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Reinvent updates #77

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merged 3 commits into from
Nov 19, 2024
Merged

Reinvent updates #77

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b64f7e0
added support for arrays
Nov 12, 2024
b3b638b
last update
Nov 18, 2024
4cf30eb
version number update
Nov 18, 2024
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4 changes: 2 additions & 2 deletions openad/app/metadata.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"banner": "OPENAD",
"title": "Welcome to the Open Accelerated Discovery CLI",
"version": "0.6.4",
"version": "0.6.5",
"commands": {
"intro": "If this is your first time, let us help you getting started.",
"? toolkits": "Learn about the toolkits.",
Expand All @@ -10,4 +10,4 @@
"? <soft>...</soft>": "List commands containing \"...\"",
"docs": "Read the docs in your browser."
}
}
}
166 changes: 51 additions & 115 deletions openad/openad_model_plugin/openad_model_toolkit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,10 +42,6 @@
oneOf,
)

# from openad.molecules.mol_functions import MOL_PROPERTIES as m_props
# from openad.helpers.general import is_notebook_mode


(
get,
lister,
Expand Down Expand Up @@ -109,6 +105,7 @@
key_val_expr_num = Word(nums)
key_val_expr_alpha = Word(alphanums + "_" + ".")
number_type = Combine(Optional("-") + Word(nums) + Word(".") + Word(nums)) | Word(nums)
array_var = Suppress(Word("[")) + delimitedList(OneOrMore(desc | number_type)) + Suppress(Word("]"))
key_val_line = Group(name_expr("key") + Suppress("=") + key_val_expr("val"))
boolean_var = Keyword("True") | Keyword("False")

Expand Down Expand Up @@ -185,25 +182,25 @@
service_command_start["get_protein_property"] = 'get + CaselessKeyword("protein") + CaselessKeyword("property")'
service_command_start["generate_data"] = 'CaselessKeyword("generate") + CaselessKeyword("with")'

service_command_merge[
"get_molecule_property"
] = '+ Optional((CaselessKeyword("merge with mols")|CaselessKeyword("merge with molecules"))("merge_with_mws"))'
service_command_merge["get_molecule_property"] = (
'+ Optional((CaselessKeyword("merge with mols")|CaselessKeyword("merge with molecules"))("merge_with_mws"))'
)
service_command_merge["get_crystal_property"] = ""
service_command_merge["get_protein_property"] = ""
service_command_merge["generate_data"] = ""

service_command_subject[
"get_molecule_property"
] = '+CaselessKeyword("for")+(mol_list("mol_list")|(Word("[")+delimitedList(molecule_identifier,delim=",")("molecules")+Word("]")|molecule_identifier("molecule")))'
service_command_subject[
"get_protein_property"
] = '+CaselessKeyword("for")+((Word("[")+ delimitedList(molecule_identifier,delim=",")("proteins")+Word("]")|molecule_identifier("protein")))'
service_command_subject[
"get_crystal_property"
] = '+CaselessKeyword("for")+((Word("[")+ delimitedList(desc,delim=",")("crystal_files")+Word("]")|desc("crystal_file")("crystal_PATH")))'
service_command_subject[
"generate_data"
] = '+CaselessKeyword("data")+<TARGET>Optional(CaselessKeyword("Sample")+Word(nums)("sample_size"))'
service_command_subject["get_molecule_property"] = (
'+CaselessKeyword("for")+(mol_list("mol_list")|(Word("[")+delimitedList(molecule_identifier,delim=",")("molecules")+Word("]")|molecule_identifier("molecule")))'
)
service_command_subject["get_protein_property"] = (
'+CaselessKeyword("for")+((Word("[")+ delimitedList(molecule_identifier,delim=",")("proteins")+Word("]")|molecule_identifier("protein")))'
)
service_command_subject["get_crystal_property"] = (
'+CaselessKeyword("for")+((Word("[")+ delimitedList(desc,delim=",")("crystal_files")+Word("]")|desc("crystal_file")("crystal_PATH")))'
)
service_command_subject["generate_data"] = (
'+CaselessKeyword("data")+<TARGET>Optional(CaselessKeyword("Sample")+Word(nums)("sample_size"))'
)

