Workstation templates: Resources and its CRUD, and workstation tasks (#95)

* coin_cell_station draft

* refactor: rename "station_resource" to "deck"

* add standardized BIOYOND resources: bottle_carrier, bottle

* refactor and add BIOYOND resources tests

* add BIOYOND deck assignment and pass all tests

* fix: update resource with correct structure; remove deprecated liquid_handler set_group action

* feat: 将新威电池测试系统驱动与配置文件并入 workstation_dev_YB2 (#92)

* feat: 新威电池测试系统驱动与注册文件

* feat: bring neware driver & battery.json into workstation_dev_YB2

* add bioyond studio draft

* bioyond station with communication init and resource sync

* fix bioyond station and registry

* create/update resources with POST/PUT for big amount/ small amount data

* refactor: add itemized_carrier instead of carrier consists of ResourceHolder

* create warehouse by factory func

* update bioyond launch json

* add child_size for itemized_carrier

* fix bioyond resource io

---------

Co-authored-by: h840473807 <47357934+h840473807@users.noreply.github.com>
Co-authored-by: Xie Qiming <97236197+Andy6M@users.noreply.github.com>

unilabos/resources/itemized_carrier.py

@@ -0,0 +1,357 @@
+"""
+自动化液体处理工作站物料类定义 - 简化版
+Automated Liquid Handling Station Resource Classes - Simplified Version
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Optional
+
+from pylabrobot.resources.coordinate import Coordinate
+from pylabrobot.resources.container import Container
+from pylabrobot.resources.resource_holder import ResourceHolder
+from pylabrobot.resources import Resource as ResourcePLR
+
+
+class Bottle(Container):
+    """瓶子类 - 简化版，不追踪瓶盖"""
+
+    def __init__(
+        self,
+        name: str,
+        diameter: float,
+        height: float,
+        max_volume: float,
+        size_x: float = 0.0,
+        size_y: float = 0.0,
+        size_z: float = 0.0,
+        barcode: Optional[str] = "",
+        category: str = "container",
+        model: Optional[str] = None,
+    ):
+        super().__init__(
+            name=name,
+            size_x=diameter,
+            size_y=diameter,
+            size_z=height,
+            max_volume=max_volume,
+            category=category,
+            model=model,
+        )
+        self.diameter = diameter
+        self.height = height
+        self.barcode = barcode
+
+    def serialize(self) -> dict:
+        return {
+            **super().serialize(),
+            "diameter": self.diameter,
+            "height": self.height,
+            "barcode": self.barcode,
+        }
+
+
+from string import ascii_uppercase as LETTERS
+from typing import Dict, List, Optional, Type, TypeVar, Union, Sequence, Tuple
+
+import pylabrobot
+from pylabrobot.resources.resource_holder import ResourceHolder
+
+T = TypeVar("T", bound=ResourceHolder)
+
+S = TypeVar("S", bound=ResourceHolder)
+
+
+class ItemizedCarrier(ResourcePLR):
+  """Base class for all carriers."""
+
+  def __init__(
+    self,
+    name: str,
+    size_x: float,
+    size_y: float,
+    size_z: float,
+    num_items_x: int = 0,
+    num_items_y: int = 0,
+    num_items_z: int = 0,
+    sites: Optional[Dict[Union[int, str], Optional[ResourcePLR]]] = None,
+    category: Optional[str] = "carrier",
+    model: Optional[str] = None,
+  ):
+    super().__init__(
+      name=name,
+      size_x=size_x,
+      size_y=size_y,
+      size_z=size_z,
+      category=category,
+      model=model,
+    )
+    self.num_items = len(sites)
+    self.num_items_x, self.num_items_y, self.num_items_z = num_items_x, num_items_y, num_items_z
+    if isinstance(sites, dict):
+      sites = sites or {}
+      self.sites: List[Optional[ResourcePLR]] = list(sites.values())
+      self._ordering = sites
+      self.child_locations: Dict[str, Coordinate] = {}
+      self.child_size: Dict[str, dict] = {}
+      for spot, resource in sites.items():
+        if resource is not None and getattr(resource, "location", None) is None:
+          raise ValueError(f"resource {resource} has no location")
+        if resource is not None:
+          self.child_locations[spot] = resource.location
+          self.child_size[spot] = {"width": resource._size_x, "height": resource._size_y, "depth": resource._size_z}
+        else:
+          self.child_locations[spot] = Coordinate.zero()
+          self.child_size[spot] = {"width": 0, "height": 0, "depth": 0}
+    elif isinstance(sites, list):
+      # deserialize时走这里；还需要根据 self.sites 索引children
+      self.child_locations = {site["label"]: Coordinate(**site["position"]) for site in sites}
+      self.child_size = {site["label"]: site["size"] for site in sites}
