ena-upload-cli 0.7.5__tar.gz → 0.9.0__tar.gz

{ena_upload_cli-0.7.5/ena_upload_cli.egg-info → ena_upload_cli-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: ena-upload-cli
-Version: 0.7.5
+Version: 0.9.0
 Summary: Command Line Interface to upload data to the European Nucleotide Archive
 Home-page: https://github.com/usegalaxy-eu/ena-upload-cli
 Author: Dilmurat Yusuf
@@ -27,6 +27,7 @@ Dynamic: description-content-type
 Dynamic: home-page
 Dynamic: keywords
 Dynamic: license
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
@@ -141,6 +142,15 @@ The command line tool will automatically fetch the correct scientific name based
 | sample_alias_4 | sample_title_2 | 2697049  | Severe acute respiratory syndrome coronavirus 2 | covid-19    | sample_description_1 | 2020-10-11      | Argentina                                |
 | sample_alias_5 | sample_title_3 | 2697049  | Severe acute respiratory syndrome coronavirus 2 | covid-19    | sample_description_2 | 2008-01-24      | Belgium                                  |
 
+#### Custom attributes
+
+Additional custom attributes (i.e. attributes not specified in the ERC checklist) can be added to the sample table by adding columns which headers are named like `sample_attribute[attribute_name]`; for example `sample_attribute[treatment]`, `sample_attribute[age]`... An example tsv file using custom attributes can be found in [example_tables/ENA_template_samples_xtra_attrs.tsv](/example_tables/ENA_template_samples_xtra_attrs.tsv). The same syntax is also applicable for xlsx input files.
+
+| alias          | ...            | sample_attribute[treatment] | sample_attribute[age]
+|----------------|----------------|---------------------|------------------------|
+| sample_alias_4 | ...            | treated             | 2 days
+| sample_alias_5 | ...            | untreated           | 2 days
+
 #### Viral submissions
 
 If you want to submit viral samples you can use the [ENA virus pathogen](https://www.ebi.ac.uk/ena/browser/view/ERC000033) checklist by adding `ERC000033` to the checklist parameter. Check out our [viral example command](#test-the-tool) as demonstration. Please use the [ENA virus pathogen](https://github.com/ELIXIR-Belgium/ENA-metadata-templates/tree/main/templates/ERC000033) checklist in our template repo to know what is allowed/possible in the `Controlled vocabulary`fields.
@@ -149,6 +159,19 @@ If you want to submit viral samples you can use the [ENA virus pathogen](https:/
 
 Please check out the [template](https://github.com/ELIXIR-Belgium/ENA-metadata-templates) of your checklist to discover which attributes are mandatory for the study, experiment and run ENA object.
 
+#### Read info run attributes
+
+Using `read_type`	and `read_label` as header in the columns of ENA run objects will allow you to set information about reads. Values are listed in a comma separated way, without spaces. `read_type` has a controlled vocabulary, which can be found in the [ENA Documentation](https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#json-manifest-file-format). An example tsv file using these attributes can be found in [example_tables/ENA_template_runs_read_info.tsv](/example_tables/ENA_template_runs_read_info.tsv). The same syntax is also applicable for xlsx input files.
+This feature is currently limited to FastQ files.
+
+#### Encrypted files
+
+When transferring encrypted files, an additional `unencrypted_checksum` column can be added in the run table. This column should contain the md5 checksum of the unencrypted file, and note that no check is performed on this value.
+This feature is currently limited to FastQ files.
+
+#### Study and experiment custom attributes
+
+Similarly to samples, additional custom attributes can be added to the experiment and study tables by adding columns which headers are named like `experiment_attribute[attribute_name]` and `study_attribute[attribute_name]` in the experiment and study tables, respectively.
 
 ### Dev instance
 
@@ -264,7 +287,7 @@ By default the updated tables after submission will have the action `added` in t
 
 * **Release submission**
   ```
-  ena-upload-cli --action release --center'your_center_name' --study example_tables/ENA_template_studies_release.tsv --dev --secret .secret.yml 
+  ena-upload-cli --action release --center 'your_center_name' --study example_tables/ENA_template_studies_release.tsv --dev --secret .secret.yml 
   ```
 
 > **Note for Windows users:** Windows, by default, does not support wildcard expansion in command-line arguments.