###################################################################
# targets for generate Data
Expand Down Expand Up @@ -240,18 +237,18 @@
# sampling_wrapper={'fraction_to_mask': mask, 'property_goal': {'<esol>': 0.234}}"""


service_command_help[
"get_molecule_property"
] = "get molecule property <property> FOR @mols | [<list of SMILES>] | <SMILES> USING (<parameter>=<value> <parameter>=<value>) (merge with mols|molecules)"
service_command_help[
"get_crystal_property"
] = "get crystal property <property> FOR <directory> USING (<parameter>=<value> <parameter>=<value>)"
service_command_help[
"get_protein_property"
] = "get protein property <property> FOR [<list of Proteins>] | <Protein> USING (<parameter>=<value> <parameter>=<value>)"
service_command_help[
"generate_data"
] = "generate with <property> data <TARGET> (sample <sample_size>) USING (<parameter>=<value> <parameter>=<value>) "
service_command_help["get_molecule_property"] = (
"get molecule property <property> FOR @mols | [<list of SMILES>] | <SMILES> USING (<parameter>=<value> <parameter>=<value>) (merge with mols|molecules)"
)
service_command_help["get_crystal_property"] = (
"get crystal property <property> FOR <directory> USING (<parameter>=<value> <parameter>=<value>)"
)
service_command_help["get_protein_property"] = (
"get protein property <property> FOR [<list of Proteins>] | <Protein> USING (<parameter>=<value> <parameter>=<value>)"
)
service_command_help["generate_data"] = (
"generate with <property> data <TARGET> (sample <sample_size>) USING (<parameter>=<value> <parameter>=<value>) "
)

service_command_description[
"get_molecule_property"
Expand Down Expand Up @@ -300,7 +297,6 @@ def service_grammar_add(statements: list, help: list, service_catalog: dict):
command = "CaselessKeyword(service)('service')+" + service_command_start[schema["service_type"]]
valid_types = None # noqa: F841
valid_type = None

# in properties this refers to generateable properties for a Target in Generators this is simple a single name of a generarion Algorithm
# for some propertyy statements there can be multiple properties in a single statement

Expand Down Expand Up @@ -536,6 +532,17 @@ def optional_parameter_list(inp_statement: dict, clause: str):
"""Create an optional parameter list for a clause"""
ii = 0
expression = " "
type_dict = {
"allOf": "key_val_expr",
"anyOf": "key_val_expr",
"string": "key_val_expr",
"desc": "desc",
"object": "input_object",
"boolean": "boolean_var",
"array": "array_var",
"number": "number_type",
"integer": "number_type",
}
for i in inp_statement[clause]:
if i in ["selected_property", "property_type", "domain", "algorithm_type"]:
continue
Expand All @@ -562,9 +569,10 @@ def optional_parameter_list(inp_statement: dict, clause: str):

else:
status = "ZeroOrMore"

if ii == 0:
expression = expression + " "
if inp_statement[clause][i] == "allOf":
if type_str in ["anyOf", "allOf"]:
expression = (
expression
+ f" {status}(Group( CaselessKeyword ('"
Expand All @@ -574,42 +582,12 @@ def optional_parameter_list(inp_statement: dict, clause: str):
+ "'))"
+ " "
)
elif inp_statement[clause][i][type_str] == "string":
expression = (
expression
+ f" {status}(Group( CaselessKeyword ('"
+ i
+ "') +Suppress('=')+key_val_expr('val'))('"
+ parameter
+ "'))"
+ " "
)
elif inp_statement[clause][i][type_str] == "desc":
expression = (
expression
+ f" {status}(Group( CaselessKeyword ('"
+ i
+ "') +Suppress('=')+desc('val'))('"
+ parameter
+ "'))"
+ " "
)
elif inp_statement[clause][i][type_str] == "object":
expression = (
expression
+ f" {status}(Group( CaselessKeyword ('"
+ i
+ "') +Suppress('=')+input_object('val'))('"
+ parameter
+ "'))"
+ " "
)
elif inp_statement[clause][i][type_str] == "boolean":
elif inp_statement[clause][i][type_str] in type_dict:
expression = (
expression
+ f" {status}(Group( CaselessKeyword ('"
+ i
+ "') +Suppress('=')+boolean_var('val'))('"
+ f"') +Suppress('=')+{type_dict[inp_statement[clause][i][type_str]]}('val'))('"
+ parameter
+ "'))"
+ " "
Expand All @@ -624,19 +602,9 @@ def optional_parameter_list(inp_statement: dict, clause: str):
+ "'))"
+ " "
)
else:
if type_str == "allOf":
expression = (
expression
+ f" & {status}(Group( CaselessKeyword ('"
+ i
+ "') +Suppress('=')+key_val_expr('val'))('"
+ parameter
+ "'))"
+ " "
)

