Upgrade script

MANIFEST.in

@@ -1,4 +1,3 @@
 include LICENSE README.rst
 recursive-include docs *
-recursive-include scripts *
 include nixio/info.json

nixio/cmd/__init__.py

@@ -1,3 +0,0 @@
-from .validate import main as validatemain
-
-__all__ = ["validatemain"]

nixio/cmd/upgrade.py

@@ -0,0 +1,219 @@
+import argparse
+import nixio as nix
+import h5py
+
+
+def get_file_version(fname):
+    with h5py.File(fname, mode="r") as hfile:
+        return tuple(hfile.attrs["version"])
+
+
+def has_valid_file_id(fname):
+    with h5py.File(fname, mode="r") as hfile:
+        fileid = hfile.attrs.get("id")
+        if fileid and nix.util.is_uuid(fileid):
+            return True
+    return False
+
+
+def add_file_id(fname):
+    """
+    Returns a closure that binds the filename if a file ID is required. When
+    the return value is called, it adds a UUID to the file header.
+    """
+    if has_valid_file_id(fname):
+        return None
+
+    def add_id():
+        "Add a UUID to the file header"
+        with h5py.File(fname, mode="a") as hfile:
+            if has_valid_file_id(fname):
+                return
+            print("Adding file id")
+            hfile.attrs["id"] = nix.util.create_id()
+    return add_id
+
+
+def update_property_values(fname):
+    """
+    Returns a closure that binds the filename if at least one Property update
+    is required. When the return value is called, it rewrites all the metadata
+    Property objects to the new format.
+    """
+    props = list()
+
+    with h5py.File(fname, mode="r") as hfile:
+        sections = hfile["metadata"]
+
+        def find_props(name, group):
+            if isinstance(group, h5py.Dataset) and len(group.dtype):
+                # structured/compound dtypes have non-zero length
+                props.append(group.name)
+
+        sections.visititems(find_props)
+
+    if not props:
+        return None
+
+    def update_props():
+        for propname in props:
+            with h5py.File(fname, mode="a") as hfile:
+                prop = hfile[propname]
+                if not (isinstance(prop, h5py.Dataset) and len(prop.dtype)):
+                    # File was possibly changed since the tasks were
+                    # collected.  File may have been submitted twice or
+                    # multiple instances of the script could be running.
+                    # skip this prop
+                    continue
+
+                print(f"Fixing {propname}")
+                # pull out the old extra attributes
+                uncertainty = prop["uncertainty"]
+                reference = prop["reference"]
+                filename = prop["filename"]
+                encoder = prop["encoder"]
+                checksum = prop["checksum"]
+
+                # replace base prop
+                values = prop["value"]
+                dt = values.dtype
+                del hfile[propname]
+                newprop = create_property(hfile, propname,
+                                          dtype=dt, data=values)
+
+                # Create properties for any extra attrs that are set
+                if len(set(uncertainty)) > 1:
+                    # multiple values, make new prop
+                    create_property(hfile, propname + ".uncertainty",
+                                    dtype=float, data=uncertainty)
+                elif any(uncertainty):
+                    # single, unique, non-zero value; add to main prop attr
+                    newprop.attrs["uncertainty"] = uncertainty[0]
+
+                if any(reference):
+                    create_property(hfile, propname + ".reference",
+                                    dtype=nix.util.vlen_str_dtype,
+                                    data=reference)
+
+                if any(filename):
+                    create_property(hfile, propname + ".filename",
+                                    dtype=nix.util.vlen_str_dtype,
+                                    data=filename)
+
+                if any(encoder):
+                    create_property(hfile, propname + ".encoder",
+                                    dtype=nix.util.vlen_str_dtype,
+                                    data=encoder)
+
+                if any(checksum):
+                    create_property(hfile, propname + ".checksum",
+                                    dtype=nix.util.vlen_str_dtype,
