Multiple changes

bu_isciii/__main__.py

@@ -456,13 +456,13 @@ def bioinfo_doc(
 @click.option(
     "-id",
     "--initial_date",
-    default=False,
+    default=None,
     help="The date from which start search (format 'YYYY-MM-DD')",
 )
 @click.option(
     "-fd",
     "--final_date",
-    default=False,
+    default=None,
     help="The date from which end search (format 'YYYY-MM-DD')",
 )
 def archive(resolution, type, option, skip_prompts, initial_date, final_date):

bu_isciii/conf/configuration.json

@@ -1,6 +1,7 @@
 {
     "global":{
-      "data_path": "/data/bi"
+      "data_path": "/data/bi",
+      "archived_path": "/archived/bi"
     },
     "sftp_copy": {
       "protocol": "rsync",
@@ -43,11 +44,15 @@
       "fastq_repo": "/srv/fastq_repo"
     },
     "scratch_copy": {
-      "command": "rsync -rlv --exclude 'service_info.txt' --exclude 'work' --exclude '*_NC' "
+      "protocol": "rsync",
+      "options": ["-rlpv"],
+      "exclusions": [
+        "'*_NC'",
+        "'service_info.txt'",
+        "'work'"
+      ]
     },
     "archive": {
-      "data_path": "/data/bi",
-      "archived_path": "/archived/bi",
       "protocol": "rsync",
       "options": ["-rv"]
     }

bu_isciii/drylab_api.py

@@ -20,7 +20,7 @@ def __init__(self, server, url, password):
         self.request_url = server + url
         self.headers = {
             "content-type": "application/json",
-            "authorization": "Basic " + password,
+            "WWW-Authenticate": "Basic " + password,
         }
 
     # TODO: this is waaay too dirty, find a way to pass variable number of parameters and values.

bu_isciii/new_service.py

@@ -54,13 +54,13 @@ def __init__(
             conf_api["server"], conf_api["api_url"], api_token
         )
         self.resolution_info = self.rest_api.get_request(
-            request_info="serviceFullData", safe=False, resolution=self.resolution_id
+            request_info="service-data", safe=False, resolution=self.resolution_id
         )
         self.service_folder = self.resolution_info["resolutions"][0][
-            "resolutionFullNumber"
+            "resolution_full_number"
         ]
         self.services_requested = self.resolution_info["resolutions"][0][
-            "availableServices"
+            "available_services"
         ]
         self.service_samples = self.resolution_info["samples"]
 
@@ -167,18 +167,19 @@ def create_samples_id(self):
                 "a",
                 encoding="utf-8",
             ) as f:
-                line = sample["sampleName"] + "\n"
+                line = sample["sample_name"] + "\n"
                 f.write(line)
 
     def create_symbolic_links(self):
         samples_files = []
         for sample in self.service_samples:
             regex = os.path.join(
-                self.conf["fastq_repo"], sample["projectName"], "{}*"
-            ).format(sample["sampleName"])
+                self.conf["fastq_repo"], sample["project_name"], "{}_*"
+            ).format(sample["sample_name"])
             sample_file = glob.glob(regex)
+
             if sample_file:
-                samples_files.appned(sample_file)
+                samples_files.append(sample_file)
             else:
                 stderr.print(
                     "[red] This regex has not output any file: %s. This maybe because the project is not yet in the fastq repo or because some of the samples are not in the project."
@@ -198,19 +199,20 @@ def create_symbolic_links(self):
             ):
                 stderr.print("Bye!")
                 sys.exit()
-        for file in samples_files:
-            try:
-                os.symlink(
-                    file,
-                    os.path.join(self.full_path, "RAW", os.path.basename(file)),
-                )
-            except OSError as e:
-                stderr.print(
-                    "[red]ERROR: Symbolic links creation failed for sample %s."
-                    % sample["sampleName"]
-                )
-                stderr.print("Traceback: %s" % e)
-                sys.exit()
+        for sample in samples_files:
+            for file in sample:
+                try:
+                    os.symlink(
+                        file,
+                        os.path.join(self.full_path, "RAW", os.path.basename(file)),
+                    )
+                except OSError as e:
+                    stderr.print(
+                        "[red]ERROR: Symbolic links creation failed for sample %s."
+                        % sample["sampleName"]
+                    )
+                    stderr.print("Traceback: %s" % e)
+                    sys.exit()
 