+      self.sites = [site["occupied_by"] for site in sites]
+      self._ordering = {site["label"]: site["position"] for site in sites}
+    else:
+      print("sites:", sites)
+
+  @property
+  def capacity(self):
+    """The number of sites on this carrier."""
+    return len(self.sites)
+
+  def __len__(self) -> int:
+    """Return the number of sites on this carrier."""
+    return len(self.sites)
+
+  def assign_child_resource(
+    self,
+    resource: ResourcePLR,
+    location: Optional[Coordinate],
+    reassign: bool = True,
+    spot: Optional[int] = None,
+  ):
+    idx = spot
+    # 如果只给 location，根据坐标和 deserialize 后的 self.sites（持有names）来寻找 resource 该摆放的位置
+    if spot is not None:
+      idx = spot
+    else:
+      for i, site in enumerate(self.sites):
+        site_location = list(self.child_locations.values())[i]
+        if type(site) == str and site == resource.name:
+          idx = i
+          break
+        if site_location == location:
+          idx = i
+          break
+        
+    if not reassign and self.sites[idx] is not None:
+      raise ValueError(f"a site with index {idx} already exists")
+    super().assign_child_resource(resource, location=location, reassign=reassign)
+    self.sites[idx] = resource
+
+  def assign_resource_to_site(self, resource: ResourcePLR, spot: int):
+    if self.sites[spot] is not None and not isinstance(self.sites[spot], ResourceHolder):
+      raise ValueError(f"spot {spot} already has a resource, {resource}")
+    self.assign_child_resource(resource, location=self.child_locations.get(str(spot)), spot=spot)
+
+  def unassign_child_resource(self, resource: ResourcePLR):
+    found = False
+    for spot, res in enumerate(self.sites):
+      if res == resource:
+        self.sites[spot] = None
+        found = True
+        break
+    if not found:
+      raise ValueError(f"Resource {resource} is not assigned to this carrier")
+    if hasattr(resource, "unassign"):
+      resource.unassign()
+
+  def __getitem__(
+    self,
+    identifier: Union[str, int, Sequence[int], Sequence[str], slice, range],
+  ) -> Union[List[T], T]:
+    """Get the items with the given identifier.
+
+    This is a convenience method for getting the items with the given identifier. It is equivalent
+    to :meth:`get_items`, but adds support for slicing and supports single items in the same
+    functional call. Note that the return type will always be a list, even if a single item is
+    requested.
+
+    Examples:
+      Getting the items with identifiers "A1" through "E1":
+
+        >>> items["A1:E1"]
+
+        [<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
+
+      Getting the items with identifiers 0 through 4 (note that this is the same as above):
+
+        >>> items[range(5)]
+
+        [<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
+
+      Getting items with a slice (note that this is the same as above):
+
+        >>> items[0:5]
+
+        [<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
+
+      Getting a single item:
+
+        >>> items[0]
+
+        [<Item A1>]
+    """
+
+    if isinstance(identifier, str):
+      if ":" in identifier:  # multiple # TODO: deprecate this, use `"A1":"E1"` instead (slice)
+        return self.get_items(identifier)
+
+      return self.get_item(identifier)  # single
+
+    if isinstance(identifier, int):
+      return self.get_item(identifier)
+
+    if isinstance(identifier, (slice, range)):
+      start, stop = identifier.start, identifier.stop
+      if isinstance(identifier.start, str):
+        start = list(self._ordering.keys()).index(identifier.start)
+      elif identifier.start is None:
+        start = 0
+      if isinstance(identifier.stop, str):
+        stop = list(self._ordering.keys()).index(identifier.stop)
+      elif identifier.stop is None:
+        stop = self.num_items
+      identifier = list(range(start, stop, identifier.step or 1))
+      return self.get_items(identifier)
+
+    if isinstance(identifier, (list, tuple)):
+      return self.get_items(identifier)
+
+    raise TypeError(f"Invalid identifier type: {type(identifier)}")
+
+  def get_item(self, identifier: Union[str, int, Tuple[int, int]]) -> T:
+    """Get the item with the given identifier.
+
+    Args:
+      identifier: The identifier of the item. Either a string, an integer, or a tuple. If an
+      integer, it is the index of the item in the list of items (counted from 0, top to bottom, left
+      to right).  If a string, it uses transposed MS Excel style notation, e.g. "A1" for the first
+      item, "B1" for the item below that, etc. If a tuple, it is (row, column).
