fix in params uri

khanlab · Jul 18, 2024 · 6d3b57b · 6d3b57b
1 parent 78d2d66
commit 6d3b57b
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Showing 3 changed files with 24 additions and 15 deletions.
diff --git a/workflow/lib/cloud_io.py b/workflow/lib/cloud_io.py
@@ -10,7 +10,6 @@ def is_remote(uri_string):
 def get_fsspec(uri_string,storage_provider_settings=None,creds=None):
     uri = Path(uri_string)
     if uri.protocol == 'gcs':
-        print('is gcs')
         from gcsfs import GCSFileSystem
         gcsfs_opts={}
         gcsfs_opts={'project': storage_provider_settings['gcs'].get_settings().project,

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -68,17 +68,6 @@ def get_extension_ome_zarr():
             return "ome.zarr"
 
 
-def strip_snakemake_touch(path):
-    """This strips the .snakemake_touch (see get_extension_ome_zarr)
-    from the given path. Use this with params to obtain a uri for the
-    remote file."""
-    suffix = ".zarr/" + ".snakemake_touch"
-    if path.endswith(suffix):
-        return path[: -len(suffix)] + ".zarr"
-    else:
-        return path
-
-
 # targets
 def get_all_targets():
     targets = []

diff --git a/workflow/rules/ome_zarr.smk b/workflow/rules/ome_zarr.smk
@@ -23,7 +23,14 @@ rule zarr_to_ome_zarr:
         scaling_method=config["ome_zarr"]["scaling_method"],
         downsampling=config["bigstitcher"]["fuse_dataset"]["downsampling"],
         stains=get_stains,
-        uri=lambda wildcards, output: strip_snakemake_touch(output.zarr),
+        uri=_bids(
+            root=root,
+            subject="{subject}",
+            datatype="micr",
+            sample="{sample}",
+            acq="{acq}",
+            suffix="SPIM.ome.zarr",
+        ),
         storage_provider_settings=workflow.storage_provider_settings,
     output:
         **get_output_ome_zarr("blaze"),
@@ -60,7 +67,14 @@ rule tif_stacks_to_ome_zarr:
         scaling_method=config["ome_zarr"]["scaling_method"],
         downsampling=config["bigstitcher"]["fuse_dataset"]["downsampling"],
         stains=get_stains,
-        uri=lambda wildcards, output: strip_snakemake_touch(output.zarr),
+        uri=_bids(
+            root=root,
+            subject="{subject}",
+            datatype="micr",
+            sample="{sample}",
+            acq="{acq}",
+            suffix="SPIM.ome.zarr",
+        ),
         storage_provider_settings=workflow.storage_provider_settings,
     output:
         **get_output_ome_zarr("prestitched"),
@@ -121,7 +135,14 @@ rule ome_zarr_to_nii:
         zarr=get_input_ome_zarr_to_nii(),
     params:
         channel_index=lambda wildcards: get_stains(wildcards).index(wildcards.stain),
-        uri=lambda wildcards, input: strip_snakemake_touch(input.zarr),
+        uri=_bids(
+            root=root,
+            subject="{subject}",
+            datatype="micr",
+            sample="{sample}",
+            acq="{acq}",
+            suffix="SPIM.ome.zarr",
+        ),
         storage_provider_settings=workflow.storage_provider_settings,
     output:
         nii=bids(