{ena_upload_cli-0.7.5 → ena_upload_cli-0.9.0}/README.md

@@ -108,6 +108,15 @@ The command line tool will automatically fetch the correct scientific name based
 | sample_alias_4 | sample_title_2 | 2697049  | Severe acute respiratory syndrome coronavirus 2 | covid-19    | sample_description_1 | 2020-10-11      | Argentina                                |
 | sample_alias_5 | sample_title_3 | 2697049  | Severe acute respiratory syndrome coronavirus 2 | covid-19    | sample_description_2 | 2008-01-24      | Belgium                                  |
 
+#### Custom attributes
+
+Additional custom attributes (i.e. attributes not specified in the ERC checklist) can be added to the sample table by adding columns which headers are named like `sample_attribute[attribute_name]`; for example `sample_attribute[treatment]`, `sample_attribute[age]`... An example tsv file using custom attributes can be found in [example_tables/ENA_template_samples_xtra_attrs.tsv](/example_tables/ENA_template_samples_xtra_attrs.tsv). The same syntax is also applicable for xlsx input files.
+
+| alias          | ...            | sample_attribute[treatment] | sample_attribute[age]
+|----------------|----------------|---------------------|------------------------|
+| sample_alias_4 | ...            | treated             | 2 days
+| sample_alias_5 | ...            | untreated           | 2 days
+
 #### Viral submissions
 
 If you want to submit viral samples you can use the [ENA virus pathogen](https://www.ebi.ac.uk/ena/browser/view/ERC000033) checklist by adding `ERC000033` to the checklist parameter. Check out our [viral example command](#test-the-tool) as demonstration. Please use the [ENA virus pathogen](https://github.com/ELIXIR-Belgium/ENA-metadata-templates/tree/main/templates/ERC000033) checklist in our template repo to know what is allowed/possible in the `Controlled vocabulary`fields.
@@ -116,6 +125,19 @@ If you want to submit viral samples you can use the [ENA virus pathogen](https:/
 
 Please check out the [template](https://github.com/ELIXIR-Belgium/ENA-metadata-templates) of your checklist to discover which attributes are mandatory for the study, experiment and run ENA object.
 
+#### Read info run attributes
+
+Using `read_type`	and `read_label` as header in the columns of ENA run objects will allow you to set information about reads. Values are listed in a comma separated way, without spaces. `read_type` has a controlled vocabulary, which can be found in the [ENA Documentation](https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#json-manifest-file-format). An example tsv file using these attributes can be found in [example_tables/ENA_template_runs_read_info.tsv](/example_tables/ENA_template_runs_read_info.tsv). The same syntax is also applicable for xlsx input files.
+This feature is currently limited to FastQ files.
+
+#### Encrypted files
+
+When transferring encrypted files, an additional `unencrypted_checksum` column can be added in the run table. This column should contain the md5 checksum of the unencrypted file, and note that no check is performed on this value.
+This feature is currently limited to FastQ files.
+
+#### Study and experiment custom attributes
+
+Similarly to samples, additional custom attributes can be added to the experiment and study tables by adding columns which headers are named like `experiment_attribute[attribute_name]` and `study_attribute[attribute_name]` in the experiment and study tables, respectively.
 
 ### Dev instance
 
@@ -231,7 +253,7 @@ By default the updated tables after submission will have the action `added` in t
 
 * **Release submission**
   ```
-  ena-upload-cli --action release --center'your_center_name' --study example_tables/ENA_template_studies_release.tsv --dev --secret .secret.yml 
+  ena-upload-cli --action release --center 'your_center_name' --study example_tables/ENA_template_studies_release.tsv --dev --secret .secret.yml 
   ```
 
 > **Note for Windows users:** Windows, by default, does not support wildcard expansion in command-line arguments.

ena_upload_cli-0.9.0/ena_upload/_version.py

@@ -0,0 +1 @@
+__version__ = "0.9.0"

