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Shortern paths and symlinks #6

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merged 4 commits into from
Sep 25, 2023
Merged

Shortern paths and symlinks #6

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1a47a68
Move 'converted' into SUFFIX constant
will-moore Aug 25, 2023
c9cb76b
Shortern paths and symlink dirs
will-moore Aug 25, 2023
9f9d1aa
Use 'mkngff' instead of 'converted' for path suffix
will-moore Aug 25, 2023
3031512
Merge remote-tracking branch 'origin/main' into HEAD
joshmoore Aug 28, 2023
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11 changes: 7 additions & 4 deletions src/omero_mkngff/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
from omero.cli import BaseControl, Parser
from omero.sys import ParametersI

SUFFIX = "mkngff"
HELP = """Plugin to swap OMERO filesets with NGFF

CLI plugin used to swap an existing OMERO fileset with
Expand Down Expand Up @@ -197,7 +198,7 @@ def sql(self, args: Namespace) -> None:
self.ctx.die(401, f"Symlink target does not exist: {args.symlink_target}")
return

# create *_converted/path/to/zarr directory containing symlink to data
# create *_SUFFIX/path/to/zarr directory containing symlink to data
if args.symlink_repo:
prefix_dir = os.path.join(args.symlink_repo, prefix)
self.ctx.err(f"Checking for prefix_dir {prefix_dir}")
Expand All @@ -206,7 +207,7 @@ def sql(self, args: Namespace) -> None:
symlink_container = f"{symlink_path.parent}"
if symlink_container.startswith("/"):
symlink_container = symlink_container[1:] # remove "/" from start
symlink_dir = os.path.join(f"{prefix_dir}_converted", symlink_container)
symlink_dir = f"{prefix_dir}_{SUFFIX}"
self.ctx.err(f"Creating dir at {symlink_dir}")
os.makedirs(symlink_dir, exist_ok=True)

Expand All @@ -219,11 +220,13 @@ def sql(self, args: Namespace) -> None:

rows = []
for row_path, row_name, row_mime in self.walk(symlink_path):
# remove common path to shorten
row_path = str(row_path).replace(f"{symlink_path.parent}", "")
if str(row_path).startswith("/"):
row_path = str(row_path)[1:] # remove "/" from start
rows.append(
ROW.format(
PATH=f"{prefix_path}/{prefix_name}_converted/{row_path}/",
PATH=f"{prefix_path}/{prefix_name}_{SUFFIX}/{row_path}/",
NAME=row_name,
MIME=row_mime,
)
Expand All @@ -232,7 +235,7 @@ def sql(self, args: Namespace) -> None:
self.ctx.out(
TEMPLATE.format(
OLD_FILESET=args.fileset_id,
PREFIX=f"{prefix_path}/{prefix_name}_converted/",
PREFIX=f"{prefix_path}/{prefix_name}_{SUFFIX}/",
ROWS=",\n".join(rows),
REPO=self.get_uuid(args),
UUID=args.secret,
Expand Down