Update search, so it works with the new after syntax. (#456)

* Update to 1.0.1

* update python version

* run new version on  3.10

* revamp search

* remove explicit model version

.github/workflows/tests.yml

@@ -35,7 +35,7 @@ jobs:
 
  matrix:
  os: [ubuntu-latest, macos-latest]
- python-version: [3.8, 3.12]
+ python-version: ["3.10", 3.12]
 
  env:
  CRIPT_HOST: https://lb-stage.mycriptapp.org/

README.md

@@ -3,7 +3,7 @@
 [![License](./CRIPT_full_logo_colored_transparent.png)](https://github.com/C-Accel-CRIPT/Python-SDK/blob/develop/LICENSE.md)
 
 [![License](https://img.shields.io/github/license/C-Accel-CRIPT/cript?style=flat-square)](https://github.com/C-Accel-CRIPT/Python-SDK/blob/develop/LICENSE.md)
-[![Python](https://img.shields.io/badge/Language-Python%203.8+-blue?style=flat-square&logo=python)](https://www.python.org/)
+[![Python](https://img.shields.io/badge/Language-Python%203.10+-blue?style=flat-square&logo=python)](https://www.python.org/)
 [![Code style is black](https://img.shields.io/badge/Code%20Style-black-000000.svg?style=flat-square&logo=python)](https://github.com/psf/black)
 [![Link to CRIPT website](https://img.shields.io/badge/platform-criptapp.org-blueviolet?style=flat-square)](https://criptapp.org/)
 [![Using Pytest](https://img.shields.io/badge/Dependencies-pytest-green?style=flat-square&logo=Pytest)](https://docs.pytest.org/en/7.2.x/)
@@ -36,7 +36,7 @@ The CRIPT Python SDK allows programmatic access to the [CRIPT platform](https://
 
 ## Installation
 
-CRIPT Python SDK requires Python 3.8+
+CRIPT Python SDK requires Python 3.10+
 
 The latest released of CRIPT Python SDK is available on [Python Package Index (PyPI)](https://pypi.org/project/cript/)
 

setup.cfg

@@ -14,13 +14,13 @@ classifiers =
  Topic :: Scientific/Engineering
  Programming Language :: Python :: 3
  Programming Language :: Python :: 3 :: Only
- Programming Language :: Python :: 3.8
+ Programming Language :: Python :: 3.10
 
 [options]
 package_dir =
  =src
 packages = find:
-python_requires = >=3.8
+python_requires = >=3.10
 include_package_data = True
 install_requires =
  requests==2.31.0

src/cript/api/api.py

@@ -787,35 +787,32 @@ def search(
  node_type = node_type.node_type_snake_case
 
  api_endpoint: str = ""
- page_number: Union[int, None] = None
-
+ limit_node_fetches: Optional[int] = None
  if search_mode == SearchModes.NODE_TYPE:
  api_endpoint = f"/search/{node_type}"
- page_number = 0
+ value_to_search = ""
 
  elif search_mode == SearchModes.CONTAINS_NAME:
  api_endpoint = f"/search/{node_type}"
- page_number = 0
 
  elif search_mode == SearchModes.EXACT_NAME:
  api_endpoint = f"/search/exact/{node_type}"
- page_number = None
+ limit_node_fetches = 1
 
  elif search_mode == SearchModes.UUID:
  api_endpoint = f"/{node_type}/{value_to_search}"
  # putting the value_to_search in the URL instead of a query
  value_to_search = ""
- page_number = None
+ limit_node_fetches = 1
 
  elif search_mode == SearchModes.BIGSMILES:
  api_endpoint = "/search/bigsmiles/"
- page_number = 0
 
  # error handling if none of the API endpoints got hit
  else:
  raise RuntimeError("Internal Error: Failed to recognize any search modes. Please report this bug on https://github.com/C-Accel-CRIPT/Python-SDK/issues.")
 
- return Paginator(api=self, url_path=api_endpoint, page_number=page_number, query=value_to_search)
+ return Paginator(api=self, url_path=api_endpoint, query=value_to_search, limit_node_fetches=limit_node_fetches)
 
  def delete(self, node) -> None:
  """

src/cript/api/paginator.py

@@ -1,5 +1,5 @@
 import json
-from typing import Dict, Union
+from typing import Dict, Optional, Tuple
 from urllib.parse import quote
 
 import requests
@@ -9,6 +9,16 @@
 from cript.nodes.util import load_nodes_from_json
 
 
+def _get_uuid_score_from_json(node_dict: Dict) -> Tuple[str, Optional[float]]:
+ """
+ Get the UUID string and search score from a JSON node representation if available.
+ """
+ node_uuid: str = node_dict["uuid"]
+ node_score: Optional[float] = node_dict.get("score", None)
+
+ return node_uuid, node_score
+
+
 class Paginator:
  """
  Paginator is used to flip through different pages of data that the API returns when searching.
@@ -29,22 +39,17 @@ class Paginator:
 
