Merge pull request #167 from mcneilco/DISCO-1604

DISCO-1604: Protocol support, salt class, metalot structure fix and logging

acasclient/CmpdReg.py

@@ -4,11 +4,57 @@
 import types
 import logging
 from .acasclient import client
+from .lsthing import convert_json, camel_to_underscore
 
 logger = logging.getLogger(__name__)
-logging.basicConfig(level=logging.INFO)
 
 
+
+class Salt():
+    """Salt class."""
+    def __init__(self, abbrev: str, name: str, mol_structure: str, id: int = None, **kwargs):
+        self.id = id
+        self.abbrev = abbrev
+        self.name = name
+        self.mol_structure = mol_structure
+
+    def save(self, client: client) -> Salt:
+        """Save the salt to the server."""
+        resp = client.create_salt(self.abbrev, self.name, self.mol_structure)
+        self.id = resp['id']
+        return self
+
+    @classmethod
+    def from_camel_dict(cls, data):
+        """Construct an AbstractModel object from a camelCase dict
+
+        :param data: dict of attributes
+        :type data: dict
+        :return: instance of class AbstractModel
+        :rtype: AbstractModel
+        """
+        snake_case_dict = convert_json(data, camel_to_underscore)
+        return cls.from_dict(snake_case_dict)
+
+    @classmethod
+    def from_dict(cls, data):
+        """Construct an AbstractModel object from a dict
+
+        :param data: dict of attributes
+        :type data: dict
+        :return: instance of class AbstractModel
+        :rtype: AbstractModel
+        """
+        return cls(**data)
+
+    def as_dict(self) -> dict:
+        return {
+            'id': self.id,
+            'abbrev': self.abbrev,
+            'name': self.name,
+            'mol_structure': self.mol_structure
+        }
+
 class AdditionalScientistType(Enum):
     """Enum for additional scientist types."""
     COMPOUND = ACASDDict('compound', 'scientist')
@@ -62,7 +108,7 @@ def meta_lots_to_dict_array(meta_lots: list[dict]) -> list[dict]:
     return [meta_lot_to_dict(meta_lot) for meta_lot in meta_lots]
 
 
-def meta_lot_to_dict(meta_lot: dict) -> dict:
+def meta_lot_to_dict(meta_lot: dict, use_parent_mol=True) -> dict:
     """Converts a meta lot to a dictionary into a flat dictionary of specific fields."""
     parent_common_names = [parent_alias["aliasName"] for parent_alias in meta_lot["lot"]["saltForm"]["parent"]["parentAliases"] if parent_alias["lsKind"] == "Common Name"]
 
@@ -80,8 +126,13 @@ def meta_lot_to_dict(meta_lot: dict) -> dict:
     # If lot amount is filled in, then we need to fill in lot barcode with the lot corp name
     lot_barcode = meta_lot["lot"]["corpName"] if meta_lot["lot"]["amount"] is not None else None
 
+    if use_parent_mol:
+        mol = meta_lot["lot"]["parent"]["molStructure"]
+    else:
+        mol = meta_lot["lot"]['asDrawnStruct'] if meta_lot["lot"]['asDrawnStruct'] is not None else meta_lot["lot"]["parent"]["molStructure"]
+
     return_dict = {
-        'mol': meta_lot["lot"]['asDrawnStruct'] if meta_lot["lot"]['asDrawnStruct'] is not None else meta_lot["lot"]["parent"]["molStructure"],
+        'mol': mol,
         "id": meta_lot["lot"]["id"],
         "name": meta_lot["lot"]["corpName"],
         "parent_common_name": '; '.join(parent_common_names) if len(parent_common_names) > 0 else None,

acasclient/acasclient.py

@@ -960,7 +960,99 @@ def get_protocols_by_label(self, label):
                                 .format(self.url, quote(label, safe='')))
         resp.raise_for_status()
         return resp.json()
+
+    def get_protocol_by_code(self, protocol_code):
+        """Get a protocol from a protocol code
+
+        Get a protocol given a protocol code
+
+        Args:
+            protocol_code (str): A protocol code
+
+        Returns: Returns a protocol object
+        """
+        resp = self.session.get("{}/api/protocols/codename/{}"
+                                .format(self.url, protocol_code))
+        if resp.status_code == 500:
+            return None
+        resp.raise_for_status()
+        return resp.json()
+
+    def get_all_protocol_stubs(self):
+        """Get all protocol stubs
+
+        Get an array of all protocols
+
+        Args:
+            None
+
+        list of dict: Returns an array of protocol stubs in the format:
+            [
+                {
+                    'id': int,
+                    'code': str,
+                    'name': str,
+                    'ignored': str
+                },
+                ...
+            ]
+        """
+        resp = self.session.get("{}/api/protocolCodes"
+                                .format(self.url))
+        resp.raise_for_status()
+        protocols = resp.json()
+        # Remove any dupes using the id (BUG in ACAS)
+        return [dict(t) for t in {tuple(d.items()) for d in protocols}]
+
+    def save_protocol(self, protocol):
+        """Save a protocol
 
