From 76bcdea090004519337f16d6f1b3bd77085816e6 Mon Sep 17 00:00:00 2001 From: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com> Date: Tue, 26 Nov 2024 16:49:28 +0000 Subject: [PATCH 1/9] bump schematic --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index 7ae5e5c9..55b5baab 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ numpy==1.26.4 pandas>=2.0.0 synapseclient>=4.3.0 -schematicpy==24.7.2 +schematicpy==24.11.2 ipython>=8.26.0 \ No newline at end of file From fbb0302013f32d6e51f26053bf7a746419f9a138 Mon Sep 17 00:00:00 2001 From: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com> Date: Tue, 26 Nov 2024 16:49:42 +0000 Subject: [PATCH 2/9] remove filled manifest --- filled-manifests/synapse_storage_manifest_individualkey.csv | 4 ---- 1 file changed, 4 deletions(-) delete mode 100644 filled-manifests/synapse_storage_manifest_individualkey.csv diff --git a/filled-manifests/synapse_storage_manifest_individualkey.csv b/filled-manifests/synapse_storage_manifest_individualkey.csv deleted file mode 100644 index 2c2d5a5b..00000000 --- a/filled-manifests/synapse_storage_manifest_individualkey.csv +++ /dev/null @@ -1,4 +0,0 @@ -Component,individualID,Id,entityId -IndividualKey,mouse1,13152b66-b026-4909-aa3f-02611c12b823, -IndividualKey,mouse2,0e98aac1-8b71-4633-8ae4-6244ef975487, -IndividualKey,mouse37,ef8911b9-ebd8-4e28-842e-86c27a927557, From f7e1de8e48663277c4aac5e242d5f39bad1719a3 Mon Sep 17 00:00:00 2001 From: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com> Date: Tue, 26 Nov 2024 16:49:50 +0000 Subject: [PATCH 3/9] add test value --- modules/ADKP/consortium.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/ADKP/consortium.csv b/modules/ADKP/consortium.csv index 9534fe69..451025c5 100644 --- a/modules/ADKP/consortium.csv +++ b/modules/ADKP/consortium.csv @@ -1,5 +1,5 @@ Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module -consortium,The name of the consortium,"CMC, PEC, AMP-AD, MODEL-AD, M2OVE-AD, Resilience-AD, BSMN, CSBC, PSON, GENIE, Synodos, DHART SPORE, CDCP, Psych-AD, ELITE, Not Applicable",,,True,ManifestColumn,,sage.annotations-sageCommunity.consortium-0.0.5,,string,ADKP +consortium,The name of the consortium,"testvalue, CMC, PEC, AMP-AD, MODEL-AD, M2OVE-AD, Resilience-AD, BSMN, CSBC, PSON, GENIE, Synodos, DHART SPORE, CDCP, Psych-AD, ELITE, Not Applicable",,,True,ManifestColumn,,sage.annotations-sageCommunity.consortium-0.0.5,,string,ADKP AMP-AD,Accelerating Medicines Partnership-Alzheimer's Disease,,,,,consortium,,https://adknowledgeportal.synapse.org/,,string,ADKP BSMN,Brain Somatic Mosaicism Network,,,,,consortium,,https://www.synapse.org/bsmn,,string,ADKP CDCP,Community Data Contribution Program,,,,,consortium,,https://adknowledgeportal.synapse.org/,,string,ADKP @@ -16,3 +16,4 @@ PSON,Physical Science in Oncology,,,,,consortium,,https://physics.cancer.gov/,,s Psych-AD,Neuropsychiatric Symptoms in Alzheimer's Disease,,,,,consortium,,https://adknowledgeportal.synapse.org/Explore/Programs/DetailsPage?Program=Psych-AD,,string,ADKP Resilience-AD,Interdisciplinary Research to Understand the Complex Biology of Resilience to Alzheimer's Disease Risk,,,,,consortium,,https://adknowledgeportal.synapse.org/,,string,ADKP Synodos,Data derived from a CTF-Funded Synodos project,,,,,consortium,,https://www.synapse.org/ctf,,string,ADKP +testvalue,not real,,,,,consortium,,nope,,string,ADKP From 7bb58146b7ce91f6fabd2a7e2c8e6c3bfa68a49b Mon Sep 17 00:00:00 2001 From: avanlinden Date: Tue, 26 Nov 2024 16:52:17 +0000 Subject: [PATCH 4/9] GitHub Action: assemble *.model.csv from modules directory --- AD.model.csv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/AD.model.csv b/AD.model.csv index 1f1815d8..b16a7b39 100644 --- a/AD.model.csv +++ b/AD.model.csv @@ -491,6 +491,7 @@ PSON,Physical Science in Oncology,,,,,consortium,,https://physics.cancer.gov/,,s Psych-AD,Neuropsychiatric