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fix formatting
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@jburel
jburel committed Apr 24, 2024
1 parent c6f9db2 commit b912061
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Showing 2 changed files with 65 additions and 43 deletions.
7 changes: 1 addition & 6 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -62,11 +62,6 @@ repos:
"--rst-roles=class,func,ref,module,const",
]

- repo: https://github.com/pre-commit/mirrors-mypy
rev: v1.9.0
hooks:
- id: mypy

- repo: https://github.com/pre-commit/mirrors-mypy
rev: v1.9.0
hooks:
Expand All @@ -75,7 +70,7 @@ repos:
--disallow-untyped-defs,
--ignore-missing-imports,
]
exclude: tests/
exclude: test/

- repo: https://github.com/adrienverge/yamllint.git
rev: v1.35.1
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101 changes: 64 additions & 37 deletions src/omero_mkngff/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,9 +43,11 @@
omero mkngff sql ${fileset} ${zarrdir} --zarr_name "nice.ome.zarr"
"""
FS_SUFFIX_HELP = ("New Fileset.templatePrefix will be old Fileset.templatePrefix + fs_suffix. "
"Default is to use _mkngff. "
"Use 'None' to specify an empty string (new templatePrefix is same as old).")
FS_SUFFIX_HELP = (
"New Fileset.templatePrefix will be old Fileset.templatePrefix + fs_suffix. "
"Default is to use _mkngff. "
"Use 'None' to specify an empty string (new templatePrefix is same as old)."
)

SETUP = """
Expand Down Expand Up @@ -151,42 +153,59 @@ def _configure(self, parser: Parser) -> None:

sql = sub.add_parser("sql", help="generate SQL statement")
sql.add_argument(
"--secret", help="DB UUID for protecting SQL statements", default="SECRETUUID"
"--secret",
help="DB UUID for protecting SQL statements",
default="SECRETUUID",
)
sql.add_argument("--zarr_name", help="Nicer name for zarr directory if desired")
sql.add_argument(
"--symlink_repo",
help=("Create symlinks from Fileset to symlink_target using"
"this ManagedRepo path, e.g. /data/OMERO/ManagedRepository")
help=(
"Create symlinks from Fileset to symlink_target using"
"this ManagedRepo path, e.g. /data/OMERO/ManagedRepository"
),
)
sql.add_argument(
"--bfoptions", action="store_true",
help=("Create data.zarr.bfoptions file if --symlink_repo has been provided")
"--bfoptions",
action="store_true",
help=(
"Create data.zarr.bfoptions file if --symlink_repo has been provided"
),
)
sql.add_argument(
"--clientpath",
help=("Base path to create clientpath/path/to/img.zarr/")
"--clientpath", help=("Base path to create clientpath/path/to/img.zarr/")
)
sql.add_argument("--fs_suffix", default="_mkngff", help=FS_SUFFIX_HELP)
sql.add_argument("fileset_id", type=int)
sql.add_argument("symlink_target")
sql.set_defaults(func=self.sql)

# symlink command to ONLY create symlinks - useful if you have previously generated
# symlink command to ONLY create symlinks
# useful if you have previously generated
# the corresponding sql for a Fileset
symlink = sub.add_parser("symlink", help="Create managed repo symlink")
symlink.add_argument("symlink_repo", help=(
"Create symlinks from Fileset to symlink_target using"
"this ManagedRepo path, e.g. /data/OMERO/ManagedRepository"))
symlink.add_argument(
"symlink_repo",
help=(
"Create symlinks from Fileset to symlink_target using"
"this ManagedRepo path, e.g. /data/OMERO/ManagedRepository"
),
)
symlink.add_argument("fileset_id", type=int)
symlink.add_argument("symlink_target")
symlink.add_argument("--bfoptions", action="store_true", help="Create data.zarr.bfoptions file")
symlink.add_argument(
"--bfoptions", action="store_true", help="Create data.zarr.bfoptions file"
)
symlink.add_argument("--fs_suffix", default="_mkngff", help=FS_SUFFIX_HELP)
symlink.set_defaults(func=self.symlink)

bfoptions = sub.add_parser("bfoptions", help="Create data.zarr.bfoptions in Fileset")
bfoptions.add_argument("symlink_repo", help=(
"The ManagedRepo path, e.g. /data/OMERO/ManagedRepository"))
bfoptions = sub.add_parser(
"bfoptions", help="Create data.zarr.bfoptions in Fileset"
)
bfoptions.add_argument(
"symlink_repo",
help=("The ManagedRepo path, e.g. /data/OMERO/ManagedRepository"),
)
bfoptions.add_argument("fileset_id", type=int)
bfoptions.add_argument("symlink_target")
bfoptions.add_argument("--fs_suffix", default="_mkngff", help=FS_SUFFIX_HELP)
Expand All @@ -207,11 +226,14 @@ def sql(self, args: Namespace) -> None:
self.ctx.die(401, f"Symlink target does not exist: {args.symlink_target}")
return