+        Save a protocol to ACAS
+
+        Args:
+            protocol (dict): A protocol object
+
+        Returns: Returns a protocol object
+        """
+        if protocol.get("id") and protocol.get("codeName"):
+            resp_dict = self.update_protocol(protocol)
+        else:
+            resp_dict = self.create_protocol(protocol)
+        return resp_dict
+
+    def update_protocol(self, protocol):
+        """Update a protocol
+
+        Update a protocol in ACAS
+
+        Args:
+            protocol (dict): A protocol object
+
+        Returns: Returns a protocol object
+        """
+        resp = self.session.put("{}/api/protocols/{}".format(self.url, protocol.get('id')),
+                                headers={'Content-Type': "application/json"},
+                                data=json.dumps(protocol))
+        resp.raise_for_status()
+        return resp.json()
+
+    def create_protocol(self, protocol):
+        """Create a protocol
+
+        Create a protocol in ACAS
+
+        Args:
+            protocol (dict): A protocol object
+
+        Returns: Returns a protocol object
+        """
+        resp = self.session.post("{}/api/protocols".format(self.url),
+                                 headers={'Content-Type': "application/json"},
+                                 data=json.dumps(protocol))
+        resp.raise_for_status()
+        return resp.json()
+
+
     def get_experiments_by_protocol_code(self, protocol_code):
         """Get all experiments for a protocol from a protocol code
 

acasclient/ddict.py

@@ -4,8 +4,6 @@
 import logging
 
 logger = logging.getLogger(__name__)
-logging.basicConfig(level=logging.INFO)
-
 
 class DDict(object):
     """The DDict class is meant as a generic interface for any implementation of a Data Dictionary that
@@ -71,3 +69,20 @@ def update_valid_values(self, client):
         self.valid_values = [val_dict['code'] for val_dict in valid_codetables]
         if not self.valid_values:
             self.raise_empty_dict_error()
+
+class ACASAuthorDDict(DDict):
+    """DDict implementation for built-in ACAS DDicts """
+
+    CODE_ORIGIN = 'ACAS authors'
+
+    def __init__(self, code_type, code_kind):
+        super(ACASAuthorDDict, self).__init__(code_type, code_kind, self.CODE_ORIGIN)
+
+    def update_valid_values(self, client):
+        """Get the valid values for the DDict."""
+        valid_authors = client.get_authors()
+        # Raise error if author does not match name
+        self.valid_values = [val_dict['code'] for val_dict in valid_authors]
+        if not self.valid_values:
+            self.raise_empty_dict_error()
+

acasclient/experiment.py

@@ -288,4 +288,4 @@ def scientist(self) -> str:
             value_kind="scientist")
         return data.get('codeValue') if data else None
 
-    as_dict = dict.__str__
+    as_dict = dict.__str__

acasclient/lsthing.py

@@ -1,7 +1,7 @@
 from __future__ import unicode_literals
 from typing import Any, Dict
 
-from .ddict import ACASDDict, ACASLsThingDDict, DDict
+from .ddict import ACASDDict, ACASLsThingDDict, DDict, ACASAuthorDDict
 from .interactions import INTERACTION_VERBS_DICT, opposite
 from .validation import validation_result, ValidationResult
 
@@ -18,12 +18,11 @@
 from six import text_type as str
 
 logger = logging.getLogger(__name__)
-logging.basicConfig(level=logging.INFO)
-
 
 ROW_NUM_KEY = 'row number'
 ACAS_DDICT = ACASDDict.CODE_ORIGIN.upper()
 ACAS_LSTHING = ACASLsThingDDict.CODE_ORIGIN.upper()
+ACAS_AUTHOR = ACASAuthorDDict.CODE_ORIGIN.upper()
 
 # JSON encoding / decoding
 
@@ -850,7 +849,31 @@ def as_camel_dict(self):
         snake_case_dict = self.as_dict()
         camel_dict = convert_json(snake_case_dict, underscore_to_camel)
         return camel_dict
+
+    def __deepcopy__(self, memo):
+        """Create a deep copy of the instance.
+
+        The 'id' and 'version' fields are nulled out to ensure that the copied object
+        is treated as a new instance rather than a duplicate of the original. This is
+        particularly useful when the copied object needs to be saved as a new record
+        in a database or used in a context where unique identifiers are required.
+
+        Args:
+            memo (dict): A dictionary of objects already copied during the current copying pass.
 