+                                    data=checksum)
+
+    update_props.__doc__ = "Update {} properties".format(len(props))
+    return update_props
+
+
+def create_property(hfile, name, dtype, data):
+    prop = hfile.create_dataset(name, dtype=dtype, data=data)
+    prop.attrs["name"] = name.split("/")[-1]
+    prop.attrs["entity_id"] = nix.util.create_id()
+    prop.attrs["created_at"] = nix.util.time_to_str(nix.util.now_int())
+    prop.attrs["updated_at"] = nix.util.time_to_str(nix.util.now_int())
+    return prop
+
+
+def update_format_version(fname):
+    """
+    Returns a closure that binds the filename. When the return value is
+    called, it updates the version in the header to the version in the library.
+    """
+    def update_ver():
+        with h5py.File(fname, mode="a") as hfile:
+            hfile.attrs["version"] = nix.file.HDF_FF_VERSION
+    lib_verstr = ".".join(str(v) for v in nix.file.HDF_FF_VERSION)
+    update_ver.__doc__ = f"Update the file format version to {lib_verstr}"
+    return update_ver
+
+
+def collect_tasks(fname):
+    file_ver = get_file_version(fname)
+    file_verstr = ".".join(str(v) for v in file_ver)
+    lib_verstr = ".".join(str(v) for v in nix.file.HDF_FF_VERSION)
+    if file_ver >= nix.file.HDF_FF_VERSION:
+        print(f"{fname}: Up to date ({file_verstr})")
+        return
+
+    # even if the version string indicates the file is old, check format
+    # details before scheduling tasks
+    tasks = list()
+    id_task = add_file_id(fname)
+    if id_task:
+        tasks.append(id_task)
+
+    props_task = update_property_values(fname)
+    if props_task:
+        tasks.append(props_task)
+
+    # always update the format last
+    tasks.append(update_format_version(fname))
+
+    # print task list
+    print(f"{fname}: {file_verstr} -> {lib_verstr}")
+    print("  - " + "\n  - ".join(t.__doc__ for t in tasks) + "\n")
+
+    return tasks
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Upgrade NIX files to newest version"
+    )
+    parser.add_argument("-f", "--force", action="store_true",
+                        help="overwrite existing files without prompting")
+    parser.add_argument("file", type=str, nargs="+",
+                        help="path to file to upgrade (at least one)")
+    args = parser.parse_args()
+    filenames = args.file
+
+    tasks = dict()
+    for fname in filenames:
+        tasklist = collect_tasks(fname)
+        if not tasklist:
+            continue
+
+        tasks[fname] = tasklist
+
+    if not tasks:
+        return
+
+    force = args.force
+    if not force:
+        print("""
+PLEASE READ CAREFULLY
+
+If you choose to continue, the changes listed above will be applied to the
+respective files. This will make the files unreadable by older NIX library
+versions. Although this procedure is generally fast and safe, interrupting it
+may leave files in a corrupted state.
+
+MAKE SURE YOUR FILES AND DATA ARE BACKED UP BEFORE CONTINUING.
+        """)
+        conf = None
+
+        while conf not in ("y", "n", "yes", "no"):
+            conf = input("Continue with changes? [yes/no] ")
+            conf = conf.lower()
+    else:
+        conf = "yes"
+
+    if conf in ("y", "yes"):
+        for fname, tasklist in tasks.items():
+            print(f"Processing {fname} ", end="", flush=True)
+            for task in tasklist:
+                task()
+            print("done")
+
+
+if __name__ == "__main__":
+    main()

nixio/cmd/validate.py

@@ -1,16 +1,8 @@
-import sys
 import os
+import argparse
 import nixio as nix
 
 
-def usage():
-    print("Usage")
-    print("  nix-validate <nixfile>...")
-    print()
-    print("Args")
-    print("  <nixfile>...    One or more NIX files")
-
-
 def format_obj(obj):
     return "{} '{}' (ID: {})".format(type(obj).__name__, obj.name, obj.id)
 
@@ -46,13 +38,15 @@ def validate(filename):
 
 
 def main():
-    args = sys.argv
-    if len(args) < 2:
-        usage()
-        sys.exit(1)
-
-    nixfnames = args[1:]
-    for nixfn in nixfnames:
+    parser = argparse.ArgumentParser(
+        description="Validate NIX files"
+    )
+    parser.add_argument("file", type=str, nargs="+",
+                        help="path to file to validate (at least one)")
+    args = parser.parse_args()
+    filenames = args.file
+
+    for nixfn in filenames:
         if os.path.exists(nixfn):
             validate(nixfn)
         else: