From ea1af91fcfb08a59a3fe67c12b7407b2512b0c6e Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Thu, 18 Apr 2024 14:05:37 +0900
Subject: [PATCH 01/21] adjust caiman dependencies

---
 studio/app/optinist/wrappers/caiman/conda/caiman.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/studio/app/optinist/wrappers/caiman/conda/caiman.yaml b/studio/app/optinist/wrappers/caiman/conda/caiman.yaml
index 2166a61bf..844cb2605 100644
--- a/studio/app/optinist/wrappers/caiman/conda/caiman.yaml
+++ b/studio/app/optinist/wrappers/caiman/conda/caiman.yaml
@@ -6,3 +6,4 @@ dependencies:
   - cython
   - numpy=1.22.*
   - caiman>=1.9.9, <=1.9.12
+  - scikit-image=0.19.*

From 6d0277fb86b482f23790d2777634b2451467766a Mon Sep 17 00:00:00 2001
From: Miles D <milesd@Miless-MacBook-Pro.local>
Date: Tue, 4 Jun 2024 09:52:34 +0900
Subject: [PATCH 02/21] Update docs about x86_64 installation

---
 docs/index.rst           |  1 +
 docs/installation/mac.md | 41 ++++++++++++++++++++++++++++++++++------
 2 files changed, 36 insertions(+), 6 deletions(-)

diff --git a/docs/index.rst b/docs/index.rst
index a99d40fd2..33a56812e 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -36,4 +36,5 @@ Main Features
   gui/index
   host_for_multiuser/index
   utils/index
+  utils/nwb_file
   for_developers/index
diff --git a/docs/installation/mac.md b/docs/installation/mac.md
index ff8f3667c..9b2de6330 100644
--- a/docs/installation/mac.md
+++ b/docs/installation/mac.md
@@ -21,15 +21,44 @@ Please follow instructions below.
 
 #### Install Anaconda
 
-- Download and install package.
-  - https://repo.anaconda.com/archive/
-    - Anaconda3-\*.\*-MacOSX-x86_64.pkg
-      - *The latest version of the module is ok.
+- Download and install the package:
+  - [Anaconda Archive](https://repo.anaconda.com/archive/)
+    - Download the latest version: `Anaconda3-*.MacOSX-x86_64.pkg`
+      - *The latest version of the module is fine.*
 
 ```{eval-rst}
 .. caution::
-   Even if you're using arm64 (Apple Sillicon, M1, M2...) architecture's Mac, x86_64 version is required.
-   Some modules cannot be installed by conda install or pip install in arm64 version.
+   Even if you're using arm64 (Apple Silicon, M1, M2...) architecture's Mac, the x86_64 version is required.
+   Some modules cannot be installed by conda install or pip install in the arm64 version.
+   Installing the x86_64 version of conda can be done using `rosetta`.
+
+   1. Install Rosetta using the terminal:
+
+        .. code-block:: bash
+
+          /usr/sbin/softwareupdate --install-rosetta --agree-to-license
+
+   2. Open a Terminal Session in Rosetta:
+      - Open your existing Terminal (which is running natively on ARM).
+      - Start a new Terminal session that emulates the x86_64 architecture using the following command:
+
+        .. code-block:: bash
+
+           arch -x86_64 /usr/bin/env bash
+
+   3. Download and install Miniconda:
+
+        .. code-block:: bash
+
+           curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
+
+           bash Miniconda3-latest-MacOSX-x86_64.sh
+
+           /Users/MYUSERNAME/miniconda3/bin/conda init
+
+           conda activate
+
+   Now continue creating the optinist environment using conda
 ```
 
 ### Create anaconda environment

From c93fa9163d7d9b7dd6c51b24cc0de769c14730b4 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Thu, 6 Jun 2024 21:30:21 +0900
Subject: [PATCH 03/21] improve logger

- enable debug level for optinist-logger
- adjust logging-format
---
 studio/__main_unit__.py              |  5 +++--
 studio/app/common/core/logger.py     | 16 ++++++++++++++--
 studio/config/logging.multiuser.yaml |  6 ++++--
 studio/config/logging.yaml           |  6 ++++--
 4 files changed, 25 insertions(+), 8 deletions(-)

diff --git a/studio/__main_unit__.py b/studio/__main_unit__.py
index 860058c2e..50b4ca7ac 100644
--- a/studio/__main_unit__.py
+++ b/studio/__main_unit__.py
@@ -1,5 +1,4 @@
 import argparse
-import logging
 
 import uvicorn
 from fastapi import Depends, FastAPI, Request
@@ -12,6 +11,7 @@
     get_admin_user,
     get_current_user,
 )
+from studio.app.common.core.logger import AppLogger
 from studio.app.common.core.mode import MODE
 from studio.app.common.core.workspace.workspace_dependencies import (
     is_workspace_available,
@@ -91,7 +91,8 @@ def skip_dependencies():
 @app.on_event("startup")
 async def startup_event():
     mode = "standalone" if MODE.IS_STANDALONE else "multiuser"
-    logging.info(f'"Studio" application startup complete. [mode: {mode}]')
+    logger = AppLogger.get_logger()
+    logger.info(f'"Studio" application startup complete. [mode: {mode}]')
 
 
 @app.get("/is_standalone", response_model=bool, tags=["others"])
diff --git a/studio/app/common/core/logger.py b/studio/app/common/core/logger.py
index 6b6a1b00c..6fba22f5c 100644
--- a/studio/app/common/core/logger.py
+++ b/studio/app/common/core/logger.py
@@ -1,5 +1,6 @@
 import logging
 import logging.config
+import os
 
 import yaml
 
@@ -12,7 +13,7 @@ class AppLogger:
     Generic Application Logger
     """
 
-    LOGGER_NAME = None  # Note: use root logger (empty name)
+    LOGGER_NAME = "optinist"
 
     @staticmethod
     def init_logger():
@@ -39,7 +40,18 @@ def init_logger():
         )
 
         with open(log_config_file) as file:
-            logging.config.dictConfig(yaml.load(file.read(), yaml.FullLoader))
+            log_config = yaml.load(file.read(), yaml.FullLoader)
+
+            # create log output directory (if none exists)
+            log_file = (
+                log_config.get("handlers", {}).get("rotating_file", {}).get("filename")
+            )
+            if log_file:
+                log_dir = os.path.dirname(log_file)
+                if not os.path.isdir(log_dir):
+                    os.makedirs(log_dir)
+
+            logging.config.dictConfig(log_config)
 
     @staticmethod
     def get_logger():
diff --git a/studio/config/logging.multiuser.yaml b/studio/config/logging.multiuser.yaml
index eb8025bb8..5341f1b41 100644
--- a/studio/config/logging.multiuser.yaml
+++ b/studio/config/logging.multiuser.yaml
@@ -3,10 +3,10 @@ disable_existing_loggers: false
 formatters:
   default:
     (): "uvicorn.logging.DefaultFormatter"
-    fmt: "%(asctime)s %(levelprefix)s %(funcName)s():%(lineno)d - %(message)s"
+    fmt: "%(asctime)s %(levelprefix)s [%(name)s] %(funcName)s():%(lineno)d - %(message)s"
   access:
     (): "uvicorn.logging.AccessFormatter"
-    fmt: "%(asctime)s %(levelprefix)s %(funcName)s():%(lineno)d - %(message)s"
+    fmt: "%(asctime)s %(levelprefix)s [%(name)s] %(funcName)s():%(lineno)d - %(message)s"
 handlers:
   console:
     class: logging.StreamHandler
@@ -21,6 +21,8 @@ handlers:
     interval: 1
     backupCount: 365
 loggers:
+  optinist:
+    level: DEBUG
   snakemake:
     level: INFO
     handlers: [rotating_file]
diff --git a/studio/config/logging.yaml b/studio/config/logging.yaml
index fef5dbc37..0e5113d74 100644
--- a/studio/config/logging.yaml
+++ b/studio/config/logging.yaml
@@ -3,16 +3,18 @@ disable_existing_loggers: false
 formatters:
   default:
     (): "uvicorn.logging.DefaultFormatter"
-    fmt: "%(asctime)s %(levelprefix)s %(funcName)s():%(lineno)d - %(message)s"
+    fmt: "%(asctime)s %(levelprefix)s [%(name)s] %(funcName)s():%(lineno)d - %(message)s"
   access:
     (): "uvicorn.logging.AccessFormatter"
-    fmt: "%(asctime)s %(levelprefix)s %(funcName)s():%(lineno)d - %(message)s"
+    fmt: "%(asctime)s %(levelprefix)s [%(name)s] %(funcName)s():%(lineno)d - %(message)s"
 handlers:
   console:
     class: logging.StreamHandler
     level: DEBUG
     formatter: default
 loggers:
+  optinist:
+    level: DEBUG
   snakemake:
     level: INFO
     handlers: [console]

From e2f3db9b04b112dcbf7152c685128f2995160b15 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Fri, 7 Jun 2024 09:47:19 +0900
Subject: [PATCH 04/21] add rule name for each rules

---
 studio/app/Snakefile | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/studio/app/Snakefile b/studio/app/Snakefile
index bf3a37748..afaa90a2e 100644
--- a/studio/app/Snakefile
+++ b/studio/app/Snakefile
@@ -26,6 +26,8 @@ else:
             FILETYPE.MICROSCOPE,
         ]:
             rule:
+                name:
+                    rule_name
                 input:
                     SmkUtils.input(details)
                 output:
@@ -36,6 +38,8 @@ else:
                     f"{DIRPATH.APP_DIR}/common/core/rules/data.py"
         else:
             rule:
+                name:
+                    rule_name
                 input:
                     SmkUtils.input(details)
                 output:

From 7a8d082a2ef0e90d06a0949555c35b3b86d20341 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Fri, 7 Jun 2024 09:50:54 +0900
Subject: [PATCH 05/21] add validation for node input data

