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indexclient

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indexclient - pypi Package Compare versions

Comparing version
1.5.8
 to
2.1.0
+1
-1
indexclient.egg-info/PKG-INFO
Metadata-Version: 1.0
Name: indexclient
Version: 1.5.8
Version: 2.1.0
Summary: UNKNOWN

@@ -5,0 +5,0 @@ Home-page: UNKNOWN

+0
-5
indexclient.egg-info/SOURCES.txt

@@ -1,6 +0,1 @@

LICENSE
MANIFEST.in
NOTICE
Pipfile
Pipfile.lock
README.md

@@ -7,0 +2,0 @@ setup.py

+221
-73
indexclient/client.py

@@ -1,14 +0,19 @@

try:
from urlparse import urljoin
except ImportError:
from urllib.parse import urljoin
import copy
import json
import warnings
import requests
from indexclient.errors import BaseIndexError
MAX_RETRIES = 10
UPDATABLE_ATTRS = [
'file_name', 'urls', 'version',
'metadata', 'acl', 'urls_metadata'
"file_name",
"urls",
"version",
"metadata",
"acl",
"authz",
"urls_metadata",
]

@@ -26,3 +31,3 @@

resp.reason = json["error"]
except KeyError:
except (json.decoder.JSONDecodeError, KeyError):
pass

@@ -33,4 +38,26 @@ finally:

def timeout_wrapper(func):
def timeout(*args, **kwargs):
kwargs.setdefault("timeout", 60)
return func(*args, **kwargs)
return timeout
def retry_and_timeout_wrapper(func):
def retry_logic_with_timeout(*args, **kwargs):
kwargs.setdefault("timeout", 60)
retries = 0
while retries < MAX_RETRIES:
try:
return func(*args, **kwargs)
except requests.exceptions.ReadTimeout:
retries += 1
if retries == MAX_RETRIES:
raise
return retry_logic_with_timeout
class IndexClient(object):
def __init__(self, baseurl, version="v0", auth=None):

@@ -42,7 +69,8 @@ self.auth = auth

def url_for(self, *path):
return urljoin(self.url, "/".join(path))
subpath = "/".join(path).lstrip("/")
return "{}/{}".format(self.url.rstrip("/"), subpath)
def check_status(self):
"""Check that the API we are trying to communicate with is online"""
resp = requests.get(self.url + '/index')
resp = requests.get(self.url + "/index")
handle_error(resp)

@@ -65,3 +93,3 @@

if no_dist:
response = self._get(did, params={'no_dist': ''})
response = self._get(did, params={"no_dist": ""})
else:

@@ -108,3 +136,3 @@ response = self._get(did)

headers = {'content-type': 'application/json'}
headers = {"content-type": "application/json"}
try:

@@ -118,6 +146,3 @@ response = self._post("bulk/documents", json=dids, headers=headers)

return [
Document(self, doc['did'], json=doc)
for doc in response.json()
]
return [Document(self, doc["did"], json=doc) for doc in response.json()]

@@ -133,16 +158,16 @@ def get_with_params(self, params=None):

params_copy = copy.deepcopy(params) or {}
if 'hashes' in params_copy:
params_copy['hash'] = params_copy.pop('hashes')
if "hashes" in params_copy:
params_copy["hash"] = params_copy.pop("hashes")
reformatted_params = dict()
for param in ['hash', 'metadata']:
for param in ["hash", "metadata"]:
if param in params_copy:
reformatted_params[param] = []
for k, v in params_copy[param].items():
reformatted_params[param].append(str(k) + ':' + str(v))
reformatted_params[param].append(str(k) + ":" + str(v))
del params_copy[param]
reformatted_params.update(params_copy)
reformatted_params['limit'] = 1
reformatted_params["limit"] = 1
try:
response = self._get('index', params=reformatted_params)
response = self._get("index", params=reformatted_params)
except requests.HTTPError as e:

@@ -153,6 +178,6 @@ if e.response.status_code == 404:

raise e
if not response.json()['records']:
if not response.json()["records"]:
return None
json = response.json()['records'][0]
did = json['did']
json = response.json()["records"][0]
did = json["did"]
return Document(self, did, json=json)

@@ -164,3 +189,10 @@

def list_with_params(self, limit=float("inf"), start=None, page_size=100, params=None, negate_params=None):
def list_with_params(
self,
limit=float("inf"),
start=None,
page_size=100,
params=None,
negate_params=None,
):
"""

@@ -175,12 +207,12 @@ Return a generator of document object corresponding to the supplied parameters, such

params_copy = copy.deepcopy(params) or {}
if 'hashes' in params_copy:
params_copy['hash'] = params_copy.pop('hashes')
if 'urls_metadata' in params_copy:
params_copy['urls_metadata'] = json.dumps(params_copy.pop('urls_metadata'))
if "hashes" in params_copy:
params_copy["hash"] = params_copy.pop("hashes")
if "urls_metadata" in params_copy:
params_copy["urls_metadata"] = json.dumps(params_copy.pop("urls_metadata"))
reformatted_params = dict()
for param in ['hash', 'metadata']:
for param in ["hash", "metadata"]:
if param in params_copy:
reformatted_params[param] = []
for k, v in params_copy[param].items():
reformatted_params[param].append(str(k) + ':' + str(v))
reformatted_params[param].append(str(k) + ":" + str(v))
del params_copy[param]

