deriva-ml 1.10.0__py3-none-any.whl → 1.11.0__py3-none-any.whl

deriva_ml/upload.py

@@ -19,22 +19,20 @@ Here is the directory layout we support:
                                    asset
                                        <asset_table>
                                            file1, file2, ...
-                           <feature_name>.csv    <- needs to have asset_name column remapped before uploading
-            table
-               <schema>
-                   <record_table>
-                      record_table.csv
-            asset
-               <schema>
-                   <asset_table>
-                     file1, file2, ....
-        asset
-            <schema>
-                <asset_table>
-                    <metadata1>
-                        <metadata2>
-                            file1, file2, ....
-
+                           <feature_name>.jsonl    <- needs to have asset_name column remapped before uploading
+                table
+                   <schema>
+                       <record_table>
+                          record_table.csv
+                asset
+                    <schema>
+                        <asset_table>
+                            <metadata1>
+                                <metadata2>
+                                    file1, file2, ....
+                asset-type
+                    <schema>
+                        file1.jsonl, file2.jsonl
 """
 
 import json
@@ -55,27 +53,21 @@ from deriva_ml.deriva_definitions import (
     DerivaMLException,
     FileUploadState,
     UploadState,
+    DerivaSystemColumns,
 )
 from deriva_ml.deriva_model import DerivaModel
 
+
+try:
+    from icecream import ic
+except ImportError:  # Graceful fallback if IceCream isn't installed.
+    ic = lambda *a: None if not a else (a[0] if len(a) == 1 else a)  # noqa
+
+
 upload_root_regex = r"(?i)^.*/deriva-ml"
 
 exec_dir_regex = upload_root_regex + r"/execution/(?P<execution_rid>[-\w]+)"
-exec_asset_dir_regex = (
-    exec_dir_regex + r"/execution-asset/(?P<execution_asset_type>[-\w]+)"
-)
-exec_asset_regex = (
-    exec_asset_dir_regex + r"/(?P<file_name>[-\w]+)[.](?P<file_ext>[a-z0-9]+)$"
-)
-exec_metadata_dir_regex = (
-    exec_dir_regex + r"/execution-metadata/(?P<execution_metadata_type>[-\w]+)"
-)
 
-# May have more than one suffix
-exec_metadata_regex = (
-    exec_metadata_dir_regex
-    + r"/(?P<filename>[-\w]+([.][\w]+)*)[.](?P<file_ext>[a-z0-9]*)$"
-)
 feature_dir_regex = exec_dir_regex + r"/feature"
 feature_table_dir_regex = (
     feature_dir_regex
@@ -89,9 +81,8 @@ feature_asset_regex = (
     feature_asset_dir_regex
     + r"/(?P<file_name>[A-Za-z0-9_-]+)[.](?P<file_ext>[a-z0-9]*)$"
 )
-asset_path_regex = (
-    upload_root_regex + r"/asset/(?P<schema>[-\w]+)/(?P<asset_table>[-\w]*)"
-)
+
+asset_path_regex = exec_dir_regex + r"/asset/(?P<schema>[-\w]+)/(?P<asset_table>[-\w]*)"
 
 asset_file_regex = r"(?P<file_name>[-\w]+)[.](?P<file_ext>[a-z0-9]*)$"
 
@@ -101,24 +92,17 @@ table_regex = (
 )
 
 
-def is_execution_metadata_dir(path: Path) -> Optional[re.Match]:
-    """Path matches the patten for execution metadata directory."""
-    return re.match(exec_metadata_dir_regex + "$", path.as_posix())
-
-
-def is_execution_asset_dir(path: Path) -> Optional[re.Match]:
-    """Path maths the pattern for execution asset directory"""
-    return re.match(exec_asset_dir_regex + "$", path.as_posix())
-
-
 def is_feature_dir(path: Path) -> Optional[re.Match]:
     """Path matches the pattern for where the table for a feature would go."""
     return re.match(feature_table_dir_regex + "$", path.as_posix())
 
