-fix DetachedInstanceError

- init project then create folder

python/biopro/db/collection.py

@@ -0,0 +1,75 @@
+from sqlalchemy import Table, Column, String, MetaData, ForeignKey, JSON
+from sqlalchemy.sql import select, func
+from sqlalchemy.types import Integer, BigInteger, String, Boolean, TIMESTAMP, Numeric
+from sqlalchemy.dialects.postgresql import JSONB
+from biopro.db.base import Session
+
+from .base import Base
+
+class Collection(Base):
+    __tablename__ = "collections"
+
+    id = Column(Integer, primary_key=True)
+    name = Column(String(255))
+    parent = Column(JSONB)
+    controller_id = Column(Integer)
+    type = Column(String(255))
+    description = Column(String(255))
+    deleted = Column(Boolean)
+    created_at = Column(TIMESTAMP(timezone=True), server_default=func.now())
+    updated_at = Column(TIMESTAMP(timezone=True), onupdate=func.now())
+
+    @classmethod
+    def create_collection(cls, collection_name, parent, duplicate=False):
+        with Session() as session:
+            name = cls.check_name_duplicate(collection_name, parent, 0, duplicate=duplicate)
+            if name == None:
+                return session.query(Collection).filter(Collection.name == collection_name, Collection.parent == parent).first()
+            else:
+                collection = Collection(
+                    name = name,
+                    parent = parent,
+                    type= "folder",
+                )
+                session.add(collection)
+                session.commit()
+                session.refresh(collection)
+                return collection
+
+    @classmethod
+    def check_name_duplicate(cls, collection_name, parent, n, _session = None, duplicate=False):
+        if _session == None:
+            with Session() as session:
+                result = session.query(Collection).filter(Collection.name == cls.generate_name(collection_name, n), Collection.parent == parent).first()
+                if result is None:
+                    return cls.generate_name(collection_name, n)
+                else:
+                    if duplicate == True:
+                        return None
+                    else:
+                        new_num = n + 1
+                        # new_name =  f"{collection_name}({new_num})" 
+                        return cls.check_name_duplicate(collection_name, parent, new_num, session)
+        else:
+            result = _session.query(Collection).filter(Collection.name == cls.generate_name(collection_name, n), Collection.parent == parent).first()
+            if result is None:
+                return cls.generate_name(collection_name, n)
+            else:
+                new_num = n + 1
+                # new_name =  f"{collection_name}({new_num})" 
+                return cls.check_name_duplicate(collection_name, parent, new_num, _session)
+
+    @classmethod
+    def generate_name(cls, collection_name, n):
+        if n==0:
+            return collection_name
+        else:
+            return f"{collection_name}({n})" 
+    
+    @classmethod
+    def find_collection(cls, collection_name, parent):
+        with Session() as session:
+            result = session.query(Collection).filter(Collection.name == collection_name, Collection.parent == parent).first()
+            return result
+    
+        

python/biopro/db/meta.py

@@ -0,0 +1,24 @@
+from sqlalchemy import Table, Column, String, MetaData, ForeignKey, JSON
+from sqlalchemy.sql import select, func
+from sqlalchemy.types import Integer, BigInteger, String, Boolean, TIMESTAMP, Numeric
+from sqlalchemy.dialects.postgresql import JSONB
+
+from .base import Base, Session
+
+class RecordingDataMeta(Base):
+    __tablename__ = "recording_data_metas"
+
+    id = Column(Integer, primary_key=True)
+    path = Column(String(255))
+    name = Column(String(255))
+    parent = Column(JSONB)
+    size = Column(String(255))
+    time_duration = (String(255))
+    raw_data = Column(JSONB)
+    project = Column(Integer)
+    deleted = Column(Boolean, default = False)
+    created_at = Column(TIMESTAMP(timezone=True), server_default=func.now())
+    updated_at = Column(TIMESTAMP(timezone=True), onupdate=func.now())
+
+    # def __repr__(self):
+    #     return f"User(id={self.id!r}, name={self.name!r}, fullname={self.task!r})"