@@ -193,3 +225,3 @@ reformatted_params.update(params_copy)

while True:
resp = self._get("index", params=reformatted_params)
resp = self._get("index", params=reformatted_params, timeout=60)
handle_error(resp)

@@ -205,4 +237,4 @@ json_str = resp.json()

return
if len(json_str['records']) == page_size:
reformatted_params['start'] = json_str['records'][-1]['did']
if len(json_str["records"]) == page_size:
reformatted_params["start"] = json_str["records"][-1]["did"]
else:

@@ -213,4 +245,15 @@ # There's no more results

def create(
self, hashes, size, did=None, urls=None, file_name=None,
metadata=None, baseid=None, acl=None, urls_metadata=None, version=None):
self,
hashes,
size,
did=None,
urls=None,
file_name=None,
metadata=None,
baseid=None,
acl=None,
urls_metadata=None,
version=None,
authz=None,
):
"""Create a new entry in indexd

@@ -225,2 +268,3 @@

acl (list): access control list
authz (str): RBAC string
file_name (str): name of the file associated with a given UUID

@@ -247,3 +291,4 @@ metadata (dict): additional key value metadata for this entry

"acl": acl,
"version": version
"authz": authz,
"version": version,
}

@@ -253,19 +298,73 @@ if did:

resp = self._post(
"index/", headers={"content-type": "application/json"},
data=json_dumps(json), auth=self.auth)
"index/",
headers={"content-type": "application/json"},
data=json_dumps(json),
auth=self.auth,
)
return Document(self, resp.json()["did"])
def add_alias_for_did(self, alias, did):
"""
Adds an alias for a document id (did). Once an alias is created for
a did, the document can be retrieved by the alias using the
`global_get(alias)` function.
:param str alias:
The alias we want to assign to the document id.
:param str did:
The document id for the index record we want to alias.
:raises BaseIndexError:
Raised if aliasing operation fails.
"""
alias_payload = {"aliases": [{"value": alias}]}
resp = self._post(
"index/{}/aliases/".format(did),
headers={"content-type": "application/json"},
data=json.dumps(alias_payload),
auth=self.auth,
)
try:
return resp.json()
except ValueError as err:
reason = json.dumps(
{"error": "invalid json payload returned: {}".format(err)}
)
raise BaseIndexError(resp.status_code, reason)
# DEPRECATED 11/2019 -- interacts with old `/alias/` endpoint.
# For creating aliases for indexd records, prefer using
# the `add_alias_for_did` function, which interacts with the new
# `/index/{GUID}/aliases` endpoint.
def create_alias(
self, record, size, hashes, release=None,
metastring=None, host_authorities=None, keeper_authority=None):
data = json_dumps({
'size': size,
'hashes': hashes,
'release': release,
'metastring': metastring,
'host_authorities': host_authorities,
'keeper_authority': keeper_authority
})
url = '/alias/' + record
headers = {'content-type': 'application/json'}
self,
record,
size,
hashes,
release=None,
metastring=None,
host_authorities=None,
keeper_authority=None,
):
warnings.warn(
(
"This function is deprecated. For creating aliases for indexd "
"records, prefer using the `add_alias_for_did` function, which "
"interacts with the new `/index/{GUID}/aliases` endpoint."
),
DeprecationWarning,
)
data = json_dumps(
{
"size": size,
"hashes": hashes,
"release": release,
"metastring": metastring,
"host_authorities": host_authorities,
"keeper_authority": keeper_authority,
}
)
url = "alias/" + record
headers = {"content-type": "application/json"}
resp = self._put(url, headers=headers, data=data, auth=self.auth)

@@ -300,3 +399,5 @@ return resp.json()

rev_doc = self._post("index", current_did, json=new_doc.to_json(), auth=self.auth).json()
rev_doc = self._post(
"index", current_did, json=new_doc.to_json(), auth=self.auth
).json()
if rev_doc and "did" in rev_doc:

@@ -315,2 +416,3 @@ return Document(self, rev_doc["did"])

@retry_and_timeout_wrapper
def _get(self, *path, **kwargs):

@@ -321,2 +423,3 @@ resp = requests.get(self.url_for(*path), **kwargs)

@timeout_wrapper
def _post(self, *path, **kwargs):

@@ -327,2 +430,3 @@ resp = requests.post(self.url_for(*path), **kwargs)

@timeout_wrapper
def _put(self, *path, **kwargs):

@@ -333,2 +437,3 @@ resp = requests.put(self.url_for(*path), **kwargs)

