bfabric_flask.py

#!/usr/bin/env python3
# -*- coding: latin1 -*-


"""
This script is thought to be used as a
Rest SOAP proxy.
In particular, it connects R shiny to https://bfabric.org


run as pfeeder
FLASK_APP=$(which bfabric_flask.py) flask run --host=0.0.0.0 

Christian Panse <cp@fgcz.ethz.ch>
Christian Trachsel

2016-07-05 1700
2017-05-11
2019-10-16 adapted to bfabric10
2022-02-04 adaptation to start flask by Debian's systemd
"""

import base64
import json
from flask import Flask, jsonify, request
from flask.json import JSONEncoder
from slugify import slugify


import bfabric

import logging
import logging.handlers
from flask.logging import default_handler


def create_logger(name="bfabric11_flask", address=("fgcz-ms.uzh.ch", 514)):
    """
    create a logger object
    """
    syslog_handler = logging.handlers.SysLogHandler(address=address)
    formatter = logging.Formatter('%(name)s %(message)s')
    syslog_handler.setFormatter(formatter)

    logger = logging.getLogger(name)
    logger.setLevel(20)
    logger.addHandler(syslog_handler)


    return logger

logger = create_logger()

class BfabricJSONEncoder(JSONEncoder):
    """
    enables to serialize (jsonify) bfabric wsdl objects
    """

    def default(self, obj):
        try:
            iterable = iter(obj)
        except TypeError:
            pass
        else:
            return(dict(iterable))

        return JSONEncoder.default(self, obj)


address=("fgcz-ms.uzh.ch", 514)
name="bfabric_flask"
formatter = logging.Formatter('%(name)s %(message)s')

syslog_handler = logging.handlers.SysLogHandler(address=address)
syslog_handler.setFormatter(formatter)



app = Flask(__name__)

app.json_encoder = BfabricJSONEncoder 
bfapp = bfabric.Bfabric()

inlcude_child_extracts = True

"""
generic query interface for read interface

example (assumes the proxy runs on localhost):

R>     rv <- POST('http://localhost:5000/query', 
               body = toJSON(list(login = login, 
                                  webservicepassword = webservicepassword,
                                  query = 'resource',
                                  containerid = 3000,
                                  applicationid = 205)), 
               encode = 'json')
    
R>    rv <- content(rv)

TODO(cp@fgcz.ethz.ch): also provide an argument for the webbase
"""
@app.route('/q', methods=['GET', 'POST'])
def q():
    try:
        content = json.loads(request.data)
    except:
        return jsonify({'error': 'could not get POST content.'})

    # TODO(cp): more finetuning on paging
    try:
        webservicepassword = content['webservicepassword'][0].replace("\t", "")
        login = content['login'][0]

        # TODO(cp): check if meaningful page
        page = content['page'][0]
        
        bf = bfabric.Bfabric(login=login, password=webservicepassword)
        res = bf.read_object(endpoint=content['endpoint'][0], obj=content['query'], page=page)
        logger.info("'{}' login success query {} ...".format(login, content['query']))
    except:
        logger.info("'{}' login failed ...".format(login))
        return jsonify({'status': 'jsonify failed: bfabric python module.'})

    try:
        return jsonify({'res': res})
    except:
        logger.info("'{}' query failed ...".format(login))
        return jsonify({'status': 'jsonify failed'})


@app.route('/s', methods=['GET', 'POST'])
def s():
    try:
        content = json.loads(request.data)
    except:
        return jsonify({'error': 'could not get POST content.'})

    bf = bfabric.Bfabric()
    print (content)
    res = bf.save_object(endpoint=content['endpoint'][0], obj=content['query'])

    try:
        return jsonify({'res': res})
    except:
        return jsonify({'status': 'jsonify failed'})
    
    

def dfs__(extract_id):
    stack = list()
    visited = dict()
    stack.append(extract_id)

    extract_dict = dict()

    while len(stack) > 0:
        o = stack.pop()
        visited[u] = True


        extract = bfapp.read_object(endpoint='extract', obj={'id': u})
        extract_dict[u] = extract[0]

        try:
           for child_extract in extract[0].childextract:
               if (child_extract._id not in visited):

                    stack.append(child_extract._id)

        except:
            pass

    return extract_dict


#def wsdl_sample(containerid):
#    try:
#        return map(lambda x: {'id': x._id, 'name': x.name},
#            bfapp.read_object(endpoint='sample', obj={'containerid': containerid}))
#    except:
#        pass

def compose_ms_queue_dataset(jsoncontent, workunitid, containerid):
    obj = {}
    try:
        obj['name'] = 'generated through http://fgcz-s-028.uzh.ch:8080/queue_generator/'
        obj['workunitid'] = workunitid
        obj['containerid'] = containerid
        obj['attribute'] = [
            {'name': 'File Name', 'position':1, 'type':'String'},
            {'name': 'Condition', 'position':2, 'type':'String'},
            {'name': 'Path', 'position': 3},
            {'name': 'Position', 'position': 4},
            {'name': 'Inj Vol', 'position': 5, 'type': 'numeric'},
            {'name': 'ExtractID', 'position': 6, 'type': 'extract'} ]

        obj['item'] = list()

        for idx in range(0, len(jsoncontent)):
            obj['item'].append({'field': map(lambda x: {'attributeposition': x + 1, 'value': jsoncontent[idx][x]}, range(0, len(jsoncontent[idx]))), 'position': idx + 1})

    except:
        pass

    return obj


@app.route('/add_resource', methods=['POST'])
def add_resource():                            
    try:
        queue_content = json.loads(request.data)
        print (queue_content)
        print("--")
    except:
        print ("failed: could not get POST content")
        return jsonify({'error': 'could not get POST content.'})

    res = bfapp.save_object('workunit', {'name': queue_content['name'],
                                         'description': "{}".format(queue_content['workunitdescription'][0]),
                                         'containerid': queue_content['containerid'],
                                         'applicationid': queue_content['applicationid']
                                         })
    print (res)

    workunit_id = res[0]._id

    print (workunit_id)

    res = bfapp.save_object('resource', {'base64': queue_content['base64'],
                                         'name': queue_content['resourcename'],
                                         'workunitid': workunit_id})

    res = bfapp.save_object('workunit', {'id': workunit_id, 'status': 'available'})

    return jsonify(dict(workunit_id=workunit_id))

