[FIX] babs-init runs without babs_singularity_run section

babs/babs.py

@@ -1865,6 +1865,38 @@ def babs_merge(self, chunk_size, trial_run):
                           + " not to push merging actions to output RIA.")
             print("\n`babs-merge` did not fully finish yet!")
 
+    def babs_unzip(container_config_yaml_file):
+        """
+        This function unzips results and extract desired files.
+        This is done in 3 steps:
+        1. Generate scripts used by `babs-unzip`
+        2. Run scripts to unzip data
+        3. Merge all branches of unzipping
+
+        Parameters:
+        --------------
+        config: dict
+            loaded container config yaml file
+        """
+
+        # ====================================================
+        # Generate scripts used by `babs-unzip`
+        # ====================================================
+
+        # Prepare input_ds_unzip:
+        # Call `babs_bootstrap()`:
+        #   !!!! using babs_proj_unzip, instead current `self`!!!
+
+        print("TODO")
+
+        # ====================================================
+        # Run scripts to unzip data
+        # ====================================================
+
+        # ====================================================
+        # Merge all branches of unzipping
+        # ====================================================
+
 
 class Input_ds():
     """This class is for input dataset(s)"""
@@ -2298,13 +2330,23 @@ def generate_bash_run_bidsapp(self, bash_path, input_ds, type_session):
 
         # check if `self.config` from the YAML file contains information we need:
         if "babs_singularity_run" not in self.config:
-            print("The key 'babs_singularity_run' was not included "
-                  "in the `container_config_yaml_file`. "
-                  "Therefore we will not refer to the yaml file for `singularity run` arguments, "
-                  "but will use regular `singularity run` command.")
-        #       "command of singularity run will be read from information "
-        #       "saved by `call-fmt` when `datalad containers-add.`")
-            cmd_singularity_flags = "\n\t"
+            # sanity check: there should be only one input ds
+            #   otherwise need to specify in this section:
+            assert input_ds.num_ds == 1, \
+                "Section 'babs_singularity_run' is missing in the provided" \
+                + " `container_config_yaml_file`. As there are more than one" \
+                + " input dataset, you must include this section to specify" \
+                + " to which argument that each input dataset will go."
+            # if there is only one input ds, fine:
+            print("Section 'babs_singularity_run' was not included "
+                  "in the `container_config_yaml_file`. ")
+            cmd_singularity_flags = ""   # should be empty
+            # Make sure other returned variables from `generate_cmd_singularityRun_from_config`
+            #   also have values:
+            # as "--fs-license-file" or "$FREESURFER_LICENSE" is not provided:
+            flag_fs_license = None
+            # copied from `generate_cmd_singularityRun_from_config`:
+            singuRun_input_dir = input_ds.df["path_data_rel"][0]
         else:
             # print("Generate singularity run command from `container_config_yaml_file`")
             # # contain \ for each key-value

babs/cli.py

@@ -701,6 +701,62 @@ def babs_merge_main():
     babs_proj.babs_merge(args.chunk_size, args.trial_run)
 