@timeout_wrapper
def _delete(self, *path, **kwargs):

@@ -345,3 +450,2 @@ resp = requests.delete(self.url_for(*path), **kwargs)

class Document(object):
def __init__(self, client, did, json=None):

@@ -355,7 +459,25 @@ self.client = client

def __eq__(self, other_doc):
return self._doc == other_doc._doc
"""
equals `==` operator overload
It doesn't matter the order of the urls list. What matters is the
existence of the urls are the same on both sides.
"""
return self._sorted_doc == other_doc._sorted_doc
def __ne__(self, other_doc):
return self._doc != other_doc._doc
"""
not equals `!=` operator overload
It doesn't matter the order of the urls list. What matters is the
existence of the urls are the same on both sides.
"""
return self._sorted_doc != other_doc._sorted_doc
def __lt__(self, other_doc):
return self.did < other_doc.did
def __gt__(self, other_doc):
return self.did > other_doc.did
def __repr__(self):

@@ -368,7 +490,6 @@ """

"""
attributes = ', '.join([
'{}={}'.format(attr, self.__dict__[attr])
for attr in self._attrs
])
return '<Document(' + attributes + ')>'
attributes = ", ".join(
["{}={}".format(attr, self.__dict__[attr]) for attr in self._attrs]
)
return "<Document(" + attributes + ")>"

@@ -382,3 +503,5 @@ def _check_deleted(self):

if not self._fetched:
raise RuntimeError("Document must be fetched from the server before being rendered as json")
raise RuntimeError(
"Document must be fetched from the server before being rendered as json"
)
return self._doc

@@ -397,3 +520,3 @@

# set attributes to current Document
for k,v in json.items():
for k, v in json.items():
self.__dict__[k] = v

@@ -408,3 +531,3 @@ self._attrs = json.keys()

"""
return {k:v for k,v in self._doc.items() if k in UPDATABLE_ATTRS}
return {k: v for k, v in self._doc.items() if k in UPDATABLE_ATTRS}

@@ -415,2 +538,11 @@ @property

@property
def _sorted_doc(self):
"""Return the _doc object but with all arrays in sorted order.
This will allow us to compare dictionaries with lists correctly. We
only care about the contents of the arrays not the order of them.
"""
return recursive_sort(self._doc)
def patch(self):

@@ -424,7 +556,10 @@ """Update attributes in an indexd Document

self._check_deleted()
self.client._put("index", self.did,
params={"rev": self.rev},
headers={"content-type": "application/json"},
auth=self.client.auth,
data=json.dumps(self._doc_for_update()))
self.client._put(
"index",
self.did,
params={"rev": self.rev},
headers={"content-type": "application/json"},
auth=self.client.auth,
data=json.dumps(self._doc_for_update()),
)
self._load() # to sync new rev from server

@@ -434,5 +569,18 @@

self._check_deleted()
self.client._delete("index", self.did,
auth=self.client.auth,
params={"rev": self.rev})
self.client._delete(
"index", self.did, auth=self.client.auth, params={"rev": self.rev}
)
self._deleted = True
def recursive_sort(value):
"""
Sort all the lists in the dictionary recursively so that we can compare a
dictionary's contents being the same instead of comparing their order.
"""
if isinstance(value, dict):
return {key: recursive_sort(value[key]) for key in value.keys()}
elif isinstance(value, list):
return sorted([recursive_sort(element) for element in value])
else:
return value
+3
-2
indexclient/errors.py
class BaseIndexError(Exception):
'''
"""
Base index error.
'''
"""
def __init__(self, code, msg):

@@ -6,0 +7,0 @@ self.code = code

+38
-42
indexclient/parsers/create.py

@@ -11,34 +11,31 @@ import sys

def create_record(host, port, form, size, urls, hashes, **kwargs):
'''
"""
Create a new record.
'''
resource = 'http://{host}:{port}/index/'.format(
host=host,
port=port,
)
"""
resource = "http://{host}:{port}/index/".format(host=host, port=port)
if size < 0:
raise ValueError('size must be non-negative')
raise ValueError("size must be non-negative")
urls_set = set(urls)
hash_set = set((h,v) for h,v in hashes)
hash_dict = {h:v for h,v in hash_set}
hash_set = set((h, v) for h, v in hashes)
hash_dict = {h: v for h, v in hash_set}
if len(hash_dict) < len(hash_set):
logging.error('multiple incompatible hashes specified')
logging.error("multiple incompatible hashes specified")
for h in hash_dict.items():
hash_set.remove(h)
for h, _ in hash_set:
logging.error('multiple values specified for {h}'.format(h=h))
raise ValueError('conflicting hashes provided')
logging.error("multiple values specified for {h}".format(h=h))
raise ValueError("conflicting hashes provided")
data = {
'form': form,
'size': size,
'urls': [u for u in urls_set],
'hashes': hash_dict,
"form": form,
"size": size,
"urls": [u for u in urls_set],
"hashes": hash_dict,
}