python/biopro/db/project.py

@@ -0,0 +1,24 @@
+from sqlalchemy import Table, Column, String, MetaData, ForeignKey, JSON
+from sqlalchemy.sql import select, func
+from sqlalchemy.types import Integer, BigInteger, String, Boolean, TIMESTAMP, Numeric
+from sqlalchemy.dialects.postgresql import JSONB
+
+from .base import Base
+
+class Project(Base):
+    __tablename__ = "project"
+
+    id = Column(Integer, primary_key=True)
+    name = Column(String)
+    desc = Column(String)
+    task = Column(JSONB)
+    cycle = Column(JSONB)
+    device = Column(JSONB)
+    uuid = Column(String(36))
+    user_auth = Column(JSONB)
+    deleted = Column(Boolean, default = False)
+    created_at = Column(TIMESTAMP(timezone=True), server_default=func.now())
+    updated_at = Column(TIMESTAMP(timezone=True), onupdate=func.now())
+
+    # def __repr__(self):
+    #     return f"User(id={self.id!r}, name={self.name!r}, fullname={self.task!r})"

python/biopro/db/project_meta.py

@@ -3,7 +3,7 @@ from sqlalchemy.sql import select, func
 from sqlalchemy.types import Integer, BigInteger, String, Boolean, TIMESTAMP, Numeric
 from sqlalchemy.dialects.postgresql import JSONB
 
-from .base import Base
+from .base import Base, Session
 
 class MetaProjectInfo(Base):
     __tablename__ = "project_metas"
@@ -17,5 +17,13 @@ class MetaProjectInfo(Base):
     created_at = Column(TIMESTAMP(timezone=True), server_default=func.now())
     updated_at = Column(TIMESTAMP(timezone=True), onupdate=func.now())
 
+    @classmethod
+    def create_project_meta(cls, project):
+        with Session() as session:
+            project_meta = MetaProjectInfo(project = project['project'], cycle= project['cycle'], task=project['task'], serial_number=int(project['serial_number']))
+            session.add(project_meta)
+            session.commit()
+            return project_meta.id
+
     # def __repr__(self):
     #     return f"User(id={self.id!r}, name={self.name!r}, fullname={self.task!r})"

python/biopro/db/recording_data.py

@@ -0,0 +1,88 @@
+from sqlalchemy import Table, Column, String, MetaData, ForeignKey, JSON
+from sqlalchemy.sql import select, func
+from sqlalchemy.types import Integer, BigInteger, String, Boolean, TIMESTAMP, Numeric, Text
+from sqlalchemy.dialects.postgresql import JSONB
+from biopro.db.base import Session
+
+from .base import Base
+
+# build a model class with a specific table name
+def get_raw_model(channel):
+    tablename = str(channel) + '_recording_data_raws'  # dynamic table name
+    class_name = 'RECORDING_DATA_RAWS' # dynamic class name
+    print('get_raw_model', tablename)
+
+    for mapper in Base.registry.mappers:
+        cls = mapper.class_
+        classname = cls.__name__
+        tblname = cls.__tablename__
+        print(cls, classname, tblname)
+        if (classname == class_name):
+            if tblname == tablename:
+                return cls
+
+    Model = type(class_name, (RECORDING_DATA_RAWS,), {
+        '__tablename__': tablename
+    })
+    return Model
+
+
+class RECORDING_DATA_RAWS(Base):
+    __abstract__ = True
+
+    id = Column(Integer, primary_key=True)
+    name = Column(String(255))
+    parent = Column(Integer)
+    size = Column(String(255))
+    path = Column(JSONB)
+    uuid = Column(String(255))
+    serial_number = Column(String(255))
+    data_format = Column(String(255))
+    channel = Column(Integer)
+    start_time = Column(String(255))
+    end_time = Column(String(255))
+    data = Column(Text)
+    compressed = Column(Boolean)
+    deleted = Column(Boolean)
+    created_at = Column(TIMESTAMP(timezone=True), server_default=func.now())
+    updated_at = Column(TIMESTAMP(timezone=True), onupdate=func.now())
+
+    # @classmethod
+    # def create_subject_data(cls, subject_id, project, meta, data):
+    #     with Session() as session:
+    #         subject = Subject(
+    #             subject_id = subject_id,
+    #             project = project,
+    #             meta= meta,
+    #             data = data
+    #         )
+    #         session.add(subject)
+    #         session.commit()
+    #         return subject
+        
+    # @classmethod
+    # def check_name_duplicate(cls, collection_name, parent, n):
+    #     with Session() as session:
+    #         result = session.query(Collection).filter(Collection.name == cls.generate_name(collection_name, n), Collection.parent == parent).first()
+    #         if result is None:
+    #             return cls.generate_name(collection_name, n)
+    #         else:
+    #             new_num = n + 1
+    #             # new_name =  f"{collection_name}({new_num})" 
+    #             return cls.check_name_duplicate(collection_name, parent, new_num)
+
+    # @classmethod
+    # def generate_name(cls, collection_name, n):
+    #     if n==0:
+    #         return collection_name
+    #     else:
+    #         return f"{collection_name}({n})" 
+    
+    # @classmethod
+    # def find_data(cls, id):
+    #     with Session() as session:
+
+    #         result = session.query(RECORDING_DATA_RAWS).first()
+    #         return result
+    
+        

