From 4d0f91fec68fb655d48f2cd903a35fd946d46282 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Thu, 14 Nov 2019 13:52:14 +0100
Subject: [PATCH] Squash the soft-links in latest nuclei table folder
---
.../default.csv | 2 +-
.../extrapolated_intensity_correction.csv | 2 +-
.../morphology.csv | 2 +-
scripts/files/copy_helper.py | 25 ++++++++++++++++---
4 files changed, 25 insertions(+), 6 deletions(-)
diff --git a/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/default.csv b/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/default.csv
index df93135..60df4ef 120000
--- a/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/default.csv
+++ b/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/default.csv
@@ -1 +1 @@
-../../../0.6.4/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/default.csv
\ No newline at end of file
+../../../0.0.0/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/default.csv
\ No newline at end of file
diff --git a/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/extrapolated_intensity_correction.csv b/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/extrapolated_intensity_correction.csv
index d687ecc..e5dd2bb 120000
--- a/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/extrapolated_intensity_correction.csv
+++ b/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/extrapolated_intensity_correction.csv
@@ -1 +1 @@
-../../../0.6.4/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/extrapolated_intensity_correction.csv
\ No newline at end of file
+../../../0.6.0/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/extrapolated_intensity_correction.csv
\ No newline at end of file
diff --git a/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/morphology.csv b/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/morphology.csv
index c1efe4a..7226fec 120000
--- a/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/morphology.csv
+++ b/data/0.6.5/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/morphology.csv
@@ -1 +1 @@
-../../../0.6.4/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/morphology.csv
\ No newline at end of file
+../../../0.0.0/tables/sbem-6dpf-1-whole-segmented-nuclei-labels/morphology.csv
\ No newline at end of file
diff --git a/scripts/files/copy_helper.py b/scripts/files/copy_helper.py
index 0ae50ae..a28229a 100644
--- a/scripts/files/copy_helper.py
+++ b/scripts/files/copy_helper.py
@@ -5,6 +5,23 @@ from .sources import get_image_names, get_segmentation_names, get_segmentations
from ..attributes.base_attributes import write_additional_table_file
+def make_squashed_link(src_file, dst_file, override=False):
+
+ if os.path.exists(dst_file):
+ if override and os.path.islink(dst_file):
+ os.unlink(dst_file)
+ elif override and not os.path.islink(dst_file):
+ raise RuntimeError("Cannot override an actual file!")
+ elif not override:
+ return
+
+ if os.path.islink(src_file):
+ src_file = os.path.realpath(src_file)
+ dst_folder = os.path.split(dst_file)[0]
+ rel_path = os.path.relpath(src_file, dst_folder)
+ os.symlink(rel_path, dst_file)
+
+
def copy_file(xml_in, xml_out):
h5path = get_h5_path_from_xml(xml_in, return_absolute_path=True)
xml_dir = os.path.split(xml_out)[0]
@@ -26,9 +43,11 @@ def copy_tables(src_folder, dst_folder, name):
src_file = os.path.join(table_in, ff)
dst_file = os.path.join(table_out, ff)
- rel_path = os.path.relpath(src_file, table_out)
- if not os.path.exists(dst_file):
- os.symlink(rel_path, dst_file)
+ make_squashed_link(src_file, dst_file)
+
+ # rel_path = os.path.relpath(src_file, table_out)
+ # if not os.path.exists(dst_file):
+ # os.symlink(rel_path, dst_file)
# write the txt file for additional tables
write_additional_table_file(table_out)
--
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