adding warning for access edge cases when linking

apps/access/__init__.py

@@ -5,7 +5,8 @@
 from pathlib import Path
 import shutil
 import requests
-
+import re
+import json
 FLAG_TO_APPS = {
     "dmpmanifest": ("access_manifest", "manifest"),
     "msi": ("access legacy MSI", "microsatellite_instability"),
@@ -54,6 +55,7 @@ def get_operator_run(app_name, app_version=None, tags=None, config=None, show_al
         "app_name": app_name
     }
 
+    operator_look_ahead(latest_operator_run, config, tags)
     if show_all_runs:
         latest_operator_run.pop("status")
 
@@ -69,13 +71,34 @@ def get_operator_run(app_name, app_version=None, tags=None, config=None, show_al
         if "igoRequestId" in tags:
             new_tag = tags.replace("igoRequestId", "requestId")
             return get_operator_run(app_name, app_version, tags=new_tag, config=config)
+
         else:
             print("There are no completed operator runs for this request in the following app: %s:%s" %
                   (str(app_name), str(app_version)), file=sys.stderr)
             return None
 
     return latest_runs[0]
 
+def operator_look_ahead(latest_operator_run, config, tags):
+    threshold = float(.90)
+    complete = float(1.0)
+    try:
+        request_id = json.loads(tags)['igoRequestId']
+    except:
+         request_id = json.loads(tags)['requestId']
+    latest_operator_run_look_ahead = latest_operator_run.copy()
+    latest_operator_run_look_ahead.pop("status")
+    response_look_ahead = requests.get(urljoin(config['beagle_endpoint'], config['api']['operator-runs']),
+                        headers={'Authorization': 'Bearer %s' % config['token']},
+                        params=latest_operator_run)
+    if response_look_ahead.json()["results"]:
+        total_r = response_look_ahead.json()["results"][0]["num_total_runs"]
+        completed_r = response_look_ahead.json()["results"][0]["num_completed_runs"]
+        percent_c =  completed_r / total_r
+        if (percent_c >= threshold) and (percent_c < complete):
+            print(f"Warning there is a more recent operator run for request {request_id} that is incomplete, but with {percent_c} of runs completed. This may be the operator run you need for analysis. Consult the request's operator run history and consider using the --all-runs flag if appropriate.")
+
+
 def open_request_file(request_ids_file): 
     try:
         with open(request_ids_file,'r') as file:
@@ -114,13 +137,11 @@ def get_runs(operator_run_id, config, show_all_runs):
         "page_size": 1000,
         "status": "COMPLETED"
     }
-
     if show_all_runs:
         run_params.pop("status")
 
     response = requests.get(urljoin(config['beagle_endpoint'], config['api']['run']),
                             headers={'Authorization': 'Bearer %s' % config['token']}, params=run_params)
-
     return response.json()["results"]
 
 def get_run_by_id(run_id, config):
@@ -162,6 +183,7 @@ def link_app(operator_run, directory, request_id, sample_id, arguments, config,
             except Exception as e:
                 print("could not delete symlink: {} ".format(path / run["id"]), file=sys.stderr)
         else:
+            is_run_manual(run, request_id)
             try:
                 os.symlink(run["output_directory"], path / run["id"])
                 print((path / run["id"]).absolute(), file=sys.stdout)
@@ -287,14 +309,20 @@ def link_bams_by_patient_id(operator_run, directory, request_id, sample_id, argu
 
     if not runs:
         return
+
+    add_bai=False 
+    if len(runs) == 1:
+        manual_name="Run Access Legacy Fastq to Bam (file outputs) - Manual"
+        if manual_name in runs[0]["name"]:
+            add_bai=True
 
     files = [] # (sample_id, /path/to/file)
-
     for run in runs:
         for file_group in get_files_by_run_id(run["id"], config):
             files = files + find_files_by_sample(file_group["value"], sample_id=sample_id)
-
+    
     accepted_file_types = ['.bam', '.bai']
+
     for (sample_id, file) in files:
         file_path = get_file_path(file)
         _, file_ext = os.path.splitext(file_path)
@@ -323,6 +351,10 @@ def link_bams_by_patient_id(operator_run, directory, request_id, sample_id, argu
             try:
                 os.symlink(file_path, sample_version_path / file_name)
                 print((sample_version_path / file_name).absolute(), file=sys.stdout)
+                if add_bai:
+                    file_name_index = file_name.replace(".bam", ".bai")
+                    os.symlink(file_path, sample_version_path / file_name_index)
+                    print((sample_version_path / file_name_index).absolute(), file=sys.stdout)
             except Exception as e:
                 print("Could not create symlink from '{}' to '{}'".format(sample_version_path / file_name, file_path), file=sys.stderr)
                 continue
@@ -339,6 +371,16 @@ def link_bams_by_patient_id(operator_run, directory, request_id, sample_id, argu
                 pass
 
     return "Completed"
+def is_run_manual(run, request_id):
+    pattern = "/work/access/production/data/bams/*"
+    match = re.match(pattern, run["output_directory"])
+    patient_dir = run["output_directory"] + '/current'
+    proj_dir = Path("./") / ("Project_" + request_id)
+    if match:
+        if Path(patient_dir).is_dir():
+            return True
+        else:
+            raise FileNotFoundError(f'The folder {patient_dir} does not exist. Bams for request {request_id} were manually imported to Voyager. Please link patients in the data folder before linking the project folder.')
 
 def find_files_by_sample(file_group, sample_id = None):
     def traverse(file_group):