Update to match neurodatascience/nipoppy:main

nipoppy_cli/nipoppy/data/descriptors/bidscoiner-4.3.2.json

@@ -0,0 +1,79 @@
+{
+    "name": "bidscoiner",
+    "description": "bidscoiner (part of BIDScoin) to run BIDS conversion based on a YAML configuration file (bidsmap). See https://bidscoin.readthedocs.io/en/latest/workflow.html#step-2-running-the-bidscoiner",
+    "tool-version": "4.3.2+qt5",
+    "schema-version": "0.5",
+    "command-line": "bidscoiner [SOURCEFOLDER] [BIDSFOLDER] [PARTICIPANT_LABEL] [BIDSMAP] [FORCE] [CLUSTER] [NATIVESPEC]",
+    "inputs": [
+        {
+            "name": "sourcefolder",
+            "id": "sourcefolder",
+            "description": "The study root folder containing the raw source data",
+            "type": "String",
+            "optional": false,
+            "value-key": "[SOURCEFOLDER]"
+        },
+        {
+            "name": "bidsfolder",
+            "id": "bidsfolder",
+            "description": "The destination / output folder with the bids data",
+            "type": "String",
+            "optional": false,
+            "value-key": "[BIDSFOLDER]"
+        },
+        {
+            "name": "participant_label",
+            "id": "participant_label",
+            "description": "Space separated list of selected sub-# names / folders to be processed (the sub-prefix can be removed). Otherwise all subjects in the sourcefolder will be selected",
+            "type": "String",
+            "list": true,
+            "optional": true,
+            "command-line-flag": "-p",
+            "value-key": "[PARTICIPANT_LABEL]"
+        },
+        {
+            "name": "bidsmap",
+            "id": "bidsmap",
+            "description": "The study bidsmap file with the mapping heuristics. If the bidsmap filename is just the basename (i.e. no \"/\" in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml",
+            "type": "String",
+            "optional": true,
+            "default-value": "bidsmap.yaml",
+            "command-line-flag": "-b",
+            "value-key": "[BIDSMAP]"
+        },
+        {
+            "name": "force",
+            "id": "force",
+            "description": "Process all subjects, regardless of existing subject folders in the bidsfolder. Otherwise these subject folders will be skipped",
+            "type": "Flag",
+            "optional": true,
+            "command-line-flag": "-f",
+            "value-key": "[FORCE]"
+        },
+        {
+            "name": "cluster",
+            "id": "cluster",
+            "description": "Use the DRMAA library to submit the bidscoiner jobs to a high-performance compute (HPC) cluster",
+            "type": "Flag",
+            "optional": true,
+            "command-line-flag": "-c",
+            "value-key": "[CLUSTER]"
+        },
+        {
+            "name": "nativespec",
+            "id": "nativespec",
+            "description": "Opaque DRMAA argument with native specifications for submitting bidscoiner jobs to the HPC cluster. NB: Use quotes and include at least one space character to prevent premature parsing (default: -l walltime=00:30:00,mem=4gb)",
+            "type": "String",
+            "optional": true,
+            "default-value": "-l walltime=00:30:00,mem=4gb",
+            "command-line-flag": "-n",
+            "value-key": "[NATIVESPEC]"
+        }
+    ],
+    "tags": {},
+    "suggested-resources": {
+        "cpu-cores": 1,
+        "ram": 1,
+        "walltime-estimate": 60
+    }
+}