python/biopro/db/subject_data.py

@@ -0,0 +1,60 @@
+from sqlalchemy import Table, Column, String, MetaData, ForeignKey, JSON
+from sqlalchemy.sql import select, func
+from sqlalchemy.types import Integer, BigInteger, String, Boolean, TIMESTAMP, Numeric
+from sqlalchemy.dialects.postgresql import JSONB
+from biopro.db.base import Session
+
+from .base import Base
+
+class SubjectData(Base):
+    __tablename__ = "subject_datas"
+
+    id = Column(Integer, primary_key=True)
+    subject_id = Column(Integer)
+    mode = Column(JSONB)
+    data = Column(JSONB)
+    user_auth = Column(JSONB)
+    meta = Column(String(255))
+    project = Column(String(255))
+    deleted = Column(Boolean)
+    created_at = Column(TIMESTAMP(timezone=True), server_default=func.now())
+    updated_at = Column(TIMESTAMP(timezone=True), onupdate=func.now())
+
+    @classmethod
+    def create_subject_data(cls, subject_id, project, meta, data):
+        with Session() as session:
+            subject = SubjectData(
+                subject_id = subject_id,
+                project = project,
+                meta= meta,
+                data = data
+            )
+            session.add(subject)
+            session.commit()
+            return subject
+        
+    # @classmethod
+    # def check_name_duplicate(cls, collection_name, parent, n):
+    #     with Session() as session:
+    #         result = session.query(Collection).filter(Collection.name == cls.generate_name(collection_name, n), Collection.parent == parent).first()
+    #         if result is None:
+    #             return cls.generate_name(collection_name, n)
+    #         else:
+    #             new_num = n + 1
+    #             # new_name =  f"{collection_name}({new_num})" 
+    #             return cls.check_name_duplicate(collection_name, parent, new_num)
+
+    # @classmethod
+    # def generate_name(cls, collection_name, n):
+    #     if n==0:
+    #         return collection_name
+    #     else:
+    #         return f"{collection_name}({n})" 
+    
+    # @classmethod
+    # def find_collection(cls, collection_name, parent):
+    #     with Session() as session:
+    #         result = session.query(Collection).filter(Collection.name == collection_name, Collection.parent == parent).first()
+    #         return result
+    
+        

python/biopro/devlib/data.py

@@ -1676,7 +1676,13 @@ class EISZeroOneDataDecoder(RecDataDecoder):
 
 
 
-        else:                                           #CV Mode
+        else:
+            if (self._mode == 1 or self._mode == 2 or self._mode == 3):
+                ch1 = ch1 * (-1)
+            if (self._mode == 4):
+                ch1 = ch1 * (-1)
+                ch3 = ch3 * (-1)
+                                                           #CV Mode
             ret.append_data(0, ch1)                     #Iin     [nA]
             ret.append_data(1, ch2)                     #Vset    [nV]
             ret.append_data(2, ch3)                     #Vout    [nV]

python/biopro/devlib/library.py

@@ -1292,6 +1292,9 @@ class CompletedDevice(Device):
 
     def central_version_get(self) -> Optional[list]:
         return self._device.central_version_get()
+    
+    def save_data_to_subject(self, project, meta, device, subject_id):
+        self._master._handler.save_data_to_subject(project, meta, device, subject_id)
 
