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HadleyKingHadleyKing
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Merge pull request #13 from biocompute-objects/dev
Long overdue updates to main
2 parents e93c675 + 9852c25 commit 986e459

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‎.gitignore‎

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cwl_run/*
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.DS_Store
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tests/notes.txt
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error.log
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*.DS_Store
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error.log
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.bco_env/
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home
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.python-version
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.vscode/

‎README.md‎

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Run the Git Clone command in the location you would like the repostory:
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1. `cd path/to/my/github/repositories`
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1. Choose location for repository
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2. `git clone https://github.com/HadleyKing/bco-tool.git`
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cd path/to/my/github/repositories
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Add the main bco-tool program to your path
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2. Clone repo
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4. `cd bco-tool`
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git clone https://github.com/biocompute-objects/bcotool.git
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5. `pip install -r requirements.txt`
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### To add the main bco-tool program to your path
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6. `cp bco-tool/bco_runner.py /usr/local/bin/bco`
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4. Enter directory
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cd bcotool
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5. Create and/or activate a [python virtual environment](https://virtualenv.pypa.io/en/latest/user_guide.html):
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virtualenv [path_to_environment]
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5. Install requirements in the virtual environment
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pip install -r requirements.txt
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6. Copy the exicutable program file to the user local bin:
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cp bco-tool/bco_runner.py /usr/local/bin/bco
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## Supported modes

‎bco-tool/library/__init__.py‎

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bco-tool/library/ConvertToSchema.py renamed to bcotool/ConvertToSchema.py

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bco-tool/library/JsonUtils.py renamed to bcotool/JsonUtils.py

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bco-tool/library/README.md renamed to bcotool/README.md

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‎bcotool/__init__.py‎

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"""
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bco app and stuff
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"""
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from .bcoutils import *
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from .validate import *

‎bcotool/apitest.py‎

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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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#bcotool
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import requests
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import json
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import bcoutils
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#______________________________________________________________________________#
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def update_bco():
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"""
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"""
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bco = '/Users/hadleyking/GitHub/hadleyking/bcotool/data_tests/cwl-blastn-homologs.json'
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headers = {'Content-type': 'application/json; charset=UTF-8'}
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bco_dict = bcoutils.load_bco(bco)
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creator = {
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'POST_create_new_object':[
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{
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'object_id': 'https://beta.portal.aws.biochemistry.gwu.edu/BCO_31/1.0',
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'table': 'bco_publish',
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'schema': 'IEEE',
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'contents': bco_dict,
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'state': 'PUBLISHED'
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}
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]
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}
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creator = json.dumps(creator)
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r = requests.post(
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'https://beta.portal.aws.biochemistry.gwu.edu/bco/objects/create/',
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data = creator, verify=False, headers=headers)
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return (r.text)
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#______________________________________________________________________________#
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def publish_bco():
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"""
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"""
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bco = '/Users/hadleyking/GitHub/hadleyking/bcotool/data_tests/cwl-blastn-homologs.json'
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headers = {'Content-type': 'application/json; charset=UTF-8'}
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bco_dict = bcoutils.load_bco(bco)
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creator = {
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'POST_create_new_object':[
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{
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'table': 'bco_publish',
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'schema': 'IEEE',
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'contents': bco_dict,
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'state': 'PUBLISHED'
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}
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]
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}
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creator = json.dumps(creator)
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r = requests.post(
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'https://beta.portal.aws.biochemistry.gwu.edu/bco/objects/create/',
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data = creator, verify=False, headers=headers)
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return (r.text
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)
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#______________________________________________________________________________#
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def read_bco():
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"""
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"""
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headers = {'Content-type': 'application/json; charset=UTF-8'}
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req_list = [
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('bco_draft', 'https://beta.portal.aws.biochemistry.gwu.edu/BCO_DRAFT_706f97bdcafa4cd89056fbbfc9d5d325'),
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('bco_publish', 'https://beta.portal.aws.biochemistry.gwu.edu/BCO_3/1.0')
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]
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req_dict = {}
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req_dict['POST_read_object'] = []
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for i in req_list:
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print(i[0])
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req_dict['POST_read_object'].append(
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{
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'table': i[0],
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'object_id': i[1]
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}
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)
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# reader = {
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# 'POST_read_object':[
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# {
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# 'table': 'bco_draft',
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# 'object_id': 'https://beta.portal.aws.biochemistry.gwu.edu/BCO_DRAFT_706f97bdcafa4cd89056fbbfc9d5d325'
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# },
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# {
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# 'table': 'bco_publish',
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# 'object_id': 'https://beta.portal.aws.biochemistry.gwu.edu/BCO_3/1.0'
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# }
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# ]
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# }
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print(req_dict)
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read = json.dumps(req_dict)
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r = requests.post(
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'https://beta.portal.aws.biochemistry.gwu.edu/bco/objects/read/',
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data = read, verify=False, headers=headers)
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return (r.text)
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#______________________________________________________________________________#
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def main():
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# resp = read_bco()
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resp = publish_bco()
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resp = update_bco()
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print(resp)
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#______________________________________________________________________________#
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if __name__ == "__main__":
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main()

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