nipoppy_cli/nipoppy/data/descriptors/bidseditor-4.3.2.json

@@ -0,0 +1,42 @@
+{
+    "name": "bidseditor",
+    "description": "bidseditor (part of BIDScoin) to edit an existing YAML configuration file (bidsmap). See https://bidscoin.readthedocs.io/en/latest/workflow.html#step-1b-running-the-bidseditor",
+    "tool-version": "4.3.2+qt5",
+    "schema-version": "0.5",
+    "command-line": "bidseditor [BIDSFOLDER] [BIDSMAP] [TEMPLATE]",
+    "inputs": [
+        {
+            "name": "bidsfolder",
+            "id": "bidsfolder",
+            "description": "The destination folder with the (future) bids data",
+            "type": "String",
+            "optional": false,
+            "value-key": "[BIDSFOLDER]"
+        },
+        {
+            "name": "bidsmap",
+            "id": "bidsmap",
+            "description": "The study bidsmap file with the mapping heuristics. If the bidsmap filename is just the basename (i.e. no \"/\" in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml",
+            "type": "String",
+            "optional": true,
+            "default-value": "bidsmap.yaml",
+            "command-line-flag": "-b",
+            "value-key": "[BIDSMAP]"
+        },
+        {
+            "name": "template",
+            "id": "template",
+            "description": "The template bidsmap file with the default heuristics (this could be provided by your institute). If the bidsmap filename is just the basename (i.e. no \"/\" in the name) then it is assumed to be located in the bidscoin config folder. Default: bidsmap_dccn",
+            "type": "String",
+            "optional": true,
+            "command-line-flag": "-t",
+            "value-key": "[TEMPLATE]"
+        }
+    ],
+    "tags": {},
+    "suggested-resources": {
+        "cpu-cores": 1,
+        "ram": 1,
+        "walltime-estimate": 60
+    }
+}

nipoppy_cli/nipoppy/data/descriptors/bidsmapper-4.3.2.json

@@ -0,0 +1,123 @@
+{
+    "name": "bidsmapper",
+    "description": "bidsmapper (part of BIDScoin) to create/edit a YAML configuration file (bidsmap). See https://bidscoin.readthedocs.io/en/latest/workflow.html#step-1a-running-the-bidsmapper",
+    "tool-version": "4.3.2+qt5",
+    "schema-version": "0.5",
+    "command-line": "bidsmapper [SOURCEFOLDER] [BIDSFOLDER] [BIDSMAP] [TEMPLATE] [PLUGINS] [SUBPREFIX] [SESPREFIX] [UNZIP] [STORE] [AUTOMATED] [FORCE] [NO_UPDATE]",
+    "inputs": [
+        {
+            "name": "sourcefolder",
+            "id": "sourcefolder",
+            "description": "The study root folder containing the raw source data folders",
+            "type": "String",
+            "optional": false,
+            "value-key": "[SOURCEFOLDER]"
+        },
+        {
+            "name": "bidsfolder",
+            "id": "bidsfolder",
+            "description": "The destination folder with the (future) bids data and the bidsfolder/code/bidscoin/bidsmap.yaml output file",
+            "type": "String",
+            "optional": false,
+            "value-key": "[BIDSFOLDER]"
+        },
+        {
+            "name": "bidsmap",
+            "id": "bidsmap",
+            "description": "The study bidsmap file with the mapping heuristics. If the bidsmap filename is just the basename (i.e. no '/' in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml",
+            "type": "String",
+            "optional": true,
+            "default-value": "bidsmap.yaml",
+            "command-line-flag": "-b",
+            "value-key": "[BIDSMAP]"
+        },
+        {
+            "name": "template",
+            "id": "template",
+            "description": "The bidsmap template file with the default heuristics (this could be provided by your institute). If the bidsmap filename is just the basename (i.e. no '/' in the name) then it is assumed to be located in the bidscoin config folder. Default: bidsmap_dccn",
+            "type": "String",
+            "optional": true,
+            "command-line-flag": "-t",
+            "value-key": "[TEMPLATE]"
+        },
+        {
+            "name": "plugins",
+            "id": "plugins",
+            "description": "List of plugins to be used. Default: the plugin list of the study/template bidsmap)",
+            "type": "String",
+            "list": true,
+            "optional": true,
+            "command-line-flag": "-p",
+            "value-key": "[PLUGINS]"
+        },
+        {
+            "name": "subprefix",
+            "id": "subprefix",
+            "description": "The prefix common for all the source subject-folders (e.g. 'Pt' is the subprefix if subject folders are named 'Pt018', 'Pt019', ...). Use '*' when your subject folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'sub-'",
+            "type": "String",
+            "optional": true,
+            "command-line-flag": "-n",
+            "value-key": "[SUBPREFIX]"
+        },
+        {
+            "name": "sesprefix",
+            "id": "sesprefix",
+            "description": "The prefix common for all the source session-folders (e.g. 'M_' is the subprefix if session folders are named 'M_pre', 'M_post', ..). Use '*' when your session folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'ses-'",
+            "type": "String",
+            "optional": true,
+            "command-line-flag": "-m",
+            "value-key": "[SESPREFIX]"
+        },
+        {
+            "name": "unzip",
+            "id": "unzip",
+            "description": "Wildcard pattern to unpack tarball/zip-files in the sub/ses sourcefolder that need to be unzipped (in a tempdir) to make the data readable. Default: the value of the study/template bidsmap",
+            "type": "String",
+            "optional": true,
+            "command-line-flag": "-u",
+            "value-key": "[UNZIP]"
+        },
+        {
+            "name": "store",
+            "id": "store",
+            "description": "Store provenance data samples in the bidsfolder/code/provenance folder (useful for inspecting e.g. zipped or transferred datasets)",
+            "type": "Flag",
+            "optional": true,
+            "command-line-flag": "-s",
+            "value-key": "[STORE]"
+        },
+        {
+            "name": "automated",
+            "id": "automated",
+            "description": "Save the automatically generated bidsmap to disk and without interactively tweaking it with the bidseditor",
+            "type": "Flag",
+            "optional": true,
+            "command-line-flag": "-a",
+            "value-key": "[AUTOMATED]"
+        },
+        {
+            "name": "force",
+            "id": "force",
+            "description": "Discard the previously saved bidsmap and logfile",
+            "type": "Flag",
+            "optional": true,
+            "command-line-flag": "-f",
+            "value-key": "[FORCE]"
+        },
+        {
+            "name": "no_update",
+            "id": "no_update",
+            "description": "Do not update any sub/sesprefixes in or prepend the sourcefolder name to the <<filepath:regex>> expression that extracts the subject/session labels. This is normally done to make the extraction more robust, but could cause problems for certain use cases",
+            "type": "Flag",
+            "optional": true,
+            "command-line-flag": "--no-update",
+            "value-key": "[NO_UPDATE]"
+        }
+    ],
+    "tags": {},
+    "suggested-resources": {
+        "cpu-cores": 1,
+        "ram": 1,
+        "walltime-estimate": 60
+    }
+}