 
-def is_feature_asset_dir(path: Path) -> Optional[re.Match]:
-    """Path matches the pattern for feature, asset, returns the feature components."""
-    return re.match(feature_asset_dir_regex + "$", path.as_posix())
+def normalize_asset_dir(path: str) -> Optional[tuple[str, str]]:
+    """Parse a path to an asset file and return the asset table name and file name"""
+
+    if not (m := re.match(asset_path_regex, path)):
+        return None
+    return f"{m['schema']}/{m['asset_table']}", Path(path).name
 
 
 def upload_root(prefix: Path | str) -> Path:
@@ -128,20 +112,6 @@ def upload_root(prefix: Path | str) -> Path:
     return path
 
 
-def asset_root(prefix: Path | str) -> Path:
-    """Return the top level directory of where to put asset directories to be uploaded."""
-    path = upload_root(prefix) / "asset"
-    path.mkdir(exist_ok=True, parents=True)
-    return path
-
-
-def asset_table_dir(prefix: Path, asset_schema, asset_table) -> Path:
-    """Return the top level directory of where to asset table will be uploaded."""
-    path = asset_root(prefix) / asset_schema / asset_table
-    path.mkdir(exist_ok=True, parents=True)
-    return path
-
-
 def execution_rids(prefix: Path | str) -> list[RID]:
     """Return a list of all the execution RIDS that have files waiting to be uploaded."""
     path = upload_root(prefix) / "execution"
@@ -155,42 +125,16 @@ def execution_root(prefix: Path | str, exec_rid) -> Path:
     return path
 
 
-def execution_asset_root(prefix: Path | str, exec_rid: str) -> Path:
-    """Path to directory into which execution assets should be located"""
-
-    path = execution_root(prefix, exec_rid) / "execution-asset"
-    path.mkdir(parents=True, exist_ok=True)
-    return path
-
-
-@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
-def execution_asset_dir(prefix: Path | str, exec_rid: str, asset_type: str) -> Path:
-    """Return the path to a directory in which to place execution assets of a specified type are to be uploaded."""
-    path = execution_asset_root(prefix, exec_rid) / asset_type
-    path.mkdir(parents=True, exist_ok=True)
-    return path
-
-
-def execution_metadata_root(prefix: Path | str, exec_rid: str) -> Path:
-    """Path to directory into which execution metadata should be located."""
-    path = execution_root(prefix, exec_rid) / "execution-metadata"
-    path.mkdir(parents=True, exist_ok=True)
-    return path
-
-
-def execution_metadata_dir(
-    prefix: Path | str, exec_rid: str, metadata_type: str
-) -> Path:
-    """Return the path to a directory in which to place execution metadata of a specified type are to be uploaded."""
-
-    path = execution_metadata_root(prefix, exec_rid) / metadata_type
+def feature_root(prefix: Path | str, exec_rid: str) -> Path:
+    """Return the path to the directory in which features for the specified execution should be placed."""
+    path = execution_root(prefix, exec_rid) / "feature"
     path.mkdir(parents=True, exist_ok=True)
     return path
 
 
-def feature_root(prefix: Path | str, exec_rid: str) -> Path:
+def asset_root(prefix: Path | str, exec_rid: str) -> Path:
     """Return the path to the directory in which features for the specified execution should be placed."""
-    path = execution_root(prefix, exec_rid) / "feature"
+    path = execution_root(prefix, exec_rid) / "asset"
     path.mkdir(parents=True, exist_ok=True)
     return path
 
@@ -221,41 +165,10 @@ def feature_value_path(
     """
     return (
         feature_dir(prefix, exec_rid, schema, target_table, feature_name)
-        / f"{feature_name}.csv"
+        / f"{feature_name}.jsonl"
     )
 