{ena_upload_cli-0.7.5 → ena_upload_cli-0.9.0}/ena_upload/ena_upload.py

@@ -214,6 +214,16 @@ def generate_stream(schema, targets, Template, center, tool):
     :return: stream
     '''
 
+    # find all columns in targets which column header matches the pattern attribute[(.*)], extract the group
+    # and return a dict[header] = group
+    # eg for header run_attribute[sex] => {'run_attribute[sex]': 'sex'}
+    pattern = re.compile(rf"{schema}_attribute\[(.*)\]")
+    extra_attributes = {}
+    for column in targets.columns:
+        match = re.match(pattern, column)
+        if match:
+            extra_attributes[column] = match.group(1)
+
     if schema == 'run':
         # These attributes are required for rendering
         # the run xml templates
@@ -221,6 +231,13 @@ def generate_stream(schema, targets, Template, center, tool):
         if 'file_format' in targets:
             targets.rename(columns={'file_format': 'file_type'}, inplace=True)
         file_attrib = ['file_name', 'file_type', 'file_checksum']
+        if 'read_type' in targets:
+            file_attrib.append('read_type')
+        if 'read_label' in targets:
+            file_attrib.append('read_label')
+        if 'unencrypted_checksum' in targets:
+            file_attrib.append('unencrypted_checksum')
+
         other_attrib = ['alias', 'experiment_alias']
         # Create groups with alias as index
         run_groups = targets[other_attrib].groupby('alias')['experiment_alias'].first().to_dict()
@@ -230,11 +247,14 @@ def generate_stream(schema, targets, Template, center, tool):
         stream = Template.generate(run_groups=run_groups,
                                    file_groups=file_groups,
                                    center=center,
+                                   extra_attributes=extra_attributes,
                                    tool_name=tool['tool_name'],
                                    tool_version=tool['tool_version'])
     else:
         stream = Template.generate(
-            df=targets, center=center, tool_name=tool['tool_name'], tool_version=tool['tool_version'])
+            df=targets, center=center, extra_attributes=extra_attributes,
+            tool_name=tool['tool_name'], tool_version=tool['tool_version']
+        )
 
     return stream
 
@@ -684,10 +704,8 @@ def process_args():
     parser = argparse.ArgumentParser(prog='ena-upoad-cli',
                                      description='''The program makes submission
                                      of data and respective metadata to European
-                                     Nucleotide Archive (ENA). The metadate
-                                     should be provided in separate tables
-                                     corresponding the ENA objects -- STUDY,
-                                     SAMPLE, EXPERIMENT and RUN.''',
+                                     Nucleotide Archive (ENA) easy. The metadata
+                                     can be provided in a xlsx spreadsheet or tsv tables.''',
                                      formatter_class=SmartFormatter)
     parser.add_argument('--version', action='version',
                         version='%(prog)s '+__version__)
@@ -982,7 +1000,7 @@ def main():
                 if pd.notna(row['scientific_name']) and pd.isna(row['taxon_id']):
                     # retrieve taxon id using scientific name
                     taxonID = get_taxon_id(row['scientific_name'])
-                    df.loc[index, 'taxon_id'] = taxonID
+                    df.loc[index, 'taxon_id'] = int(taxonID)
                 elif pd.notna(row['taxon_id']) and pd.isna(row['scientific_name']):
                     # retrieve scientific name using taxon id
                     scientificName = get_scientific_name(row['taxon_id'])
@@ -1022,9 +1040,9 @@ def main():
         print("No submission will be performed, remove `--draft' argument to perform submission.")
     else:
         if dev:
-            url = 'https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA'
+            url = 'https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/'
         else:
-            url = 'https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA'
+            url = 'https://www.ebi.ac.uk/ena/submit/drop-box/submit/'
 
         print(f'\nSubmitting XMLs to ENA server: {url}')
         receipt = send_schemas(schema_xmls, url, webin_id, password).text