nipoppy_cli/nipoppy/data/examples/sample_global_config-all_pipelines.json

@@ -75,6 +75,27 @@
                     "UPDATE_DOUGHNUT": true
                 }
             ]
+        },
+        {
+            "NAME": "bidscoin",
+            "VERSION": "4.3.2",
+            "STEPS": [
+                {
+                    "NAME": "prepare",
+                    "INVOCATION_FILE": "[[NIPOPPY_DPATH_INVOCATIONS]]/[[NIPOPPY_PIPELINE_NAME]]-[[NIPOPPY_PIPELINE_VERSION]]-prepare.json",
+                    "DESCRIPTOR_FILE": "[[NIPOPPY_DPATH_DESCRIPTORS]]/bidsmapper-[[NIPOPPY_PIPELINE_VERSION]].json"
+                },
+                {
+                    "NAME": "edit",
+                    "INVOCATION_FILE": "[[NIPOPPY_DPATH_INVOCATIONS]]/[[NIPOPPY_PIPELINE_NAME]]-[[NIPOPPY_PIPELINE_VERSION]]-edit.json",
+                    "DESCRIPTOR_FILE": "[[NIPOPPY_DPATH_DESCRIPTORS]]/bidseditor-[[NIPOPPY_PIPELINE_VERSION]].json"
+                },
+                {
+                    "NAME": "convert",
+                    "INVOCATION_FILE": "[[NIPOPPY_DPATH_INVOCATIONS]]/[[NIPOPPY_PIPELINE_NAME]]-[[NIPOPPY_PIPELINE_VERSION]]-convert.json",
+                    "DESCRIPTOR_FILE": "[[NIPOPPY_DPATH_DESCRIPTORS]]/bidscoiner-[[NIPOPPY_PIPELINE_VERSION]].json"
+                }
+            ]
         }
     ],
     "PROC_PIPELINES": [

