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Merge pull request #89 from INCATools/additional-sources2
additional sources
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -61,6 +61,7 @@ PREFIX_YAML_PATH = $(PREFIX_DIR)/prefixes.yaml | |
| gzip -f $*-$(RGSUFFIX).tsv && \ | ||
| cat $(THIS_DIR)/indexes/*.sql | sqlite3 $@.tmp && \ | ||
| echo "ALTER TABLE statements ADD COLUMN graph TEXT;" | sqlite3 $@.tmp && \ | ||
| (test -d views && find views -maxdepth 1 -name '$(notdir $*)*.sql' -type f -print0 | xargs -0 -I{} sh -c 'sqlite3 [email protected]< "$$1"' sh {} || echo no views ) && \ | ||
| mv $@.tmp $@ | ||
| .PRECIOUS: %.db | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -4,14 +4,14 @@ | |
| import shutil | ||
| import subprocess | ||
| from pathlib import Path | ||
| from typing import Optional, TextIO | ||
| from typing import List, Optional, TextIO | ||
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| import requests | ||
| from linkml_runtime.loaders import yaml_loader | ||
| from sqlalchemy import create_engine | ||
| from sqlalchemy.orm import sessionmaker | ||
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| from semsql.builder.registry import registry_schema | ||
| from semsql.builder.registry import path_to_ontology_registry, registry_schema | ||
| from semsql.builder.registry.registry_schema import (CompressionEnum, Makefile, | ||
| MakefileRule, Ontology) | ||
| from semsql.utils.makefile_utils import makefile_to_string | ||
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@@ -117,6 +117,27 @@ def connect(owl_file: str): | |
| return session | ||
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| def get_postprocessing_steps( | ||
| ontology: str, db: str, registry_path: str = None | ||
| ) -> List[str]: | ||
| """ | ||
| Get postprocessing steps for an ontology | ||
| :param registry_path: | ||
| :param ontology: | ||
| :return: | ||
| """ | ||
| if registry_path is None: | ||
| registry_path = path_to_ontology_registry() | ||
| registry: registry_schema.Registry | ||
| registry = yaml_loader.load( | ||
| str(registry_path), target_class=registry_schema.Registry | ||
| ) | ||
| # steps = [step.format(ont=ontology, db=db) for step in registry.ontologies.get(ontology, []).post_processing_steps] | ||
| steps = registry.ontologies.get(ontology, []) | ||
| return steps | ||
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| def compile_registry(registry_path: str, local_prefix_file: TextIO = None) -> str: | ||
| """ | ||
| Generate makefile content from registry | ||
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@@ -139,7 +160,7 @@ def compile_registry(registry_path: str, local_prefix_file: TextIO = None) -> st | |
| elif ont.zip_extract_file: | ||
| command = ( | ||
| f"curl -L -s {ont.url} > [email protected] && " | ||
| "unzip -p [email protected] {ont.zip_extract_file} " | ||
| f"unzip -p [email protected] {ont.zip_extract_file} " | ||
| "> [email protected] && rm [email protected]" | ||
| ) | ||
| elif ont.compression: | ||
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@@ -169,9 +190,8 @@ def compile_registry(registry_path: str, local_prefix_file: TextIO = None) -> st | |
| command = "robot merge -i $< -o $@" | ||
| else: | ||
| command = "cp $< $@" | ||
| rule = MakefileRule( | ||
| target=target, dependencies=dependencies, commands=[command] | ||
| ) | ||
| commands = [command] | ||
| rule = MakefileRule(target=target, dependencies=dependencies, commands=commands) | ||
| makefile.rules.append(rule) | ||
| if not ont.suppress: | ||
| onts.append(ont.id) | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -98,10 +98,24 @@ ontologies: | |
| url: https://openenergyplatform.org/ontology/oeo/releases/oeo-full.owl | ||
| prefixmap: | ||
| OEO: http://openenergy-platform.org/ontology/oeo/OEO_ | ||
| taxslim: | ||
| url: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.obo | ||
| build_command: "robot convert -i $< -o $@" | ||
| goldterms: | ||
| url: https://raw.githubusercontent.com/cmungall/gold-ontology/main/gold.owl | ||
| build_command: "robot relax -i $< reason -o $@" | ||
| prefixmap: | ||
| GOLDTERMS: https://w3id.org/gold.path/ | ||
| GOLDVOCAB: https://w3id.org/gold.vocab/ | ||
| sdgio: | ||
| url: https://raw.githubusercontent.com/SDG-InterfaceOntology/sdgio/master/sdgio.owl | ||
| prefixmap: | ||
| SDGIO: http://purl.unep.org/sdg/SDGIO_ | ||
| kin: | ||
| url: http://purl.org/ga4gh/kin.owl | ||
| build_command: "robot reason -i $< -o $@" | ||
| prefixmap: | ||
| KIN: "http://purl.org/ga4gh/kin.owl#KIN_" | ||
| biovoices: | ||
| url: https://zenodo.org/record/5589773/files/ontology.owl?download=1 | ||
| build_command: "robot relax -i $< merge -o $@" | ||
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@@ -110,6 +124,11 @@ ontologies: | |
| omop: | ||
| prefixmap: | ||
| omop: https://athena.ohdsi.org/search-terms/terms/ | ||
| comet: | ||
| url: https://raw.githubusercontent.com/linkml/linkml-common/main/project/owl/linkml_common.owl.ttl | ||
| build_command: "robot relax -i $< merge -o $@" | ||
| prefixmap: | ||
| comet: https://w3id.org/linkml-common/ | ||
| cco: | ||
| url: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AllCoreOntology | ||
| build_command: "robot merge -i $< relax -o $@" | ||
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@@ -166,9 +185,16 @@ ontologies: | |
| ito: | ||
| url: https://github.com/OpenBioLink/ITO/raw/master/ITO.owl.zip | ||
| zip_extract_file: ITO.owl | ||
| reactome-Homo-sapiens: | ||
| reactome-hs: | ||
| url: https://reactome.org/download/current/biopax.zip | ||
| zip_extract_file: Homo_sapiens.owl | ||
| #post_processing_steps: | ||
| # - "sqlite3 {db} < views/reactome.sql" | ||
| reactome-mm: | ||
| url: https://reactome.org/download/current/biopax.zip | ||
| zip_extract_file: Mus_musculus.owl | ||
| post_processing_steps: | ||
| - "sqlite3 {db} < views/reactome.sql" | ||
| efo: | ||
| url: http://www.ebi.ac.uk/efo/efo.owl | ||
| has_imports: true | ||
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@@ -327,6 +353,17 @@ ontologies: | |
| url: "'https://data.bioontology.org/ontologies/NANDO/submissions/15/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb'" | ||
| prefixmap: | ||
| NANDO: http://nanbyodata.jp/ontology/NANDO_ | ||
| ecso: | ||
| url: "'https://data.bioontology.org/ontologies/ECSO/submissions/64/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb'" | ||
| prefixmap: | ||
| ECSO: http://purl.dataone.org/odo/ECSO_ | ||
| enigma_context: | ||
| url: https://raw.githubusercontent.com/jmchandonia/CORAL/main/example/enigma/ontologies/context_measurement_ontology.obo | ||
| build_command: "robot merge -i $< -o $@" | ||
| #meo: | ||
| # url: "'https://data.bioontology.org/ontologies/MEO/submissions/9/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb'" | ||
| # prefixmap: | ||
| # MEO: http://purl.jp/bio/11/meo/MEO_ | ||
| ontie: | ||
| url: https://ontology.iedb.org/file/ontie.owl | ||
| prefixmap: | ||
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@@ -349,8 +386,8 @@ ontologies: | |
| linkml: https://w3id.org/linkml/ | ||
| mixs: https://w3id.org/mixs/ | ||
| mixs: | ||
| url: https://raw.githubusercontent.com/microbiomedata/mixs-6-2-release-candidate/main/schema-derivatives/mixs_6_2_rc.owl.ttl | ||
| build_command: "robot merge -i $< reason -o $@.tmp.owl && perl -npe 's@_6_2_rc@@g;s@-6-2-rc@@g' [email protected] > $@" | ||
| url: https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/main/project/owl/mixs.owl.ttl | ||
| build_command: "robot merge -i $< reason -o $@" | ||
| prefixmap: | ||
| mixs: https://w3id.org/mixs/ | ||
| fibo: | ||
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@@ -363,6 +400,9 @@ ontologies: | |
| # BFO variant products | ||
| bfo2020: | ||
| url: http://purl.obolibrary.org/obo/bfo/2020/bfo.owl | ||
| #post_processing_steps: | ||
| # - "echo hello {db}" | ||
| # - "echo goodbye {db}" | ||
| bfo2020_core: | ||
| url: http://purl.obolibrary.org/obo/bfo/2020/bfo-core.owl | ||
| bfo2020_notime: | ||
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