@@ -48,9 +45,11 @@

try: res.raise_for_status()
try:
res.raise_for_status()
except Exception as err:
raise BaseIndexError(res.status_code, res.text)
try: doc = res.json()
try:
doc = res.json()
except ValueError as err:
reason = json.dumps({'error': 'invalid json payload returned'})
reason = json.dumps({"error": "invalid json payload returned"})
raise BaseIndexError(res.status_code, reason)

@@ -62,34 +61,31 @@

def config(parser):
'''
"""
Configure the create command.
'''
"""
parser.set_defaults(func=create_record)
parser.add_argument('form',
choices=['object', 'container', 'multipart'],
help='record format',
parser.add_argument(
"form", choices=["object", "container", "multipart"], help="record format"
)
parser.add_argument('--size',
required=True,
type=int,
help='size in bytes',
)
parser.add_argument("--size", required=True, type=int, help="size in bytes")
parser.add_argument('--hash',
parser.add_argument(
"--hash",
required=True,
nargs=2,
metavar=('TYPE', 'VALUE'),
action='append',
dest='hashes',
metavar=("TYPE", "VALUE"),
action="append",
dest="hashes",
default=[],
help='hash type and value',
help="hash type and value",
)
parser.add_argument('--url',
metavar='URL',
action='append',
dest='urls',
parser.add_argument(
"--url",
metavar="URL",
action="append",
dest="urls",
default=[],
help='known URLs associated with data',
help="known URLs associated with data",
)
+11
-19
indexclient/parsers/delete.py

@@ -12,33 +12,25 @@ import sys

def delete_record(host, port, did, rev, **kwargs):
'''
"""
Create a new record.
'''
resource = 'http://{host}:{port}/index/{did}'.format(
host=host,
port=port,
did=did,
)
"""
resource = "http://{host}:{port}/index/{did}".format(host=host, port=port, did=did)
params = {
'rev': rev,
}
params = {"rev": rev}
res = requests.delete(resource, params=params)
try: res.raise_for_status()
try:
res.raise_for_status()
except Exception as err:
raise BaseIndexError(res.status_code, res.text)
def config(parser):
'''
"""
Configure the delete command.
'''
"""
parser.set_defaults(func=delete_record)
parser.add_argument('did',
help='id of record to delete',
)
parser.add_argument("did", help="id of record to delete")
parser.add_argument('rev',
help='current revision of record',
)
parser.add_argument("rev", help="current revision of record")
+25
-14
indexclient/parsers/info.py

@@ -5,2 +5,3 @@ import sys

import argparse
import warnings

@@ -12,21 +13,33 @@ import requests

# DEPRECATED 11/2019 -- interacts with old `/alias/` endpoint.
# For creating aliases for indexd records, prefer using
# the `add_alias` function, which interacts with the new
# `/index/{GUID}/aliases` endpoint.
def info(host, port, name, **kwargs):
'''
"""
Retrieve info by name.
'''
resource = 'http://{host}:{port}/alias/{name}'.format(
host=host,
port=port,
name=name,
"""
warnings.warn(
(
"This function is deprecated. For creating aliases for indexd "
"records, prefer using the `add_alias_for_did` function, which "
"interacts with the new `/index/{GUID}/aliases` endpoint."
),
DeprecationWarning,
)
resource = "http://{host}:{port}/alias/{name}".format(
host=host, port=port, name=name
)
res = requests.get(resource)
try: res.raise_for_status()
try:
res.raise_for_status()
except Exception as err:
raise errors.BaseIndexError(res.status_code, res.text)
try: doc = res.json()
try:
doc = res.json()
except ValueError as err:
reason = json.dumps({'error': 'invalid json payload returned'})
reason = json.dumps({"error": "invalid json payload returned"})
raise errors.BaseIndexError(res.status_code, reason)

@@ -38,9 +51,7 @@

def config(parser):
'''
"""
Configure the info command.
'''
"""
parser.set_defaults(func=info)
parser.add_argument('name',
help='name of information to retrieve',
)
parser.add_argument("name", help="name of information to retrieve")
+61
-61
indexclient/parsers/name.py
import sys
import json
import argparse
import warnings