 
-def feature_asset_dir(
-    prefix: Path | str,
-    exec_rid: str,
-    schema: str,
-    target_table: str,
-    feature_name: str,
-    asset_table: str,
-) -> Path:
-    """Return the path to a directory in which to place feature assets for a named feature are to be uploaded.
-
-    Args:
-        prefix: Location of upload root directory
-        exec_rid: RID of the execution for the feature asset
-        schema: Domain schema
-        target_table: Name of the target table for the feature.
-        feature_name: Name of the feature
-        asset_table: Name of the asset table for the feature.
-
-    Returns:
-        Path to directory in which feature asset files are placed.
-    """
-    path = (
-        feature_dir(prefix, exec_rid, schema, target_table, feature_name)
-        / "asset"
-        / asset_table
-    )
-
-    path.mkdir(parents=True, exist_ok=True)
-    return path
-
-
 def table_path(prefix: Path | str, schema: str, table: str) -> Path:
     """Return the path to a CSV file in which to place table values that are to be uploaded.
 
@@ -286,7 +199,7 @@ def asset_table_upload_spec(model: DerivaModel, asset_table: str | Table):
     asset_table = model.name_to_table(asset_table)
     schema = model.name_to_table(asset_table).schema.name
     metadata_path = "/".join([rf"(?P<{c}>[-\w]+)" for c in metadata_columns])
-    asset_path = f"{upload_root_regex}/asset/{schema}/{asset_table.name}/{metadata_path}/{asset_file_regex}"
+    asset_path = f"{exec_dir_regex}/asset/{schema}/{asset_table.name}/{metadata_path}/{asset_file_regex}"
     asset_table = model.name_to_table(asset_table)
     schema = model.name_to_table(asset_table).schema.name
     return {
@@ -321,72 +234,7 @@ def bulk_upload_configuration(model: DerivaModel) -> dict[str, Any]:
         if model.asset_metadata(t)
     ]
     return {
-        "asset_mappings": [
-            {
-                # Upload  any files that may have been created by the program execution.  These are  in the
-                # Execution_Metadata directory
-                "column_map": {
-                    "MD5": "{md5}",
-                    "URL": "{URI}",
-                    "Length": "{file_size}",
-                    "Filename": "{file_name}",
-                    "Execution_Metadata_Type": "{execution_metadata_type_name}",
-                },
-                "file_pattern": exec_metadata_regex,
-                "target_table": ["deriva-ml", "Execution_Metadata"],
-                "checksum_types": ["sha256", "md5"],
-                "hatrac_options": {"versioned_urls": True},
-                "hatrac_templates": {
-                    "hatrac_uri": "/hatrac/execution_metadata/{md5}.{file_name}",
-                    "content-disposition": "filename*=UTF-8''{file_name}.{file_ext}",
-                },
-                "record_query_template": "/entity/{target_table}/MD5={md5}&Filename={file_name}",
-                "metadata_query_templates": [
-                    "/attribute/deriva-ml:Execution_Metadata_Type/Name={execution_metadata_type}/execution_metadata_type_name:=Name"
-                ],
-            },
-            {
-                # Upload the contents of the Execution_Asset directory.
-                "column_map": {
-                    "MD5": "{md5}",
-                    "URL": "{URI}",
-                    "Length": "{file_size}",
-                    "Filename": "{file_name}",
-                    "Execution_Asset_Type": "{execution_asset_type_name}",
-                },
-                "file_pattern": exec_asset_regex,
-                "target_table": ["deriva-ml", "Execution_Asset"],
-                "checksum_types": ["sha256", "md5"],
-                "hatrac_options": {"versioned_urls": True},
-                "hatrac_templates": {
-                    "hatrac_uri": "/hatrac/execution_asset/{md5}.{file_name}",
-                    "content-disposition": "filename*=UTF-8''{file_name}.{file_ext}",
-                },
-                "record_query_template": "/entity/{target_table}/MD5={md5}&Filename={file_name}",
-                "metadata_query_templates": [
-                    "/attribute/deriva-ml:Execution_Asset_Type/Name={execution_asset_type}/execution_asset_type_name:=Name"
-                ],
-            },
-            {
-                # Upload the assets for a feature table.
-                "column_map": {
-                    "MD5": "{md5}",
-                    "URL": "{URI}",
-                    "Length": "{file_size}",
-                    "Filename": "{file_name}",
-                },
-                "file_pattern": feature_asset_regex,  # Sets target_table, feature_name, asset_table
-                "target_table": ["{schema}", "{asset_table}"],
-                "checksum_types": ["sha256", "md5"],
-                "hatrac_options": {"versioned_urls": True},
-                "hatrac_templates": {
-                    "hatrac_uri": "/hatrac/{asset_table}/{md5}.{file_name}",
-                    "content-disposition": "filename*=UTF-8''{file_name}",
-                },
-                "record_query_template": "/entity/{target_table}/MD5={md5}&Filename={file_name}",
-            },
-        ]
-        + asset_tables_with_metadata
+        "asset_mappings": asset_tables_with_metadata
         + [
             {
                 # Upload assets into an asset table of an asset table without any metadata
@@ -396,7 +244,8 @@ def bulk_upload_configuration(model: DerivaModel) -> dict[str, Any]:
                     "Length": "{file_size}",
                     "Filename": "{file_name}",
                 },
-                "target_table": [model.domain_schema, "{asset_table}"],
+                "asset_type": "fetch",
+                "target_table": ["{schema}", "{asset_table}"],
                 "file_pattern": asset_path_regex
                 + "/"
                 + asset_file_regex,  # Sets schema, asset_table, file_name, file_ext
@@ -548,49 +397,63 @@ def upload_asset(
         raise e
 