---
 studio/app/common/core/rules/runner.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/studio/app/common/core/rules/runner.py b/studio/app/common/core/rules/runner.py
index 6961ef004..ab4bdf1cf 100644
--- a/studio/app/common/core/rules/runner.py
+++ b/studio/app/common/core/rules/runner.py
@@ -150,6 +150,10 @@ def read_input_info(cls, input_files):
         input_info = {}
         for filepath in input_files:
             load_data = PickleReader.read(filepath)
+
+            # validate load_data content
+            assert type(load_data) is dict, "Invalid node input data content."
+
             merged_nwb = cls.deep_merge(
                 load_data.pop("nwbfile", {}), input_info.pop("nwbfile", {})
             )

From c580332f90aafb9a53b2f101d499976c9519ef90 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Fri, 7 Jun 2024 14:14:19 +0900
Subject: [PATCH 06/21] refactor snakemake modules

- improve error message
- use constants
---
 studio/app/common/core/rules/runner.py             | 4 +++-
 studio/app/common/core/snakemake/snakemake_rule.py | 8 +++++---
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/studio/app/common/core/rules/runner.py b/studio/app/common/core/rules/runner.py
index ab4bdf1cf..cb30d4c9b 100644
--- a/studio/app/common/core/rules/runner.py
+++ b/studio/app/common/core/rules/runner.py
@@ -152,7 +152,9 @@ def read_input_info(cls, input_files):
             load_data = PickleReader.read(filepath)
 
             # validate load_data content
-            assert type(load_data) is dict, "Invalid node input data content."
+            assert (
+                type(load_data) is dict
+            ), f"Invalid node input data content. [{filepath}]"
 
             merged_nwb = cls.deep_merge(
                 load_data.pop("nwbfile", {}), input_info.pop("nwbfile", {})
diff --git a/studio/app/common/core/snakemake/snakemake_rule.py b/studio/app/common/core/snakemake/snakemake_rule.py
index 5aff39666..e09217afc 100644
--- a/studio/app/common/core/snakemake/snakemake_rule.py
+++ b/studio/app/common/core/snakemake/snakemake_rule.py
@@ -44,14 +44,16 @@ def __init__(
         )
 
     def image(self) -> Rule:
-        return self.builder.set_type("image").build()
+        return self.builder.set_type(FILETYPE.IMAGE).build()
 
-    def csv(self, nodeType="csv") -> Rule:
+    def csv(self, nodeType=FILETYPE.CSV) -> Rule:
         return self.builder.set_type(nodeType).build()
 
     def hdf5(self) -> Rule:
         return (
-            self.builder.set_type("hdf5").set_hdf5Path(self._node.data.hdf5Path).build()
+            self.builder.set_type(FILETYPE.HDF5)
+            .set_hdf5Path(self._node.data.hdf5Path)
+            .build()
         )
 
     def mat(self) -> Rule:

From a37bf5eb67d5b1a7660e4a4dab65a890a93df2a4 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Thu, 13 Jun 2024 17:10:26 +0900
Subject: [PATCH 07/21] improve workflow runner

- Clarify definition and determination of NodeType (Data or Algo)
---
 studio/app/Snakefile                          | 11 +--
 studio/app/common/core/rules/data.py          | 19 ++---
 studio/app/common/core/snakemake/smk_utils.py | 25 ++----
 studio/app/common/core/workflow/workflow.py   | 44 +++++++++-
 .../common/core/workflow/workflow_runner.py   | 83 ++++++-------------
 5 files changed, 88 insertions(+), 94 deletions(-)

diff --git a/studio/app/Snakefile b/studio/app/Snakefile
index afaa90a2e..ac7f1cc17 100644
--- a/studio/app/Snakefile
+++ b/studio/app/Snakefile
@@ -1,9 +1,9 @@
 from studio.app.common.core.snakemake.smk_utils import SmkUtils
 from studio.app.common.core.utils.filepath_creater import join_filepath
 from studio.app.optinist.core.edit_ROI import EditRoiUtils
-from studio.app.const import FILETYPE
 from studio.app.dir_path import DIRPATH
 
+from studio.app.common.core.workflow.workflow import NodeType
 
 if config.get('type') == "EDIT_ROI":
     rule edit_ROI:
@@ -17,14 +17,7 @@ else:
 
 
     for rule_name, details in config["rules"].items():
-        if details["type"] in [
-            FILETYPE.IMAGE,
-            FILETYPE.CSV,
-            FILETYPE.BEHAVIOR,
-            FILETYPE.HDF5,
-            FILETYPE.MATLAB,
-            FILETYPE.MICROSCOPE,
-        ]:
+        if NodeType.check_nodetype_from_filetype(details["type"]) == NodeType.DATA:
             rule:
                 name:
                     rule_name
diff --git a/studio/app/common/core/rules/data.py b/studio/app/common/core/rules/data.py
index c8c3da363..01ec47e92 100644
--- a/studio/app/common/core/rules/data.py
+++ b/studio/app/common/core/rules/data.py
@@ -12,22 +12,21 @@
 from studio.app.common.core.rules.file_writer import FileWriter
 from studio.app.common.core.snakemake.snakemake_reader import RuleConfigReader
 from studio.app.common.core.utils.pickle_handler import PickleWriter
+from studio.app.common.core.workflow.workflow import NodeType
 from studio.app.const import FILETYPE
 
 if __name__ == "__main__":
     last_output = snakemake.config["last_output"]
 
     rule_config = RuleConfigReader.read(snakemake.params.name)
-    if rule_config.type in [FILETYPE.IMAGE]:
-        rule_config.input = snakemake.input
-    elif rule_config.type in [
-        FILETYPE.CSV,
-        FILETYPE.BEHAVIOR,
-        FILETYPE.HDF5,
-        FILETYPE.MATLAB,
-        FILETYPE.MICROSCOPE,
-    ]:
-        rule_config.input = snakemake.input[0]
+
+    if NodeType.check_nodetype_from_filetype(rule_config.type) == NodeType.DATA:
+        if rule_config.type in [FILETYPE.IMAGE]:
+            rule_config.input = snakemake.input
+        else:
+            rule_config.input = snakemake.input[0]
+    else:
+        assert False, f"Invalid rule type: {rule_config.type}"
 
     rule_config.output = snakemake.output[0]
 
diff --git a/studio/app/common/core/snakemake/smk_utils.py b/studio/app/common/core/snakemake/smk_utils.py
index c7484f9fe..91e03f978 100644
--- a/studio/app/common/core/snakemake/smk_utils.py
+++ b/studio/app/common/core/snakemake/smk_utils.py
@@ -2,6 +2,7 @@
 
 from studio.app.common.core.utils.filepath_creater import join_filepath
 from studio.app.common.core.utils.filepath_finder import find_condaenv_filepath
+from studio.app.common.core.workflow.workflow import NodeType
 from studio.app.const import FILETYPE
 from studio.app.dir_path import DIRPATH
 from studio.app.wrappers import wrapper_dict
@@ -10,16 +11,11 @@
 class SmkUtils:
     @classmethod
     def input(cls, details):
-        if details["type"] in [FILETYPE.IMAGE]:
-            return [join_filepath([DIRPATH.INPUT_DIR, x]) for x in details["input"]]
-        elif details["type"] in [
-            FILETYPE.CSV,
-            FILETYPE.BEHAVIOR,
-            FILETYPE.HDF5,
-            FILETYPE.MATLAB,
-            FILETYPE.MICROSCOPE,
-        ]:
-            return join_filepath([DIRPATH.INPUT_DIR, details["input"]])
+        if NodeType.check_nodetype_from_filetype(details["type"]) == NodeType.DATA:
+            if details["type"] in [FILETYPE.IMAGE]:
+                return [join_filepath([DIRPATH.INPUT_DIR, x]) for x in details["input"]]
+            else:
+                return join_filepath([DIRPATH.INPUT_DIR, details["input"]])
         else:
             return [join_filepath([DIRPATH.OUTPUT_DIR, x]) for x in details["input"]]
 
@@ -29,14 +25,7 @@ def output(cls, details):
 
     @classmethod
     def conda(cls, details):
-        if details["type"] in [
-            FILETYPE.IMAGE,
-            FILETYPE.CSV,
-            FILETYPE.BEHAVIOR,
-            FILETYPE.HDF5,
-            FILETYPE.MATLAB,
-            FILETYPE.MICROSCOPE,
-        ]:
+        if NodeType.check_nodetype_from_filetype(details["type"]) == NodeType.DATA:
             return None
 
         wrapper = cls.dict2leaf(wrapper_dict, details["path"].split("/"))
diff --git a/studio/app/common/core/workflow/workflow.py b/studio/app/common/core/workflow/workflow.py
index e7efd7979..b21b7ae96 100644
--- a/studio/app/common/core/workflow/workflow.py
+++ b/studio/app/common/core/workflow/workflow.py
@@ -4,19 +4,61 @@
 from pydantic import BaseModel
 
 from studio.app.common.core.snakemake.smk import ForceRun
+from studio.app.const import FILETYPE
 
 
 @dataclass
 class NodeType:
+    # Data Types
     IMAGE: str = "ImageFileNode"
     CSV: str = "CsvFileNode"
     FLUO: str = "FluoFileNode"
     BEHAVIOR: str = "BehaviorFileNode"
     HDF5: str = "HDF5FileNode"
-    MAT: str = "MatlabFileNode"
+    MATLAB: str = "MatlabFileNode"
     MICROSCOPE: str = "MicroscopeFileNode"
+    # Data Type (Includs above DataType Nodes)
+    DATA: str = "DataNode"
+    # Algo Type
     ALGO: str = "AlgorithmNode"
 