@@ -10,43 +11,52 @@ import requests

def name_record(host, port, name, rev, size, hashes,
release, metadata, hosts, keeper, **kwargs):
'''
# DEPRECATED 11/2019 -- interacts with old `/alias/` endpoint.
# For creating aliases for indexd records, prefer using
# the `add_alias` function, which interacts with the new
# `/index/{GUID}/aliases` endpoint.
def name_record(
host, port, name, rev, size, hashes, release, metadata, hosts, keeper, **kwargs
):
"""
Alias a record.
'''
resource = 'http://{host}:{port}/alias/{name}'.format(
host=host,
port=port,
name=name,
"""
warnings.warn(
(
"This function is deprecated. For creating aliases for indexd "
"records, prefer using the `add_alias_for_did` function, which "
"interacts with the new `/index/{GUID}/aliases` endpoint."
),
DeprecationWarning,
)
resource = "http://{host}:{port}/alias/{name}".format(
host=host, port=port, name=name
)
params = {
'rev': rev,
}
params = {"rev": rev}
if size is not None and size < 0:
raise ValueError('size must be non-negative')
raise ValueError("size must be non-negative")
host_set = set(hosts)
hash_set = set((h,v) for h,v in hashes)
hash_dict = {h:v for h,v in hash_set}
hash_set = set((h, v) for h, v in hashes)
hash_dict = {h: v for h, v in hash_set}
if len(hash_dict) < len(hash_set):
logging.error('multiple incompatible hashes specified')
logging.error("multiple incompatible hashes specified")
for h in hash_dict.items():
hash_set.remove(h)
for h, _ in hash_set:
logging.error('multiple values specified for {h}'.format(h=h))
raise ValueError('conflicting hashes provided')
logging.error("multiple values specified for {h}".format(h=h))
raise ValueError("conflicting hashes provided")
data = {
'size': size,
'hashes': hash_dict,
'release': release,
'metadata': metadata,
'host_authorities': [h for h in host_set],
'keeper_authority': keeper,
"size": size,
"hashes": hash_dict,
"release": release,
"metadata": metadata,
"host_authorities": [h for h in host_set],
"keeper_authority": keeper,
}

@@ -56,9 +66,11 @@

try: res.raise_for_status()
try:
res.raise_for_status()
except Exception as err:
raise errors.BaseIndexError(res.status_code, res.text)
try: doc = res.json()
try:
doc = res.json()
except ValueError as err:
reason = json.dumps({'error': 'invalid json payload returned'})
reason = json.dumps({"error": "invalid json payload returned"})
raise errors.BaseIndexError(res.status_code, reason)

@@ -70,49 +82,37 @@

def config(parser):
'''
"""
Configure the name command.
'''
"""
parser.set_defaults(func=name_record)
parser.add_argument('name',
help='name to assign',
)
parser.add_argument("name", help="name to assign")
parser.add_argument('rev',
nargs='?',
help='revision of name',
)
parser.add_argument("rev", nargs="?", help="revision of name")
parser.add_argument('--size',
default=None,
type=int,
help='size of underlying data',
parser.add_argument(
"--size", default=None, type=int, help="size of underlying data"
)
parser.add_argument('--hash',
parser.add_argument(
"--hash",
nargs=2,
metavar=('TYPE', 'VALUE'),
action='append',
dest='hashes',
metavar=("TYPE", "VALUE"),
action="append",
dest="hashes",
default=[],
help='hash type and value',
help="hash type and value",
)
parser.add_argument('--release',
choices=['public', 'private', 'controlled'],
help='data release type',
parser.add_argument(
"--release",
choices=["public", "private", "controlled"],
help="data release type",
)
parser.add_argument('--metadata',
help='metadata string',
)
parser.add_argument("--metadata", help="metadata string")
parser.add_argument('--host',
action='append',
dest='hosts',
default=[],
help='host authority',
parser.add_argument(
"--host", action="append", dest="hosts", default=[], help="host authority"
)
parser.add_argument('--keeper',
help='data keeper authority',
)
parser.add_argument("--keeper", help="data keeper authority")
+11
-15
indexclient/parsers/retrieve.py

@@ -12,20 +12,18 @@ import sys

def retrieve_record(host, port, did, **kwargs):
'''
"""
Retrieve a record by id.
'''
resource = 'http://{host}:{port}/index/{did}'.format(
host=host,
port=port,
did=did,
)
"""
resource = "http://{host}:{port}/index/{did}".format(host=host, port=port, did=did)
res = requests.get(resource)
try: res.raise_for_status()
try:
res.raise_for_status()
except Exception as err:
raise errors.BaseIndexError(res.status_code, res.text)
try: doc = res.json()
try:
doc = res.json()
except ValueError as err:
reason = json.dumps({'error': 'invalid json payload returned'})
reason = json.dumps({"error": "invalid json payload returned"})
raise errors.BaseIndexError(res.status_code, reason)

@@ -37,9 +35,7 @@

def config(parser):
'''
"""
Configure the retrieve command.
'''
"""
parser.set_defaults(func=retrieve_record)
parser.add_argument('did',
help='id of record to retrieve',
)
parser.add_argument("did", help="id of record to retrieve")
+73
-81
indexclient/parsers/search.py