 
-class UploadAssetDirectory:
-    def __init__(self, model: DerivaModel, schema: str, table: str, prefix: Path):
-        self.prefix = prefix
-        self.path = asset_table_dir(
-            prefix=prefix, asset_schema=schema, asset_table=table
+def asset_file_path(
+    prefix: Path | str,
+    exec_rid: RID,
+    asset_table: Table,
+    file_name: str,
+    metadata: dict[str, Any],
+) -> Path:
+    """Return the file in which to place  assets of a specified type are to be uploaded.
+
+    Args:
+        prefix: Path prefix to use.
+        exec_rid: RID to use.
+        asset_table: Table in which to place assets.
+        file_name: File name to use.
+        metadata: Any additional metadata to add to the asset
+    Returns:
+        Path to directory in which to place assets of type asset_type.
+    """
+    schema = asset_table.schema.name
+    asset_name = asset_table.name
+
+    path = execution_root(prefix, exec_rid) / "asset" / schema / asset_name
+    metadata = metadata or {}
+    asset_columns = {
+        "Filename",
+        "URL",
+        "Length",
+        "MD5",
+        "Description",
+    }.union(set(DerivaSystemColumns))
+    asset_metadata = {c.name for c in asset_table.columns} - asset_columns
+    if not (asset_metadata >= set(metadata.keys())):
+        raise DerivaMLException(
+            f"Metadata {metadata} does not match asset metadata {asset_metadata}"
         )
-        self.table = table
-        self.schema = schema
-        self.model = model
-
-    def create_file(self, file_name: str, metadata: dict[str, Any]) -> Path:
-        """Return the file in which to place  assets of a specified type are to be uploaded.
-
-        Args:
-            file_name: Name of file to which the contents of the asset will be placed
-            metadata: Any additional metadata to add to the asset
-        Returns:
-            Path to directory in which to place assets of type asset_type.
-        """
-        metadata = metadata or {}
-        asset_metadata = self.model.asset_metadata(self.table)
-        if not (asset_metadata >= set(metadata.keys())):
-            raise DerivaMLException(
-                f"Metadata {metadata} does not match asset metadata {asset_metadata}"
-            )
 
-        path = self.path
-        for m in self.model.asset_metadata(self.table):
-            path = path / metadata.get(m, "None")
-        path.mkdir(parents=True, exist_ok=True)
-        return path / file_name
+    for m in asset_metadata:
+        path = path / metadata.get(m, "None")
+    path.mkdir(parents=True, exist_ok=True)
+    return path / file_name
+
 
+def asset_type_path(prefix: Path | str, exec_rid: RID, asset_table: Table) -> Path:
+    """Return the path to a JSON line file in which to place asset_type information.
 