+    @classmethod
+    def check_nodetype(cls, node_type: str) -> str:
+        """
+        Check NodeType (DATA or ALGO) from detailed node type
+        """
+        if node_type in [
+            cls.IMAGE,
+            cls.CSV,
+            cls.FLUO,
+            cls.BEHAVIOR,
+            cls.HDF5,
+            cls.MATLAB,
+            cls.MICROSCOPE,
+        ]:
+            return cls.DATA
+        elif node_type == cls.ALGO:
+            return cls.ALGO
+        else:
+            None
+
+    @classmethod
+    def check_nodetype_from_filetype(cls, file_type: str) -> str:
+        """
+        Check NodeType (DATA or ALGO) from file type
+        """
+        if file_type in [
+            FILETYPE.IMAGE,
+            FILETYPE.CSV,
+            FILETYPE.BEHAVIOR,
+            FILETYPE.HDF5,
+            FILETYPE.MATLAB,
+            FILETYPE.MICROSCOPE,
+        ]:
+            return cls.DATA
+        else:
+            None
+
 
 @dataclass
 class OutputType:
diff --git a/studio/app/common/core/workflow/workflow_runner.py b/studio/app/common/core/workflow/workflow_runner.py
index c11116cfd..f6ef40dd5 100644
--- a/studio/app/common/core/workflow/workflow_runner.py
+++ b/studio/app/common/core/workflow/workflow_runner.py
@@ -78,76 +78,47 @@ def rulefile(self):
         last_outputs = []
 
         for node in self.nodeDict.values():
-            if node.type == NodeType.IMAGE:
-                rule_dict[node.id] = SmkRule(
+            if NodeType.check_nodetype(node.type) == NodeType.DATA:
+                data_common_rule = SmkRule(
                     workspace_id=self.workspace_id,
                     unique_id=self.unique_id,
                     node=node,
                     edgeDict=self.edgeDict,
                     nwbfile=nwbfile,
-                ).image()
-            elif node.type == NodeType.CSV:
-                rule_dict[node.id] = SmkRule(
-                    workspace_id=self.workspace_id,
-                    unique_id=self.unique_id,
-                    node=node,
-                    edgeDict=self.edgeDict,
-                    nwbfile=nwbfile,
-                ).csv()
-            elif node.type == NodeType.FLUO:
-                rule_dict[node.id] = SmkRule(
-                    workspace_id=self.workspace_id,
-                    unique_id=self.unique_id,
-                    node=node,
-                    edgeDict=self.edgeDict,
-                    nwbfile=nwbfile,
-                ).csv()
-            elif node.type == NodeType.BEHAVIOR:
-                rule_dict[node.id] = SmkRule(
-                    workspace_id=self.workspace_id,
-                    unique_id=self.unique_id,
-                    node=node,
-                    edgeDict=self.edgeDict,
-                    nwbfile=nwbfile,
-                ).csv(nodeType="behavior")
-            elif node.type == NodeType.HDF5:
-                rule_dict[node.id] = SmkRule(
-                    workspace_id=self.workspace_id,
-                    unique_id=self.unique_id,
-                    node=node,
-                    edgeDict=self.edgeDict,
-                    nwbfile=nwbfile,
-                ).hdf5()
-            elif node.type == NodeType.MAT:
-                rule_dict[node.id] = SmkRule(
-                    workspace_id=self.workspace_id,
-                    unique_id=self.unique_id,
-                    node=node,
-                    edgeDict=self.edgeDict,
-                    nwbfile=nwbfile,
-                ).mat()
-            elif node.type == NodeType.MICROSCOPE:
-                rule_dict[node.id] = SmkRule(
-                    workspace_id=self.workspace_id,
-                    unique_id=self.unique_id,
-                    node=node,
-                    edgeDict=self.edgeDict,
-                    nwbfile=nwbfile,
-                ).microscope()
-            elif node.type == NodeType.ALGO:
-                rule = SmkRule(
+                )
+                data_rule = None
+
+                if node.type == NodeType.IMAGE:
+                    data_rule = data_common_rule.image()
+                elif node.type == NodeType.CSV:
+                    data_rule = data_common_rule.csv()
+                elif node.type == NodeType.FLUO:
+                    data_rule = data_common_rule.csv()
+                elif node.type == NodeType.BEHAVIOR:
+                    data_rule = data_common_rule.csv(nodeType="behavior")
+                elif node.type == NodeType.HDF5:
+                    data_rule = data_common_rule.hdf5()
+                elif node.type == NodeType.MATLAB:
+                    data_rule = data_common_rule.mat()
+                elif node.type == NodeType.MICROSCOPE:
+                    data_rule = data_common_rule.microscope()
+
+                rule_dict[node.id] = data_rule
+
+            elif NodeType.check_nodetype(node.type) == NodeType.ALGO:
+                algo_rule = SmkRule(
                     workspace_id=self.workspace_id,
                     unique_id=self.unique_id,
                     node=node,
                     edgeDict=self.edgeDict,
                 ).algo(nodeDict=self.nodeDict)
 
-                rule_dict[node.id] = rule
+                rule_dict[node.id] = algo_rule
 
                 if node.id in endNodeList:
-                    last_outputs.append(rule.output)
+                    last_outputs.append(algo_rule.output)
             else:
-                assert False, "NodeType doesn't exists"
+                assert False, f"NodeType doesn't exists: {node.type}"
 
         return rule_dict, last_outputs
 

From dcc791dd40b81030a4f4b323602cb297ff030f75 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Thu, 13 Jun 2024 17:40:08 +0900
Subject: [PATCH 08/21] improve workflow runner

- Clarify definition and determination of NodeType (Data or Algo)
---
 studio/app/Snakefile                          |  4 +--
 studio/app/common/core/rules/data.py          | 14 ++++----
 studio/app/common/core/snakemake/smk_utils.py |  6 ++--
 studio/app/common/core/workflow/workflow.py   | 34 +++++++++++--------
 .../common/core/workflow/workflow_runner.py   |  6 ++--
 5 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/studio/app/Snakefile b/studio/app/Snakefile
index ac7f1cc17..a94bc9183 100644
--- a/studio/app/Snakefile
+++ b/studio/app/Snakefile
@@ -3,7 +3,7 @@ from studio.app.common.core.utils.filepath_creater import join_filepath
 from studio.app.optinist.core.edit_ROI import EditRoiUtils
 from studio.app.dir_path import DIRPATH
 
-from studio.app.common.core.workflow.workflow import NodeType
+from studio.app.common.core.workflow.workflow import NodeType, NodeTypeUtil
 
 if config.get('type') == "EDIT_ROI":
     rule edit_ROI:
@@ -17,7 +17,7 @@ else:
 
 
     for rule_name, details in config["rules"].items():
-        if NodeType.check_nodetype_from_filetype(details["type"]) == NodeType.DATA:
+        if NodeTypeUtil.check_nodetype_from_filetype(details["type"]) == NodeType.DATA:
             rule:
                 name:
                     rule_name
diff --git a/studio/app/common/core/rules/data.py b/studio/app/common/core/rules/data.py
index 01ec47e92..686defe07 100644
--- a/studio/app/common/core/rules/data.py
+++ b/studio/app/common/core/rules/data.py
@@ -12,7 +12,7 @@
 from studio.app.common.core.rules.file_writer import FileWriter
 from studio.app.common.core.snakemake.snakemake_reader import RuleConfigReader
 from studio.app.common.core.utils.pickle_handler import PickleWriter
-from studio.app.common.core.workflow.workflow import NodeType
+from studio.app.common.core.workflow.workflow import NodeType, NodeTypeUtil
 from studio.app.const import FILETYPE
 
 if __name__ == "__main__":
@@ -20,7 +20,7 @@
 
     rule_config = RuleConfigReader.read(snakemake.params.name)
 
-    if NodeType.check_nodetype_from_filetype(rule_config.type) == NodeType.DATA:
+    if NodeTypeUtil.check_nodetype_from_filetype(rule_config.type) == NodeType.DATA:
         if rule_config.type in [FILETYPE.IMAGE]:
             rule_config.input = snakemake.input
         else:
@@ -30,18 +30,18 @@
 
     rule_config.output = snakemake.output[0]
 
+    outputfile = None
     if rule_config.type in [FILETYPE.CSV, FILETYPE.BEHAVIOR]:
         outputfile = FileWriter.csv(rule_config, rule_config.type)
-        PickleWriter.write(rule_config.output, outputfile)
     elif rule_config.type == FILETYPE.IMAGE:
         outputfile = FileWriter.image(rule_config)
-        PickleWriter.write(rule_config.output, outputfile)
     elif rule_config.type == FILETYPE.HDF5:
         outputfile = FileWriter.hdf5(rule_config)
-        PickleWriter.write(rule_config.output, outputfile)
     elif rule_config.type == FILETYPE.MATLAB:
         outputfile = FileWriter.mat(rule_config)
-        PickleWriter.write(rule_config.output, outputfile)
     elif rule_config.type == FILETYPE.MICROSCOPE:
         outputfile = FileWriter.microscope(rule_config)
-        PickleWriter.write(rule_config.output, outputfile)
+    else:
+        assert False, f"Invalid file type: {rule_config.type}"
+
+    PickleWriter.write(rule_config.output, outputfile)
diff --git a/studio/app/common/core/snakemake/smk_utils.py b/studio/app/common/core/snakemake/smk_utils.py
index 91e03f978..c26bc2415 100644
--- a/studio/app/common/core/snakemake/smk_utils.py
+++ b/studio/app/common/core/snakemake/smk_utils.py
@@ -2,7 +2,7 @@
 
 from studio.app.common.core.utils.filepath_creater import join_filepath
 from studio.app.common.core.utils.filepath_finder import find_condaenv_filepath
-from studio.app.common.core.workflow.workflow import NodeType
+from studio.app.common.core.workflow.workflow import NodeType, NodeTypeUtil
 from studio.app.const import FILETYPE
 from studio.app.dir_path import DIRPATH
 from studio.app.wrappers import wrapper_dict
@@ -11,7 +11,7 @@
 class SmkUtils:
     @classmethod
     def input(cls, details):
-        if NodeType.check_nodetype_from_filetype(details["type"]) == NodeType.DATA:
+        if NodeTypeUtil.check_nodetype_from_filetype(details["type"]) == NodeType.DATA:
             if details["type"] in [FILETYPE.IMAGE]:
                 return [join_filepath([DIRPATH.INPUT_DIR, x]) for x in details["input"]]
             else:
@@ -25,7 +25,7 @@ def output(cls, details):
 
