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| author | CoprDistGit <infra@openeuler.org> | 2023-05-15 05:05:21 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-15 05:05:21 +0000 |
| commit | 70af38dc5e9df29a86feae26f5e164a74503d3c0 (patch) | |
| tree | 4841d0dda16bc74a3ee33efb50a8d0a80291fdd6 | |
| parent | 81cc5881af48e3231fc9e7e96b47785b59bc6cb7 (diff) | |
automatic import of python-bioclients
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-bioclients.spec | 261 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 263 insertions, 0 deletions
@@ -0,0 +1 @@ +/BioClients-0.2.11.tar.gz diff --git a/python-bioclients.spec b/python-bioclients.spec new file mode 100644 index 0000000..2bb1b71 --- /dev/null +++ b/python-bioclients.spec @@ -0,0 +1,261 @@ +%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` <img align="right" src="doc/images/BioClients_logo.png" height="120" alt="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 <https://github.com/jeremyjyang/BioClients>; +releases available via `pypi.org`: +<https://pypi.org/project/BioClients/> +(`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` <img align="right" src="doc/images/BioClients_logo.png" height="120" alt="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 <https://github.com/jeremyjyang/BioClients>; +releases available via `pypi.org`: +<https://pypi.org/project/BioClients/> +(`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` <img align="right" src="doc/images/BioClients_logo.png" height="120" alt="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 <https://github.com/jeremyjyang/BioClients>; +releases available via `pypi.org`: +<https://pypi.org/project/BioClients/> +(`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 +* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 0.2.11-1 +- Package Spec generated @@ -0,0 +1 @@ +99f179762a95ec18903815c3f363022f BioClients-0.2.11.tar.gz |
