reconfigured Resource class and added get_resource() to the ResourceP…

…ool class

CPAC/_entrypoints/run.py

@@ -782,12 +782,12 @@ def run_main():
                 only_one_anat=False,
             )
             # Initializing the bidstable on the bids_directory
-            bids_table = bids2table(bids_dir, workers=10)
+            bids_table = bids2table(bids_dir, workers=10).flat
 
             try:
                 # fillna
-                bids_table['ent__ses'] = bids_table['ent__ses'].fillna('None')
-                grouped_tab = bids_table.groupby(["ent__sub", "ent__ses"])
+                bids_table['ses'] = bids_table['ses'].fillna('None')
+                grouped_tab = bids_table.groupby(["sub", "ses"])
             except Exception as e:
                 WFLOGGER.warning("Could not create bids table: %s", e)
                 print("Could not create bids table: %s", e)

CPAC/pipeline/engine/engine.py

@@ -1347,10 +1347,24 @@ def initiate_rpool(wf, cfg, data_paths=None, part_id=None):
     # rpool = ingress_pipeconfig_paths(cfg, rpool, unique_id, creds_path)
 
     # output files with 4 different scans
-    print(rpool.get_resource("T1w"))
+    resource_description = {
+        "suffix": "T1w",
+        "desc": "preproc",
+        "space": "MNI152NLin6ASym"
+    }
+    resource_content = rpool.get_resource(resource_description)
     #print(dir(rpool.get_resource("T1w")[0]))
     #rpool.write_to_disk(cfg.pipeline_setup["working_directory"]["path"])
     #print(rpool.get_resource("T1w"))
+
+    # Ensure the directory exists
+    os.makedirs('/code/output', exist_ok=True)
+
+    # Now, safely open the file. It will be created if it does not exist.
+    with open('/code/output/output.txt', 'w') as file:
+
+        # Write the content to the file
+        file.write(str(resource_content))
     import sys
     sys.exit()
 

CPAC/pipeline/engine/resource.py

@@ -3,7 +3,7 @@
 from dataclasses import dataclass
 import pandas as pd
 
-class Resource(BIDSFile):
+class Resource():
     row: dict
     CpacProvenance: tuple
     ds: dict
@@ -17,90 +17,25 @@ class Resource(BIDSFile):
     def __init__(self, row, CpacProvenance):
 
         self.cpac_provenance = CpacProvenance
-        self.metadata = row['meta__json'] if isinstance(row['meta__json'], dict) else {}
+        self.metadata = {}#row['json'] if isinstance(row['json'], dict) else {}
         self.row = row
-        #extra stuff
-        self.ds = {k: v for k, v in row.items() if k.startswith('ds')}
-        self.entity = {k: v for k, v in row.items() if k.startswith('ent')}
-        self.finfo = {k: v for k, v in row.items() if k.startswith('finfo')}
+        for key, value in self.row.items():
+            setattr(self, key, value)
 
-        self.filename = self.finfo['finfo__file_path'].split("/")[-1]
-        self.file_path = self.finfo['finfo__file_path']
-        self.rel_path = f"sub-{self.entity['ent__sub']}"
-        if self.entity['ent__ses'] != "None":
-            self.rel_path += f"/ses-{self.entity['ent__ses']}"
-        self.rel_path += f"/{self.entity['ent__datatype']}"
-
-        self.category = self.entity['ent__suffix']
-
-        super().__init__(
-            self.ds['ds__dataset'],
-            self.ds['ds__dataset_path'],
-            self.finfo['finfo__file_path'],
-            self.entity,
-            self.metadata,           
-        )
+        self.filename = self.file_path.split("/")[-1]
+        self.rel_path = f"sub-{self.sub}"
+        if self.ses != "None":
+            self.rel_path += f"/ses-{self.ses}"
+        self.rel_path += f"/{self.datatype}"
 