  _url_path: str
  _query: str
- _initial_page_number: Union[int, None]
  _current_position: int
  _fetched_nodes: list
+ _uuid_search_score_map: Dict
  _number_fetched_pages: int = 0
- _limit_page_fetches: Union[int, None] = None
- _num_skip_pages: int = 0
+ _limit_node_fetches: Optional[int] = None
+ _start_after_uuid: Optional[str] = None
+ _start_after_score: Optional[float] = None
  auto_load_nodes: bool = True
 
  @beartype
- def __init__(
- self,
- api,
- url_path: str,
- page_number: Union[int, None],
- query: str,
- ):
+ def __init__(self, api, url_path: str, query: str, limit_node_fetches: Optional[int] = None):
  """
  create a paginator
 
@@ -53,34 +58,33 @@ def __init__(
 
  Parameters
  ----------
- http_headers: dict
- get already created http headers from API and just use them in paginator
- api_endpoint: str
- api endpoint to send the search requests to
- it already contains what node the user is looking for
- current_page_number: int
- page number to start from. Keep track of current page for user to flip back and forth between pages of data
+ api: cript.API
+ Object through which the API call is routed.
+ url_path: str
+ query URL used.
  query: str
  the value the user is searching for
+ limit_node_fetches: Optional[int] = None
+ limits the number of nodes fetches through this call.
 
  Returns
  -------
  None
  instantiate a paginator
  """
  self._api = api
- self._initial_page_number = page_number
- self._number_fetched_pages = 0
  self._fetched_nodes = []
  self._current_position = 0
+ self._limit_node_fetches = limit_node_fetches
+ self._uuid_search_score_map = {}
 
  # check if it is a string and not None to avoid AttributeError
  try:
- self._url_path = quote(url_path.rstrip("/").strip())
+ self._url_path = url_path.rstrip("/").strip()
  except Exception as exc:
  raise RuntimeError(f"Invalid type for api_endpoint {self._url_path} for a paginator.") from exc
 
- self._query = quote(query)
+ self._query = query
 
  @beartype
  def _fetch_next_page(self) -> None:
@@ -105,16 +109,36 @@ def _fetch_next_page(self) -> None:
  None
  """
 
- # Check if we are supposed to fetch more pages
- if self._limit_page_fetches and self._number_fetched_pages >= self._limit_page_fetches:
- raise StopIteration
-
  # Composition of the query URL
- temp_url_path: str = self._url_path
- temp_url_path += f"/?q={self._query}"
- if self._initial_page_number is not None:
- temp_url_path += f"&page={self.page_number}"
- self._number_fetched_pages += 1
+ temp_url_path: str = self._url_path + "/"
+
+ query_list = []
+
+ if len(self._query) > 0:
+ query_list += [f"q={self._query}"]
+
+ if self._limit_node_fetches is None or self._limit_node_fetches > 1: # This limits these parameters
+ if self._start_after_uuid is not None:
+ query_list += [f"after={self._start_after_uuid}"]
+ if self._start_after_score is not None: # Always None for none BigSMILES searches
+ query_list += [f"score={self._start_after_score}"]
+
+ # Reset to allow normal search to continue
+ self._start_after_uuid = None
+ self._start_after_score = None
+
+ elif len(self._fetched_nodes) > 0: # Use known last element
+ node_uuid, node_score = _get_uuid_score_from_json(self._fetched_nodes[-1])
+ query_list += [f"after={node_uuid}"]
+ if node_score is not None:
+ query_list += [f"score={node_score}"]
+
+ for i, query in enumerate(query_list):
+ if i == 0:
+ temp_url_path += "?"
+ else:
+ temp_url_path += "&"
+ temp_url_path += quote(query, safe="/=&?")
 
  response: requests.Response = self._api._capsule_request(url_path=temp_url_path, method="GET")
 
@@ -153,18 +177,18 @@ def _fetch_next_page(self) -> None:
  self._fetched_nodes += json_list
 
  def __next__(self):
+ if self._limit_node_fetches and self._current_position >= self._limit_node_fetches:
+ raise StopIteration
+
  if self._current_position >= len(self._fetched_nodes):
- # Without a page number argument, we can only fetch once.
- if self._initial_page_number is None and self._number_fetched_pages > 0:
- raise StopIteration
  self._fetch_next_page()
 
  try:
  next_node_json = self._fetched_nodes[self._current_position - 1]
- except IndexError: # This is not a random access iteration.
+ except IndexError as exc: # This is not a random access iteration.
  # So if fetching a next page wasn't enough to get the index inbound,
  # The iteration stops
- raise StopIteration
+ raise StopIteration from exc
 
  if self.auto_load_nodes:
  return_data = load_nodes_from_json(next_node_json)
@@ -181,65 +205,53 @@ def __iter__(self):
  self._current_position = 0
  return self
 
- @property
- def page_number(self) -> Union[int, None]:
- """Obtain the current page number the paginator is fetching next.
-
- Returns
- -------
- int
- positive number of the next page this paginator is fetching.
- None
- if no page number is associated with the pagination
- """
- page_number = self._num_skip_pages + self._number_fetched_pages
- if self._initial_page_number is not None:
- page_number += self._initial_page_number
- return page_number
-
  @beartype
- def limit_page_fetches(self, max_num_pages: Union[int, None]) -> None:
+ def limit_node_fetches(self, max_num_nodes: Optional[int]) -> None:
  """Limit pagination to a maximum number of pages.
 