Symptoms in Alzheimer's Disease,,,,,consortium,,https://adknowledgeportal.synapse.org/Explore/Programs/DetailsPage?Program=Psych-AD,,string,ADKP Resilience-AD,Interdisciplinary Research to Understand the Complex Biology of Resilience to Alzheimer's Disease Risk,,,,,consortium,,https://adknowledgeportal.synapse.org/,,string,ADKP Synodos,Data derived from a CTF-Funded Synodos project,,,,,consortium,,https://www.synapse.org/ctf,,string,ADKP +testvalue,not real,,,,,consortium,,nope,,string,ADKP AIBL pool,"The Australian Imaging, Biomarkers, and Lifestyle Flagship Study of Ageing (AIBL) reference pool.",,,,,controlType,,https://aibl.csiro.au/,,string,experimentalData Baker pool,The Baker Institute Metabolomics Laboratory reference pool.,,,,,controlType,,https://baker.edu.au/research/laboratories/metabolomics,,string,experimentalData blank injection,blank injection,,,,,controlType,,-,,string,experimentalData @@ -863,7 +864,7 @@ chromosome,A structure composed of a very long molecule of DNA and associated pr climbID,Identifying string linked to an animal in Climb database,,,,True,ManifestColumn,,sage.annotations-neuro.climbID-0.0.1,,string,MODEL-AD cohort,A study group population where the members are human beings who meet inclusion criteria.,"ABC-DS,ACT,ADNI,ADRC,Banner,BEAM,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,MARS-WI,Mayo Clinic,MC,MCJ,MCR,MIND,MSBB,NYBB,Pitt ADRC,POINTER,RADC,ROSMAP,SMRI,Tulsa LIBR-1000,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP",,,False,ManifestColumn,,http://purl.obolibrary.org/obo/STATO_0000203,,string,clinical conservationMethod,The conservation method,"noConservation, fixed tissues only, frozen tissue only, both fixed and frozen tissue, missing or unknown",,,True,ManifestColumn,,sage-annotations-clinical.conservationMethod-0.0.2,string,,clinical -consortium,The name of the consortium,"CMC, PEC, AMP-AD, MODEL-AD, M2OVE-AD, Resilience-AD, BSMN, CSBC, PSON, GENIE, Synodos, DHART SPORE, CDCP, Psych-AD, ELITE, Not Applicable",,,True,ManifestColumn,,sage.annotations-sageCommunity.consortium-0.0.5,,string,ADKP +consortium,The name of the consortium,"testvalue, CMC, PEC, AMP-AD, MODEL-AD, M2OVE-AD, Resilience-AD, BSMN, CSBC, PSON, GENIE, Synodos, DHART SPORE, CDCP, Psych-AD, ELITE, Not Applicable",,,True,ManifestColumn,,sage.annotations-sageCommunity.consortium-0.0.5,,string,ADKP contrastAgent,Substance administered during an imaging procedure that allows delineation of internal structures.,,,,False,ManifestColumn,,sage.annotations-experimentalData.contrastAgent-0.0.2,,string,imaging controlType,Control samples suitable for normalization and batch correction,"AIBL pool, Baker pool, blank injection, GIS, GoldenWest, NIST SRM 1950, qc mix, Replicate, study pool, water plus Baker ISTD",,,False,ManifestColumn,,sage.annotations-experimentalData.controlType-0.0.5,,string,experimentalData CVD_ART,Arteriolosclerosis,"No CVD_ART, Mild, Moderate, Severe, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.CVD_ART-0.0.2,string,,clinical From 187583c08af68d8a8c2befc264ade993beef309a Mon Sep 17 00:00:00 2001 From: avanlinden Date: Tue, 26 Nov 2024 16:52:35 +0000 Subject: [PATCH 5/9] GitHub Action: convert *.model.csv to *.model.jsonld --- AD.model.jsonld | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/AD.model.jsonld b/AD.model.jsonld index 645a855f..d3c2fa8d 100644 --- a/AD.model.jsonld +++ b/AD.model.jsonld @@ -11247,6 +11247,9 @@ "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ + { + "@id": "bts:Testvalue" + }, { "@id": "bts:CMC" }, @@ -11850,6 +11853,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Testvalue", + "@type": "rdfs:Class", + "rdfs:comment": "not real", + "rdfs:label": "Testvalue", + "rdfs:subClassOf": [ + { + "@id": "bts:Consortium" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "testvalue", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:AIBLpool", "@type": "rdfs:Class", From 