@app.route('/add_dataset/<int:containerid>', methods=['GET', 'POST'])
def add_dataset(containerid):
    try:
        queue_content = json.loads(request.data)
    except:
        return jsonify({'error': 'could not get POST content.'})

    try:
        obj = {}
        obj['name'] = 'autogenerated dataset by http://fgcz-s-028.uzh.ch:8080/queue_generator/'
        obj['containerid'] = containerid
        obj['attribute'] = [ {'name':'File Name', 'position':1, 'type':'String'},
            {'name':'Path', 'position':2},
            {'name':'Position', 'position':3},
            {'name':'Inj Vol', 'position':4, 'type':'numeric'},
            {'name':'ExtractID', 'position':5, 'type':'extract'} ]

        obj['item'] = list()

        for idx in range(0, len(queue_content)):
            obj['item']\
            .append({'field': map(lambda x: {'attributeposition': x + 1, 'value': queue_content[idx][x]}, range(0, len(queue_content[idx]))), 'position': idx + 1})

            print (obj)

    except:
        return jsonify({'error': 'composing bfabric object failed.'})

    try:
        res = bfapp.save_object(endpoint='dataset', obj=obj)[0]
        print ("added dataset {} to bfabric.".format(res._id))
        return (jsonify({'id':res._id}))

    except:
        print(res)
        return jsonify({'error': 'beaming dataset to bfabric failed.'})



@app.route('/user/<int:containerid>', methods=['GET'])
def get_user(containerid):

    users = bfapp.read_object(endpoint='user', obj={'containerid': containerid})
    #not users or
    if not users or len(users) == 0:
        return jsonify({'error': 'no resources found.'})
        # abort(404)

    return jsonify({'user': users})


@app.route('/sample/<int:containerid>', methods=['GET'])
def get_all_sample(containerid):

    samples = []
    rv = list(map(lambda p: bfapp.read_object(endpoint='sample', obj={'containerid': containerid}, page=p), range(1,10)))
    rv = list(map(lambda x: [] if x is None else x, rv))
    for el in rv: samples.extend(el)


    try:
        annotationDict = {}
        for annotationId in filter(lambda x: x is not None, set(map(lambda x: x.groupingvar._id if "groupingvar" in x else None, samples))):
            print (annotationId)
            annotation = bfapp.read_object(endpoint='annotation', obj={'id': annotationId})
            annotationDict[annotationId] = annotation[0].name
    except:
        pass

    for sample in samples:
        try:
            sample['condition'] = annotationDict[sample.groupingvar._id]
        except:
            sample['condition'] = None

    if len(samples) == 0:
        return jsonify({'error': 'no extract found.'})
        # abort(404)

    return jsonify({'samples': samples})

"""
example
curl http://localhost:5000/zip_resource_of_workunitid/154547
"""
@app.route('/zip_resource_of_workunitid/<int:workunitid>', methods=['GET'])
def get_zip_resources_of_workunit(workunitid):
    res = map(lambda x: x.relativepath, bfapp.read_object(endpoint='resource', obj={'workunitid': workunitid}))
    print (res)
    res = filter(lambda x: x.endswith(".zip"), res)
    return jsonify(res)


@app.route('/query', methods=['GET', 'POST'])
def query():
    try:
        content = json.loads(request.data)
    except:
        return jsonify({'error': 'could not get POST content.', 'appid': appid})

    print ("PASSWORD CLEARTEXT", content['webservicepassword'])
    
    bf = bfabric.Bfabric(login=content['login'], 
      password=content['webservicepassword'], 
      webbase='http://fgcz-bfabric.uzh.ch/bfabric')

    for i in content.keys():
      print ("{}\t{}".format(i, content[i]))

    if 'containerid' in content:
      workunits = bf.read_object(endpoint='workunit', 
        obj={'applicationid': content['applicationid'],
          'containerid': content['containerid']})
      print (workunits)
      return jsonify({'workunits': map(lambda x: x._id, workunits)})
    #elif 'query' in content and "{}".format(content['query']) is 'project':
    else:
      user = bf.read_object(endpoint='user', obj={'login': content['login']})[0]
      projects = map(lambda x: x._id, user.project)
      return jsonify({'projects': projects})

    return jsonify({'error': 'could not process query'})
  
@app.route('/addworkunit', methods=['GET', 'POST'])
def add_workunit():
    appid = request.args.get('appid', None)
    pid = request.args.get('pid', None)
    rname = request.args.get('rname', None)

    try:
        content = json.loads(request.data)
        # print content
    except:
        return jsonify({'error': 'could not get POST content.', 'appid': appid})

    resource_base64 = content['base64']
    #base64.b64encode(content)
    print (resource_base64)

    return jsonify({'rv': 'ok'})

if __name__ == '__main__':
    app.run(debug=False, host="0.0.0.0", port=5000)