From 36ae4680d1f91eaed00f433a9f5f78b3de0d26ce Mon Sep 17 00:00:00 2001 From: sameeul Date: Wed, 17 Jul 2024 12:02:27 -0400 Subject: [PATCH 01/15] test new ome-converter-image --- cwl_adapters/ome-converter.cwl | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index 7dd5607..989dc37 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -10,7 +10,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: polusai/ome-converter-plugin:0.3.2-dev2 + dockerPull: sameeul/ome-converter-tool:0.3.2-dev1 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: @@ -26,8 +26,6 @@ requirements: # set HOME here so that at runtime we get a cache hit on the maven install. EnvVarRequirement: # See https://www.commonwl.org/user_guide/topics/environment-variables.html - envDef: - HOME: /home/polusai inputs: inpDir: From c46378b13e3fa1699823dc8e23ba755147f536f3 Mon Sep 17 00:00:00 2001 From: Sameeul Bashir Samee Date: Wed, 14 Aug 2024 20:10:31 -0400 Subject: [PATCH 02/15] Update ome-converter.cwl --- cwl_adapters/ome-converter.cwl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index 989dc37..997d8e7 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -5,7 +5,7 @@ cwlVersion: v1.0 label: OME Zarr Converter doc: |- - This WIPP plugin converts BioFormats supported data types to the OME Zarr file format. + This WIPP plugin converts BioFormats supported data types to the OME Zarr file format. https://github.com/PolusAI/polus-plugins/tree/master/formats/ome-converter-plugin requirements: @@ -76,4 +76,4 @@ $namespaces: $schemas: - https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl -# manifest: https://raw.githubusercontent.com/PolusAI/polus-plugins/master/formats/ome-converter-plugin/plugin.json \ No newline at end of file +# manifest: https://raw.githubusercontent.com/PolusAI/polus-plugins/master/formats/ome-converter-plugin/plugin.json From 3ec0c54abc45c89cd11e02cf195b5e3a5ebcd4a6 Mon Sep 17 00:00:00 2001 From: Sameeul Bashir Samee Date: Wed, 14 Aug 2024 20:15:31 -0400 Subject: [PATCH 03/15] Update ome-converter.cwl --- cwl_adapters/ome-converter.cwl | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index 997d8e7..95adc3f 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -5,7 +5,7 @@ cwlVersion: v1.0 label: OME Zarr Converter doc: |- - This WIPP plugin converts BioFormats supported data types to the OME Zarr file format. + This WIPP plugin converts BioFormats supported data types to the OME Zarr file format. https://github.com/PolusAI/polus-plugins/tree/master/formats/ome-converter-plugin requirements: @@ -17,15 +17,6 @@ requirements: - entry: $(inputs.outDir) writable: true # Output directories must be writable InlineJavascriptRequirement: {} -# NOTE: polusai/ome-converter-plugin:0.3.1 uses the base image -# polusai/bfio:2.3.2 which now un-bundles the java maven package -# ome:formats-gpl:7.1.0 due to licensing reasons. -# To avoid requiring network access at runtime, in the bfio Dockerfile -# it is pre-installed and saved in ~/.m2/ However, by default -# CWL hides all environment variables (including HOME), so we need to -# set HOME here so that at runtime we get a cache hit on the maven install. - EnvVarRequirement: -# See https://www.commonwl.org/user_guide/topics/environment-variables.html inputs: inpDir: From 8bfe812c673fe7c7cd51a0b537a6100a664fc1a2 Mon Sep 17 00:00:00 2001 From: Sameeul Bashir Samee Date: Thu, 3 Oct 2024 09:47:46 -0400 Subject: [PATCH 04/15] Update ome-converter.cwl --- cwl_adapters/ome-converter.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index 95adc3f..e9b9a10 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -10,7 +10,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: sameeul/ome-converter-tool:0.3.2-dev1 + dockerPull: sameeul/ome-converter-plugin:0.3.2-dev3 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: From bc48d8744ae3530fa523e3439d7f4886aafd22f5 Mon Sep 17 00:00:00 2001 From: Sameeul Bashir Samee Date: Thu, 3 Oct 2024 13:37:02 -0400 Subject: [PATCH 05/15] Update ome-converter.cwl --- cwl_adapters/ome-converter.