Add ont file reorganization

scripts/ONTDataOrganization.py

@@ -0,0 +1,96 @@
+import os
+import shutil
+import requests
+import config
+
+def isBarcoded(experiment_directory):
+    for root, dirs, files in os.walk(experiment_directory):
+        if 'barcode01' in dirs:
+            return True
+    return False
+
+def renameBarcodedSamples(experiment_directory):
+    #search lims db for pool name if pool name is an IGO ID (data -> experiment -> pool name)
+    #fetch parent samples of pool, find their barcodes
+    #match parent sample IGO IDs to barcoded directories
+    #rename
+
+    # for if sample name is [pool ID] + ["_barcode_..."]
+    pass
+
+
+def reorganizeExperiment(experiment_path):
+        sample_list = os.listdir(experiment_path)
+        for sample_dir in sample_list:
+            sample_path = os.path.join(experiment_path, sample_dir)
+            if not os.path.isdir(sample_path):
+                continue
+            for alias_dir in os.listdir(sample_path):
+                alias_path = os.path.join(sample_path, alias_dir)
+                if not os.path.isdir(alias_path):
+                    continue
+                for fastq_pod5_dir in os.listdir(alias_path):
+                    fastq_pod5_path = os.path.join(alias_path,fastq_pod5_dir)
+                    if not os.path.isdir(fastq_pod5_path):
+                        continue
+                    for barcode_dir in os.listdir(fastq_pod5_path):
+                        barcode_path = os.path.join(fastq_pod5_path,barcode_dir)
+                        if not os.path.isdir(barcode_path):
+                            continue
+                        files_in_barcode = os.listdir(barcode_path)
+                        if len(files_in_barcode) > 1:
+                            #make new directories
+                            new_sample_dir = sample_dir + "_" + barcode_dir
+                            new_sample_path = os.path.join(experiment_path, new_sample_dir)
+                            new_alias_path = os.path.join(new_sample_path, alias_dir)
+                            new_fastq_pod5_path = os.path.join(new_alias_path, fastq_pod5_dir)
+                            os.makedirs(new_fastq_pod5_path, exist_ok=True)
+                            #copy
+                            for file in files_in_barcode:
+                                file_path = os.path.join(barcode_path, file)
+                                print("File Path: ",file_path)
+                                print("Dest Path: ", new_fastq_pod5_path)
+                                shutil.copy2(file_path, new_fastq_pod5_path)
+
+def renameNonBarcodeSamples():
+    # for if sample name is IGO ID
+    # make sample name full deliverable name
+    pass
+
+
+def OrganizeData(data_path):
+    for experiment in os.listdir(data_path):
+        experiment_path = os.path.join(data_path, experiment)
+        if os.path.isdir(experiment_path):
+            if isBarcoded(experiment_path):
+                reorganizeExperiment(experiment_path)
+                renameBarcodedSamples(experiment_path)
+    renameNonBarcodeSamples()
+
+'''
+Returns list of run summary objects in JSON format.
+The run summary objects are individual library and pooled library samples going for pooling (sample status = Ready for - Pooling of Sample Libraries for Sequencing)   
+'''
+def get_run_summary(poolId):
+
+    url = "https://igolims:8443/LimsRest/api/getPoolsBarcodes?poolId=%s" % (poolId)
+    try:
+            resp = requests.get(url, auth=(config.LIMS_USER, config.LIMS_PASSWORD), verify=False)
+            return resp
+    except:
+        print("Request Failed: %s" % url)
+
+    content = json.loads(resp.content)
+    if (resp.status_code != 200 or len(content) == 0):
+        # Warning
+        print("Plan runs failed to return data. Service Response: %s" %
+            (resp.status_code))
+
+#/getNearestParentLibrarySamplesForPool(pooled sample, user)
+#/getBarcodeList
+
+if __name__ == "__main__":
+    data_path = "/Users/desmondlambe/data"
+    OrganizeData(data_path)
+
+