     @classmethod
     def conda(cls, details):
-        if NodeType.check_nodetype_from_filetype(details["type"]) == NodeType.DATA:
+        if NodeTypeUtil.check_nodetype_from_filetype(details["type"]) == NodeType.DATA:
             return None
 
         wrapper = cls.dict2leaf(wrapper_dict, details["path"].split("/"))
diff --git a/studio/app/common/core/workflow/workflow.py b/studio/app/common/core/workflow/workflow.py
index b21b7ae96..8d5935083 100644
--- a/studio/app/common/core/workflow/workflow.py
+++ b/studio/app/common/core/workflow/workflow.py
@@ -17,33 +17,37 @@ class NodeType:
     HDF5: str = "HDF5FileNode"
     MATLAB: str = "MatlabFileNode"
     MICROSCOPE: str = "MicroscopeFileNode"
+
     # Data Type (Includs above DataType Nodes)
     DATA: str = "DataNode"
+
     # Algo Type
     ALGO: str = "AlgorithmNode"
 
-    @classmethod
-    def check_nodetype(cls, node_type: str) -> str:
+
+class NodeTypeUtil:
+    @staticmethod
+    def check_nodetype(node_type: str) -> str:
         """
         Check NodeType (DATA or ALGO) from detailed node type
         """
         if node_type in [
-            cls.IMAGE,
-            cls.CSV,
-            cls.FLUO,
-            cls.BEHAVIOR,
-            cls.HDF5,
-            cls.MATLAB,
-            cls.MICROSCOPE,
+            NodeType.IMAGE,
+            NodeType.CSV,
+            NodeType.FLUO,
+            NodeType.BEHAVIOR,
+            NodeType.HDF5,
+            NodeType.MATLAB,
+            NodeType.MICROSCOPE,
         ]:
-            return cls.DATA
-        elif node_type == cls.ALGO:
-            return cls.ALGO
+            return NodeType.DATA
+        elif node_type == NodeType.ALGO:
+            return NodeType.ALGO
         else:
             None
 
-    @classmethod
-    def check_nodetype_from_filetype(cls, file_type: str) -> str:
+    @staticmethod
+    def check_nodetype_from_filetype(file_type: str) -> str:
         """
         Check NodeType (DATA or ALGO) from file type
         """
@@ -55,7 +59,7 @@ def check_nodetype_from_filetype(cls, file_type: str) -> str:
             FILETYPE.MATLAB,
             FILETYPE.MICROSCOPE,
         ]:
-            return cls.DATA
+            return NodeType.DATA
         else:
             None
 
diff --git a/studio/app/common/core/workflow/workflow_runner.py b/studio/app/common/core/workflow/workflow_runner.py
index f6ef40dd5..bde1fc107 100644
--- a/studio/app/common/core/workflow/workflow_runner.py
+++ b/studio/app/common/core/workflow/workflow_runner.py
@@ -10,7 +10,7 @@
 from studio.app.common.core.snakemake.snakemake_reader import SmkParamReader
 from studio.app.common.core.snakemake.snakemake_rule import SmkRule
 from studio.app.common.core.snakemake.snakemake_writer import SmkConfigWriter
-from studio.app.common.core.workflow.workflow import NodeType, RunItem
+from studio.app.common.core.workflow.workflow import NodeType, NodeTypeUtil, RunItem
 from studio.app.common.core.workflow.workflow_params import get_typecheck_params
 from studio.app.common.core.workflow.workflow_reader import WorkflowConfigReader
 from studio.app.common.core.workflow.workflow_writer import WorkflowConfigWriter
@@ -78,7 +78,7 @@ def rulefile(self):
         last_outputs = []
 
         for node in self.nodeDict.values():
-            if NodeType.check_nodetype(node.type) == NodeType.DATA:
+            if NodeTypeUtil.check_nodetype(node.type) == NodeType.DATA:
                 data_common_rule = SmkRule(
                     workspace_id=self.workspace_id,
                     unique_id=self.unique_id,
@@ -105,7 +105,7 @@ def rulefile(self):
 
                 rule_dict[node.id] = data_rule
 
-            elif NodeType.check_nodetype(node.type) == NodeType.ALGO:
+            elif NodeTypeUtil.check_nodetype(node.type) == NodeType.ALGO:
                 algo_rule = SmkRule(
                     workspace_id=self.workspace_id,
                     unique_id=self.unique_id,

From 6e4e2074cf77d339cf38581f02f44df265917718 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Thu, 13 Jun 2024 19:25:46 +0900
Subject: [PATCH 09/21] refactor ACCEPT_FILE_EXT

Use Enum, simplify implementation
---
 studio/app/common/routers/files.py   | 35 +++++++++++-----------------
 studio/app/common/routers/outputs.py |  4 ++--
 studio/app/const.py                  | 15 ++++++++----
 3 files changed, 25 insertions(+), 29 deletions(-)

diff --git a/studio/app/common/routers/files.py b/studio/app/common/routers/files.py
index 87cc459c9..1e2e80392 100644
--- a/studio/app/common/routers/files.py
+++ b/studio/app/common/routers/files.py
@@ -27,14 +27,7 @@
     FilePath,
     TreeNode,
 )
-from studio.app.const import (
-    ACCEPT_CSV_EXT,
-    ACCEPT_HDF5_EXT,
-    ACCEPT_MATLAB_EXT,
-    ACCEPT_MICROSCOPE_EXT,
-    ACCEPT_TIFF_EXT,
-    FILETYPE,
-)
+from studio.app.const import ACCEPT_FILE_EXT, FILETYPE
 from studio.app.dir_path import DIRPATH
 
 router = APIRouter(prefix="/files", tags=["files"])
@@ -61,7 +54,9 @@ def get_tree(
         )
 
         IMAGE_SHAPE_DICT = (
-            get_image_shape_dict(workspace_id) if file_types == ACCEPT_TIFF_EXT else {}
+            get_image_shape_dict(workspace_id)
+            if file_types == ACCEPT_FILE_EXT.TIFF_EXT.value
+            else {}
         )
 
         for node_name in sorted_listdir:
@@ -74,7 +69,7 @@ def get_tree(
 
             if os.path.isfile(search_dirpath) and node_name.endswith(tuple(file_types)):
                 shape = IMAGE_SHAPE_DICT.get(relative_path, {}).get("shape")
-                if shape is None and file_types == ACCEPT_TIFF_EXT:
+                if shape is None and file_types == ACCEPT_FILE_EXT.TIFF_EXT.value:
                     shape = update_image_shape(workspace_id, relative_path)
                 nodes.append(
                     TreeNode(
@@ -152,15 +147,17 @@ def update_image_shape(workspace_id, relative_file_path):
 )
 async def get_files(workspace_id: str, file_type: str = None):
     if file_type == FILETYPE.IMAGE:
-        return DirTreeGetter.get_tree(workspace_id, ACCEPT_TIFF_EXT)
+        return DirTreeGetter.get_tree(workspace_id, ACCEPT_FILE_EXT.TIFF_EXT.value)
     elif file_type == FILETYPE.CSV:
-        return DirTreeGetter.get_tree(workspace_id, ACCEPT_CSV_EXT)
+        return DirTreeGetter.get_tree(workspace_id, ACCEPT_FILE_EXT.CSV_EXT.value)
     elif file_type == FILETYPE.HDF5:
-        return DirTreeGetter.get_tree(workspace_id, ACCEPT_HDF5_EXT)
+        return DirTreeGetter.get_tree(workspace_id, ACCEPT_FILE_EXT.HDF5_EXT.value)
     elif file_type == FILETYPE.MICROSCOPE:
-        return DirTreeGetter.get_tree(workspace_id, ACCEPT_MICROSCOPE_EXT)
+        return DirTreeGetter.get_tree(
+            workspace_id, ACCEPT_FILE_EXT.MICROSCOPE_EXT.value
+        )
     elif file_type == FILETYPE.MATLAB:
-        return DirTreeGetter.get_tree(workspace_id, ACCEPT_MATLAB_EXT)
+        return DirTreeGetter.get_tree(workspace_id, ACCEPT_FILE_EXT.MATLAB_EXT.value)
     else:
         return []
 
@@ -222,13 +219,7 @@ async def download_file(
     background_tasks: BackgroundTasks,
 ):
     path = PurePath(urlparse(file.url).path)
-    if path.suffix not in {
-        *ACCEPT_CSV_EXT,
-        *ACCEPT_HDF5_EXT,
-        *ACCEPT_TIFF_EXT,
-        *ACCEPT_MATLAB_EXT,
-        *ACCEPT_MICROSCOPE_EXT,
-    }:
+    if path.suffix not in ACCEPT_FILE_EXT.AlL_EXT.value:
         raise HTTPException(status_code=400, detail="Invalid url")
 
     create_directory(join_filepath([DIRPATH.INPUT_DIR, workspace_id]))
diff --git a/studio/app/common/routers/outputs.py b/studio/app/common/routers/outputs.py
index 850ed4d4c..d82587363 100644
--- a/studio/app/common/routers/outputs.py
+++ b/studio/app/common/routers/outputs.py
@@ -12,7 +12,7 @@
 )
 from studio.app.common.core.utils.json_writer import JsonWriter, save_tiff2json
 from studio.app.common.schemas.outputs import JsonTimeSeriesData, OutputData
-from studio.app.const import ACCEPT_TIFF_EXT
+from studio.app.const import ACCEPT_FILE_EXT
 from studio.app.dir_path import DIRPATH
 
 router = APIRouter(prefix="/outputs", tags=["outputs"])
@@ -121,7 +121,7 @@ async def get_image(
     end_index: Optional[int] = 10,
 ):
     filename, ext = os.path.splitext(os.path.basename(filepath))
-    if ext in ACCEPT_TIFF_EXT:
+    if ext in ACCEPT_FILE_EXT.TIFF_EXT.value:
         if not filepath.startswith(join_filepath([DIRPATH.OUTPUT_DIR, workspace_id])):
             filepath = join_filepath([DIRPATH.INPUT_DIR, workspace_id, filepath])
 
diff --git a/studio/app/const.py b/studio/app/const.py
index dab8efa67..d2a846761 100644
--- a/studio/app/const.py
+++ b/studio/app/const.py
@@ -1,4 +1,5 @@
 from dataclasses import dataclass
+from enum import Enum
 