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index e9b9a10..cad20f8 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -10,7 +10,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: sameeul/ome-converter-plugin:0.3.2-dev3 + dockerPull: polusai/ome-converter-tool:0.3.3-dev2 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: From c2b7f8d2fe1212d27fc869f6c7661eaa1be150aa Mon Sep 17 00:00:00 2001 From: Sameeul Bashir Samee Date: Thu, 3 Oct 2024 15:18:18 -0400 Subject: [PATCH 06/15] Update ome-converter.cwl --- cwl_adapters/ome-converter.cwl | 9 --------- 1 file changed, 9 deletions(-) diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index cad20f8..0739216 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -35,15 +35,6 @@ inputs: inputBinding: prefix: --filePattern - fileExtension: - label: The file extension - doc: |- - The file extension - type: string - inputBinding: - prefix: --fileExtension - default: "default" # enum: .ome.tiff, .ome.zarr, default - outDir: label: Output collection doc: |- From 017ab55cbfb10a5e7a5fec4edfe07a337aaf945d Mon Sep 17 00:00:00 2001 From: sameeul Date: Thu, 3 Oct 2024 15:50:07 -0400 Subject: [PATCH 07/15] remove old parameter --- workflows/bbbc.py | 1 - workflows/bbbc.wic | 1 - 2 files changed, 2 deletions(-) diff --git a/workflows/bbbc.py b/workflows/bbbc.py index 53edb54..de03ccd 100644 --- a/workflows/bbbc.py +++ b/workflows/bbbc.py @@ -22,7 +22,6 @@ def workflow() -> Workflow: omeconverter = Step(clt_path='../image-workflows/cwl_adapters/ome-converter.cwl') omeconverter.inpDir = filerenaming.outDir omeconverter.filePattern = '.*.tif' - omeconverter.fileExtension = '.ome.tif' omeconverter.outDir = Path('omeconverter.outDir') montage = Step(clt_path='../image-workflows/cwl_adapters/montage.cwl') diff --git a/workflows/bbbc.wic b/workflows/bbbc.wic index 7f650d9..67cde4b 100644 --- a/workflows/bbbc.wic +++ b/workflows/bbbc.wic @@ -21,7 +21,6 @@ steps: - outDir: !& file-renaming.outDir ome-converter: in: - fileExtension: !ii .ome.tif filePattern: !ii .*.tif inpDir: !* file-renaming.outDir outDir: !ii omeconverter.outDir From 4066b98b0171aba77dd4160dc1ab1bc0434fdfbd Mon Sep 17 00:00:00 2001 From: sameeul Date: Thu, 3 Oct 2024 16:44:31 -0400 Subject: [PATCH 08/15] disable precompute_slide --- workflows/bbbc.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/workflows/bbbc.py b/workflows/bbbc.py index de03ccd..bc8130e 100644 --- a/workflows/bbbc.py +++ b/workflows/bbbc.py @@ -35,11 +35,11 @@ def workflow() -> Workflow: image_assembler.imgPath = omeconverter.outDir image_assembler.outDir = Path('image_assembler.outDir') - precompute_slide = Step(clt_path='../image-workflows/cwl_adapters/precompute_slide.cwl') - precompute_slide.inpDir = image_assembler.outDir - precompute_slide.pyramidType = 'Zarr' - precompute_slide.imageType = 'image' - precompute_slide.outDir = Path('precompute_slide.outDir') + # precompute_slide = Step(clt_path='../image-workflows/cwl_adapters/precompute_slide.cwl') + # precompute_slide.inpDir = image_assembler.outDir + # precompute_slide.pyramidType = 'Zarr' + # precompute_slide.imageType = 'image' + # precompute_slide.outDir = Path('precompute_slide.outDir') steps = [bbbcdownload, subdirectory, @@ -47,7 +47,8 @@ def workflow() -> Workflow: omeconverter, montage, image_assembler, - precompute_slide] + # precompute_slide + ] filename = 'bbbc_py' # .yml viz = Workflow(steps, filename) return viz From 81eacd38564feeafcb215a4a4345da68bea024be Mon Sep 17 00:00:00 2001 From: Sameeul Bashir Samee Date: Fri, 4 Oct 2024 07:14:16 -0400 Subject: [PATCH 09/15] Update ome-converter.cwl --- cwl_adapters/ome-converter.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index 0739216..b1a7532 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -10,7 +10,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: polusai/ome-converter-tool:0.3.3-dev2 + dockerPull: sameeul/ome-converter-tool:0.3.3-dev0 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: From bce9f674d3786e95746e4c644a940c8a943c2f83 Mon Sep 17 00:00:00 2001 From: Sameeul Bashir Samee Date: Fri, 4 Oct 2024 07:31:23 -0400 Subject: [PATCH 10/15] Update bbbc.py --- workflows/bbbc.