 
+def babs_unzip_cli():
+    """ CLI for babs-unzip """
+
+    parser = argparse.ArgumentParser(
+        description="``babs-unzip`` unzips results zip files and extracts desired files",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument(
+        "--project_root", "--project-root",
+        help="Absolute path to the root of BABS project."
+        " For example, '/path/to/my_BABS_project/'.",
+        required=True)
+    parser.add_argument(
+        '--container_config_yaml_file', '--container-config-yaml-file',
+        help="Path to a YAML file of the BIDS App container that contains information of"
+        " what files to unzip etc.")
+
+    return parser
+
+
+def babs_unzip_main():
+    """
+    This is the core function of babs-unzip, which unzip results zip files
+    and extracts desired files.
+
+    project_root: str
+        Absolute path to the root of BABS project.
+        For example, '/path/to/my_BABS_project/'.
+    container_config_yaml_file: str
+        path to container's configuration YAML file.
+        These two sections will be used:
+        1. 'unzip_desired_filenames' - must be included
+        2. 'rename_conflict_files' - optional
+    """
+
+    # Get arguments:
+    args = babs_unzip_cli().parse_args()
+    project_root = args.project_root
+    container_config_yaml_file = args.container_config_yaml_file
+
+    # container config:
+    config = read_yaml(container_config_yaml_file)
+    # ^^ not to use filelock here - otherwise will create `*.lock` file in user's folder
+
+    # Sanity checks:
+    if "unzip_desired_filenames" not in config:
+        raise Exception("Section 'unzip_desired_filenames' is not included"
+                        " in `--container_config_yaml_file`. This section is required."
+                        " Path to this YAML file: '" + container_config_yaml_file + "'.")
+
+    # Get class `BABS` based on saved `analysis/code/babs_proj_config.yaml`:
+    babs_proj, _ = get_existing_babs_proj(project_root)
+
+    # Call method `babs_unzip()`:
+    babs_proj.babs_unzip(config)
+
+
 def get_existing_babs_proj(project_root):
     """
     This is to get `babs_proj` (class `BABS`) and `input_ds` (class `Input_ds`)
@@ -730,7 +786,7 @@ def get_existing_babs_proj(project_root):
     babs_proj_config_yaml = op.join(project_root,
                                     "analysis/code/babs_proj_config.yaml")
     if op.exists(babs_proj_config_yaml) is False:
-        raise Exception( \
+        raise Exception(
             "`babs-init` was not successful;"
             + " there is no 'analysis/code/babs_proj_config.yaml' file!"
             + " Please rerun `babs-init` to finish the setup.")

docs/source/preparation_config_yaml_file.rst

@@ -29,6 +29,12 @@ Sections in the configuration YAML file
 
 Among these sections, these sections are optional:
 
+* **babs_singularity_run**
+
+  * Only if you are sure that besides arguments handled by BABS, you don't need any other argument,
+    you may exclude this section from the YAML file.
+  * You must include this section if there are more one input dataset.
+
 * **required_files**
 * **keywords_alert**
 

notebooks/example_container_fmriprepfake.yaml

@@ -0,0 +1,44 @@
+# This is an example config yaml file for fmriprep-fake version 0.1.0.
+# fmriprep-fake's Docker image is publicly available at: https://hub.docker.com/r/djarecka/fmriprep_fake
+# fmriprep-fake generates fMRIPrep outputs without running fMRIPrep itself. You may use it to check fmriprep outputs.
+#     More details please see: https://github.com/djarecka/fmriprep-fake
+# Thanks to Dorota Jarecka for preparing and sharing this BIDS App!
+
+# Warning!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the toy BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# 'babs_singularity_run': There is no such section for fmriprep-fake
+#   as all commands needed by fmriprep-fake have been handled by BABS.
+
+babs_zip_foldername:   # the foldername(s) to get zipped and the version string(s)
+    fmriprepfake: "0-1-1"     # should be the same as in `babs-init`'s argument `container_name`; better using "-" instead of "."
+
+cluster_resources:
+    interpreting_shell: /bin/bash   # "-S /bin/bash" on cubic
+    hard_memory_limit: 2G   # "-l h_vmem=25G" on cubic
+    temporary_disk_space: 20G   # "-l tmpfree=50G" on cubic  # this is highly-recommended on cubic
+    hard_runtime_limit: "24:00:00"   # needed by cubic for PennLINC lab members; otherwise jobs will be sent to generic nodes 
+    customized_text: |
+        #$ -R y
+
+# Users need to add their customized bash command below,
+#   they will be used as preambles in `participant_job.sh`
+#   the commands should not be quoted!
+script_preamble: |
+    source ${CONDA_PREFIX}/bin/activate mydatalad    # Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
+
+# Where to run the jobs:
+job_compute_space: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
+
+# Below is to filter out subjects (or sessions)
+#   right now we only filter based on unzipped dataset
+required_files:
+    $INPUT_DATASET_#1:
+        - "func/*_bold.nii*"
+        - "anat/*_T1w.nii*"
+
+# Keywords for alerting messages in log files:
+# 'keywords_alert': not to include this section for now.