+
+    Raises:
+      IndexError: If the identifier is out of range. The range is 0 to self.num_items-1 (inclusive).
+    """
+
+    if isinstance(identifier, tuple):
+      row, column = identifier
+      identifier = LETTERS[row] + str(column + 1)  # standard transposed-Excel style notation
+    if isinstance(identifier, str):
+      try:
+        identifier = list(self._ordering.keys()).index(identifier)
+      except ValueError as e:
+        raise IndexError(
+          f"Item with identifier '{identifier}' does not exist on " f"resource '{self.name}'."
+        ) from e
+
+    if not 0 <= identifier < self.capacity:
+      raise IndexError(
+        f"Item with identifier '{identifier}' does not exist on " f"resource '{self.name}'."
+      )
+
+    # Cast child to item type. Children will always be `T`, but the type checker doesn't know that.
+    return self.sites[identifier]
+
+  def get_items(self, identifiers: Union[str, Sequence[int], Sequence[str]]) -> List[T]:
+    """Get the items with the given identifier.
+
+    Args:
+      identifier: Deprecated. Use `identifiers` instead. # TODO(deprecate-ordered-items)
+      identifiers: The identifiers of the items. Either a string range or a list of integers. If a
+        string, it uses transposed MS Excel style notation. Regions of items can be specified using
+        a colon, e.g. "A1:H1" for the first column. If a list of integers, it is the indices of the
+        items in the list of items (counted from 0, top to bottom, left to right).
+
+    Examples:
+      Getting the items with identifiers "A1" through "E1":
+
+        >>> items.get_items("A1:E1")
+
+        [<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
+
+      Getting the items with identifiers 0 through 4:
+
+        >>> items.get_items(range(5))
+
+        [<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
+    """
+
+    if isinstance(identifiers, str):
+      identifiers = pylabrobot.utils.expand_string_range(identifiers)
+    return [self.get_item(i) for i in identifiers]
+
+  def __setitem__(self, idx: Union[int, str], resource: Optional[ResourcePLR]):
+    """Assign a resource to this carrier."""
+    if resource is None:  # setting to None
+      assigned_resource = self[idx]
+      if assigned_resource is not None:
+        self.unassign_child_resource(assigned_resource)
+    else:
+      idx = list(self._ordering.keys()).index(idx) if isinstance(idx, str) else idx
+      self.assign_resource_to_site(resource, spot=idx)
+
+  def __delitem__(self, idx: int):
+    """Unassign a resource from this carrier."""
+    assigned_resource = self[idx]
+    if assigned_resource is not None:
+      self.unassign_child_resource(assigned_resource)
+
+  def get_resources(self) -> List[ResourcePLR]:
+    """Get all resources assigned to this carrier."""
+    return [resource for resource in self.sites.values() if resource is not None]
+
+  def __eq__(self, other):
+    return super().__eq__(other) and self.sites == other.sites
+
+  def get_free_sites(self) -> List[int]:
+    return [spot for spot, resource in self.sites.items() if resource is None]
+
+  def serialize(self):
+    return {
+      **super().serialize(),
+      "num_items_x": self.num_items_x,
+      "num_items_y": self.num_items_y,
+      "num_items_z": self.num_items_z,
+      "sites": [{
+        "label": str(identifier),
+        "visible": True if self[identifier] is not None else False,
+        "occupied_by": self[identifier].name 
+                        if isinstance(self[identifier], ResourcePLR) and not isinstance(self[identifier], ResourceHolder) else 
+                        self[identifier] if isinstance(self[identifier], str) else None,
+        "position": {"x": location.x, "y": location.y, "z": location.z},
+        "size": self.child_size[identifier],
+        "content_type": ["bottle", "container", "tube", "bottle_carrier", "tip_rack"]
+      } for identifier, location in self.child_locations.items()]
+    }
+
+
+class BottleCarrier(ItemizedCarrier):
+    """瓶载架 - 直接继承自 TubeCarrier"""
+
+    def __init__(
+        self,
+        name: str,
+        size_x: float,
+        size_y: float,
+        size_z: float,
+        sites: Optional[Dict[Union[int, str], ResourceHolder]] = None,
+        category: str = "bottle_carrier",
+        model: Optional[str] = None,
+    ):
+        super().__init__(
+            name=name,
+            size_x=size_x,
+            size_y=size_y,
+            size_z=size_z,
+            sites=sites,
+            category=category,
+            model=model,
+        )