     # utility method
 

python/biopro/project/project.py

@@ -15,6 +15,9 @@ from .instruction import Instruction
 from biopro.device.manager import DeviceManager
 from biopro.text import *
 
+from biopro.db.base import Session
+from biopro.db.collection import Collection
+
 key_list = {
   'deviceList': 'device',
 }
@@ -46,6 +49,9 @@ class Project(threading.Thread):
 
     self._count = 1 #流水號
 
+    self._project_meta_id = -1
+    self._subject = []
+
     self.log_verbose = log_verbose
     self._logger = logging.getLogger('project')
     self._logger.setLevel('DEBUG')
@@ -60,6 +66,17 @@ class Project(threading.Thread):
     fh = logging.FileHandler(f'/home/pi/logger/project/{self.uuid}.log', mode="w")
     fh.setFormatter(self._formatter)
     self._logger.addHandler(fh)
+
+    default_name = 'admin'
+    default_parent = {"folder": [1]}
+    collection = Collection.find_collection(default_name, default_parent)
+    parent = {"folder": [collection.id]}
+    # create project folder
+    folder_name_duplicate = False
+    if len(self._subject) > 0:
+      folder_name_duplicate = True
+    collection = Collection.create_collection(self.name, parent, folder_name_duplicate)
+    self.setup_collection(collection)
     
   def setup_project(self, project):
     for (key, value) in project.items():
@@ -79,6 +96,9 @@ class Project(threading.Thread):
       complete_device = self._device_manager.get_device(mac_address)
       complete_device.occupied_by_project = self._uuid
       self._complete_device[device] = complete_device
+    
+  def setup_collection(self, collection):
+    self._task_manager.create_collection(collection)
 
   @property
   def id(self) -> int:
@@ -87,6 +107,22 @@ class Project(threading.Thread):
   @id.setter
   def id(self, new_id):
     self._id = new_id
+
+  @property
+  def project_meta_id(self) -> int:
+    return self._project_meta_id
+  
+  @project_meta_id.setter
+  def project_meta_id(self, new_project_meta_id):
+    self._project_meta_id = new_project_meta_id
+
+  @property
+  def subject(self) -> object:
+    return self._subject
+  
+  @subject.setter
+  def subject(self, new_subject):
+    self._subject = new_subject
   
   @property
   def uuid(self) -> str:
@@ -264,6 +300,9 @@ class Project(threading.Thread):
                       args = list(map(lambda arg: task_info[arg], instruction['arguments']))
                       target=getattr(device, instruction['method'])(*args)
                       print('instruction 2', device, instruction, datetime.now())
+                    if (action.type == 'stop'):
+                      if (len(self._subject) > 0):
+                         target=getattr(device, "save_data_to_subject")(self.id, self.project_meta_id, device, self._subject[0])
                     if action.type == 'start':
                       self._count += 1
             

python/biopro/project/task_manager.py

@@ -5,6 +5,7 @@ from xml.dom.expatbuilder import parseString
 import paho.mqtt.client as mqtt
 from biopro.text import *
 from .task import Task
+from biopro.db.collection import Collection
 
 _RUNTIME_COMPILE = False
 
@@ -67,6 +68,13 @@ class TaskManager():
         if cycle['range'][1] == task.uuid:
           return index
 
+    def check_task_in_cycle(self, task_index):
+      for index, cycle in enumerate(self._cycle_list):
+        if self.get_index_by_uuid(cycle['range'][0]) <= task_index:
+          if self.get_index_by_uuid(cycle['range'][1]) >= task_index:
+            return True
+      return False
+
     @property
     def check_list(self):
       return [self._running_task, *self._next_task]
@@ -162,4 +170,12 @@ class TaskManager():
 
     def get_task(self, task_id):
       return self._task_list[task_id]
-  
+  
+    def create_collection(self, parent):
+      for index, task in enumerate(self._task_list):
+        if self.check_task_in_cycle(index) == True:
+          if task.type == '':
+            collection = Collection.create_collection(task.name, {"folder": [parent.id]}, False)
+            task.parent = {"folder": [collection.id]}
+        else:
+          task.parent = {"folder": [parent.id]}

python/biopro/server/data.py

@@ -362,14 +362,14 @@ class DataServer(SocketServer, DataAPI):
         self.log_verbose('device ID', device_id)
 