3f2c1c951584a0c4e1b2ca503c80db39ec552f40 Mon Sep 17 00:00:00 2001 From: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com> Date: Tue, 26 Nov 2024 16:57:38 +0000 Subject: [PATCH 6/9] remove test value --- modules/ADKP/consortium.csv | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/ADKP/consortium.csv b/modules/ADKP/consortium.csv index 451025c5..9534fe69 100644 --- a/modules/ADKP/consortium.csv +++ b/modules/ADKP/consortium.csv @@ -1,5 +1,5 @@ Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module -consortium,The name of the consortium,"testvalue, CMC, PEC, AMP-AD, MODEL-AD, M2OVE-AD, Resilience-AD, BSMN, CSBC, PSON, GENIE, Synodos, DHART SPORE, CDCP, Psych-AD, ELITE, Not Applicable",,,True,ManifestColumn,,sage.annotations-sageCommunity.consortium-0.0.5,,string,ADKP +consortium,The name of the consortium,"CMC, PEC, AMP-AD, MODEL-AD, M2OVE-AD, Resilience-AD, BSMN, CSBC, PSON, GENIE, Synodos, DHART SPORE, CDCP, Psych-AD, ELITE, Not Applicable",,,True,ManifestColumn,,sage.annotations-sageCommunity.consortium-0.0.5,,string,ADKP AMP-AD,Accelerating Medicines Partnership-Alzheimer's Disease,,,,,consortium,,https://adknowledgeportal.synapse.org/,,string,ADKP BSMN,Brain Somatic Mosaicism Network,,,,,consortium,,https://www.synapse.org/bsmn,,string,ADKP CDCP,Community Data Contribution Program,,,,,consortium,,https://adknowledgeportal.synapse.org/,,string,ADKP @@ -16,4 +16,3 @@ PSON,Physical Science in Oncology,,,,,consortium,,https://physics.cancer.gov/,,s Psych-AD,Neuropsychiatric Symptoms in Alzheimer's Disease,,,,,consortium,,https://adknowledgeportal.synapse.org/Explore/Programs/DetailsPage?Program=Psych-AD,,string,ADKP Resilience-AD,Interdisciplinary Research to Understand the Complex Biology of Resilience to Alzheimer's Disease Risk,,,,,consortium,,https://adknowledgeportal.synapse.org/,,string,ADKP Synodos,Data derived from a CTF-Funded Synodos project,,,,,consortium,,https://www.synapse.org/ctf,,string,ADKP -testvalue,not real,,,,,consortium,,nope,,string,ADKP From efc530a5c9b886ad795ddaa8bd687e8f316767bb Mon Sep 17 00:00:00 2001 From: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com> Date: Tue, 26 Nov 2024 17:22:51 +0000 Subject: [PATCH 7/9] use python container instead of universal --- .devcontainer/devcontainer.json | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 5c658046..03b1b96a 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,10 +1,5 @@ { - "image": "mcr.microsoft.com/devcontainers/universal:2", - "hostRequirements": { - "cpus": 4, - "memory": "4gb", - "storage": "16gb" - }, + "image": "mcr.microsoft.com/devcontainers/python:3.10", "features": { }, "postCreateCommand": "bash ./.devcontainer/post-create.sh", From d2bc80ce496a24fc770a932c727fbea203e7eba1 Mon Sep 17 00:00:00 2001 From: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com> Date: Tue, 26 Nov 2024 17:23:18 +0000 Subject: [PATCH 8/9] use full path to install req.txt --- .devcontainer/post-create.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.devcontainer/post-create.sh b/.devcontainer/post-create.sh index 2e149f32..9725d6b5 100644 --- a/.devcontainer/post-create.sh +++ b/.devcontainer/post-create.sh @@ -1,4 +1,4 @@ #!/bin/bash # install schematic and other packages -pip install -r ../requirements.txt \ No newline at end of file +pip install -r /workspaces/data-models/requirements.txt \ No newline at end of file From abbf944d4c495f1cca448e120da7cedef1ebc373 Mon Sep 17 00:00:00 2001 From: Abby Vander Linden <11965371+avanlinden@users.noreply.github.com> Date: Tue, 26 Nov 2024 17:28:55 +0000 Subject: [PATCH 9/9] generate data models without test value --- AD.model.csv | 3 +-- AD.model.jsonld | 20 -------------------- 2 files changed, 1 insertion(+), 22 deletions(-) diff --git a/AD.model.csv b/AD.model.csv index b16a7b39..1f1815d8 100644 --- a/AD.model.csv +++ b/AD.model.csv @@ -491,7 +491,6 @@ PSON,Physical Science in Oncology,,,,,consortium,,https://physics.cancer.gov/,,s Psych-AD,Neuropsychiatric Symptoms in Alzheimer's Disease,,,,,consortium,,https://adknowledgeportal.synapse.org/Explore/Programs/DetailsPage?Program=Psych-AD,,string,ADKP Resilience-AD,Interdisciplinary Research to Understand the Complex Biology of Resilience to Alzheimer's Disease Risk,,,,,consortium,,https://adknowledgeportal.synapse.org/,,string,ADKP Synodos,Data derived from a CTF-Funded Synodos project,,,,,consortium,,https://www.synapse.org/ctf,,string,ADKP -testvalue,not real,,,,,consortium,,nope,,string,ADKP AIBL pool,"The Australian Imaging, Biomarkers, and Lifestyle Flagship Study of Ageing (AIBL) reference pool.",,,,,controlType,,https://aibl.csiro.au/,,string,experimentalData Baker pool,The Baker Institute Metabolomics Laboratory reference pool.,,,,,controlType,,https://baker.edu.au/research/laboratories/metabolomics,,string,experimentalData blank injection,blank injection,,,,,controlType,,-,,string,experimentalData @@ -864,7 +863,7 @@ chromosome,A structure composed of a very long molecule of DNA and associated pr climbID,Identifying string linked to an animal in Climb database,,,,True,ManifestColumn,,sage.annotations-neuro.climbID-0.0.1,,string,MODEL-AD cohort,A study group population where the members are human beings who meet inclusion criteria.,"ABC-DS,ACT,ADNI,ADRC,Banner,BEAM,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,MARS-WI,Mayo Clinic,MC,MCJ,MCR,MIND,MSBB,NYBB,Pitt ADRC,POINTER,RADC,ROSMAP,SMRI,Tulsa LIBR-1000,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP",,,False,ManifestColumn,,http://purl.obolibrary.org/obo/STATO_0000203,,string,clinical conservationMethod,The conservation method,"noConservation, fixed tissues only, frozen tissue only, both fixed and frozen tissue, missing or unknown",,,True,ManifestColumn,,sage-annotations-clinical.conservationMethod-0.0.2,string,,clinical -consortium,The name of the consortium,"testvalue, CMC, PEC, AMP-AD, MODEL-AD, M2OVE-AD, Resilience-AD, BSMN, CSBC, PSON, GENIE, Synodos, DHART SPORE, CDCP, Psych-AD, ELITE, Not Applicable",,,True,ManifestColumn,,sage.annotations-sageCommunity.consortium-0.0.5,,string,ADKP +consortium,The name of the consortium,"CMC, PEC, AMP-AD, MODEL-AD, M2OVE-AD, Resilience-AD, BSMN, CSBC, PSON, GENIE, Synodos, DHART SPORE, CDCP, Psych-AD, ELITE, Not Applicable",,,True,ManifestColumn,,sage.annotations-sageCommunity.consortium-0.0.5,,string,ADKP contrastAgent,Substance administered during an imaging procedure that allows delineation of internal structures.,,,,False,ManifestColumn,,sage.annotations-experimentalData.contrastAgent-0.0.2,,string,imaging controlType,Control samples suitable for normalization and batch correction,"AIBL pool, Baker pool, blank injection, GIS, GoldenWest, NIST SRM 1950, qc mix, Replicate, study pool, water plus Baker ISTD",,,False,ManifestColumn,,sage.annotations-experimentalData.controlType-0.0.5,,string,experimentalData CVD_ART,Arteriolosclerosis,"No CVD_ART, Mild, Moderate, Severe, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.CVD_ART-0.0.2,string,,clinical diff --git a/AD.model.jsonld b/AD.model.jsonld index d3c2fa8d..645a855f 100644 --- a/AD.model.jsonld +++ b/AD.model.jsonld @@ -11247,9 +11247,6 @@ "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ - { - "@id": "bts:Testvalue" - }, { "@id": "bts:CMC" }, @@ -11853,23 +11850,6 @@ "sms:required": "sms:false", "sms:validationRules": [] }, - { - "@id": "bts:Testvalue", - "@type": "rdfs:Class", - "rdfs:comment": "not real", - "rdfs:label": "Testvalue", - "rdfs:subClassOf": [ - { - "@id": "bts:Consortium" - } - ], - "schema:isPartOf": { - "@id": "http://schema.biothings.io" - }, - "sms:displayName": "testvalue", - "sms:required": "sms:false", - "sms:validationRules": [] - }, { "@id": "bts:AIBLpool", "@type": "rdfs:Class",