-def test_upload():
-    """ """
-    ead = execution_asset_dir("foo", "my-rid", "my-asset")
-    emd = execution_metadata_dir("foo", "my-rid", "my-metadata")
-    _fp = feature_value_path("foo", "my-rid", "my-schema", "my-target", "my-feature")
-    fa = feature_asset_dir(
-        "foo", "my-rid", "my-schema", "my-target", "my-feature", "my-asset"
+    Args:
+        prefix: Location of upload root directory
+        exec_rid: Execution RID
+        asset_table: Table in which to place assets.
+
+    Returns:
+        Path to the file in which to place asset_type values for the named asset..
+    """
+    path = (
+        execution_root(prefix, exec_rid=exec_rid)
+        / "asset-type"
+        / asset_table.schema.name
     )
-    _tp = table_path("foo", "my-schema", "my-table")
-    #   _ad = create_asset_dir("foo", "my-schema", "my-asset")
-    _is_md = is_execution_metadata_dir(emd)
-    _is_ea = is_execution_asset_dir(ead)
-    _is_fa = is_feature_asset_dir(fa)
+    path.mkdir(parents=True, exist_ok=True)
+    return path / f"{asset_table.name}.jsonl"

{deriva_ml-1.10.0.dist-info → deriva_ml-1.11.0.dist-info}/METADATA

@@ -1,11 +1,12 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.10.0
+Version: 1.11.0
 Summary: Utilities to simplify use of Dervia and Pandas to create reproducable ML pipelines
 Author-email: ISRD <isrd-dev@isi.edu>
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: bump-my-version
 Requires-Dist: deriva~=1.7.7
 Requires-Dist: pandas
 Requires-Dist: regex~=2024.7.24

deriva_ml-1.11.0.dist-info/RECORD

@@ -0,0 +1,27 @@
+deriva_ml/__init__.py,sha256=r1Z9N5vtZkAET7emqhpAx2bf_xJUp5wHOc4_DIplsG8,1082
+deriva_ml/database_model.py,sha256=58iweWRteLeKKjjeNA9_e7TbUb4Av92lxH2zKvZzwA8,14823
+deriva_ml/dataset.py,sha256=HXzu30n42bDPWhyYC1n87uovU1ThXeafmZ3cqUD1gYw,60827
+deriva_ml/dataset_aux_classes.py,sha256=YxjQnu2kS9kK_f8bGqhmgE6ty9GNeitCxfvReT9vaM0,6537
+deriva_ml/dataset_bag.py,sha256=rA5BrcR1_j3-aj50vzfnoMTxaT2-CkNktYB-6HbunwQ,11848
+deriva_ml/demo_catalog.py,sha256=9Qo3JD4bUIwnL3ngPctc2QBeWApvMR_5UyaK9ockTrY,11536
+deriva_ml/deriva_definitions.py,sha256=2eSbTFQ-9rpctphN4PLo8WdtkzMfhfZr3vJeywt6xPM,8897
+deriva_ml/deriva_ml_base.py,sha256=abATy0Qju3uyJnq9FdAXD3JjZqms04j1HBxdranox58,46265
+deriva_ml/deriva_model.py,sha256=k6P74S0-7yMJw0KDt3apErTjIpCkCwz1f_1t3T-hbLE,12981
+deriva_ml/execution.py,sha256=7xEg8oHyfVVD5TWPYGHM1Vj2CGPJhzhgPqprvm8E2-c,34187
+deriva_ml/execution_configuration.py,sha256=ZdLHLTUcg5V1id1sVjbp7Nm5bjh42ATG7hOGKaiCSj4,4013
+deriva_ml/execution_environment.py,sha256=bCRKrCELDbGQDo7_FKfw7e8iMzVjSRZK3baKkqH5-_0,3264
+deriva_ml/feature.py,sha256=07g0uSrhumdopJluWuWSRMrzagaikAOihqB09bzXBP4,5475
+deriva_ml/history.py,sha256=qTDLDs8Ow_6r7mDO0gZm0Fg81SWKOAgtCU5pzZoDRgM,2828
+deriva_ml/test_functions.py,sha256=-eqLHjjCQCLBNAr1ofbZekNiCOfMISSACRxT_YHER8I,4396
+deriva_ml/upload.py,sha256=RJLZjJrbDEfONbxsxt_tYChQU77FkJeByyONrFKjvAc,16143
+deriva_ml/schema_setup/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+deriva_ml/schema_setup/annotations.py,sha256=v0gTpmWYxRqsQ-bcnQzsr8WowGv2pi9pZUsO3WWnu1U,9528
+deriva_ml/schema_setup/create_schema.py,sha256=hNMc-v5tferd0UjfdB6nBw7Rc_o-Mg6NkPqQGie9YOw,11700
+deriva_ml/schema_setup/policy.json,sha256=77sf0Imy6CAQV0_VwwbA56_KROJ05WXsvT-Wjtkk538,1633
+deriva_ml/schema_setup/table_comments_utils.py,sha256=-2_ubEpoH7ViLVb-ZfW9wZbQ26DTKNgjkCABMzGu4i4,2140
+deriva_ml-1.11.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+deriva_ml-1.11.0.dist-info/METADATA,sha256=H7JTu9ZNl-soQeX0oj2N_AELNu2r6n3NCP5o5LFF5M4,973
+deriva_ml-1.11.0.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+deriva_ml-1.11.0.dist-info/entry_points.txt,sha256=ZiOvrYj022x544TQwi018ujeHRRDahNmwJnzn5ThacM,242
+deriva_ml-1.11.0.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
+deriva_ml-1.11.0.dist-info/RECORD,,