         # project binding meta file
-        project_id = None
-        _project = None
-        if project_info != None:
-            _project = json.loads(project_info)
-            self.database_process.put_queue(['project_insert', device_id, _project])
-            result = self._queue_ds_dict[int(device_id)].get()
-            if result[0] == 'project_id':
-                project_id =  result[1]
+        # project_id = None
+        # _project = None
+        # if project_info != None:
+        #     _project = json.loads(project_info)
+        #     self.database_process.put_queue(['project_insert', device_id, _project])
+        #     result = self._queue_ds_dict[int(device_id)].get()
+        #     if result[0] == 'project_id':
+        project_id =  project_info
 
         # while len(self._configurations) <= device_id:
         #     self._configurationsappend(None)

python/biopro/server/database.py

@@ -222,7 +222,8 @@ class DataBaseProcess(Process):
 
                 try:
                     sql_cursor.execute(sql_str, sql_set)
-                except:
+                except BaseException as e:
+                    print('meta create error', e)
                     self._psql_conn.commit()
                     sql_cursor.close()
                     self._queue_error.put(device_id)
@@ -249,7 +250,8 @@ class DataBaseProcess(Process):
 
                 try:
                     sql_cursor.execute(sql_str, sql_set)
-                except:
+                except BaseException as e:
+                    print('meta update error', e)
                     self._psql_conn.commit()
                     sql_cursor.close()
                     self._queue_error.put(device_id)

python/biopro/server/main.py

@@ -35,7 +35,11 @@ from biopro.project.project_manager import ProjectManager
 from biopro.db.base import Base, Session, engine
 from biopro.db.project_report import ProjectReport
 from biopro.db.project_meta import MetaProjectInfo
-
+# from biopro.db.device import Device
+from biopro.db.recording_data import get_raw_model
+from biopro.db.subject_data import SubjectData
+from biopro.db.meta import RecordingDataMeta
+import random
 
 _RUNTIME_COMPILE = False
 
@@ -328,6 +332,18 @@ class ControlServer(SocketServer, ControlServerAPI):
         finally:
             self.led_thread.set_state(LED.AVAILABLE)
 
+            # version_info = [0, 2, 1, 7, 23, 2]
+            # serial_number = DeviceSerialNumber(version_info[0],
+            #                             version_info[1],
+            #                             version_info[2],
+            #                             version_info[3],
+            #                             version_info[4],
+            #                             version_info[5])
+            # response = DeviceResponseInfo('Elite-EDC', serial_number, (164, 218, 50, 212, 231, 12), addr_type=0)
+            # print('setup done', response)
+            # ret = self.device_manager.connect(response)
+            # print('ret', ret)
+
     def _setup_get_available_channel(self) -> Optional[List[int]]:
         client = self.data_server.client()
 
@@ -557,8 +573,15 @@ class ControlServer(SocketServer, ControlServerAPI):
             response = content
         else:
             response = to_device_info(content)
-
         try:
+            # version_info = [0, 2, 1, 7, 23, 2]
+            # serial_number = DeviceSerialNumber(version_info[0],
+            #                             version_info[1],
+            #                             version_info[2],
+            #                             version_info[3],
+            #                             version_info[4],
+            #                             version_info[5])
+            # response = DeviceResponseInfo('Elite-EDC', serial_number, (164, 218, 50, 212, 231, 12))
             ret = self.device_manager.connect(response)
         except DeviceInstructionError as e:
             '''when device reset fail error'''
@@ -1102,6 +1125,7 @@ class ControlServer(SocketServer, ControlServerAPI):
 
         client = self.data_server.client()
         project = None
+        _project_meta_id = None
         if client is not None:
             info = self.file_manager.use(device)
 
