Small update and bug fixing pre-release 2.0.0

CHANGELOG.md

@@ -4,7 +4,47 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [2.0.0] - 2024-02-28 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.0.0
+## [2.1.0dev] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.1.X
+
+### Credits
+
+Code contributions to the hotfix:
+
+### Template fixes and updates
+
+### Modules
+
+#### Added enhancements
+
+#### Fixes
+
+#### Changed
+
+#### Removed
+
+### Requirements
+
+## [2.X.1hot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.1
+
+### Credits
+
+Code contributions to the hotfix:
+
+### Template fixes and updates
+
+### Modules
+
+#### Added enhancements
+
+#### Fixes
+
+#### Changed
+
+#### Removed
+
+### Requirements
+
+## [2.0.0] - 2024-03-01 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.0.0
 
 ### Credits
 
@@ -31,6 +71,8 @@ Code contributions to the release:
 - Added finish module
 - Added json files: sftp_user.json
 - Added delivery jinja templates
+- Added IRMA template to services.json
+- Scratch module now executes rsync using SLURM's srun 
 
 #### Fixes
 

bu_isciii/conf/configuration.json

@@ -21,10 +21,10 @@
     },
     "xtutatis_api_settings": {
         "api_url": "/drylab/api/",
-        "server": "http://iskylims.isciiides.es"
+        "server": "https://iskylims.isciii.es"
     },
     "api_settings": {
-        "server": "http://iskylims.isciiides.es",
+        "server": "https://iskylims.isciii.es",
         "api_url": "/drylab/api/"
     },
     "bioinfo_doc": {

bu_isciii/scratch.py

@@ -71,9 +71,6 @@ def __init__(
             "resolution_full_number"
         ]
         self.scratch_tmp_path = os.path.join(self.tmp_dir, self.service_folder)
-        self.out_file = os.path.join(
-            self.tmp_dir, self.scratch_tmp_path, "DOC", "service_info.txt"
-        )
         # params like --chdir, --partition and --time
         srun_params = self.conf["srun_settings"].items()
         self.srun_settings = [arg for param in srun_params for arg in param]
@@ -98,12 +95,13 @@ def __init__(
             )
 
         self.full_path = os.path.join(self.path, self.service_folder)
+        self.out_file = os.path.join(self.full_path, "DOC", "service_info.txt")
 
     def srun_command(self, srun_settings, command):
         command_list = [["srun"], srun_settings, command]
         srun_command = [arg for command in command_list for arg in command]
-        subprocess.run(srun_command, check=True, shell=True)
-        return
+        exit_code = subprocess.call(srun_command)
+        return exit_code
 
     def copy_scratch(self):
         stderr.print("[blue]I will copy the service from %s" % self.full_path)
@@ -114,31 +112,35 @@ def copy_scratch(self):
                 if protocol == "rsync":
                     rsync_command = sysrsync.get_rsync_command(
                         source=self.full_path,
-                        destination=self.conf["scratch_path"],
+                        destination=self.conf["scratch_path"] + "/",
                         options=self.conf["options"],
                         exclusions=self.conf["exclusions"],
                         sync_source_contents=False,
                     )
-                    self.srun_command(self.srun_settings, rsync_command)
+                    exit_code = self.srun_command(self.srun_settings, rsync_command)
+
+                else:
+                    stderr.print(
+                        "[ref] This protocol is not allowed at the moment",
+                        highlight=False,
+                    )
+                    sys.exit()
+                if exit_code == 0:
                     stderr.print(
                         "[green] Data copied to the sftp folder successfully",
                         highlight=False,
                     )
-                else:
+                    f = open(self.out_file, "w")
+                    f.write("Temporal directory: " + self.scratch_tmp_path + "\n")
+                    f.write("Origin service directory: " + self.full_path + "\n")
+                    f.close()
                     stderr.print(
-                        "[ref] This protocol is not allowed at the moment",
+                        "[green]Successfully copied the directory to %s"
+                        % self.scratch_tmp_path,
                         highlight=False,
                     )
-                    sys.exit()
-                f = open(self.out_file, "w")
-                f.write("Temporal directory: " + self.scratch_tmp_path + "\n")
-                f.write("Origin service directory: " + self.full_path + "\n")
-                f.close()
-                stderr.print(
-                    "[green]Successfully copied the directory to %s"
-                    % self.scratch_tmp_path,
-                    highlight=False,
-                )
+                else:
+                    stderr.print(f"[red]Errors while copying {self.full_path}")
             except Exception as e:
                 stderr.print(e)
                 stderr.print(
@@ -173,7 +175,7 @@ def revert_copy_scratch(self):
                     if self.conf["protocol"] == "rsync":
                         # scratch_tmp cannot be used due to permission issues
                         scratch_bi_path = "".join(
-                            self.conf["scratch_path"], self.service_folder
+                            [self.conf["scratch_path"], self.service_folder]
                         )
                         rsync_command = sysrsync.get_rsync_command(
                             source=scratch_bi_path,

bu_isciii/templates/services.json

@@ -304,5 +304,22 @@
       "last_folder":"RESULTS",
       "delivery_md": "",
       "results_md": ""
-    }
+    },
+    "IRMA": {
+      "label": "",
+      "template": "IRMA",
+      "url": "",
+      "order": 1,
+      "begin": "",
+      "end": "",
+      "description": "",
+      "clean": {
+        "folders":["02-preprocessing"],
+        "files":[]
+      },
+      "no_copy": ["RAW", "TMP"],
+      "last_folder":"REFERENCES",
+      "delivery_md": "",
+      "results_md": ""
+  }
 }