refactor rename path variable names

arayabrain · Jun 28, 2023 · 17801d9 · 17801d9
1 parent 4b8d401
commit 17801d9
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Showing 24 changed files with 53 additions and 55 deletions.
diff --git a/run_cluster.py b/run_cluster.py
@@ -12,15 +12,16 @@ def main(args):
     # copy config file
     if args.config is not None:
         shutil.copyfile(
-            args.config, join_filepath([DIRPATH.ROOT_DIR, DIRPATH.SNAKEMAKE_CONFIG_YML])
+            args.config,
+            join_filepath([DIRPATH.STUDIO_DIR, DIRPATH.SNAKEMAKE_CONFIG_YML]),
         )
 
     snakemake(
         DIRPATH.SNAKEMAKE_FILEPATH,
         forceall=args.forceall,
         cores=args.cores,
         use_conda=args.use_conda,
-        workdir=f"{os.path.dirname(DIRPATH.ROOT_DIR)}",
+        workdir=f"{os.path.dirname(DIRPATH.STUDIO_DIR)}",
     )
 
 

diff --git a/studio/Snakefile b/studio/Snakefile
@@ -4,14 +4,14 @@ from studio.core.models import FILETYPE
 from studio.core.snakemake.smk_utils import SmkUtils
 from studio.core.utils.filepath_creater import join_filepath
 
-configfile: join_filepath([DIRPATH.ROOT_DIR, 'config.yaml'])
+configfile: join_filepath([DIRPATH.STUDIO_DIR, 'config.yaml'])
 
 if config.get('type') == ACTION.EDIT_ROI:
     rule edit_ROI:
         conda:
             EditRoiUtils.conda(config)
         script:
-            f"{DIRPATH.ROOT_DIR}/core/rules/edit_ROI.py"
+            f"{DIRPATH.STUDIO_DIR}/core/rules/edit_ROI.py"
 else:
     rule all:
         input: [join_filepath([DIRPATH.OUTPUT_DIR, x]) for x in config["last_output"]]
@@ -27,7 +27,7 @@ else:
                 params:
                     name = details
                 script:
-                    f"{DIRPATH.ROOT_DIR}/core/rules/data.py"
+                    f"{DIRPATH.STUDIO_DIR}/core/rules/data.py"
         else:
             rule:
                 input:
@@ -39,4 +39,4 @@ else:
                 conda:
                     SmkUtils.conda(details)
                 script:
-                    f"{DIRPATH.ROOT_DIR}/core/rules/func.py"
+                    f"{DIRPATH.STUDIO_DIR}/core/rules/func.py"
diff --git a/studio/__main_unit__.py b/studio/__main_unit__.py
@@ -26,7 +26,7 @@
     allow_headers=["*"],
 )
 
-FRONTEND_DIRPATH = DIRPATH.PKG_DIR + "/frontend"
+FRONTEND_DIRPATH = DIRPATH.ROOT_DIR + "/frontend"
 
 app.mount(
     "/static",

diff --git a/studio/core/dir_path.py b/studio/core/dir_path.py
@@ -5,16 +5,10 @@
 
 
 class DIRPATH:
-    OPTINIST_DIR = _DEFAULT_DIR if _ENV_DIR is None else _ENV_DIR
-    INPUT_DIR = f"{OPTINIST_DIR}/input"
-    OUTPUT_DIR = f"{OPTINIST_DIR}/output"
+    DATA_DIR = _DEFAULT_DIR if _ENV_DIR is None else _ENV_DIR
 
-    CONDAENV_DIR = (
-        f"{os.path.dirname(os.path.dirname(os.path.dirname(__file__)))}/conda"
-    )
-
-    PKG_DIR = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
-    ROOT_DIR = os.path.dirname(os.path.dirname(__file__))
+    INPUT_DIR = f"{DATA_DIR}/input"
+    OUTPUT_DIR = f"{DATA_DIR}/output"
 
     if not os.path.exists(INPUT_DIR):
         os.makedirs(INPUT_DIR)
@@ -24,6 +18,13 @@ class DIRPATH:
         os.makedirs(OUTPUT_DIR)
     assert os.path.exists(OUTPUT_DIR)
 