nipoppy_cli/nipoppy/data/examples/sample_global_config-latest_pipelines.json

@@ -75,6 +75,27 @@
                     "UPDATE_DOUGHNUT": true
                 }
             ]
+        },
+        {
+            "NAME": "bidscoin",
+            "VERSION": "4.3.2",
+            "STEPS": [
+                {
+                    "NAME": "prepare",
+                    "INVOCATION_FILE": "[[NIPOPPY_DPATH_INVOCATIONS]]/[[NIPOPPY_PIPELINE_NAME]]-[[NIPOPPY_PIPELINE_VERSION]]-prepare.json",
+                    "DESCRIPTOR_FILE": "[[NIPOPPY_DPATH_DESCRIPTORS]]/bidsmapper-[[NIPOPPY_PIPELINE_VERSION]].json"
+                },
+                {
+                    "NAME": "edit",
+                    "INVOCATION_FILE": "[[NIPOPPY_DPATH_INVOCATIONS]]/[[NIPOPPY_PIPELINE_NAME]]-[[NIPOPPY_PIPELINE_VERSION]]-edit.json",
+                    "DESCRIPTOR_FILE": "[[NIPOPPY_DPATH_DESCRIPTORS]]/bidseditor-[[NIPOPPY_PIPELINE_VERSION]].json"
+                },
+                {
+                    "NAME": "convert",
+                    "INVOCATION_FILE": "[[NIPOPPY_DPATH_INVOCATIONS]]/[[NIPOPPY_PIPELINE_NAME]]-[[NIPOPPY_PIPELINE_VERSION]]-convert.json",
+                    "DESCRIPTOR_FILE": "[[NIPOPPY_DPATH_DESCRIPTORS]]/bidscoiner-[[NIPOPPY_PIPELINE_VERSION]].json"
+                }
+            ]
         }
     ],
     "PROC_PIPELINES": [

nipoppy_cli/nipoppy/data/examples/sample_invocations/bidscoin-4.3.2-convert.json

@@ -0,0 +1,7 @@
+{
+    "sourcefolder": "[[NIPOPPY_DPATH_SOURCEDATA]]",
+    "bidsfolder": "[[NIPOPPY_DPATH_BIDS]]",
+    "participant_label": [
+        "[[NIPOPPY_PARTICIPANT_ID]]"
+    ]
+}

nipoppy_cli/nipoppy/data/examples/sample_invocations/bidscoin-4.3.2-edit.json

@@ -0,0 +1,3 @@
+{
+    "bidsfolder": "[[NIPOPPY_DPATH_BIDS]]"
+}

nipoppy_cli/nipoppy/data/examples/sample_invocations/bidscoin-4.3.2-prepare.json

@@ -0,0 +1,4 @@
+{
+    "sourcefolder": "[[NIPOPPY_DPATH_SOURCEDATA]]",
+    "bidsfolder": "[[NIPOPPY_DPATH_BIDS]]"
+}

nipoppy_cli/tests/test_default_config.py

@@ -116,6 +116,9 @@ def test_pipeline_runner(
         ("heudiconv", "0.12.2", "convert"),
         ("dcm2bids", "3.1.0", "prepare"),
         ("dcm2bids", "3.1.0", "convert"),
+        ("bidscoin", "4.3.2", "prepare"),
+        ("bidscoin", "4.3.2", "edit"),
+        ("bidscoin", "4.3.2", "convert"),
     ],
 )
 def test_bids_conversion_runner(
@@ -131,7 +134,9 @@ def test_bids_conversion_runner(
         simulate=True,
     )
 
-    runner.pipeline_config.get_fpath_container().touch()
+    fpath_container = runner.pipeline_config.get_fpath_container()
+    if fpath_container is not None:
+        runner.pipeline_config.get_fpath_container().touch()
 
     invocation_str, descriptor_str = runner.run_single(
         participant_id=participant_id, session_id=session_id