Python ArborFileManager Examples

Example #1

File: import_analyses.py Project: gitter-badger/ProjectManager

"""
Created December 2013

@author: [email protected]

This script loads Visomics-style analyses into the Arbor TreeStore database.

Requirements:
    - xmltodict (can be pip installed)
"""

from ArborFileManagerAPI import ArborFileManager
api = ArborFileManager()
api.initDatabaseConnection()

import json
import os
import sys
import xmltodict

# check that analysis directory has been passed in via the command line
if len(sys.argv) < 2:
  print sys.argv[0] + " <path/to/xml_dir>"
  sys.exit(1)

xml_dir = sys.argv[1]
xml_files = os.listdir(xml_dir)

for xml_file in xml_files:
  if not xml_file.endswith(".xml"):
    continue

Example #2

File: projmgr.py Project: gitter-badger/ProjectManager

import tangelo
import pymongo
import bson.json_util

from ArborFileManagerAPI import ArborFileManager
api = ArborFileManager()
api.initDatabaseConnection()

@tangelo.restful
def get(*pargs, **query_args):
    if len(pargs) == 0:
        return tangelo.HTTPStatusCode(400, "Missing resource type")

    resource_type = pargs[0]
    allowed = ["project", "analysis","collection", "workflow"]
    if resource_type == "project":
        if len(pargs) == 1:
            return api.getListOfProjectNames()
        elif len(pargs) == 2:
            project = pargs[1]
            return api.getListOfTypesForProject(project)
        elif len(pargs) == 3:
            project = pargs[1]
            datatype = pargs[2]
            return api.getListOfDatasetsByProjectAndType(project, datatype)
        elif len(pargs) == 4:
            project = pargs[1]
            datatype = pargs[2]
            dataset = pargs[3]
            coll = api.db[api.returnCollectionForObjectByName(project, datatype, dataset)]
            return bson.json_util.dumps(list(coll.find()))

Example #3

File: import_analyses.py Project: gitter-badger/ProjectManager

"""
Created December 2013

@author: [email protected]

This script loads Visomics-style analyses into the Arbor TreeStore database.

Requirements:
    - xmltodict (can be pip installed)
"""

from ArborFileManagerAPI import ArborFileManager
api = ArborFileManager()
api.initDatabaseConnection()

import json
import os
import sys
import xmltodict

# check that analysis directory has been passed in via the command line
if len(sys.argv) < 2:
    print sys.argv[0] + " <path/to/xml_dir>"
    sys.exit(1)

xml_dir = sys.argv[1]
xml_files = os.listdir(xml_dir)

for xml_file in xml_files:
    if not xml_file.endswith(".xml"):
        continue

Example #4

File: projmgr.py Project: gitter-badger/ProjectManager

import tangelo
import pymongo
import bson.json_util

from ArborFileManagerAPI import ArborFileManager

api = ArborFileManager()
api.initDatabaseConnection()


@tangelo.restful
def get(*pargs, **query_args):
    if len(pargs) == 0:
        return tangelo.HTTPStatusCode(400, "Missing resource type")

    resource_type = pargs[0]
    allowed = ["project", "analysis", "collection", "workflow"]
    if resource_type == "project":
        if len(pargs) == 1:
            return api.getListOfProjectNames()
        elif len(pargs) == 2:
            project = pargs[1]
            return api.getListOfTypesForProject(project)
        elif len(pargs) == 3:
            project = pargs[1]
            datatype = pargs[2]
            return api.getListOfDatasetsByProjectAndType(project, datatype)
        elif len(pargs) == 4:
            project = pargs[1]
            datatype = pargs[2]
            dataset = pargs[3]