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/bbbc.py b/workflows/bbbc.py index bc8130e..90b885f 100644 --- a/workflows/bbbc.py +++ b/workflows/bbbc.py @@ -45,8 +45,8 @@ def workflow() -> Workflow: subdirectory, filerenaming, omeconverter, - montage, - image_assembler, + # montage, + # image_assembler, # precompute_slide ] filename = 'bbbc_py' # .yml From 4f12df4a05c89ed3612051d98a0a4b3b6a68d421 Mon Sep 17 00:00:00 2001 From: Sameeul Bashir Samee Date: Thu, 17 Oct 2024 11:39:02 -0400 Subject: [PATCH 11/15] Update ome-converter.cwl --- cwl_adapters/ome-converter.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index b1a7532..88d1b83 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -10,7 +10,7 @@ doc: |- requirements: DockerRequirement: - dockerPull: sameeul/ome-converter-tool:0.3.3-dev0 + dockerPull: polusai/ome-converter-tool:0.3.3-dev4 # See https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement InitialWorkDirRequirement: listing: From 4a32db61fceda86eadb2180c163237eb3316f09e Mon Sep 17 00:00:00 2001 From: Sameeul Bashir Samee Date: Thu, 17 Oct 2024 12:00:48 -0400 Subject: [PATCH 12/15] Update ome-converter.cwl --- cwl_adapters/ome-converter.cwl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index 88d1b83..41cf294 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -18,6 +18,8 @@ requirements: writable: true # Output directories must be writable InlineJavascriptRequirement: {} +baseCommand: ['python3', '-m', 'polus.images.formats.ome_converter'] + inputs: inpDir: label: Input generic data collection to be processed by this plugin From 94f212265f8b0901321402ffa253dca869e599c2 Mon Sep 17 00:00:00 2001 From: Sameeul Bashir Samee Date: Thu, 17 Oct 2024 12:39:54 -0400 Subject: [PATCH 13/15] Update ome-converter.cwl --- cwl_adapters/ome-converter.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index 41cf294..6635482 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -18,7 +18,7 @@ requirements: writable: true # Output directories must be writable InlineJavascriptRequirement: {} -baseCommand: ['python3', '-m', 'polus.images.formats.ome_converter'] +baseCommand: python3 -m polus.images.formats.ome_converter inputs: inpDir: From cbaad571d6d74d8ada19babed9a90f1d5718b51e Mon Sep 17 00:00:00 2001 From: Sameeul Bashir Samee Date: Fri, 8 Nov 2024 11:48:14 -0500 Subject: [PATCH 14/15] Update ome-converter.cwl --- cwl_adapters/ome-converter.cwl | 2 -- 1 file changed, 2 deletions(-) diff --git a/cwl_adapters/ome-converter.cwl b/cwl_adapters/ome-converter.cwl index 6635482..88d1b83 100644 --- a/cwl_adapters/ome-converter.cwl +++ b/cwl_adapters/ome-converter.cwl @@ -18,8 +18,6 @@ requirements: writable: true # Output directories must be writable InlineJavascriptRequirement: {} -baseCommand: python3 -m polus.images.formats.ome_converter - inputs: inpDir: label: Input generic data collection to be processed by this plugin From ef294b43504d98afeabf119da43d4808287ff0dc Mon Sep 17 00:00:00 2001 From: sameeul Date: Fri, 8 Nov 2024 12:56:34 -0500 Subject: [PATCH 15/15] Update workflow --- workflows/bbbc.py | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/workflows/bbbc.py b/workflows/bbbc.py index 90b885f..de03ccd 100644 --- a/workflows/bbbc.py +++ b/workflows/bbbc.py @@ -35,20 +35,19 @@ def workflow() -> Workflow: image_assembler.imgPath = omeconverter.outDir image_assembler.outDir = Path('image_assembler.outDir') - # precompute_slide = Step(clt_path='../image-workflows/cwl_adapters/precompute_slide.cwl') - # precompute_slide.inpDir = image_assembler.outDir - # precompute_slide.pyramidType = 'Zarr' - # precompute_slide.imageType = 'image' - # precompute_slide.outDir = Path('precompute_slide.outDir') + precompute_slide = Step(clt_path='../image-workflows/cwl_adapters/precompute_slide.cwl') + precompute_slide.inpDir = image_assembler.outDir + precompute_slide.pyramidType = 'Zarr' + precompute_slide.imageType = 'image' + precompute_slide.outDir = Path('precompute_slide.outDir') steps = [bbbcdownload, subdirectory, filerenaming, omeconverter, - # montage, - # image_assembler, - # precompute_slide - ] + montage, + image_assembler, + precompute_slide] filename = 'bbbc_py' # .yml viz = Workflow(steps, filename) return viz