAnalysis, FreshMicro, HBI_scRNAseq, HBTRC, HDAC1-cKOBrain, HumanFC, IL10_APPmouse, iNiAstshRNA, IntegrativePathwayAnalysis, iPSC, iPSC-HiC, iPSCAstrocytes, iPSCMicroglia, Jax.IU.Pitt_APOE4.Trem2.R47H, Jax.IU.Pitt_APP.PS1, Jax.IU.Pitt_Levetiracetam-5XFAD, Jax.IU.Pitt_LOAD2.PrimaryScreen, Jax.IU.Pitt_MicrobiomePilot, Jax.IU.Pitt_PrimaryScreen, Jax.IU.Pitt_StrainValidation, Jax.IU.Pitt_Verubecestat_5XFAD, Jax.IU.Pitt.Proteomics_Metabolomics_Pilot, LBP, LillyMicroglia, LLFS, lncRNA Pilot, MARS WISCONSIN, MayoeGWAS, MayoHippocampus, MayoLOADGWAS, MayoPilotRNAseq, MayoRNAseq, MC_snRNA, MC-BrAD, MC-CAA, MCMPS, MEF2_Resilience, MindPhenomeKB, miR155, MIT_ROSMAP_Multiomics, MOA-PAD, MODEL-AD_5XFAD, MODEL-AD_Abca7_APOE4_Trem2, MODEL-AD_APOE4_KI, MODEL-AD_APOE4_Trem2, MODEL-AD_Ceacam_KO_APOE4_Trem2, MODEL-AD_hAbeta_KI, MODEL-AD_Harmonization, MODEL-AD_hCR1_KI_on_APOE4_Trem2, MODEL-AD_hTau_Trem2, MODEL-AD_Il1rapKO_APOE4_Trem2_exon2KO, MODEL-AD_Mthfr_APOE4_Trem2, MODEL-AD_Rat_F344, MODEL-AD_Trem2_R47H, MouseHAL, MRGWAS, MSBB, MSBB_ArrayTissuePanel, MSDM, MSMM, MSSMiPSC, mtDNA_AD, NAPS, NHP-Chimpanzee, NHP-Macaque, NPS-AD, OFMM, omicsADDS, Organoid_scRNAseq, Plxnb1_KO, RADEL, RNAseq_Harmonization, rnaSeqReprocessing, rnaSeqSampleSwap, ROSMAP, ROSMAP_bsSeq, ROSMAP_CellTypeSpecificHA, ROSMAP_CognitiveResilience, ROSMAP_Lipidomics_Emory, ROSMAP_MammillaryBody, ROSMAP_nucleus_hashing, ROSMAP-IA, ROSMAP-IN, RR_APOE4, scRNAseq_microglia_wild_ADmice, SEA-AD, SMIB-AD, snRNAseqAD_TREM2, StJude_BannerSun, SUNYStrokeModel, SuperAgerEpiMap, SV_xQTL, SWS, SY5Y_Emory, SY5Y_REST, TASTPM, TAUAPPms, TauD35, Trisomy21iN, TS-RNAseq, TWAS, TyrobpKO, TyrobpKO_AppPs1, U1-70_PrimaryCellCulture, UAB_ADRC, UCI_3xTg-AD, UCI_ABCA7, UCI_Apoe-Ch, UCI_BIN1, UCI_CCLines, UCI_Microbiome, UCI_Multiomics, UCI_PrimaryScreen, UCI_StrainValidation, UCI_Trem2_Cuprizone, UCI_Trem2-R47H_NSS, UCLA-ASD, UCSF_MAC, UFLOR_ABI3_GNGT2, UPenn, VirusResilience_Banner, VirusResilience_iPSC, VirusResilience_LCL, VirusResilience_Mayo.MSBB.ROSMAP, VMC, WallOfTargets, WGBS Pilot, WGS_Harmonization, Yale-ASD",,,True,ManifestColumn,,sage.annotations-neuro.study-0.0.57,,string,ADKP TDP43,TDP Whole Brain (dichotomous). Calculated using the categories in TDP_3 - if any of the amygdala hippocampus entorhinal or neocortex are positive it is yes. If assessed and negative for the above it is no,"No, Yes, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.TDP43-0.0.2,,string,clinical TDP_3,TDP-3 Component,"No TDP_3, Amygdala, Hippocampus or Etorhinal, Neocortex, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.TDP_3-0.0.2,string,,clinical TDP_5,TDP Stage; Assumes that TDP progresses from brainstem>amygdala>hippocampus>inferior temporal cortex>neocortex,"No TDP_5, Brainstem/Spinal Cord, Amygdala, Hippocampus, Entorhinal, Neocortex, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.TDP_5-0.0.2,string,,clinical @@ -1376,7 +1376,6 @@ CMC,CommonMind Consortium,,,,,study,,https://www.synapse.org/#!Synapse:syn275979 CMC-PEC,Data from the CMC cohorts funded through PsychENCODE grants,,,,,study,,https://www.synapse.org/#!Synapse:syn21961394,,string,ADKP CMC_HBCC,The CommonMind Consortium Human Brain Collection Core Cohort,,,,,study,,,,string,ADKP CNON,Cultured Neuronal cells derived from Olfactory Neuroepithelium,,,,,study,,https://www.synapse.org/#!Synapse:syn4590897,,string,ADKP -DELETEME," ""DELETEME""",,,,,study,,https://www.deleteme.edu,,string,ADKP