elif inp_statement[clause][i][type_str] == "string":
else:
if type_str in ["anyOf", "allOf"]:
expression = (
expression
+ f" & {status}(Group( CaselessKeyword ('"
Expand All @@ -646,32 +614,12 @@ def optional_parameter_list(inp_statement: dict, clause: str):
+ "'))"
+ " "
)
elif inp_statement[clause][i][type_str] == "desc":
elif inp_statement[clause][i][type_str] in type_dict:
expression = (
expression
+ f" & {status}(Group( CaselessKeyword ('"
+ i
+ "') +Suppress('=')+desc('val'))('"
+ parameter
+ "'))"
+ " "
)
elif inp_statement[clause][i][type_str] == "object":
expression = (
expression
+ f" & {status}(Group( CaselessKeyword ('"
+ i
+ "') +Suppress('=')+input_object('val'))('"
+ parameter
+ "'))"
+ " "
)
elif inp_statement[clause][i][type_str] == "boolean":
expression = (
expression
+ f" & {status}(Group( CaselessKeyword ('"
+ i
+ "') +Suppress('=')+boolean_var('val'))('"
+ f"') +Suppress('=')+{type_dict[inp_statement[clause][i][type_str]]}('val'))('"
+ parameter
+ "'))"
+ " "
Expand All @@ -686,6 +634,7 @@ def optional_parameter_list(inp_statement: dict, clause: str):
+ "'))"
+ " "
)

ii = 1

return expression
Expand Down Expand Up @@ -788,7 +737,8 @@ def request_generate(cmd_pointer, request_input):
)
elif actual_param.split("@")[1] == "integer":
template["parameters"][actual_param.split("@")[0]] = bool(request_input.as_dict()[param]["val"])

elif actual_param.split("@")[1] == "string":
template["parameters"][actual_param.split("@")[0]] = str(request_input.as_dict()[param]["val"])
else:
template["parameters"][actual_param.split("@")[0]] = request_input.as_dict()[param]["val"]
return template
Expand All @@ -807,21 +757,7 @@ def openad_model_requestor(cmd_pointer, parser):
service_name = None

a_request = request_generate(cmd_pointer, parser)
# request_params = get_service_requester(service_name)
# api_key = get_service_api_key(service_name)
# headers = {"Inference-Service": service_name, "Authorization": f"Bearer {get_service_api_key(service_name)}"}

# if Endpoint is not None and len((Endpoint.strip())) > 0:
# if "http" not in Endpoint:
# Endpoint = "http://" + Endpoint
# Endpoint = "http://34.205.69.8:8080"
# else:
# Endpoint = None

# if Endpoint is None:
# return output_error(
# "No Service Cataloged or service not up. \n Check Service Status <cmd>model service status</cmd> "
# )

spinner = Spinner(GLOBAL_SETTINGS["VERBOSE"])
spinner.start("Executing Request Against Server")

Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[tool.poetry]
name = "openad"
version = "0.6.4"
version = "0.6.5"
description = "Open Accelerated Discovery Client"
authors = ["Phil Downey <[email protected]>"]
readme = "README.md"
Expand Down
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