-        self.entity_to_bids_key = {
-
-            # These are the keys that are used in generating the Resource names.
-            # The order of the keys does matter and affects the Resource names.
-            # Some of the keys can me commented or uncommented to include or exclude them from the Resource names.
-            # If the keys are duplicated then the values are appended as a list.
-
-            #'ent__sub': 'sub',
-            #'ent__ses': 'ses',
-            'ent__sample': 'sample',
-            #'ent__task': 'task', 
-            #'ent__acq': 'acq', 
-            'ent__ce': 'ce', 
-            'ent__trc': 'trc', 
-            'ent__stain': 'stain', 
-            'ent__rec': 'rec', 
-            'ent__dir': 'dir',  
-            'ent__mod': 'mod', 
-            'ent__echo': 'echo', 
-            'ent__flip': 'flip', 
-            'ent__inv': 'inv', 
-            'ent__mt': 'mt', 
-            'ent__part': 'part', 
-            'ent__proc': 'proc', 
-            'ent__hemi': 'hemi', 
-            'ent__space': 'space', 
-            'ent__split': 'split', 
-            'ent__recording': 'recording', 
-            'ent__chunk': 'chunk', 
-            'ent__res': 'res', 
-            'ent__den': 'den', 
-            'ent__label': 'label',
-            'ent__extra_entities': 'extra_entities', 
-            'ent__desc': 'desc',  
-            'ent__suffix': 'suffix',
-            #'ent__ext': 'ext'
-        }
+        self.suffix = self.suffix
 
-        self.name = self.generate_resource_name()
+        self.name = self.filename.split(".")[0]
         self.strats = {
             str(self.cpac_provenance) : self.file_path
         }
         for key, value in self.metadata.items():
             setattr(self, key, value)
-
-    def generate_resource_name(self):
-        bids_key_value_pairs = []
-        for col, bids_key in self.entity_to_bids_key.items():
-            if pd.notnull(self.row[col]) and self.row[col] != '':
-                value = self.row[col] if pd.notna(self.row[col]) else {}
-                if bids_key in ['suffix']:
-                    bids_key_value_pairs.append(value)
-                elif bids_key in ['extra_entities']:
-                    for key, value in value.items():
-                        bids_key_value_pairs.append(f"{key}-{value}")
-                else:
-                    bids_key_value_pair = f"{bids_key}-{value}"
-                    bids_key_value_pairs.append(bids_key_value_pair)
-        bids_style_combined = '_'.join(bids_key_value_pairs)
-        return bids_style_combined
 
     def __repr__(self):
         exclude_list = ['CpacConfig', 'CpacConfigHash', 'CpacProvenance', 'metadata', 'cpac_provenance', 'ds', 'entity', 'finfo', 'row', 'filename', 'file_path', 'rel_path', 'entities', 'path', 'entity_to_bids_key', ]  # Add attribute names to exclude
@@ -114,7 +49,7 @@ def write_to_disk(self, path):
             path_to_write = os.path.join(path, self.rel_path)
             os.makedirs(path_to_write, exist_ok=True)
             # Copy the NIFTI file
-            shutil.copy(self.finfo['finfo__file_path'], path_to_write)
+            shutil.copy(self.finfo['file_path'], path_to_write)
             # Write the JSON file only if the ext is .nii.gz
             if self.filename.endswith('.nii.gz'):
                 json_path = os.path.join(path_to_write, f"{self.filename.replace('.nii.gz', '.json')}")

CPAC/pipeline/engine/resource_pool.py

@@ -1429,8 +1429,8 @@ def build_rpool(
                 CpacProvenance = default_CpacProvenance
             resource = Resource(row, CpacProvenance)
             # making the rpool a list so that the duplicates are appended rather than overwritten
-            self.rpool.setdefault(resource.category, [])
-            self.rpool[resource.category].append(resource)
+            self.rpool.setdefault(resource.suffix, [])
+            self.rpool[resource.suffix].append(resource)
             # count += 1
             # if count >10:
             #     break
@@ -1441,8 +1441,28 @@ def write_to_disk(self, path):
             for item in resources:
                 print(item['resource'].write_to_disk(path))
 
-    def get_resource(self, name):
-        return self.rpool.get(name, None)
+    def get_resource(self, description):
+        matching_resources = []
+        for resources in self.rpool.get(description['suffix'], []):
+            # Initialize a flag to True, assuming the resource matches until proven otherwise
+            is_match = True
+            for key, val in description.items():
+                # Skip the 'suffix' key as it's used to select the pool, not to match resources
+                if key == 'suffix':
+                    continue
+                # Check if the resource matches the description criteria
+                # Use getattr for object attributes or resources.get for dictionary keys
+                resource_val = getattr(resources, key, None)
+                if resource_val != val:
+                    is_match = False
+                    break  # Break out of the inner loop if any criteria does not match
+            if is_match:
+                # If the resource matches all criteria, append its name to the matching_resources list
+                matching_resources.append(resources.name)
+        for items in matching_resources: 
+            print(items)
+        return matching_resources
+
 
     def set_resource(self, name, value):
         self.rpool[name] = value