@@ -1114,10 +1138,13 @@ class ControlServer(SocketServer, ControlServerAPI):
                 info = self.file_manager.save(device, filename)
             
             if device.occupied_by_project != None:
-                project = json.dumps(self.project_manager.get(device.occupied_by_project).info_pass_data_server())
-
+                project = self.project_manager.get(device.occupied_by_project).info_pass_data_server()
+                _project_meta_id = MetaProjectInfo.create_project_meta(project)
+                new_project = self.project_manager.get(device.occupied_by_project)
+                new_project.project_meta_id = _project_meta_id
+                
             with client:
-                client.update_device_configuration(device, info.meta_file, value, project)
+                client.update_device_configuration(device, info.meta_file, value, _project_meta_id)
 
     def _device_set_disable_cache(self, device: CompletedDevice, disable):
         if disable:
@@ -1347,6 +1374,57 @@ class ControlServer(SocketServer, ControlServerAPI):
                 } for pkg in PipPackage.list()]
 
             return ret
+        
+        def save_data_to_subject(self, project, meta, device, subject):
+            mode =  device.get_parameter('MODE')
+            library = device.library_name
+            device = {
+                "library": library,
+                "mode": mode
+            }
+
+                # "pattern": {
+                #     "id": number,
+                #     "name": string,
+                #     "parameter": object,
+                # },
+                # "data": {
+                #     "id": list[int],
+                #     "channel: list[int]
+                # }
+
+            with Session() as session:
+                meta_result = session.query(RecordingDataMeta).filter(RecordingDataMeta.project == meta).first()
+                self.mqtt_thread.publish('', json.dumps({
+                    "pattern": {
+                        "id": 4,
+                    },
+                    "data": {
+                        "id": [meta_result.id],
+                        "channel": ['Time', 6]
+                    },
+                    "others": {
+                        "subject": subject,
+                        "device": device,
+                        "project": project,
+                        "project_meta": meta,
+                    }
+                }), analysis= True)
+                # result = session.query(recording_raws).order_by(recording_raws.id.desc()).first()
+                # value = result.data.split(' ')[1:-1:2]
+                # _value = list(map(int, value))
+                # sum_value = sum(_value)
+                # average_value = sum_value / len(_value)
+                # subject_data = SubjectData(
+                #     subject_id= subject['id'],
+                #     project = project,
+                #     meta = meta,
+                #     mode= device,
+                #     data= average_value
+                # )
+                # # Execute the update query
+                # session.add(subject_data)
+                # session.commit()
 
         def _hardware_send_test_hardware(self, section: Optional[str] = None) -> Dict[str, Any]:
             if section is not None:
@@ -1391,7 +1469,6 @@ class ControlServer(SocketServer, ControlServerAPI):
             if client is not None:
                 with client:
                     client.show_data(device)
-
 class _RandomCrashThread(ServerThread):
     def __init__(self):
         super().__init__('Crash')

python/biopro/server/mqtt.py

@@ -170,9 +170,11 @@ class MqttThread(threading.Thread):
         self.sleep(3)
         self._mqtt_client_local.reconnect()
 
-    def publish(self, topic: str, payload: str, inter = False, qos = 2):
+    def publish(self, topic: str, payload: str, inter = False, analysis=False, qos = 2):
         if inter:
             _topic = self.__controller_ID + '_user'
+        elif analysis:
+            _topic = self.__controller_ID + '_data_analysis/get_analysis_data'
         else:
             _topic = self.__controller_ID + '/' + topic
         if self._mqtt_client_local is not None:

update_db_package.sh

@@ -27,3 +27,6 @@ sudo su -c "psql -d postgres -c \"ALTER TABLE IF EXISTS project_report RENAME TO
 
 # change table project_meta column cycle to type jsonb
 sudo su -c "psql -d postgres -c \"ALTER TABLE project_metas ALTER COLUMN cycle type jsonb USING (cycle::jsonb);\"" postgres
+
+# add column subject in project
+sudo su -c "psql -d postgres -c \"ALTER TABLE projects ADD COLUMN IF NOT EXISTS subject JSONB;\"" postgres