+        Returns:
+            object: A deep copy of the instance with 'id' and 'version' fields set to None.
+        """
+        # Create a deep copy of the instance first
+        copied_obj = copy.copy(self)  # Shallow copy of self
+        # Then deep copy the attributes individually
+        copied_obj.__dict__ = copy.deepcopy(self.__dict__, memo)
+        # Set the 'id' attribute to None
+        copied_obj.id = None
+        copied_obj.version = None
+        return copied_obj
+
+
     def as_json(self, **kwargs):
         """Serialize instance into a JSON string with camelCase keys
 
@@ -2136,6 +2159,8 @@ def _get_ddicts(self):
                             ddict = ACASDDict(value.code_type, value.code_kind)
                         elif value.code_origin.upper() == ACAS_LSTHING:
                             ddict = ACASLsThingDDict(value.code_type, value.code_kind)
+                        elif value.code_origin.upper() == ACAS_AUTHOR:
+                            ddict = ACASAuthorDDict(value.code_type, value.code_kind)
                         else:
                             raise ValueError(f'Unsupported code_origin: {value.code_origin}')
                         ddicts[(ddict.code_type, ddict.code_kind, ddict.code_origin.upper())] = ddict

acasclient/protocol.py

@@ -0,0 +1,69 @@
+from acasclient.lsthing import (CodeValue, SimpleLsThing, LsThing, clob, ACAS_DDICT, ACAS_AUTHOR)
+
+from datetime import datetime
+
+# Constants
+META_DATA = 'protocol metadata'
+LS_TYPE = 'default'
+LS_KIND = 'default'
+PREFERRED_LABEL = 'protocol name'
+STATUS = 'protocol status'
+NOTEBOOK_PAGE = 'notebook page'
+PROJECT = 'project'
+COMMENTS = 'comments'
+ASSAY_TREE_RULE = 'assay tree rule'
+PROTOCOL_STATUS = 'protocol status'
+ASSAY_STAGE = 'assay stage'
+SCIENTIST = 'scientist'
+ASSAY_PRINCIPLE = 'assay principle'
+CREATION_DATE = 'creation date'
+PROTOCOL_DETAILS = 'protocol details'
+NOTEBOOK = 'notebook'
+
+
+class Protocol(SimpleLsThing):
+    ls_type = LS_TYPE
+    ls_kind = LS_KIND
+    preferred_label_kind = PREFERRED_LABEL
+
+    def __init__(self, name=None, scientist=None, recorded_by=None, assay_principle=None, assay_stage='unassigned', creation_date=None, protocol_details=None,
+                 notebook=None, comments=None, assay_tree_rule=None, protocol_status='created', notebook_page=None, project='unassigned', ls_thing=None):
+        names = {PREFERRED_LABEL: name}
+
+        if not creation_date:
+            creation_date = datetime.now()
+
+        metadata = {
+            META_DATA: {
+                ASSAY_PRINCIPLE: clob(assay_principle),
+                ASSAY_STAGE: CodeValue(assay_stage, 'assay', 'stage', ACAS_DDICT),
+                SCIENTIST: CodeValue(scientist, 'assay', 'scientist', ACAS_AUTHOR),
+                CREATION_DATE: creation_date,
+                PROTOCOL_DETAILS: clob(protocol_details),
+                NOTEBOOK: notebook,
+                COMMENTS: clob(comments),
+                ASSAY_TREE_RULE: assay_tree_rule,
+                PROTOCOL_STATUS: CodeValue(protocol_status, 'protocol', 'status', ACAS_DDICT),
+                NOTEBOOK_PAGE: notebook_page,
+                PROJECT: CodeValue(project, 'project', 'biology', ACAS_DDICT)
+            }
+        }
+        super(Protocol, self).__init__(ls_type=self.ls_type, ls_kind=self.ls_kind, names=names, recorded_by=recorded_by,
+                                       preferred_label_kind=self.preferred_label_kind, metadata=metadata, ls_thing=ls_thing)
+
+    def save(self, client, skip_validation=False):
+        """Persist changes to the ACAS server.
+
+        :param client: Authenticated instances of acasclient.client
+        :type client: acasclient.client
+        """
+        # Run validation
+        if not skip_validation:
+            self.validate(client)
+        self._prepare_for_save(client)
+        # Persist
+        protocol_dict = self._ls_thing.as_camel_dict()
+        resp_dict = client.save_protocol(protocol_dict)
+        self._ls_thing = LsThing.from_camel_dict(resp_dict)
+        self._cleanup_after_save()
+        return self

acasclient/selfile.py

@@ -61,8 +61,11 @@
 ################################################################################
 # Logging
 ################################################################################
-logger = logging.getLogger(__name__).addHandler(logging.NullHandler())
+# Initialize the logger
+logger = logging.getLogger(__name__)
 
+# Add a NullHandler to avoid errors if no other handlers are configured
+logger.addHandler(logging.NullHandler())
 
 ################################################################################
 # Functions