  This can be used for very large searches with the paginator, so the search can be split into
  smaller portions.
 
  Parameters
  ----------
- max_num_pages: Union[int, None],
+ max_num_nodes: Optional[int],
  positive integer with maximum number of page fetches.
  or None, indicating unlimited number of page fetches are permitted.
  """
- self._limit_page_fetches = max_num_pages
+ self._limit_node_fetches = max_num_nodes
 
- def skip_pages(self, skip_pages: int) -> int:
- """Skip pages in the pagination.
-
- Warning this function is advanced usage and may not produce the results you expect.
- In particular, every search is different, even if we search for the same values there is
- no guarantee that the results are in the same order. (And results can change if data is
- added or removed from CRIPT.) So if you break up your search with `limit_page_fetches` and
- `skip_pages` there is no guarantee that it is the same as one continuous search.
- If the paginator associated search does not accept pages, there is no effect.
+ @beartype
+ def start_after_uuid(self, start_after_uuid: str, start_after_score: Optional[float] = None):
+ """
+ This can be used to continue a search from a last known node.
 
  Parameters
  ----------
- skip_pages:int
- Number of pages that the paginator skips now before fetching the next page.
- The parameter is added to the internal state, so repeated calls skip more pages.
+ start_after_uuid: str
+ UUID string of the last node from a previous search
+ start_after_score: float
+ required for BigSMILES searches, the last score from a BigSMILES search.
+ Must be None if not a BigSMILES search.
 
  Returns
  -------
- int
- The number this paginator is skipping. Internal skip count.
+ None
+ """
+ self._start_after_uuid = start_after_uuid
+ self._start_after_score = start_after_score
 
- Raises
- ------
- RuntimeError
- If the total number of skipped pages is negative.
+ @beartype
+ def get_bigsmiles_search_score(self, uuid: str):
  """
- num_skip_pages = self._num_skip_pages + skip_pages
- if self._num_skip_pages < 0:
- RuntimeError(f"Invalid number of skipped pages. The total number of pages skipped is negative {num_skip_pages}, requested to skip {skip_pages}.")
- self._num_skip_pages = num_skip_pages
- return self._num_skip_pages
+ Get the ranking score for nodes from the BigSMILES search.
+ Will return None if not a BigSMILES search or raise an Exception.
+ """
+ if uuid not in self._uuid_search_score_map.keys():
+ start = len(self._uuid_search_score_map.keys())
+ for node_json in self._fetched_nodes[start:]:
+ node_uuid, node_score = _get_uuid_score_from_json(node_json)
+ self._uuid_search_score_map[node_uuid] = node_score
+ try:
+ return self._uuid_search_score_map[uuid]
+ except KeyError as exc:
+ raise RuntimeError(f"The requested UUID {uuid} is not know from the search. Search scores are limited only to current search.") from exc

src/cript/nodes/core.py

@@ -174,6 +174,10 @@ def _from_json(cls, json_dict: dict):
  pass
  else:
  arguments[field] = json_dict[field]
+ try: # TODO remove this hack to work with compatible model versions
+ del arguments["model_version"]
+ except KeyError:
+ pass
 
  # add omitted fields from default (necessary if they are required)
  for field_name in [field.name for field in dataclasses.fields(default_dataclass)]:

src/cript/nodes/primary_nodes/computation_process.py

@@ -521,7 +521,7 @@ def property(self) -> List[Any]:
  Examples
  --------
  >>> import cript
- >>> my_property = cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")
+ >>> my_property = cript.Property(key="enthalpy", type="min", value=1.23, unit="J")
  >>> my_computation_process.property = [my_property] # doctest: +SKIP
 
  Returns

src/cript/nodes/primary_nodes/material.py

@@ -540,7 +540,7 @@ def property(self) -> List[Any]:
  ... name="my component material 1",
  ... smiles = "component 1 smiles",
  ... )
- >>> my_property = cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")
+ >>> my_property = cript.Property(key="enthalpy", type="min", value=1.23, unit="J")
  >>> my_material.property = [my_property]
 
  Returns

src/cript/nodes/primary_nodes/process.py

@@ -580,7 +580,7 @@ def property(self) -> List[Any]:
  --------
  >>> import cript
  >>> my_process = cript.Process(name="my process name", type="affinity_pure")
- >>> my_property = cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")
+ >>> my_property = cript.Property(key="enthalpy", type="min", value=1.23, unit="J")
  >>> my_process.property = [my_property]
 
  Returns