     def samples_json(self):
         json_samples = json.dumps(self.service_samples, indent=4)
@@ -229,7 +231,7 @@ def create_new_service(self):
         self.create_symbolic_links()
         self.samples_json()
         self.rest_api.put_request(
-            "updateState", "resolution", self.resolution_id, "state", "In%20Progress"
+            "update-state", "resolution", self.resolution_id, "state", "in_progress"
         )
 
     def get_resolution_id(self):

bu_isciii/scratch.py

@@ -13,7 +13,7 @@
 # Local imports
 import bu_isciii
 import bu_isciii.utils
-from bu_isciii.drylab_api import RestServiceApi
+import bu_isciii.drylab_api
 import bu_isciii.config_json
 
 log = logging.getLogger(__name__)
@@ -54,18 +54,21 @@ def __init__(
             self.direction = direction
 
         # Load conf
-        conf_api = bu_isciii.config_json.ConfigJson().get_configuration(
-            "xtutatis_api_settings"
-        )
+        conf_api = bu_isciii.config_json.ConfigJson().get_configuration("api_settings")
         # Obtain info from iskylims api
-        rest_api = RestServiceApi(conf_api["server"], conf_api["api_url"], api_token)
+        rest_api = bu_isciii.drylab_api.RestServiceApi(
+            conf_api["server"],
+            conf_api["api_url"],
+            api_token,
+        )
         self.conf = bu_isciii.config_json.ConfigJson().get_configuration("scratch_copy")
         self.rsync_command = self.conf["command"]
 
         self.resolution_info = rest_api.get_request(
-            request_info="serviceFullData", safe=False, resolution=self.resolution_id
+            request_info="resolutionFullData", safe=False, resolution=self.resolution_id
         )
-        self.service_folder = self.resolution_info["resolutions"][0][
+
+        self.service_folder = self.resolution_info["resolutions"][
             "resolutionFullNumber"
         ]
         self.scratch_path = os.path.join(self.tmp_dir, self.service_folder)
@@ -89,7 +92,9 @@ def __init__(
             )
             sys.exit()
         else:
-            self.path = bu_isciii.utils.get_service_paths(self.resolution_info)
+            self.path = bu_isciii.utils.get_service_paths(
+                "services_and_colaborations", self.resolution_info, "non_archived_path"
+            )
 
         self.full_path = os.path.join(self.path, self.service_folder)
 

bu_isciii/utils.py

@@ -149,9 +149,9 @@ def get_service_ids(services_requested):
     service_id_list = []
     service_id_list_all = []
     for services in services_requested:
-        if services["serviceId"] is not None:
-            service_id_list.append(services["serviceId"])
-            service_id_list_all.append(services["serviceId"])
+        if services["service_id"] is not None:
+            service_id_list.append(services["service_id"])
+            service_id_list_all.append(services["service_id"])
     service_id_list_all.append("all")
     stderr.print("Which selected service do you want to manage?")
     services_sel = [prompt_selection("Service label:", service_id_list_all)]
@@ -170,20 +170,33 @@ def ask_password(msg):
     return password
 
 
-def get_service_paths(resolution_info):
+def get_service_paths(service_type, resolution_info, archived_status):
     """
     Given a service, a conf and a type,
     get the path it would have service
     """
     global_conf = bu_isciii.config_json.ConfigJson().get_configuration("global")
-    service_path = os.path.join(
-        global_conf["data_path"],
-        "services_and_colaborations",
-        resolution_info["serviceUserId"]["profile"]["profileCenter"],
-        resolution_info["serviceUserId"]["profile"][
-            "profileClassificationArea"
-        ].lower(),
-    )
+    service_path = None
+
+    if service_type == "services_and_colaborations":
+        if archived_status == "archived_path":
+            service_path = os.path.join(
+                global_conf["archived_path"],
+                service_type,
+                resolution_info["serviceUserId"]["profile"]["profileCenter"],
+                resolution_info["serviceUserId"]["profile"][
+                    "profileClassificationArea"
+                ].lower(),
+            )
+        if archived_status == "non_archived_path":
+            service_path = os.path.join(
+                global_conf["data_path"],
+                service_type,
+                resolution_info["Service"]["serviceUserId"]["profile"]["profileCenter"],
+                resolution_info["serviceUserId"]["profile"][
+                    "profileClassificationArea"
+                ].lower(),
+            )
     return service_path