 
 @dataclass
@@ -11,11 +12,15 @@ class FILETYPE:
     MICROSCOPE: str = "microscope"
 
 
-ACCEPT_TIFF_EXT = [".tif", ".tiff", ".TIF", ".TIFF"]
-ACCEPT_CSV_EXT = [".csv"]
-ACCEPT_HDF5_EXT = [".hdf5", ".nwb", ".HDF5", ".NWB"]
-ACCEPT_MATLAB_EXT = [".mat"]
-ACCEPT_MICROSCOPE_EXT = [".nd2", ".oir", ".isxd", ".thor.zip"]
+class ACCEPT_FILE_EXT(Enum):
+    TIFF_EXT = [".tif", ".tiff", ".TIF", ".TIFF"]
+    CSV_EXT = [".csv"]
+    HDF5_EXT = [".hdf5", ".nwb", ".HDF5", ".NWB"]
+    MATLAB_EXT = [".mat"]
+    MICROSCOPE_EXT = [".nd2", ".oir", ".isxd", ".thor.zip"]
+
+    AlL_EXT = TIFF_EXT + CSV_EXT + HDF5_EXT + MATLAB_EXT + MICROSCOPE_EXT
+
 
 NOT_DISPLAY_ARGS_LIST = ["params", "output_dir", "nwbfile", "kwargs"]
 

From a71045ae97486c2951ee9ef2a723760e94bfe70d Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Thu, 13 Jun 2024 20:07:48 +0900
Subject: [PATCH 10/21] fix typo

---
 studio/app/common/core/workflow/workflow.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/studio/app/common/core/workflow/workflow.py b/studio/app/common/core/workflow/workflow.py
index 8d5935083..df310ed3c 100644
--- a/studio/app/common/core/workflow/workflow.py
+++ b/studio/app/common/core/workflow/workflow.py
@@ -18,7 +18,7 @@ class NodeType:
     MATLAB: str = "MatlabFileNode"
     MICROSCOPE: str = "MicroscopeFileNode"
 
-    # Data Type (Includs above DataType Nodes)
+    # Data Type (Includes above DataType Nodes)
     DATA: str = "DataNode"
 
     # Algo Type

From 2e157a0801aecc0738e7e6b7d438101096dd8d96 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Thu, 13 Jun 2024 22:32:06 +0900
Subject: [PATCH 11/21] fix typo

---
 studio/app/common/routers/files.py | 2 +-
 studio/app/const.py                | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/studio/app/common/routers/files.py b/studio/app/common/routers/files.py
index 1e2e80392..6ed572b22 100644
--- a/studio/app/common/routers/files.py
+++ b/studio/app/common/routers/files.py
@@ -219,7 +219,7 @@ async def download_file(
     background_tasks: BackgroundTasks,
 ):
     path = PurePath(urlparse(file.url).path)
-    if path.suffix not in ACCEPT_FILE_EXT.AlL_EXT.value:
+    if path.suffix not in ACCEPT_FILE_EXT.ALL_EXT.value:
         raise HTTPException(status_code=400, detail="Invalid url")
 
     create_directory(join_filepath([DIRPATH.INPUT_DIR, workspace_id]))
diff --git a/studio/app/const.py b/studio/app/const.py
index d2a846761..90fdb4631 100644
--- a/studio/app/const.py
+++ b/studio/app/const.py
@@ -19,7 +19,7 @@ class ACCEPT_FILE_EXT(Enum):
     MATLAB_EXT = [".mat"]
     MICROSCOPE_EXT = [".nd2", ".oir", ".isxd", ".thor.zip"]
 
-    AlL_EXT = TIFF_EXT + CSV_EXT + HDF5_EXT + MATLAB_EXT + MICROSCOPE_EXT
+    ALL_EXT = TIFF_EXT + CSV_EXT + HDF5_EXT + MATLAB_EXT + MICROSCOPE_EXT
 
 
 NOT_DISPLAY_ARGS_LIST = ["params", "output_dir", "nwbfile", "kwargs"]

From ef3bc3558695f5cb60a8aaff1377054f5ca95787 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Fri, 21 Jun 2024 17:12:28 +0900
Subject: [PATCH 12/21] modify poetry option on dockerfile

---
 studio/config/docker/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/studio/config/docker/Dockerfile b/studio/config/docker/Dockerfile
index 3bb50eff9..e2e727269 100644
--- a/studio/config/docker/Dockerfile
+++ b/studio/config/docker/Dockerfile
@@ -26,7 +26,8 @@ RUN echo 'alias ll="ls -la --color=auto"' >> /root/.bashrc && \
 # setup optinist
 COPY pyproject.toml poetry.lock ./
 RUN pip3 install --no-cache-dir --upgrade pip && \
-    pip3 install poetry
+    pip3 install poetry && \
+    poetry config virtualenvs.create false
 RUN poetry install --no-root
 
 # copy optinist files

From ddd1f09ee741c058eedca1bec640dea878d0f761 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Fri, 21 Jun 2024 17:30:44 +0900
Subject: [PATCH 13/21] modify poetry option on dockerfile

---
 studio/config/docker/Dockerfile.dev  | 3 ++-
 studio/config/docker/Dockerfile.test | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/studio/config/docker/Dockerfile.dev b/studio/config/docker/Dockerfile.dev
index 2a1bc1a84..560baadbf 100644
--- a/studio/config/docker/Dockerfile.dev
+++ b/studio/config/docker/Dockerfile.dev
@@ -26,7 +26,8 @@ RUN echo 'alias ll="ls -la --color=auto"' >> /root/.bashrc && \
 # setup optinist
 COPY pyproject.toml poetry.lock ./
 RUN pip3 install --no-cache-dir --upgrade pip && \
-    pip3 install poetry
+    pip3 install poetry && \
+    poetry config virtualenvs.create false
 RUN poetry install --no-root --with dev
 
 EXPOSE 8000
diff --git a/studio/config/docker/Dockerfile.test b/studio/config/docker/Dockerfile.test
index c04459d19..2a727ab0f 100644
--- a/studio/config/docker/Dockerfile.test
+++ b/studio/config/docker/Dockerfile.test
@@ -6,8 +6,8 @@ RUN apt-get --allow-releaseinfo-change update && \
     apt-get install --no-install-recommends -y git gcc g++ libgl1 && \
     apt-get purge git -y && apt-get autoremove -y && apt-get clean
 
-
 RUN pip3 install --no-cache-dir --upgrade pip && \
-    pip3 install poetry
+    pip3 install poetry && \
+    poetry config virtualenvs.create false
 
 COPY pyproject.toml poetry.lock ./

From c434c55795ebced360814f68024e68a2945f3057 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Mon, 24 Jun 2024 10:43:50 +0900
Subject: [PATCH 14/21] update vscode settings (for prettier)

---
 .vscode/settings.example.json | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.vscode/settings.example.json b/.vscode/settings.example.json
index 1989c4133..eacc15168 100644
--- a/.vscode/settings.example.json
+++ b/.vscode/settings.example.json
@@ -11,6 +11,8 @@
     }
   },
   "eslint.workingDirectories": ["frontend"],
+  "editor.defaultFormatter": "esbenp.prettier-vscode",
+  "editor.formatOnSave": true,
   "flake8.args": ["--config=.flake8"],
   // NOTE: Uncomment following line and fix "optinist_dev" to your conda env name
   // "flake8.path": ["conda", "run", "-n", "optinist_dev", "python", "-m", "flake8"],

From a8afd5b2943163f80f14031f0153541bcc358be6 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Tue, 25 Jun 2024 11:29:20 +0900
Subject: [PATCH 15/21] update settings for multiuser mode

