Develop merge for 2.3.1 release

CHANGELOG.md

@@ -4,6 +4,31 @@ 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).
 
+## [2.3.1] - 2026-02-26 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.3.1
+
+### Credits
+
+- [Pau Pascual](https://github.com/PauPascualMas)
+- [Victor Lopez](https://github.com/victor5lm)
+
+### Template fixes and updates
+
+- Modified `create_assembly_stats.R` to group by sample in viralrecon template [#631](https://github.com/BU-ISCIII/buisciii-tools/pull/631).
+- Fixed error handling in finish module and automatic logging for new_service [#632](https://github.com/BU-ISCIII/buisciii-tools/pull/632).
+- Solved symlink path for TBProfiler results lablog [#634](https://github.com/BU-ISCIII/buisciii-tools/pull/634)
+
+
+### Modules
+
+#### Added enhancements
+
+#### Fixes
+
+#### Changed
+
+#### Removed
+
+### Requirements
 
 ## [2.3.0] - 2025-02-09 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.3.0
 

buisciii/__main__.py

@@ -66,7 +66,7 @@ def run_buisciii():
         highlight=False,
     )
 
-    __version__ = "2.3.0"
+    __version__ = "2.3.1"
     stderr.print(
         "[grey39]    BUISCIII-tools version {}".format(__version__), highlight=False
     )
@@ -140,7 +140,9 @@ def setup_automatic_logging(service_path, resolution_id, command_name, conf):
     try:
         # Path verification
         if command_name == "new_service" and not os.path.exists(service_path):
-            stderr.print(f"[red]Service path does not exist: {service_path}!")
+            stderr.print(
+                f"[red]Service path does not exist: {service_path}! Please check the service folder was created correctly."
+            )
             sys.exit(1)
 
         timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
@@ -628,80 +630,94 @@ def finish(ctx, resolution, path, ask_path, sftp_folder, tmp_dir):
     if resolution is None:
         resolution = buisciii.utils.prompt_resolution_id()
 
-    clean_tmp_dir = tmp_dir
-    if tmp_dir == "/scratch/bi/":
-        clean_tmp_dir = "/data/ucct/bi/scratch_tmp/bi"
+    debug = ctx.obj.get("debug", False)
+    try:
+        clean_tmp_dir = tmp_dir
+        if tmp_dir == "/scratch/bi/":
+            clean_tmp_dir = "/data/ucct/bi/scratch_tmp/bi"
 
-    conf = buisciii.config_json.ConfigJson()
-    conf_api = conf.get_configuration("xtutatis_api_settings")
-    rest_api = buisciii.drylab_api.RestServiceApi(
-        conf_api["server"],
-        conf_api["api_url"],
-        ctx.obj["api_user"],
-        ctx.obj["api_password"],
-    )
-    resolution_info = rest_api.get_request(
-        request_info="service-data", safe=True, resolution=resolution
-    )
-    service_folder = resolution_info["resolutions"][0]["resolution_full_number"]
-    service_path = os.path.join(
-        buisciii.utils.get_service_paths(
-            conf, "services_and_colaborations", resolution_info, "non_archived_path"
-        ),
-        service_folder,
-    )
+        conf = buisciii.config_json.ConfigJson()
+        conf_api = conf.get_configuration("xtutatis_api_settings")
+        rest_api = buisciii.drylab_api.RestServiceApi(
+            conf_api["server"],
+            conf_api["api_url"],
+            ctx.obj["api_user"],
+            ctx.obj["api_password"],
+        )
+        resolution_info = rest_api.get_request(
+            request_info="service-data", safe=True, resolution=resolution
+        )
+        service_folder = resolution_info["resolutions"][0]["resolution_full_number"]
+        service_path = os.path.join(
+            buisciii.utils.get_service_paths(
+                conf, "services_and_colaborations", resolution_info, "non_archived_path"
+            ),
+            service_folder,
+        )
 
-    if not ctx.obj.get("manual_log_file"):
-        setup_automatic_logging(service_path, resolution, "finish", ctx.obj["conf"])
-
-    print("Starting cleaning scratch directory: " + clean_tmp_dir)
-    clean_scratch = buisciii.clean.CleanUp(
-        resolution,
-        clean_tmp_dir,
-        ask_path,
-        "clean",
-        ctx.obj["api_user"],
-        ctx.obj["api_password"],
-        ctx.obj["conf"],
-    )
-    clean_scratch.handle_clean()
-    print("Starting copy from scratch directory: " + tmp_dir + " to service directory.")
-    copy_scratch2service = buisciii.scratch.Scratch(
-        resolution,
-        path,
-        tmp_dir,
-        "scratch_to_service",
-        ask_path,
-        ctx.obj["api_user"],
-        ctx.obj["api_password"],
-        ctx.obj["conf"],
-    )
-    copy_scratch2service.handle_scratch()
-    print("Starting renaming of the service directory.")
-    rename_databi = buisciii.clean.CleanUp(
-        resolution,
-        path,
-        ask_path,
-        "rename",
-        ctx.obj["api_user"],
-        ctx.obj["api_password"],
-        ctx.obj["conf"],
-    )
-    rename_databi.handle_clean()
-    print("Starting copy of the service directory to the SFTP folder")
-    copy_sftp = buisciii.copy_sftp.CopySftp(
-        resolution,
-        path,
-        ask_path,
-        sftp_folder,
-        ctx.obj["api_user"],
-        ctx.obj["api_password"],
-        ctx.obj["conf"],
-    )
-    copy_sftp.copy_sftp()
+        if not ctx.obj.get("manual_log_file"):
+            setup_automatic_logging(service_path, resolution, "finish", ctx.obj["conf"])
+
+        print("Starting cleaning scratch directory: " + clean_tmp_dir)
+        clean_scratch = buisciii.clean.CleanUp(
+            resolution,
+            clean_tmp_dir,
+            ask_path,
+            "clean",
+            ctx.obj["api_user"],
+            ctx.obj["api_password"],
+            ctx.obj["conf"],
+        )
+        clean_scratch.handle_clean()
+        print(
+            "Starting copy from scratch directory: "
+            + tmp_dir
+            + " to service directory."
+        )
+        copy_scratch2service = buisciii.scratch.Scratch(
+            resolution,
+            path,
+            tmp_dir,
+            "scratch_to_service",
+            ask_path,
+            ctx.obj["api_user"],
+            ctx.obj["api_password"],
+            ctx.obj["conf"],
+        )
+        copy_scratch2service.handle_scratch()
+        print("Starting renaming of the service directory.")
+        rename_databi = buisciii.clean.CleanUp(
+            resolution,
+            path,
+            ask_path,
+            "rename",
+            ctx.obj["api_user"],
+            ctx.obj["api_password"],
+            ctx.obj["conf"],
+        )
+        rename_databi.handle_clean()
+        print("Starting copy of the service directory to the SFTP folder")
+        copy_sftp = buisciii.copy_sftp.CopySftp(
+            resolution,
+            path,
+            ask_path,
+            sftp_folder,
+            ctx.obj["api_user"],
+            ctx.obj["api_password"],
+            ctx.obj["conf"],
+        )
+        copy_sftp.copy_sftp()
 
-    print("Service correctly stored in the SFTP folder")
-    print("Remember to generate delivery docs after setting delivery in iSkyLIMS!")
+        print("Service correctly stored in the SFTP folder")
+        print("Remember to generate delivery docs after setting delivery in iSkyLIMS!")
+    except Exception as e:
+        if debug:
+            log.exception(f"EXCEPTION FOUND: {e}")
+            raise
+        else:
+            log.exception(f"EXCEPTION FOUND: {e}")
+            stderr.print(f"EXCEPTION FOUND: {e}")
+            sys.exit(1)
 