-    SNAKEMAKE_FILEPATH = f"{ROOT_DIR}/Snakefile"
+    ROOT_DIR = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
+    STUDIO_DIR = os.path.dirname(os.path.dirname(__file__))
+
+    CONDAENV_DIR = (
+        f"{os.path.dirname(os.path.dirname(os.path.dirname(__file__)))}/conda"
+    )
+
+    SNAKEMAKE_FILEPATH = f"{STUDIO_DIR}/Snakefile"
     EXPERIMENT_YML = "experiment.yaml"
     SNAKEMAKE_CONFIG_YML = "config.yaml"
diff --git a/studio/core/edit_ROI/edit_ROI.py b/studio/core/edit_ROI/edit_ROI.py
@@ -40,8 +40,7 @@ def get_algo(self):
 
         if (
             not os.path.exists(filepath)
-            and os.path.commonpath([DIRPATH.OPTINIST_DIR, filepath])
-            != DIRPATH.OPTINIST_DIR
+            and os.path.commonpath([DIRPATH.DATA_DIR, filepath]) != DIRPATH.DATA_DIR
         ):
             raise HTTPException(status_code=status.HTTP_404_NOT_FOUND)
         if os.path.basename(filepath) != "cell_roi.json":
@@ -61,7 +60,7 @@ def excute(self):
             DIRPATH.SNAKEMAKE_FILEPATH,
             use_conda=True,
             cores=2,
-            workdir=f"{os.path.dirname(DIRPATH.ROOT_DIR)}",
+            workdir=f"{os.path.dirname(DIRPATH.STUDIO_DIR)}",
         )
 
     def set_smk_config(self):
@@ -73,7 +72,7 @@ def set_smk_config(self):
             "params": self.params,
         }
         ConfigWriter.write(
-            dirname=DIRPATH.ROOT_DIR,
+            dirname=DIRPATH.STUDIO_DIR,
             filename=DIRPATH.SNAKEMAKE_CONFIG_YML,
             config=config,
         )

diff --git a/studio/core/rules/const.py b/studio/core/rules/const.py
@@ -1,6 +1,3 @@
-import os
+from os.path import abspath, dirname
 
-optinist_dirname = os.path.dirname(
-    os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-)
-OPTINIST_DIRPATH = f"{optinist_dirname}"
+ROOT_DIRPATH = dirname(dirname(dirname(dirname(abspath(__file__)))))
diff --git a/studio/core/rules/data.py b/studio/core/rules/data.py
@@ -5,9 +5,9 @@
 # - F821: do not import snakemake
 import sys
 
-from const import OPTINIST_DIRPATH
+from const import ROOT_DIRPATH
 
-sys.path.append(OPTINIST_DIRPATH)
+sys.path.append(ROOT_DIRPATH)
 
 from studio.core.models import FILETYPE
 from studio.core.rules.file_writer import FileWriter

diff --git a/studio/core/rules/edit_ROI.py b/studio/core/rules/edit_ROI.py
@@ -5,9 +5,9 @@
 # - F821: do not import snakemake
 import sys
 
-from const import OPTINIST_DIRPATH
+from const import ROOT_DIRPATH
 
-sys.path.append(OPTINIST_DIRPATH)
+sys.path.append(ROOT_DIRPATH)
 
 from studio.core.edit_ROI import EditRoiUtils
 

diff --git a/studio/core/rules/func.py b/studio/core/rules/func.py
@@ -5,9 +5,9 @@
 # - F821: do not import snakemake
 import sys
 
-from const import OPTINIST_DIRPATH
+from const import ROOT_DIRPATH
 
-sys.path.append(OPTINIST_DIRPATH)
+sys.path.append(ROOT_DIRPATH)
 
 from studio.core.dir_path import DIRPATH
 from studio.core.rules.runner import Runner

diff --git a/studio/core/snakemake/snakemake_executor.py b/studio/core/snakemake/snakemake_executor.py
@@ -17,7 +17,7 @@ def snakemake_execute(unique_id: str, params: SmkParam):
         forceall=params.forceall,
         cores=params.cores,
         use_conda=params.use_conda,
-        workdir=f"{os.path.dirname(DIRPATH.ROOT_DIR)}",
+        workdir=f"{os.path.dirname(DIRPATH.STUDIO_DIR)}",
         log_handler=[Logger(unique_id).smk_logger],
     )
 

diff --git a/studio/core/snakemake/snakemake_writer.py b/studio/core/snakemake/snakemake_writer.py
@@ -7,7 +7,7 @@ class SmkConfigWriter:
     @classmethod
     def write(cls, unique_id, flow_config):
         ConfigWriter.write(
-            dirname=DIRPATH.ROOT_DIR,
+            dirname=DIRPATH.STUDIO_DIR,
             filename=DIRPATH.SNAKEMAKE_CONFIG_YML,
             config=flow_config,
         )