DiCAD,"Interdisciplinary Research to Understand the Interplay of Diabetes, Cerebrovascular disease and Alzheimer's disease",,,,,study,,https://www.synapse.org/#!Synapse:syn9944859,,string,ADKP diseasePseudotime,The diseasePseudotime study,,,,,study,,https://www.synapse.org/#!Synapse:syn22822673,,string,ADKP DukeAD_PTSD,"The Duke Study of Shared Genetic, Epigenetic, and Transcriptomic Profiles Between AD and PTSD study",,,,,study,,https://www.synapse.org/#!Synapse:syn23585917,,string,ADKP From 94f47ca5c979c4920bfe7d030898ccd418e64159 Mon Sep 17 00:00:00 2001 From: MasterPastures Date: Tue, 1 Oct 2024 17:12:40 +0000 Subject: [PATCH 4/5] GitHub Action: convert *.model.csv to *.model.jsonld --- AD.model.jsonld | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/AD.model.jsonld b/AD.model.jsonld index 711d9d1..1de2c54 100644 --- a/AD.model.jsonld +++ b/AD.model.jsonld @@ -8435,9 +8435,6 @@ { "@id": "bts:CNON" }, - { - "@id": "bts:DELETEME" - }, { "@id": "bts:DiCAD" }, @@ -26158,23 +26155,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:DELETEME", - "@type": "rdfs:Class", - "rdfs:comment": "\"DELETEME\"", - "rdfs:label": "DELETEME", - "rdfs:subClassOf": [ - { - "@id": "bts:Study" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "DELETEME", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:DiseasePseudotime", "@type": "rdfs:Class", From 267afa9415bf1d3fb224a7c34a1890fc7bd4fd0c Mon Sep 17 00:00:00 2001 From: Victor Baham <83256374+MasterPastures@users.noreply.github.com> Date: Tue, 1 Oct 2024 13:15:33 -0400 Subject: [PATCH 5/5] Added step 5 to the 'Automation' section in README.md to explain how the newly edited generate-current-manifests.yml file works --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 391c917..7f90a91 100644 --- a/README.md +++ b/README.md @@ -80,7 +80,8 @@ When you open a PR that includes any changes to files in the `modules/` director 1. Runs the `assemble_csv_data_model.py` script to concatenate the modular attribute csvs into one data frame, sort alphabetically by `Parent` and then `Attribute`, and write the combined dataframe to `AD.model.csv`. The action then commits the changes to the master data model csv. 2. Installs the latest version of `schematic` from PyPi and runs `schema convert` on the newly-concatenated data model csv to generate a new version of the jsonld file `AD.model.jsonld`. The action also commits the changes to the jsonld. 3. Collects the names of any module attributes or templates changed by your PR, then uses the schematic CLI to generate Google sheet versions of those templates. -4. Makes a new comment in the PR consisting of an Rmd report with the template generation status and link to each template, so you can physically view the new template and verify that any changes you made look as intended. +4. Makes a new comment in the PR consisting of an Rmd report with the template generation status and link to each template, so you can physically view the new template and verify that any changes you made look as intended. +5. Due to branch protection rules set on the `main` branch, a branch called `update-manifests` containing the updated manifests is created, and a PR is automatically generated for a member of the repo to review and manually merge afterwards. If this automated workflow fails, then the data model may be invalid and further investigation is needed.