@@ -5,2 +5,3 @@ import sys

import argparse
import warnings

@@ -13,48 +14,42 @@ import requests

def search_record(host, port, limit, start, size, hashes, **kwargs):
'''
"""
Finds records matching specified search criteria.
'''
"""
if size is not None and size < 0:
raise ValueError('size must be non-negative')
raise ValueError("size must be non-negative")
if limit is not None and limit < 0:
raise ValueError('limit must be non-negative')
raise ValueError("limit must be non-negative")
hash_set = set((h,v) for h,v in hashes)
hash_dict = {h:v for h,v in hash_set}
hash_set = set((h, v) for h, v in hashes)
hash_dict = {h: v for h, v in hash_set}
if len(hash_dict) < len(hash_set):
logging.error('multiple incompatible hashes specified')
logging.error("multiple incompatible hashes specified")
for h in hash_dict.items():
hash_set.remove(h)
for h, _ in hash_set:
logging.error('multiple values specified for {h}'.format(h=h))
raise ValueError('conflicting hashes provided')
logging.error("multiple values specified for {h}".format(h=h))
hashes = [':'.join([h,v]) for h,v in hash_dict.items()]
raise ValueError("conflicting hashes provided")
resource = 'http://{host}:{port}/index/'.format(
host=host,
port=port,
)
hashes = [":".join([h, v]) for h, v in hash_dict.items()]
params = {
'limit': limit,
'start': start,
'hash': hashes,
'size': size,
}
resource = "http://{host}:{port}/index/".format(host=host, port=port)
params = {"limit": limit, "start": start, "hash": hashes, "size": size}
res = requests.get(resource, params=params)
try: res.raise_for_status()
try:
res.raise_for_status()
except Exception as err:
raise errors.BaseIndexError(res.status_code, res.text)
try: doc = res.json()
try:
doc = res.json()
except ValueError as err:
reason = json.dumps({'error': 'invalid json payload returned'})
reason = json.dumps({"error": "invalid json payload returned"})
raise errors.BaseIndexError(res.status_code, reason)

@@ -64,49 +59,56 @@

# DEPRECATED 11/2019 -- interacts with old `/alias/` endpoint.
# For creating aliases for indexd records, prefer using
# the `add_alias` function, which interacts with the new
# `/index/{GUID}/aliases` endpoint.
def search_names(host, port, limit, start, size, hashes, **kwargs):
'''
"""
Finds records matching specified search criteria.
'''
"""
warnings.warn(
(
"This function is deprecated. For creating aliases for indexd "
"records, prefer using the `add_alias_for_did` function, which "
"interacts with the new `/index/{GUID}/aliases` endpoint."
),
DeprecationWarning,
)
if size is not None and size < 0:
raise ValueError('size must be non-negative')
raise ValueError("size must be non-negative")
if limit is not None and limit < 0:
raise ValueError('limit must be non-negative')
raise ValueError("limit must be non-negative")
hash_set = set((h,v) for h,v in hashes)
hash_dict = {h:v for h,v in hash_set}
hash_set = set((h, v) for h, v in hashes)
hash_dict = {h: v for h, v in hash_set}
if len(hash_dict) < len(hash_set):
logging.error('multiple incompatible hashes specified')
logging.error("multiple incompatible hashes specified")
for h in hash_dict.items():
hash_set.remove(h)
for h, _ in hash_set:
logging.error('multiple values specified for {h}'.format(h=h))
raise ValueError('conflicting hashes provided')
logging.error("multiple values specified for {h}".format(h=h))
hashes = [':'.join([h,v]) for h,v in hash_dict.items()]
raise ValueError("conflicting hashes provided")
resource = 'http://{host}:{port}/alias/'.format(
host=host,
port=port,
)
hashes = [":".join([h, v]) for h, v in hash_dict.items()]
params = {
'limit': limit,
'start': start,
'size': size,
'hashes': hashes,
}
resource = "http://{host}:{port}/alias/".format(host=host, port=port)
params = {"limit": limit, "start": start, "size": size, "hashes": hashes}
res = requests.get(resource, params=params)
try: res.raise_for_status()
try:
res.raise_for_status()
except Exception as err:
raise errors.BaseIndexError(res.status_code, res.text)
try: doc = res.json()
try:
doc = res.json()
except ValueError as err:
reason = json.dumps({'error': 'invalid json payload returned'})
reason = json.dumps({"error": "invalid json payload returned"})
raise errors.BaseIndexError(res.status_code, reason)

@@ -118,45 +120,35 @@

def config(parser):
'''
"""
Configure the search command.
'''
"""
parser.set_defaults(func=search_record)
parser.add_argument('--names',
action='store_const',
parser.add_argument(
"--names",
action="store_const",
const=search_names,
dest='func',
help='search names instead of records',
dest="func",
help="search names instead of records",
)
parser.add_argument('--limit',
default=None,
type=int,
help='limit on number of ids to retrieve',
parser.add_argument(
"--limit", default=None, type=int, help="limit on number of ids to retrieve"
)
parser.add_argument('--start',
default=None,
help='starting id or alias',
)
parser.add_argument("--start", default=None, help="starting id or alias")
parser.add_argument('--size',
default=None,
type=int,
help='filter based on size',
)
parser.add_argument("--size", default=None, type=int, help="filter based on size")
parser.add_argument('--hash',
parser.add_argument(
"--hash",
nargs=2,
metavar=('TYPE', 'VALUE'),
action='append',
dest='hashes',
metavar=("TYPE", "VALUE"),
action="append",
dest="hashes",
default=[],
help='filter based on hash values',
help="filter based on hash values",
)
parser.add_argument('--url',
action='append',
dest='urls',
default=[],
help='filter based on urls',
parser.add_argument(
"--url", action="append", dest="urls", default=[], help="filter based on urls"
)
+36
-50
indexclient/parsers/update.py