{deriva_ml-1.10.0.dist-info → deriva_ml-1.11.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.0.2)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

deriva_ml-1.10.0.dist-info/RECORD

@@ -1,27 +0,0 @@
-deriva_ml/__init__.py,sha256=r1Z9N5vtZkAET7emqhpAx2bf_xJUp5wHOc4_DIplsG8,1082
-deriva_ml/database_model.py,sha256=58iweWRteLeKKjjeNA9_e7TbUb4Av92lxH2zKvZzwA8,14823
-deriva_ml/dataset.py,sha256=h7Zkhnhy66GhPg6O1ud-YCx-jFKAabWF-nwuIDsR8SU,60785
-deriva_ml/dataset_aux_classes.py,sha256=YxjQnu2kS9kK_f8bGqhmgE6ty9GNeitCxfvReT9vaM0,6537
-deriva_ml/dataset_bag.py,sha256=aOJxFA9t5apjE5BNBrk8Pi9R1Cp8AWnnaL-10P8ELrQ,11515
-deriva_ml/demo_catalog.py,sha256=1442Lbxmlq45_fgFx0SZPag6dZLimXCk57-TRFee3VA,11064
-deriva_ml/deriva_definitions.py,sha256=jNiInYA2Cb1GE4OOT1CofxBygdLDSOmNsw5Wl6NbZQE,8943
-deriva_ml/deriva_ml_base.py,sha256=Yo52Sb_9rujH7ew9aJ_Ys84NZU-Tc3TGV_O--wnaUQA,47307
-deriva_ml/deriva_model.py,sha256=B4gwr3-92IQU-mEZlusgNEnRyulD96esWGS67q9MzHk,12024
-deriva_ml/execution.py,sha256=nPTQ__QHoBTz0gUu8k4CSEeCD4UvttZfy2oDJr9HxKY,30294
-deriva_ml/execution_configuration.py,sha256=yksebWFjAfrar2955L8_D6vUnQlfuvcyrqjOIrvWW90,3368
-deriva_ml/execution_environment.py,sha256=bCRKrCELDbGQDo7_FKfw7e8iMzVjSRZK3baKkqH5-_0,3264
-deriva_ml/feature.py,sha256=7e8WYPCfJSrGxJh9oUTduYSnB5ekybRhXa_0HIigS_w,5459
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