---
 docker-compose.dev.multiuser.yml | 58 ++++++++++++++++++++++++++++++++
 docker-compose.dev.yml           |  3 ++
 studio/config/.env.example       |  3 +-
 3 files changed, 63 insertions(+), 1 deletion(-)
 create mode 100644 docker-compose.dev.multiuser.yml

diff --git a/docker-compose.dev.multiuser.yml b/docker-compose.dev.multiuser.yml
new file mode 100644
index 000000000..3ae033212
--- /dev/null
+++ b/docker-compose.dev.multiuser.yml
@@ -0,0 +1,58 @@
+version: "3"
+
+services:
+  db:
+    image: mysql:8.4
+    ports:
+      - "127.0.0.1:13306:3306"
+    env_file:
+      - studio/config/.env
+    volumes:
+      - db_data:/var/lib/mysql
+    environment:
+      TZ: Asia/Tokyo
+    healthcheck:
+      test: ["CMD", "mysqladmin", "ping", "-h", "127.0.0.1"]
+      interval: 10s
+      timeout: 5s
+      retries: 3
+
+  studio-dev-be:
+    build:
+      context: .
+      dockerfile: studio/config/docker/Dockerfile.dev
+    working_dir: /app
+    volumes:
+      - .:/app
+      # optinist data outputs directories
+      - ../optinist-docker-volumes/.snakemake/:/app/.snakemake
+      - ../optinist-docker-volumes/logs/:/app/logs
+      - ../optinist-docker-volumes/studio_data/:/app/studio_data
+    ports:
+      - "127.0.0.1:8000:8000"
+    command: >
+        bash -c "
+          alembic upgrade head &&
+          poetry run python main.py --reload --host 0.0.0.0 --port 8000
+        "
+    environment:
+      PYTHONPATH: /app/
+      TZ: Asia/Tokyo
+      OPTINIST_DIR: /app/studio_data
+    depends_on:
+      db:
+        condition: service_healthy
+
+  studio-dev-fe:
+    image: node:20.8.0-alpine3.18
+    working_dir: /app/frontend
+    volumes:
+      - ./frontend/:/app/frontend/:cached
+    ports:
+      - "127.0.0.1:3000:3000"
+    command: ash -c 'yarn install && yarn start'
+    environment:
+      TZ: Asia/Tokyo
+
+volumes:
+  db_data:
diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
index 91daa1535..3bebb8f77 100644
--- a/docker-compose.dev.yml
+++ b/docker-compose.dev.yml
@@ -8,6 +8,9 @@ services:
     working_dir: /app
     volumes:
       - .:/app
+      # optinist data outputs directories
+      - ../optinist-docker-volumes/.snakemake/:/app/.snakemake
+      - ../optinist-docker-volumes/logs/:/app/logs
       - ../optinist-docker-volumes/studio_data/:/app/studio_data
     ports:
       - "127.0.0.1:8000:8000"
diff --git a/studio/config/.env.example b/studio/config/.env.example
index 1bb1cd886..ae36187c4 100644
--- a/studio/config/.env.example
+++ b/studio/config/.env.example
@@ -5,8 +5,9 @@ REFRESH_TOKEN_EXPIRE_MINUTES=1440 # 24 hours
 IS_STANDALONE=True
 
 # NOTE: Uncomment and set your own values when using for multiple user
-# MYSQL_SERVER=db
+# MYSQL_SERVER=db:3306
 # MYSQL_ROOT_PASSWORD=db_root_password
 # MYSQL_DATABASE=studio
 # MYSQL_USER=studio_db_user
 # MYSQL_PASSWORD=studio_db_password
+# ECHO_SQL=False

From 3af0e0742c8e8e4ea4b87014d36e6308d120490e Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Tue, 25 Jun 2024 11:31:29 +0900
Subject: [PATCH 16/21] update docs for multiuser mode

---
 docs/host_for_multiuser/setup.md              | 159 +++++++++---------
 docs/installation/docker_for_developer.md     |   6 +
 .../each_platforms_for_developer.md           |   8 +-
 3 files changed, 97 insertions(+), 76 deletions(-)

diff --git a/docs/host_for_multiuser/setup.md b/docs/host_for_multiuser/setup.md
index 9645de140..5e8fac3c9 100644
--- a/docs/host_for_multiuser/setup.md
+++ b/docs/host_for_multiuser/setup.md
@@ -16,18 +16,20 @@ Follow the steps below to setup `multiuser` mode.
     ```
 2. copy config files
     ```bash
-    cp studio/config/.env.example studio/config.env
+    cp studio/config/.env.example studio/config/.env
     cp studio/config/auth/firebase_config.example.json studio/config/auth/firebase_config.json
     ```
 
-### Create your Firebase Project
+###  Setup Firebase Authentication
+
+#### Create your Firebase Project
 1. Go to [https://console.firebase.google.com/](https://console.firebase.google.com/)
 2. Click "Add project".
 3. Enter your project name, and click "Continue".
 4. Google Analytics is optional. You can choose "Enable Google Analytics for this project" or not.
 5. After your project is ready, click "Continue".
 
-### Setup Firebase Authentication
+#### Setup Firebase Authentication
 1. Select "Build > Authentication" from the left menu.
 2. Select "Get started".
 3. Select "Sign-in method" tab.
@@ -35,7 +37,7 @@ Follow the steps below to setup `multiuser` mode.
 5. Click "Email/Password" and enable it.
 6. Click "Save".
 
-### Create admin user for the project
+#### Create admin user for the project
 1. Select "Authentication" from the left menu.
 2. Select "Users" tab.
 3. Click "Add user" button.
@@ -45,7 +47,7 @@ Follow the steps below to setup `multiuser` mode.
 
 - Created user's "User UID" is required later.
 
-### Get Firebase tokens
+#### Get Firebase tokens
 1. Click setting icon(besides Project Overview), then select "Project settings" from the left menu.
 2. Select "General" tab.
 3. Select "web app" in "Your apps" section.
@@ -64,88 +66,95 @@ Follow the steps below to setup `multiuser` mode.
 8. Click "Generate new private key" in "Firebase Admin SDK" section.
 9. Put the downloaded file to `studio/config/auth/firebase_private.json`.
 
-### Setup mysql(or mariadb)
-1. Install mysql(or mariadb) server.
-2. Connect mysql server.
+### Setup Database
+- Set up your own mysql (or mariadb) server or use docker compose mysql
+- Below are the instructions for using mysql with docker compose.
+
+1. Edit configs.
+    - Edit studio/config/.env
+      - Set `MYSQL_SERVER` to db server host or ip
+        - \*For docker platform, the fixed value `db:3306` is fine.
+      - Set `MYSQL_ROOT_PASSWORD` to {DB_ROOT_PASSWORD}, which you have decided.
+      - Set `MYSQL_DATABASE` to {YOUR_DATABASE_NAME}, which you have decided.
+      - Set `MYSQL_USER` to {DB_USER_NAME}, which you have decided.
+      - Set `MYSQL_PASSWORD` to {DB_USER_PASSWORD}, which you have decided.
+2. Install & run mysql server.
     ```bash
-    mysql -u root -p
-    ```
-3. Create database for your project.
-    ```sql
-    CREATE DATABASE YOUR_DATABASE_NAME;
-    ```
-4. Create user for your project.
-    ```sql
-    CREATE USER 'DB_USER_NAME'@'localhost' IDENTIFIED BY 'DB_USER_PASSWORD';
+    docker compose -f docker-compose.dev.multiuser.yml up db -d
     ```
-5. Grant all privileges to the user for the database.
-    ```sql
-    GRANT ALL PRIVILEGES ON YOUR_DATABASE_NAME.* TO 'DB_USER_NAME'@'localhost';
+    - The database and db_user are automatically generated based on the .env settings.
+3. Connect to mysql server.
+    ```bash
+    docker exec -it {DB_DOCKER_CONTAINER_NAME} mysql -u {DB_USER_NAME} -p {YOUR_DATABASE_NAME}
     ```
+    - If a connection to the database server is available, the setup was successful.
+
+### Setup & Run OptiNiSt
 
-### Set OptiNiSt config
-1. Edit `studio/config/.env`
+#### For Docker Platform
+
+##### Setup Backend
+- See [OptiNiSt installation guide](../installation/docker_for_developer.md).
+- After building the docker environment, run following commands
+
+###### 1. Set OptiNiSt config
+- Edit `studio/config/.env`
     - Change `SECRET_KEY` to any random string.
     - Change `USE_FIREBASE_TOKEN` to `True`.
     - Change `IS_STANDALONE` to `False`
-    - Set `MYSQL_SERVER` to your host
-    - Set `MYSQL_DATABASE` to {YOUR_DATABASE_NAME}, which you created in the previous step.
-    - Set `MYSQL_USER` to {DB_USER_NAME}, which you created in the previous step.
-    - Set `MYSQL_PASSWORD` to {DB_USER_PASSWORD}, which you created in the previous step.
-    - `MYSQL_ROOT_PASSWORD` can be left commented.
-
-### Setup Frontend
-1. Install node.js(version 20)
-    - https://nodejs.org
-2. Install yarn
-    ```bash
-    npm install -g yarn
-    ```
-3. Install frontend requirements
-    ```bash
-    cd frontend
-    yarn install
-    ```
-4. Build frontend
-    ```bash
-    yarn build
-    ```
 
-### Setup Backend
-- See OptiNiSt installation guide.
+###### 2. Start backend (Database is set up on startup)
+```bash
+docker compose -f docker-compose.dev.multiuser.yml up studio-dev-be -d
+```
+
+###### 3. Insert initial data
+```bash
+docker exec -it {DB_DOCKER_CONTAINER_NAME} mysql -u {DB_USER_NAME} -p {YOUR_DATABASE_NAME}
+```
+```sql
+INSERT INTO organization (name) VALUES ('{YOUR_ORGANIZATION_NAME}');
+INSERT INTO roles (id, role) VALUES (1, 'admin'), (20, 'operator');
+INSERT INTO users (uid, organization_id, name, email, active) VALUES ('{FIREBASE_UID}', 1, '{YOUR_NAME}', '{YOUR_EMAIL}', true);
+INSERT INTO user_roles (user_id, role_id) VALUES (1, 1);
+```
+- USER_UID is the user uid you created in the previous step ([Create admin user for the project](#create-admin-user-for-the-project)).
+- Only 2 roles, "admin" and "operator" are supported for now.
+  - "admin"
+    - can manage other users
+  - "operator"
+    - general user
+
+##### Run OptiNiSt
+```bash
+docker compose -f docker-compose.dev.multiuser.yml up -d
+```
+
+1. Access to `http://{YOUR_HOST}:8000` from your browser.
+2. Confirm that you can SingIn with your Firebase Authentication account.
+
+#### For Other Platforms
+
+##### Setup Backend
+- See [OptiNiSt installation guide](../installation/index.rst).
 - After create and activate conda environment for the project, run following commands
 