# If symlink dir exists, we assume that this fileset has been processed -> skip...
# If symlink dir exists, we assume that
# this fileset has been processed -> skip...
if args.symlink_repo:
symlink_dir = self.get_symlink_dir(args.symlink_repo, prefix)
if os.path.exists(symlink_dir):
self.ctx.err(f"Symlink dir exists at {symlink_dir} - skipping sql output")
self.ctx.err(
f"Symlink dir exists at {symlink_dir} - skipping sql output"
)
return

rows = []
Expand All @@ -221,16 +243,21 @@ def sql(self, args: Namespace) -> None:
row_clientpath = "unknown"
if args.clientpath:
# zarr_path is relative URL from .zarr /to/file/
zarr_path = str(row_path).replace(args.symlink_target, '')
zarr_path = str(row_path).replace(args.symlink_target, "")
row_clientpath = f"{args.clientpath}{zarr_path}/{row_name}"

# remove common path to shorten
row_path = str(row_path).replace(f"{symlink_path.parent}", "")
row_path = str(row_path).replace(f"{symlink_path.parent}", "") # type: ignore # noqa
if str(row_path).startswith("/"):
row_path = str(row_path)[1:] # remove "/" from start
# remove "/" from start
row_path = str(row_path)[1:] # type: ignore
row_full_path = f"{prefix}{self.suffix}/{row_path}"
# pick the first .zattrs file we find, then update to ome.xml if we find it
if setid_target is None and row_name == ".zattrs" or row_name == "METADATA.ome.xml":
if (
setid_target is None
and row_name == ".zattrs"
or row_name == "METADATA.ome.xml"
):
setid_target = [row_full_path, row_name]
rows.append(
ROW.format(
Expand All @@ -241,10 +268,13 @@ def sql(self, args: Namespace) -> None:
)
)

# Add a command to update the Pixels table with path/name using old Fileset ID *before* new Fileset is created
fpath = setid_target[0]
fname = setid_target[1]
self.ctx.out(f"UPDATE pixels SET name = '{fname}', path = '{fpath}' where image in (select id from Image where fileset = {args.fileset_id});")
# Add a command to update the Pixels table with
# path/name using old Fileset ID *before* new Fileset is created
fpath = setid_target[0] # type: ignore
fname = setid_target[1] # type: ignore
self.ctx.out(
f"UPDATE pixels SET name = '{fname}', path = '{fpath}' where image in (select id from Image where fileset = {args.fileset_id});" # noqa
)

self.ctx.out(
TEMPLATE.format(
Expand Down Expand Up @@ -274,7 +304,7 @@ def symlink(self, args: Namespace) -> None:
if args.bfoptions:
self.write_bfoptions(args.symlink_repo, prefix, args.symlink_target)

def get_prefix(self, args):
def get_prefix(self, args): # type: ignore

conn = self.ctx.conn(args) # noqa
q = conn.sf.getQueryService()
Expand All @@ -296,36 +326,33 @@ def get_prefix(self, args):

return prefix

def get_symlink_dir(self, symlink_repo, prefix):
def get_symlink_dir(self, symlink_repo, prefix): # type: ignore
prefix_dir = os.path.join(symlink_repo, prefix)
self.ctx.err(f"Checking for prefix_dir {prefix_dir}")
if not os.path.exists(prefix_dir):
self.ctx.die(402, f"Fileset dir does not exist: {prefix_dir}")
symlink_dir = f"{prefix_dir}{self.suffix}"
return symlink_dir

def write_bfoptions(self, managed_repo, fsprefix, symlink_target):
def write_bfoptions(self, managed_repo, fsprefix, symlink_target): # type: ignore # noqa
file_path = Path(symlink_target)
mkngff_dir = self.get_symlink_dir(managed_repo, fsprefix)
# os.makedirs(mkngff_dir, exist_ok=True)
zarr_path = os.path.join(mkngff_dir, file_path.name)
bfoptions_path = f"{zarr_path}.bfoptions"
self.ctx.err("write bfoptions to: %s" % bfoptions_path)
with open(bfoptions_path, "w") as f:
f.writelines(["omezarr.list_pixels=false",
"\nomezarr.quick_read=true"])
f.writelines(["omezarr.list_pixels=false", "\nomezarr.quick_read=true"])

def create_symlink(self, symlink_repo, prefix, symlink_target):
def create_symlink(self, symlink_repo, prefix, symlink_target): # type: ignore # noqa
symlink_path = Path(symlink_target)
symlink_dir = self.get_symlink_dir(symlink_repo, prefix)
self.ctx.err(f"Creating dir at {symlink_dir}")
os.makedirs(symlink_dir, exist_ok=True)

symlink_source = os.path.join(symlink_dir, symlink_path.name)
target_is_directory = os.path.isdir(symlink_target)
self.ctx.err(
f"Creating symlink {symlink_source} -> {symlink_target}"
)
self.ctx.err(f"Creating symlink {symlink_source} -> {symlink_target}")
# ignore if symlink exists
if not os.path.exists(symlink_source):
os.symlink(symlink_target, symlink_source, target_is_directory)
Expand Down

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