%global _empty_manifest_terminate_build 0 Name: python-BioClients Version: 0.2.11 Release: 1 Summary: Clients for online biomedical resources, usually REST APIs. License: MIT License URL: https://github.com/jeremyjyang/BioClients Source0: https://mirrors.nju.edu.cn/pypi/web/packages/5b/3b/d8e72d59166c43ba184fb4ea3d040a6b5b0b6408d88e2e232c882aa53d92/BioClients-0.2.11.tar.gz BuildArch: noarch %description # `BioClients` BioClients logo Python package for access to online biomedical resources, usually via REST APIs. Modules generally include `Client.py` for command-line use and `Utils.py` for integration into other code. With the advent of HTTP web services, first SOAP/XML and then mostly REST/JSON, many online APIs require very similar methods for data search, requests and transforms into usable formats, often TSV. ## Availability and installation Source at ; releases available via `pypi.org`: (`pip3 install BioClients`). However, current development snapshot recommended. ___(First download or clone.)___ ``` $ cd BioClients $ python3 setup.py install ``` ## Dependencies * Python 3.7+ * Python packages: `pandas`, `requests`, `urllib`, `json`, `xml`, `yaml`, `psycopg2`, `tqdm`, etc. ## Modules [__Allen__](doc/allen.md) • [__AMP-T2D__](doc/amp__t2d.md) • [__BindingDb__](doc/bindingdb.md) • [__BioGrid__](doc/biogrid.md) • [__Bioregistry__](doc/bioregistry.md) • [__BRENDA__](doc/brenda.md) • [__CAS__](doc/cas.md) • [__CDC__](doc/cdc.md) • [__CFDE__](doc/cfde.md) • [__Chem2Bio2RDF__](doc/chem2bio2rdf.md) • [__ChEBI__](doc/chebi.md) • [__ChEMBL__](doc/chembl.md) • [__ChemIdPlus__](doc/chemidplus.md) • [__ClinicalTrials.gov__](doc/clinicaltrials.md) • [__Disease Ontology__](doc/diseaseontology.md) • [__DisGeNet__](doc/disgenet.md) • [__DNorm__](doc/dnorm.md) • [__DrugCentral__](doc/drugcentral.md) • [__EMBL-EBI__](doc/emblebi.md) • [__EnsEMBL__](doc/ensembl.md) • [__FDA__](doc/fda.md) • [__Gene Ontology__](doc/geneontology.md) • [__GTEx__](doc/gtex.md) • [__GWAS Catalog__](doc/gwascatalog.md) • [__HUGO__](doc/hugo.md) • [__HumanBase__](doc/humanbase.md) • [__iCite__](doc/icite.md) • [__IDG__](doc/idg.md) • [__JensenLab__](doc/jensenlab.md) • [__LINCS__](doc/lincs.md) • [__MaayanLab__](doc/maayanlab.md) • [__Medline__](doc/medline.md) • [__MeSH__](doc/mesh.md) • [__MONARCH__](doc/monarch.md) • [__MyGene__](doc/mygene.md) • [__NCBO__](doc/ncbo.md) • [__NCATS__](doc/ncats.md) • [__OMIM__](doc/omim.md) • [__Open Targets__](doc/opentargets.md) • [__Panther__](doc/panther.md) • [__PDB__](doc/pdb.md) • [__PubChem__](doc/pubchem.md) • [__PubMed__](doc/pubmed.md) • [__PubTator__](doc/pubtator.md) • [__Reactome__](doc/reactome.md) • [__RXNorm__](doc/rxnorm.md) • [__STRINGDB__](doc/stringdb.md) • [__TCGA__](doc/tcga.md) • [__UMLS__](doc/umls.md) • [__UniProt__](doc/uniprot.md) • [__Wikidata__](doc/wikidata.md) • [__WikiPathways__](doc/wikipathways.md) Miscellaneous utilities: [__UTIL__](doc/util.md) ## Usage Example ``` $ python3 -m BioClients.pubchem.Client -h ``` ## Design pattern Generally each module includes command-line app `Client.py` which calls functions in a corresponding `Utils.py`, providing all capabilities by import of the module. Command-line apps not API clients are generally named `App.py`. Functions can write to an output file or return a Pandas dataframe (if output file unspecified). ## Data structures and formats, XML, JSON, and TSV BioClients is designed to be simple and practical, and XML, JSON and TSV are likewise simple in many respects, yet a great deal of conceptual and technological progress is reflected. XML and JSON can represent arbitrarily complex data objects, comprised of nested lists, dictionaries, and trees of primary types. TSV represents tables of rows and columns, related by common keys, reflecting the development of SQL and relational databases. Transforming JSON to TSV, as these clients generally do, projects data objects to tables useful for many applications (e.g. machine learning). %package -n python3-BioClients Summary: Clients for online biomedical resources, usually REST APIs. Provides: python-BioClients BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-BioClients # `BioClients` BioClients logo Python package for access to online biomedical resources, usually via REST APIs. Modules generally include `Client.py` for command-line use and `Utils.py` for integration into other code. With the advent of HTTP web services, first SOAP/XML and then mostly REST/JSON, many online APIs require very similar methods for data search, requests and transforms into usable formats, often TSV. ## Availability and installation Source at ; releases available via `pypi.org`: (`pip3 install BioClients`). However, current development snapshot recommended. ___(First download or clone.)___ ``` $ cd BioClients $ python3 setup.py install ``` ## Dependencies * Python 3.7+ * Python packages: `pandas`, `requests`, `urllib`, `json`, `xml`, `yaml`, `psycopg2`, `tqdm`, etc. ## Modules [__Allen__](doc/allen.md) • [__AMP-T2D__](doc/amp__t2d.md) • [__BindingDb__](doc/bindingdb.md) • [__BioGrid__](doc/biogrid.md) • [__Bioregistry__](doc/bioregistry.md) • [__BRENDA__](doc/brenda.md) • [__CAS__](doc/cas.md) • [__CDC__](doc/cdc.md) • [__CFDE__](doc/cfde.md) • [__Chem2Bio2RDF__](doc/chem2bio2rdf.md) • [__ChEBI__](doc/chebi.md) • [__ChEMBL__](doc/chembl.md) • [__ChemIdPlus__](doc/chemidplus.md) • [__ClinicalTrials.gov__](doc/clinicaltrials.md) • [__Disease Ontology__](doc/diseaseontology.md) • [__DisGeNet__](doc/disgenet.md) • [__DNorm__](doc/dnorm.md) • [__DrugCentral__](doc/drugcentral.md) • [__EMBL-EBI__](doc/emblebi.md) • [__EnsEMBL__](doc/ensembl.md) • [__FDA__](doc/fda.md) • [__Gene Ontology__](doc/geneontology.md) • [__GTEx__](doc/gtex.md) • [__GWAS Catalog__](doc/gwascatalog.md) • [__HUGO__](doc/hugo.md) • [__HumanBase__](doc/humanbase.md) • [__iCite__](doc/icite.md) • [__IDG__](doc/idg.md) • [__JensenLab__](doc/jensenlab.md) • [__LINCS__](doc/lincs.md) • [__MaayanLab__](doc/maayanlab.md) • [__Medline__](doc/medline.md) • [__MeSH__](doc/mesh.md) • [__MONARCH__](doc/monarch.md) • [__MyGene__](doc/mygene.md) • [__NCBO__](doc/ncbo.md) • [__NCATS__](doc/ncats.md) • [__OMIM__](doc/omim.md) • [__Open Targets__](doc/opentargets.md) • [__Panther__](doc/panther.md) • [__PDB__](doc/pdb.md) • [__PubChem__](doc/pubchem.md) • [__PubMed__](doc/pubmed.md) • [__PubTator__](doc/pubtator.md) • [__Reactome__](doc/reactome.md) • [__RXNorm__](doc/rxnorm.md) • [__STRINGDB__](doc/stringdb.md) • [__TCGA__](doc/tcga.md) • [__UMLS__](doc/umls.md) • [__UniProt__](doc/uniprot.md) • [__Wikidata__](doc/wikidata.md) • [__WikiPathways__](doc/wikipathways.md) Miscellaneous utilities: [__UTIL__](doc/util.md) ## Usage Example ``` $ python3 -m BioClients.pubchem.Client -h ``` ## Design pattern Generally each module includes command-line app `Client.py` which calls functions in a corresponding `Utils.py`, providing all capabilities by import of the module. Command-line apps not API clients are generally named `App.py`. Functions can write to an output file or return a Pandas dataframe (if output file unspecified). ## Data structures and formats, XML, JSON, and TSV BioClients is designed to be simple and practical, and XML, JSON and TSV are likewise simple in many respects, yet a great deal of conceptual and technological progress is reflected. XML and JSON can represent arbitrarily complex data objects, comprised of nested lists, dictionaries, and trees of primary types. TSV represents tables of rows and columns, related by common keys, reflecting the development of SQL and relational databases. Transforming JSON to TSV, as these clients generally do, projects data objects to tables useful for many applications (e.g. machine learning). %package help Summary: Development documents and examples for BioClients Provides: python3-BioClients-doc %description help # `BioClients` BioClients logo Python package for access to online biomedical resources, usually via REST APIs. Modules generally include `Client.py` for command-line use and `Utils.py` for integration into other code. With the advent of HTTP web services, first SOAP/XML and then mostly REST/JSON, many online APIs require very similar methods for data search, requests and transforms into usable formats, often TSV. ## Availability and installation Source at ; releases available via `pypi.org`: (`pip3 install BioClients`). However, current development snapshot recommended. ___(First download or clone.)___ ``` $ cd BioClients $ python3 setup.py install ``` ## Dependencies * Python 3.7+ * Python packages: `pandas`, `requests`, `urllib`, `json`, `xml`, `yaml`, `psycopg2`, `tqdm`, etc. ## Modules [__Allen__](doc/allen.md) • [__AMP-T2D__](doc/amp__t2d.md) • [__BindingDb__](doc/bindingdb.md) • [__BioGrid__](doc/biogrid.md) • [__Bioregistry__](doc/bioregistry.md) • [__BRENDA__](doc/brenda.md) • [__CAS__](doc/cas.md) • [__CDC__](doc/cdc.md) • [__CFDE__](doc/cfde.md) • [__Chem2Bio2RDF__](doc/chem2bio2rdf.md) • [__ChEBI__](doc/chebi.md) • [__ChEMBL__](doc/chembl.md) • [__ChemIdPlus__](doc/chemidplus.md) • [__ClinicalTrials.gov__](doc/clinicaltrials.md) • [__Disease Ontology__](doc/diseaseontology.md) • [__DisGeNet__](doc/disgenet.md) • [__DNorm__](doc/dnorm.md) • [__DrugCentral__](doc/drugcentral.md) • [__EMBL-EBI__](doc/emblebi.md) • [__EnsEMBL__](doc/ensembl.md) • [__FDA__](doc/fda.md) • [__Gene Ontology__](doc/geneontology.md) • [__GTEx__](doc/gtex.md) • [__GWAS Catalog__](doc/gwascatalog.md) • [__HUGO__](doc/hugo.md) • [__HumanBase__](doc/humanbase.md) • [__iCite__](doc/icite.md) • [__IDG__](doc/idg.md) • [__JensenLab__](doc/jensenlab.md) • [__LINCS__](doc/lincs.md) • [__MaayanLab__](doc/maayanlab.md) • [__Medline__](doc/medline.md) • [__MeSH__](doc/mesh.md) • [__MONARCH__](doc/monarch.md) • [__MyGene__](doc/mygene.md) • [__NCBO__](doc/ncbo.md) • [__NCATS__](doc/ncats.md) • [__OMIM__](doc/omim.md) • [__Open Targets__](doc/opentargets.md) • [__Panther__](doc/panther.md) • [__PDB__](doc/pdb.md) • [__PubChem__](doc/pubchem.md) • [__PubMed__](doc/pubmed.md) • [__PubTator__](doc/pubtator.md) • [__Reactome__](doc/reactome.md) • [__RXNorm__](doc/rxnorm.md) • [__STRINGDB__](doc/stringdb.md) • [__TCGA__](doc/tcga.md) • [__UMLS__](doc/umls.md) • [__UniProt__](doc/uniprot.md) • [__Wikidata__](doc/wikidata.md) • [__WikiPathways__](doc/wikipathways.md) Miscellaneous utilities: [__UTIL__](doc/util.md) ## Usage Example ``` $ python3 -m BioClients.pubchem.Client -h ``` ## Design pattern Generally each module includes command-line app `Client.py` which calls functions in a corresponding `Utils.py`, providing all capabilities by import of the module. Command-line apps not API clients are generally named `App.py`. Functions can write to an output file or return a Pandas dataframe (if output file unspecified). ## Data structures and formats, XML, JSON, and TSV BioClients is designed to be simple and practical, and XML, JSON and TSV are likewise simple in many respects, yet a great deal of conceptual and technological progress is reflected. XML and JSON can represent arbitrarily complex data objects, comprised of nested lists, dictionaries, and trees of primary types. TSV represents tables of rows and columns, related by common keys, reflecting the development of SQL and relational databases. Transforming JSON to TSV, as these clients generally do, projects data objects to tables useful for many applications (e.g. machine learning). %prep %autosetup -n BioClients-0.2.11 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-BioClients -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Tue May 30 2023 Python_Bot - 0.2.11-1 - Package Spec generated