Merge pull request #19 from EBI-Metagenomics/empty_loc_fix

Refining multiple metadata fields exceptions

README.md

@@ -61,23 +61,25 @@ where
   * `---genome_info METADATA_FILE` : genomes metadata file in tsv format
   * `-m, --mags, --b, --bins`: select for bin or MAG upload. If in doubt, look at [their definition according to ENA](<https://ena-docs.readthedocs.io/en/latest/submit/assembly/metagenome.html>)
   * `--out`: output folder (default: working directory)
-  * `--force`: forces reset of sample xmls generation
-  * `--live`: registers genomes on ENA's live server. Omitting this option allows to validate samples beforehand (it will need the `-test` option in the upload command for the test submission to work)
+  * `--force`: forces reset of submission xml and ENA backup
+  * `--live`: registers genomes on ENA's live server. Omitting this option allows to validate samples beforehand (it will need the `-test` option in the upload command for test submissions to work)
   * `--webin WEBIN_ID`: webin id (format: Webin_XXXXX)
   * `--password PASSWORD`: webin password
   * `--centre_name CENTRE_NAME`: name of the centre generating and uploading genomes
   * `--tpa`: if uploading TPA (Third PArty) generated genomes
 
 It is recommended to validate your genomes in test mode (i.e. without `--live` in the registration step and with `-test` during the upload) before attempting the final upload. Launching the registration in test mode will add a timestamp to the genome name to allow multiple executions of the test process. 
 
-Sample xmls won't be regenerated automatically if a previous xml already exists. If any metadata or value in the tsv table changes, `--force` will allow xml regeneration. 
+`submission.xml` and `ENA_backup.json` won't be regenerated automatically if a previous run already exists,. To regenerate them, select `--force`. 
 
 ### Produced files:
 The script produces the following files and folders:
 ```bash
 bin_upload/MAG_upload
 ├── manifests
 │    └── ...
+├── manifests_test                  # folder generated for validation in test mode
+│    └── ...
 ├── ENA_backup.json                 # backup file to prevent re-download of metadata from ENA. Regeneration can be forced with --force
 ├── genome_samples.xml              # xml generated to register samples on ENA before the upload
 ├── registered_bins/MAGs.tsv        # list of genomes registered on ENA in live mode - needed for manifest generation

genomeuploader/__init__.py

@@ -1 +1 @@
-__version__ = '2.1.1'
+__version__ = '2.2.0'

genomeuploader/constants.py

@@ -452,7 +452,7 @@
     "Glorioso Islands",
     "Greece",
     "Greenland",
-    "GrENAda",
+    "Grenada",
     "Guadeloupe",
     "Guam",
     "Guatemala",
@@ -568,11 +568,11 @@
     "Ross Sea",
     "Russia",
     "Rwanda",
-    "Saint HelENA",
+    "Saint Helena",
     "Saint Kitts and Nevis",
     "Saint Lucia",
     "Saint Pierre and Miquelon",
-    "Saint Vincent and the GrENAdines",
+    "Saint Vincent and the Grenadines",
     "Samoa",
     "San Marino",
     "Sao Tome and Principe",

genomeuploader/ena.py

@@ -106,7 +106,7 @@ def get_run(self, run_accession, webin, password, attempt=0, search_params=None)
         except (IndexError, TypeError, ValueError):
             raise ValueError("Could not find run {} in ENA.".format(run_accession))
         except:
-            raise Exception("Could not query ENA API: {}".format(response.text))
+            raise Exception("Could not query ENA API for run {}: {}".format(run_accession, response.text))
 
         return run