@@ -11,49 +11,41 @@ import sys

def update_record(host, port, did, rev, size, hashes, urls, **kwargs):
'''
"""
Update a record.
'''
resource = 'http://{host}:{port}/index/{did}'.format(
host=host,
port=port,
did=did,
)
"""
resource = "http://{host}:{port}/index/{did}".format(host=host, port=port, did=did)
params = {
'rev': rev,
}
params = {"rev": rev}
if size < 0:
raise ValueError('size must be non-negative')
raise ValueError("size must be non-negative")
urls_set = set(urls)
hash_set = set((h,v) for h,v in hashes)
hash_dict = {h:v for h,v in hash_set}
hash_set = set((h, v) for h, v in hashes)
hash_dict = {h: v for h, v in hash_set}
if len(hash_dict) < len(hash_set):
logging.error('multiple incompatible hashes specified')
logging.error("multiple incompatible hashes specified")
for h in hash_dict.items():
hash_set.remove(h)
for h, _ in hash_set:
logging.error('multiple values specified for {h}'.format(h=h))
raise ValueError('conflicting hashes provided')
logging.error("multiple values specified for {h}".format(h=h))
data = {
'size': size,
'urls': [u for u in urls_set],
'hashes': hash_dict,
}
raise ValueError("conflicting hashes provided")
data = {"size": size, "urls": [u for u in urls_set], "hashes": hash_dict}
res = requests.put(resource, params=params, json=data)
try: res.raise_for_status()
try:
res.raise_for_status()
except Exception as err:
raise BaseIndexError(res.status_code, res.text)
try: doc = res.json()
try:
doc = res.json()
except ValueError as err:
reason = json.dumps({'error': 'invalid json payload returned'})
reason = json.dumps({"error": "invalid json payload returned"})
raise BaseIndexError(res.status_code, reason)

@@ -65,36 +57,30 @@

def config(parser):
'''
"""
Configure the update command.
'''
"""
parser.set_defaults(func=update_record)
parser.add_argument('did',
help='document id',
)
parser.add_argument("did", help="document id")
parser.add_argument('rev',
help='document revision',
)
parser.add_argument("rev", help="document revision")
parser.add_argument('--size',
required=True,
type=int,
help='size in bytes',
)
parser.add_argument("--size", required=True, type=int, help="size in bytes")
parser.add_argument('--hash',
parser.add_argument(
"--hash",
required=True,
nargs=2,
metavar=('TYPE', 'VALUE'),
action='append',
dest='hashes',
help='hash type and value',
metavar=("TYPE", "VALUE"),
action="append",
dest="hashes",
help="hash type and value",
)
parser.add_argument('--url',
metavar='URL',
action='append',
dest='urls',
parser.add_argument(
"--url",
metavar="URL",
action="append",
dest="urls",
default=[],
help='known URLs associated with data',
help="known URLs associated with data",
)
+1
-1
PKG-INFO
Metadata-Version: 1.0
Name: indexclient
Version: 1.5.8
Version: 2.1.0
Summary: UNKNOWN

@@ -5,0 +5,0 @@ Home-page: UNKNOWN

+129
-12
README.md

@@ -1,6 +0,6 @@

Index
Indexclient
===
![version](https://img.shields.io/badge/version-0.0.1-orange.svg?style=flat) [![Apache license](http://img.shields.io/badge/license-Apache-blue.svg?style=flat)](LICENSE) [![Travis](https://travis-ci.org/LabAdvComp/index.svg?branch=master)](https://travis-ci.org/LabAdvComp/index)
![version](https://img.shields.io/badge/version-2.0.0-green.svg?style=flat) [![Apache license](http://img.shields.io/badge/license-Apache-blue.svg?style=flat)](LICENSE) [![Travis](https://travis-ci.org/uc-cdis/indexclient.svg?branch=master)](https://travis-ci.org/uc-cdis/indexclient)
Index is a prototype data indexing and tracking client. It is intended to
Indexclient is a prototype data indexing and tracking client. It is intended to
provide a simple means of interactively investigating

@@ -77,4 +77,6 @@ [indexd](https://github.com/LabAdvComp/indexd) deployments. It is built upon

## Making Queries
All queries to the index are made through HTTP using JSON data payloads.

@@ -86,20 +88,135 @@ This gives a simple means of interaction that is easily accessible to any