diff --git a/studio/core/utils/filepath_finder.py b/studio/core/utils/filepath_finder.py
@@ -10,15 +10,15 @@ def find_filepath(name, category) -> Optional[str]:
     name, _ = os.path.splitext(name)
 
     filepaths = glob(
-        join_filepath([DIRPATH.ROOT_DIR, "wrappers", "**", category, f"{name}.yaml"]),
+        join_filepath([DIRPATH.STUDIO_DIR, "wrappers", "**", category, f"{name}.yaml"]),
         recursive=True,
     )
     return filepaths[0] if len(filepaths) > 0 else None
 
 
 def find_param_filepath(name: str):
     if name in ["snakemake", "nwb"]:
-        return join_filepath([DIRPATH.ROOT_DIR, "core", name, f"{name}.yaml"])
+        return join_filepath([DIRPATH.STUDIO_DIR, "core", name, f"{name}.yaml"])
     else:
         return find_filepath(name, "params")
 

diff --git a/studio/tests/core/experiment/test_expt_reader.py b/studio/tests/core/experiment/test_expt_reader.py
@@ -3,7 +3,7 @@
 from studio.core.experiment.experiment_reader import ExptConfigReader
 from studio.core.workflow.workflow import Edge, Node, NodeData, NodePosition, Style
 
-expt_filepath = f"{DIRPATH.OPTINIST_DIR}/output_test/0123/experiment.yaml"
+expt_filepath = f"{DIRPATH.DATA_DIR}/output_test/0123/experiment.yaml"
 
 
 def test_read():

diff --git a/studio/tests/core/experiment/test_expt_writer.py b/studio/tests/core/experiment/test_expt_writer.py
@@ -37,7 +37,7 @@
     )
 }
 
-dirpath = f"{DIRPATH.OPTINIST_DIR}/output/unique_id"
+dirpath = f"{DIRPATH.DATA_DIR}/output/unique_id"
 
 
 def test_create_config() -> ExptConfig:

diff --git a/studio/tests/core/snakemake/test_snakemake_executor.py b/studio/tests/core/snakemake/test_snakemake_executor.py
@@ -22,8 +22,8 @@
 )
 
 shutil.copyfile(
-    f"{DIRPATH.OPTINIST_DIR}/config.yaml",
-    f"{DIRPATH.ROOT_DIR}/config.yaml",
+    f"{DIRPATH.DATA_DIR}/config.yaml",
+    f"{DIRPATH.STUDIO_DIR}/config.yaml",
 )
 
 
@@ -84,7 +84,7 @@ def test_snakemake_execute():
     ),
 }
 
-output_dirpath = f"{DIRPATH.OPTINIST_DIR}/output/snakemake"
+output_dirpath = f"{DIRPATH.DATA_DIR}/output/snakemake"
 
 
 def test_snakemake_delete_dependencies():

diff --git a/studio/tests/core/snakemake/test_snakemake_writer.py b/studio/tests/core/snakemake/test_snakemake_writer.py
@@ -4,7 +4,7 @@
 from studio.core.snakemake.snakemake_writer import SmkConfigWriter
 
 unique_id = "smk_test"
-output_fileapth = f"{DIRPATH.OPTINIST_DIR}/output/{unique_id}/config.yaml"
+output_fileapth = f"{DIRPATH.DATA_DIR}/output/{unique_id}/config.yaml"
 
 
 def test():

diff --git a/studio/tests/core/test_dir_path.py b/studio/tests/core/test_dir_path.py
@@ -4,5 +4,5 @@
 
 
 def test_dir_path():
-    assert os.path.exists(DIRPATH.OPTINIST_DIR)
-    assert os.path.exists(DIRPATH.ROOT_DIR)
+    assert os.path.exists(DIRPATH.DATA_DIR)
+    assert os.path.exists(DIRPATH.STUDIO_DIR)
diff --git a/studio/tests/core/utils/test_config_handler.py b/studio/tests/core/utils/test_config_handler.py
@@ -5,7 +5,7 @@
 from studio.core.utils.filepath_creater import join_filepath
 from studio.core.utils.filepath_finder import find_param_filepath
 
-dirpath = f"{DIRPATH.OPTINIST_DIR}/output"
+dirpath = f"{DIRPATH.DATA_DIR}/output"
 filename = "test.yaml"
 