-1. Install backend requirements
-    ```bash
-    cd studio
-    pip install .
-    ```
-2. Setup database
-    ```bash
-    alembic upgrade head
-    ```
-3. Insert initial data
+###### 1. Set OptiNiSt config
+- Same as [[Set OptiNiSt config]](#set-optinist-config) procedure.
 
-    ```bash
-    mysql -u DB_USER_NAME -p
-    ```
-    ```sql
-    USE YOUR_DATABASE_NAME;
-    INSERT INTO organization (name) VALUES ('YOUR_ORGANIZATION_NAME');
-    INSERT INTO roles (id, role) VALUES (1, 'admin'), (20, 'operator');
-    INSERT INTO users (uid, organization_id, name, email, active, ) VALUES ('USER_UID', 1, 'YOUR_EMAIL', 'YOUR_PASSWORD', 1);
-    INSERT INTO user_roles (user_id, role_id) VALUES (1, 1);
-    ```
-    - USER_UID is the user uid you created in the previous step ([Create admin user for the project](#create-admin-user-for-the-project)).
-    - Only 2 roles, "admin" and "operator" are supported for now.
-      - "admin"
-        - can manage other users
-      - "operator"
-        - general user
-
-### Run OptiNiSt
+###### 2. Setup database
+```bash
+cd {OPTINIST_ROOT_PATH}
+alembic upgrade head
+```
+
+###### 3. Insert initial data
+- Same as [[Insert initial data]](#insert-initial-data) procedure.
+
+##### Run OptiNiSt
 ```bash
 python main.py
 ```
 
-- Access to `http://{YOUR_HOST}:8000` from your browser.
+1. Access to `http://{YOUR_HOST}:8000` from your browser.
+2. Confirm that you can SingIn with your Firebase Authentication account.
diff --git a/docs/installation/docker_for_developer.md b/docs/installation/docker_for_developer.md
index 5d48856f0..33e12281f 100644
--- a/docs/installation/docker_for_developer.md
+++ b/docs/installation/docker_for_developer.md
@@ -24,6 +24,12 @@ git clone https://github.com/oist/optinist.git
 cd ./optinist
 ```
 
+- copy config files
+  ```
+  cp studio/config/.env.example studio/config/.env
+  cp frontend/.env.example frontend/.env
+  ```
+
 ### Start docker container
 
 ```
diff --git a/docs/installation/each_platforms_for_developer.md b/docs/installation/each_platforms_for_developer.md
index 7c1d3e85f..daedd9873 100644
--- a/docs/installation/each_platforms_for_developer.md
+++ b/docs/installation/each_platforms_for_developer.md
@@ -34,7 +34,7 @@ Get node with version 20
 You can also install node via [nvm](https://github.com/nvm-sh/nvm)
 
 After install node, install yarn.
-```bash
+```
 npm install -g yarn
 ```
 
@@ -45,6 +45,12 @@ git clone https://github.com/oist/optinist.git
 cd ./optinist
 ```
 
+- copy config files
+  ```
+  cp studio/config/.env.example studio/config/.env
+  cp frontend/.env.example frontend/.env
+  ```
+
 ### Create anaconda environment
 
 ```

From 56124c3d47a658f343ff215d4bb0578310c949da Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Tue, 25 Jun 2024 12:19:14 +0900
Subject: [PATCH 17/21] corrected grammar

---
 docs/host_for_multiuser/setup.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/host_for_multiuser/setup.md b/docs/host_for_multiuser/setup.md
index 5e8fac3c9..c3fdd663c 100644
--- a/docs/host_for_multiuser/setup.md
+++ b/docs/host_for_multiuser/setup.md
@@ -64,7 +64,7 @@ Follow the steps below to setup `multiuser` mode.
     - (keep databaseURL blank)
 7. Select "Service accounts" tab.
 8. Click "Generate new private key" in "Firebase Admin SDK" section.
-9. Put the downloaded file to `studio/config/auth/firebase_private.json`.
+9. Save the downloaded file to `studio/config/auth/firebase_private.json`.
 
 ### Setup Database
 - Set up your own mysql (or mariadb) server or use docker compose mysql

From 49cec3258553b6b52a6b95503447e48a5b061875 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Thu, 27 Jun 2024 14:15:05 +0900
Subject: [PATCH 18/21] update multiuser mode setup docs

---
 docs/host_for_multiuser/setup.md | 68 ++++++++++++++++++++------------
 1 file changed, 43 insertions(+), 25 deletions(-)

diff --git a/docs/host_for_multiuser/setup.md b/docs/host_for_multiuser/setup.md
index c3fdd663c..981f7ff54 100644
--- a/docs/host_for_multiuser/setup.md
+++ b/docs/host_for_multiuser/setup.md
@@ -16,8 +16,8 @@ Follow the steps below to setup `multiuser` mode.
     ```
 2. copy config files
     ```bash
-    cp studio/config/.env.example studio/config/.env
-    cp studio/config/auth/firebase_config.example.json studio/config/auth/firebase_config.json
+    cp -i studio/config/.env.example studio/config/.env
+    cp -i studio/config/auth/firebase_config.example.json studio/config/auth/firebase_config.json
     ```
 
 ###  Setup Firebase Authentication
@@ -73,29 +73,38 @@ Follow the steps below to setup `multiuser` mode.
 1. Edit configs.
     - Edit studio/config/.env
       - Set `MYSQL_SERVER` to db server host or ip
+        - Format: `{DB_HOST}:{DB_PORT}`
         - \*For docker platform, the fixed value `db:3306` is fine.
-      - Set `MYSQL_ROOT_PASSWORD` to {DB_ROOT_PASSWORD}, which you have decided.
-      - Set `MYSQL_DATABASE` to {YOUR_DATABASE_NAME}, which you have decided.
-      - Set `MYSQL_USER` to {DB_USER_NAME}, which you have decided.
-      - Set `MYSQL_PASSWORD` to {DB_USER_PASSWORD}, which you have decided.
+      - Set `MYSQL_ROOT_PASSWORD` to database root password, which you have decided.
+      - Set `MYSQL_DATABASE` to `{YOUR_DATABASE_NAME}`, which you have decided.
+      - Set `MYSQL_USER` to `{DB_USER_NAME}`, which you have decided.
+      - Set `MYSQL_PASSWORD` to `{DB_USER_PASSWORD}`, which you have decided.
 2. Install & run mysql server.
     ```bash
     docker compose -f docker-compose.dev.multiuser.yml up db -d
     ```
     - The database and db_user are automatically generated based on the .env settings.
-3. Connect to mysql server.
-    ```bash
-    docker exec -it {DB_DOCKER_CONTAINER_NAME} mysql -u {DB_USER_NAME} -p {YOUR_DATABASE_NAME}
-    ```
+3. Check connection to mysql server.
+    - Connecting via docker command
+      ```bash
+      docker exec -it {DB_CONTAINER_NAME} mysql -u {DB_USER_NAME} -p {YOUR_DATABASE_NAME}
+      mysql> exit
+      ```
+      - Note: `{DB_CONTAINER_NAME}` is the container name or container ID of the database docker container. (Can be confirmed with `docker ps`)
+    - Connect via mysql command (requires mysql-client)
+      ```bash
+      mysql -h {DB_HOST} --port={DB_PORT} -u {DB_USER_NAME} -p {YOUR_DATABASE_NAME}
+      mysql> exit
+      ```
     - If a connection to the database server is available, the setup was successful.
 
 ### Setup & Run OptiNiSt
 
 #### For Docker Platform
 
+To use multiuser mode with Docker, perform the following steps.
+
 ##### Setup Backend
-- See [OptiNiSt installation guide](../installation/docker_for_developer.md).
-- After building the docker environment, run following commands
 
 ###### 1. Set OptiNiSt config
 - Edit `studio/config/.env`
@@ -110,20 +119,27 @@ docker compose -f docker-compose.dev.multiuser.yml up studio-dev-be -d
 
 ###### 3. Insert initial data
 ```bash
-docker exec -it {DB_DOCKER_CONTAINER_NAME} mysql -u {DB_USER_NAME} -p {YOUR_DATABASE_NAME}
+docker exec -it {DB_CONTAINER_NAME} mysql -u {DB_USER_NAME} -p {YOUR_DATABASE_NAME}
 ```
 ```sql
 INSERT INTO organization (name) VALUES ('{YOUR_ORGANIZATION_NAME}');
 INSERT INTO roles (id, role) VALUES (1, 'admin'), (20, 'operator');
-INSERT INTO users (uid, organization_id, name, email, active) VALUES ('{FIREBASE_UID}', 1, '{YOUR_NAME}', '{YOUR_EMAIL}', true);
+INSERT INTO users (uid, organization_id, name, email, active) VALUES ('{FIREBASE_USER_UID}', 1, '{YOUR_NAME}', '{YOUR_EMAIL}', true);
 INSERT INTO user_roles (user_id, role_id) VALUES (1, 1);
 ```
-- USER_UID is the user uid you created in the previous step ([Create admin user for the project](#create-admin-user-for-the-project)).
-- Only 2 roles, "admin" and "operator" are supported for now.
-  - "admin"
-    - can manage other users
-  - "operator"
-    - general user
+  - Note of Variables
+    - `{FIREBASE_USER_UID}` ... The user uid you created in the previous step ([Create admin user for the project](#create-admin-user-for-the-project)).
+    - `{YOUR_ORGANIZATION_NAME}` ... Display name on system (Any text)
+    - `{YOUR_NAME}` ... Display name on system (Any text)
+    - `{YOUR_EMAIL}` ... Email address corresponding to `{FIREBASE_USER_UID}`
+
+- About Roles
+  - Only 2 roles, "admin" and "operator" are supported for now.
+    - "admin"
+      - can manage other users
+    - "operator"
+      - general user
+  - More information is [here](usage.md).
 
 ##### Run OptiNiSt
 ```bash
@@ -133,23 +149,25 @@ docker compose -f docker-compose.dev.multiuser.yml up -d
 1. Access to `http://{YOUR_HOST}:8000` from your browser.
 2. Confirm that you can SingIn with your Firebase Authentication account.
 