 
 # CREATE DOCS IN BIOINFO_DOC

buisciii/new_service.py

@@ -322,10 +322,10 @@ def create_new_service(self):
             Run the whole service creation workflow.
         """
         if len(self.service_samples) > 0:
-            if self.setup_logging_cb is not None:
-                self.setup_logging_cb(self.full_path)
             self.check_md5()
             self.create_folder()
+            if self.setup_logging_cb is not None:
+                self.setup_logging_cb(self.full_path)
             self.copy_template()
             self.create_samples_id()
             self.create_symbolic_links()

buisciii/templates/tbprofiler/RESULTS/lablog_tbprofiler_results

@@ -4,4 +4,4 @@ mkdir -p $DELIVERY_FOLDER/tbprofiler
 
 cd $DELIVERY_FOLDER/tbprofiler
 
-ln -s ../../../ANALYSIS/*TBPROFILER/results/tbprofiler.* .
+ln -s ../../../ANALYSIS/*TBPROFILER/tbprofiler.* .

buisciii/templates/viralrecon/ANALYSIS/create_assembly_stats.R

@@ -124,8 +124,30 @@ df_final[, columnas_ch] <- apply(df_final[, columnas_ch], 2, function(x) as.char
 columnas_nu <- as.vector(6:length(colnames(df_final)))
 df_final[, columnas_nu] <- apply(df_final[, columnas_nu], 2, function(x) as.numeric(as.character(x)))
 
+# group by sample
+df_grouped <- df_final %>%
+  group_by(sample) %>%
+  summarise(
+    run = first(run),
+    user = first(user),
+    host = first(host),
+
+    Virussequence = paste(unique(Virussequence), collapse = ","),
+
+    totalreads = first(totalreads),
+    readshostR1 = first(readshostR1),
+    readshost = first(readshost),
+    `%readshost` = first(`%readshost`),
+    `Non-host-reads` = first(`Non-host-reads`),
+    `%Non-host-reads` = first(`%Non-host-reads`),
+    Contigs = if (all(is.na(Contigs))) NA else max(Contigs, na.rm = TRUE),
+    Largest_contig = if (all(is.na(Largest_contig))) NA else max(Largest_contig, na.rm = TRUE),
+    `%Genome_fraction` = if (all(is.na(`%Genome_fraction`))) NA else max(`%Genome_fraction`, na.rm = TRUE),
+    .groups = "drop"
+  )
+
 # Write table csv
-write.table(df_final, "assembly_stats.csv", row.names = F, col.names = T, sep = "\t", quote = F)
+write.table(df_grouped, "assembly_stats.csv", row.names = F, col.names = T, sep = "\t", quote = F)
 
 # Write table xlsx
-write_xlsx(df_final, "assembly_stats.xlsx", format_headers = F)
+write_xlsx(df_grouped, "assembly_stats.xlsx", format_headers = F)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "buisciii-tools"
-version = "2.3.0"
+version = "2.3.1"
 dynamic = ["dependencies"]
 
 authors = [
@@ -22,7 +22,8 @@ authors = [
     {name = "Alejandro Bernabeu", email = "abernabeu@isciii.es"},
     {name = "Alba Talavera", email = "alba.talavera@externos.isciii.es"},
     {name = "Magdalena Matito", email = "mmatito@externos.isciii.es"},
-    {name = "Pau Pascual", email = "ppascual@externos.isciii.es"}
+    {name = "Pau Pascual", email = "ppascual@externos.isciii.es"},
+    {name = "Enrique Sapena Ventura", email = "enrique.sapena@isciii.es"}
 ]
 
 maintainers = [
@@ -40,7 +41,8 @@ maintainers = [
     {name = "Alejandro Bernabeu", email = "abernabeu@isciii.es"},
     {name = "Alba Talavera", email = "alba.talavera@externos.isciii.es"},
     {name = "Magdalena Matito", email = "mmatito@externos.isciii.es"},
-    {name = "Pau Pascual", email = "ppascual@externos.isciii.es"}
+    {name = "Pau Pascual", email = "ppascual@externos.isciii.es"},
+    {name = "Enrique Sapena Ventura", email = "enrique.sapena@isciii.es"}
 ]
 
 description = "Tools for managing and resolution of buisciii services."