### Create a record
***TODO***
### Create a record
### Name a record
***TODO***
#### Method: `create`
### Retrieve a record
Example:
***TODO***
```python
indexclient.create(
hashes = {'md5': ab167e49d25b488939b1ede42752458b'},
size = 5,
# optional arguments
acl = ["a", "b"]
)
```
### Update a record
***TODO***
### Retrieve a record
#### Method: `get`
Example:
```python
indexclient.get("dg.1234/03eed607-acb0-4532-b0ee-9e3766b1aa6e")
```
#### Method: `global_get`
Example:
```python
indexclient.global_get("dg.1234/03eed607-acb0-4532-b0ee-9e3766b1aa6e")
```
or
```python
indexclient.global_get("dg.1234/03eed607-acb0-4532-b0ee-9e3766b1aa6e", no_dist=True)
```
`global_get` can also be used to retrieve records by alias. See [Add an alias for a record](#add-an-alias-for-a-record).
```python
# Retrieve a document by its alias, "10.1000/182"
doc = indexclient.global_get("10.1000/182")
print(doc.did) # >> "g.1234/03eed607-acb0-4532-b0ee-9e3766b1aa6e"
```
#### Method: `get_with_params`
Example:
```python
params = {
'hashes': {'md5': ab167e49d25b488939b1ede42752458b'},
'size': 5
# or any other params (metadata, acl, authz, etc.)
}
indexclient.get_with_params(params)
```
### Retrieve multiple records
#### Method: `bulk_request`
Example:
```python
dids = [
"03eed607-acb0-4532-b0ee-9e3766b1aa6e",
"15684515-15b0-4532-b0ee-9e3766b65515",
"03ee4857-acb0-4123-b0ee-9e3766bffa23",
"1258d607-acb0-4532-b0ee-9e3766bffa23"
]
indexclient.bulk_request(dids)
```
### Update a record
First: get a Document object of the desired record with one of the get methods
Second: Update any of the records updatable attributes.
- the format to do this is: `doc.attr = value`
- eg: `doc.file_name = new_file_name`
- Updatable attributes are: file_name urls, version, metadata, acl, authz, urls_metadata, uploader
Lastly: Update all the local changes that were made to indexd using the
Document patch method: doc.patch()
Example:
```python
doc = indexclient.get("dg.1234/03eed607-acb0-4532-b0ee-9e3766b1aa6e"')
# or any other get method (global_get, etc.)
doc.metadata["dummy_field"] = "dummy var"
doc.acl = ['a', 'b']
doc.version = '2'
doc.patch()
```
### Delete a record
***TODO***
First: get a Document object of the desired record with one of the get methods
Second: Delete the record from indexd with the delete method: `doc.delete()`
Lastly: Check if the record was deleted with: `if doc._deleted`
Example:
```python
doc = indexclient.get("dg.1234/03eed607-acb0-4532-b0ee-9e3766b1aa6e")
# or any other get method (global_get, etc.)
doc.delete()
if doc._deleted == False:
return "Record is not deleted"
```
### Add an alias for a record
You can use `indexclient` to create aliases for documents in `indexd`, which enable you to retrieve documents by the alias instead of by the Document identifier (`did` / `GUID`). Aliases can be created using `indexclient.add_alias_for_did(alias=alias, did=did)` and can be retrieved using `indexclient.global_get(alias)`.
Example:
```python
res = indexclient.add_alias_for_did("10.1000/182", "g.1234/03eed607-acb0-4532-b0ee-9e3766b1aa6e")
if res.status_code != 200:
# alias creation failed -- handle error
doc = indexclient.global_get("10.1000/182")
print(doc.did) # >> "g.1234/03eed607-acb0-4532-b0ee-9e3766b1aa6e"
```
+22
-9
setup.py

@@ -0,13 +1,26 @@

from subprocess import check_output
from setuptools import setup
def get_version():
# https://github.com/uc-cdis/dictionaryutils/pull/37#discussion_r257898408
try:
tag = check_output(
["git", "describe", "--tags", "--abbrev=0", "--match=[0-9]*"]
)
return tag.decode("utf-8").strip("\n")
except Exception:
raise RuntimeError(
"The version number cannot be extracted from git tag in this source "
"distribution; please either download the source from PyPI, or check out "
"from GitHub and make sure that the git CLI is available."
)
setup(
name='indexclient',
version='1.5.8',
packages=[
'indexclient',
'indexclient.parsers',
],
install_requires=[
'requests>=2.5.2,<3.0.0',
],
name="indexclient",
version='2.1.0',
packages=["indexclient", "indexclient.parsers"],
install_requires=["requests>=2.5.2,<3.0.0"],
)
-202
LICENSE
Apache License
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-4
MANIFEST.in
include LICENSE
include NOTICE
include Pipfile
include Pipfile.lock
-8
NOTICE
Copyright 2015 University of Chicago
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
-12
Pipfile
[[source]]
name = "pypi"
url = "https://pypi.org/simple"
verify_ssl = true
[dev-packages]
[packages]
indexclient = {editable = true,path = "."}
[requires]
python_version = "2.7"
-60
Pipfile.lock
{
"_meta": {
"hash": {
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