-#### For Other Platforms
+#### For Non-Docker Platforms
+
+Below are the steps for a case using Non-Docker platforms (Windows, Mac, Linux).
 
 ##### Setup Backend
 - See [OptiNiSt installation guide](../installation/index.rst).
-- After create and activate conda environment for the project, run following commands
+- After creating and activating a conda environment for the project, run following commands
 
 ###### 1. Set OptiNiSt config
-- Same as [[Set OptiNiSt config]](#set-optinist-config) procedure.
+- Same as [Set OptiNiSt config](#set-optinist-config) procedure.
 
 ###### 2. Setup database
 ```bash
-cd {OPTINIST_ROOT_PATH}
+cd {OPTINIST_ROOT_PATH}  # root path of repository cloned
 alembic upgrade head
 ```
 
 ###### 3. Insert initial data
-- Same as [[Insert initial data]](#insert-initial-data) procedure.
+- Same as [Insert initial data](#insert-initial-data) procedure.
 
 ##### Run OptiNiSt
 ```bash

From af8bc92f26b228899c36d7522780458f656aed8a Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Thu, 27 Jun 2024 18:40:22 +0900
Subject: [PATCH 19/21] add ExptDataWriter

---
 .../core/experiment/experiment_reader.py      | 22 ---------
 .../core/experiment/experiment_writer.py      | 47 +++++++++++++++++++
 studio/app/common/routers/experiment.py       | 26 +++++-----
 3 files changed, 61 insertions(+), 34 deletions(-)

diff --git a/studio/app/common/core/experiment/experiment_reader.py b/studio/app/common/core/experiment/experiment_reader.py
index d092a77fb..6789d4ba4 100644
--- a/studio/app/common/core/experiment/experiment_reader.py
+++ b/studio/app/common/core/experiment/experiment_reader.py
@@ -54,25 +54,3 @@ def read_output_paths(cls, config) -> Dict[str, OutputPath]:
             }
         else:
             return None
-
-    @classmethod
-    def rename(cls, filepath, new_name: str) -> ExptConfig:
-        with open(filepath, "r") as f:
-            config = yaml.safe_load(f)
-            config["name"] = new_name
-
-        with open(filepath, "w") as f:
-            yaml.dump(config, f, sort_keys=False)
-
-        return ExptConfig(
-            workspace_id=config["workspace_id"],
-            unique_id=config["unique_id"],
-            name=config["name"],
-            started_at=config.get("started_at"),
-            finished_at=config.get("finished_at"),
-            success=config.get("success", "running"),
-            hasNWB=config["hasNWB"],
-            function=cls.read_function(config["function"]),
-            nwb=config.get("nwb"),
-            snakemake=config.get("snakemake"),
-        )
diff --git a/studio/app/common/core/experiment/experiment_writer.py b/studio/app/common/core/experiment/experiment_writer.py
index 4d49a1c67..004ae01bc 100644
--- a/studio/app/common/core/experiment/experiment_writer.py
+++ b/studio/app/common/core/experiment/experiment_writer.py
@@ -1,8 +1,11 @@
 import os
+import shutil
 from dataclasses import asdict
 from datetime import datetime
 from typing import Dict
 
+import yaml
+
 from studio.app.common.core.experiment.experiment import ExptConfig, ExptFunction
 from studio.app.common.core.experiment.experiment_builder import ExptConfigBuilder
 from studio.app.common.core.experiment.experiment_reader import ExptConfigReader
@@ -98,3 +101,47 @@ def function_from_nodeDict(self) -> ExptConfig:
                 func_dict[node.id].success = "success"
 
         return self.builder.set_function(func_dict).build()
+
+
+class ExptDataWriter:
+    def __init__(
+        self,
+        workspace_id: str,
+        unique_id: str,
+    ):
+        self.workspace_id = workspace_id
+        self.unique_id = unique_id
+
+    def delete_data(self) -> bool:
+        shutil.rmtree(
+            join_filepath([DIRPATH.OUTPUT_DIR, self.workspace_id, self.unique_id])
+        )
+        return True
+
+    def rename(self, new_name: str) -> ExptConfig:
+        filepath = join_filepath(
+            [
+                DIRPATH.OUTPUT_DIR,
+                self.workspace_id,
+                self.unique_id,
+                DIRPATH.EXPERIMENT_YML,
+            ]
+        )
+
+        with open(filepath, "r+") as f:
+            config = yaml.safe_load(f)
+            config["name"] = new_name
+            yaml.dump(config, f, sort_keys=False)
+
+        return ExptConfig(
+            workspace_id=config["workspace_id"],
+            unique_id=config["unique_id"],
+            name=config["name"],
+            started_at=config.get("started_at"),
+            finished_at=config.get("finished_at"),
+            success=config.get("success", "running"),
+            hasNWB=config["hasNWB"],
+            function=ExptConfigReader.read_function(config["function"]),
+            nwb=config.get("nwb"),
+            snakemake=config.get("snakemake"),
+        )
diff --git a/studio/app/common/routers/experiment.py b/studio/app/common/routers/experiment.py
index c8b8a6738..04d4e9518 100644
--- a/studio/app/common/routers/experiment.py
+++ b/studio/app/common/routers/experiment.py
@@ -1,5 +1,4 @@
 import os
-import shutil
 from glob import glob
 from typing import Dict
 
@@ -8,6 +7,7 @@
 
 from studio.app.common.core.experiment.experiment import ExptConfig
 from studio.app.common.core.experiment.experiment_reader import ExptConfigReader
+from studio.app.common.core.experiment.experiment_writer import ExptDataWriter
 from studio.app.common.core.utils.filepath_creater import join_filepath
 from studio.app.common.core.workspace.workspace_dependencies import (
     is_workspace_available,
@@ -45,12 +45,10 @@ async def get_experiments(workspace_id: str):
     dependencies=[Depends(is_workspace_owner)],
 )
 async def rename_experiment(workspace_id: str, unique_id: str, item: RenameItem):
-    config = ExptConfigReader.rename(
-        join_filepath(
-            [DIRPATH.OUTPUT_DIR, workspace_id, unique_id, DIRPATH.EXPERIMENT_YML]
-        ),
-        new_name=item.new_name,
-    )
+    config = ExptDataWriter(
+        workspace_id,
+        unique_id,
+    ).rename(item.new_name)
     config.nodeDict = []
     config.edgeDict = []
 
@@ -64,7 +62,10 @@ async def rename_experiment(workspace_id: str, unique_id: str, item: RenameItem)
 )
 async def delete_experiment(workspace_id: str, unique_id: str):
     try:
-        shutil.rmtree(join_filepath([DIRPATH.OUTPUT_DIR, workspace_id, unique_id]))
+        ExptDataWriter(
+            workspace_id,
+            unique_id,
+        ).delete_data()
         return True
     except Exception:
         return False
@@ -77,10 +78,11 @@ async def delete_experiment(workspace_id: str, unique_id: str):
 )
 async def delete_experiment_list(workspace_id: str, deleteItem: DeleteItem):
     try:
-        [
-            shutil.rmtree(join_filepath([DIRPATH.OUTPUT_DIR, workspace_id, uid]))
-            for uid in deleteItem.uidList
-        ]
+        for unique_id in deleteItem.uidList:
+            ExptDataWriter(
+                workspace_id,
+                unique_id,
+            ).delete_data()
         return True
     except Exception:
         return False

From 74d885b3002160130fcd371e059f311d3f88d147 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Fri, 28 Jun 2024 10:45:49 +0900
Subject: [PATCH 20/21] corrected wording

---
 docs/host_for_multiuser/setup.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/host_for_multiuser/setup.md b/docs/host_for_multiuser/setup.md
index 981f7ff54..fe9d9b143 100644
--- a/docs/host_for_multiuser/setup.md
+++ b/docs/host_for_multiuser/setup.md
@@ -127,7 +127,7 @@ INSERT INTO roles (id, role) VALUES (1, 'admin'), (20, 'operator');
 INSERT INTO users (uid, organization_id, name, email, active) VALUES ('{FIREBASE_USER_UID}', 1, '{YOUR_NAME}', '{YOUR_EMAIL}', true);
 INSERT INTO user_roles (user_id, role_id) VALUES (1, 1);
 ```
-  - Note of Variables
+  - Note on Variables
     - `{FIREBASE_USER_UID}` ... The user uid you created in the previous step ([Create admin user for the project](#create-admin-user-for-the-project)).
     - `{YOUR_ORGANIZATION_NAME}` ... Display name on system (Any text)
     - `{YOUR_NAME}` ... Display name on system (Any text)

From 91dcdb8799e73d6f873a1793148d168eec2749c0 Mon Sep 17 00:00:00 2001
From: tienday <develop@itutu.local>
Date: Fri, 28 Jun 2024 12:18:56 +0900
Subject: [PATCH 21/21] Fixed ExptDataWriter bug

- A seek(0) was needed before file write in rename().
---
 studio/app/common/core/experiment/experiment_writer.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/studio/app/common/core/experiment/experiment_writer.py b/studio/app/common/core/experiment/experiment_writer.py
index 004ae01bc..b8b87d6ae 100644
--- a/studio/app/common/core/experiment/experiment_writer.py
+++ b/studio/app/common/core/experiment/experiment_writer.py
@@ -131,6 +131,7 @@ def rename(self, new_name: str) -> ExptConfig:
         with open(filepath, "r+") as f:
             config = yaml.safe_load(f)
             config["name"] = new_name
+            f.seek(0)  # requires seek(0) before write.
             yaml.dump(config, f, sort_keys=False)
 
         return ExptConfig(