 

diff --git a/studio/tests/core/utils/test_filepath_creater.py b/studio/tests/core/utils/test_filepath_creater.py
@@ -2,7 +2,7 @@
 
 from studio.core.dir_path import DIRPATH
 
-filepath = f"{DIRPATH.OPTINIST_DIR}/output/test.txt"
+filepath = f"{DIRPATH.DATA_DIR}/output/test.txt"
 
 
 def test_create_filepath():

diff --git a/studio/tests/core/utils/test_pickle_handler.py b/studio/tests/core/utils/test_pickle_handler.py
@@ -3,7 +3,7 @@
 from studio.core.dir_path import DIRPATH
 from studio.core.utils.pickle_handler import PickleReader, PickleWriter
 
-filepath = f"{DIRPATH.OPTINIST_DIR}/output/0123/func2/func2.pkl"
+filepath = f"{DIRPATH.DATA_DIR}/output/0123/func2/func2.pkl"
 
 
 def test_PickleWriter():
@@ -15,7 +15,7 @@ def test_PickleWriter():
     assert os.path.exists(filepath)
 
 
-filepath = f"{DIRPATH.OPTINIST_DIR}/output_test/0123/func1/func1.pkl"
+filepath = f"{DIRPATH.DATA_DIR}/output_test/0123/func1/func1.pkl"
 
 
 def test_PickleReader():

diff --git a/studio/tests/core/workflow/test_workflow_result.py b/studio/tests/core/workflow/test_workflow_result.py
@@ -8,14 +8,14 @@
 unique_id = "result_test"
 node_id_list = ["func1", "func2"]
 
-workflow_dirpath = f"{DIRPATH.OPTINIST_DIR}/output_test/{unique_id}"
-pickle_path = f"{DIRPATH.OPTINIST_DIR}/output_test/{unique_id}/func1/func1.pkl"
+workflow_dirpath = f"{DIRPATH.DATA_DIR}/output_test/{unique_id}"
+pickle_path = f"{DIRPATH.DATA_DIR}/output_test/{unique_id}/func1/func1.pkl"
 
 
 def test_WorkflowResult_get():
     shutil.copytree(
         workflow_dirpath,
-        f"{DIRPATH.OPTINIST_DIR}/output/{unique_id}",
+        f"{DIRPATH.DATA_DIR}/output/{unique_id}",
         dirs_exist_ok=True,
     )
     output = WorkflowResult(unique_id=unique_id).get(node_id_list)

diff --git a/studio/tests/routers/test_experiment.py b/studio/tests/routers/test_experiment.py
@@ -11,7 +11,7 @@
 
 unique_id = "0123"
 
-output_test_dir = f"{DIRPATH.OPTINIST_DIR}/output_test"
+output_test_dir = f"{DIRPATH.DATA_DIR}/output_test"
 
 shutil.copytree(
     f"{output_test_dir}/{unique_id}",
@@ -39,7 +39,7 @@ def test_import():
 
 def test_delete():
     dirname = "delete_dir"
-    dirpath = join_filepath([f"{DIRPATH.OPTINIST_DIR}/output", dirname])
+    dirpath = join_filepath([f"{DIRPATH.DATA_DIR}/output", dirname])
     os.makedirs(dirpath, exist_ok=True)
     assert os.path.exists(dirpath)
     response = client.delete(f"/experiments/{dirname}")

diff --git a/studio/tests/routers/test_hdf5.py b/studio/tests/routers/test_hdf5.py
@@ -19,7 +19,7 @@ def test_hdf5():
 
 
 def test_HDF5Getter():
-    output = HDF5Getter.get(f"{DIRPATH.OPTINIST_DIR}/input/files/test.nwb")
+    output = HDF5Getter.get(f"{DIRPATH.DATA_DIR}/input/files/test.nwb")
 
     assert isinstance(output, list)
     assert isinstance(output[0], HDF5Node)
diff --git a/studio/tests/routers/test_outputs.py b/studio/tests/routers/test_outputs.py
@@ -5,7 +5,7 @@
 
 client = TestClient(router)
 
-timeseries_dirpath = f"{DIRPATH.OPTINIST_DIR}/output/0123/func1/fluorescence.json"
+timeseries_dirpath = f"{DIRPATH.DATA_DIR}/output/0123/func1/fluorescence.json"
 
 
 def test_inittimedata():