ena_upload_cli-0.9.0/ena_upload/templates/ENA_template_FASTQFILE.xml

@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?python
+import pandas as pd
+def attributetest(row, column):
+    if hasattr(row, column) and pd.notna(row[column]) and not str(row[column]).isspace():
+        return True
+?>
+<py:choose xmlns:py="http://genshi.edgewall.org/" test="" xmlns:xi="http://www.w3.org/2001/XInclude">
+<py:when test="attributetest(row, 'unencrypted_checksum')">
+    <FILE filename="${row.file_name}" filetype="fastq" checksum_method="MD5" checksum="${row.file_checksum}" unencrypted_checksum="${row.unencrypted_checksum}">
+    <py:if test="attributetest(row, 'read_label')">
+        <py:for each="rlabel in row.read_label.split(',')">
+        <READ_LABEL>${rlabel.strip()}</READ_LABEL>
+        </py:for>
+    </py:if>
+    <py:if test="attributetest(row, 'read_type')">
+        <py:for each="rtype in row.read_type.split(',')">
+        <xi:include href="ENA_template_READ_TYPE.xml" />
+        </py:for>
+    </py:if>
+    </FILE>
+</py:when>
+<py:otherwise>
+    <FILE filename="${row.file_name}" filetype="fastq" checksum_method="MD5" checksum="${row.file_checksum}">
+    <py:if test="attributetest(row, 'read_label')">
+        <py:for each="rlabel in row.read_label.split(',')">
+        <READ_LABEL>${rlabel.strip()}</READ_LABEL>
+        </py:for>
+    </py:if>
+    <py:if test="attributetest(row, 'read_type')">
+        <py:for each="rtype in row.read_type.split(',')">
+        <xi:include href="ENA_template_READ_TYPE.xml" />
+        </py:for>
+    </py:if>
+    </FILE>
+</py:otherwise>
+</py:choose>

{ena_upload_cli-0.7.5 → ena_upload_cli-0.9.0}/ena_upload/templates/ENA_template_PLATFORM.xml

@@ -26,6 +26,7 @@
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'illumina miseq'">Illumina MiSeq</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'illumina miniseq'">Illumina MiniSeq</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'illumina novaseq x'">Illumina NovaSeq X</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'illumina novaseq x plus'">Illumina NovaSeq X Plus</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'illumina novaseq 6000'">Illumina NovaSeq 6000</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'nextseq 500'">NextSeq 500</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'nextseq 550'">NextSeq 550</INSTRUMENT_MODEL>
@@ -101,6 +102,7 @@
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'dnbseq-g400'">DNBSEQ-G400</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'dnbseq-g50'">DNBSEQ-G50</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'dnbseq-g400 fast'">DNBSEQ-G400 FAST</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'dnbseq-t10x4rs'">DNBSEQ-T10x4RS</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'unspecified'">unspecified</INSTRUMENT_MODEL>
 </DNBSEQ>
 <ELEMENT py:when="row.platform.lower().strip() == 'element'" py:choose="">

ena_upload_cli-0.9.0/ena_upload/templates/ENA_template_READ_TYPE.xml

@@ -0,0 +1,9 @@
+<py:choose xmlns:py="http://genshi.edgewall.org/" test="">
+<READ_TYPE py:when="rtype.strip().lower() == 'single'">single</READ_TYPE>
+<READ_TYPE py:when="rtype.strip().lower() == 'paired'">paired</READ_TYPE>
+<READ_TYPE py:when="rtype.strip().lower() == 'cell_barcode'">cell_barcode</READ_TYPE>
+<READ_TYPE py:when="rtype.strip().lower() == 'umi_barcode'">umi_barcode</READ_TYPE>
+<READ_TYPE py:when="rtype.strip().lower() == 'feature_barcode'">feature_barcode</READ_TYPE>
+<READ_TYPE py:when="rtype.strip().lower() == 'sample_barcode'">sample_barcode</READ_TYPE>
+<READ_TYPE py:when="rtype.strip().lower() == 'spatial_barcode'">spatial_barcode</READ_TYPE>
+</py:choose>

ena_upload_cli-0.9.0/ena_upload/templates/ENA_template_experiments.xml

@@ -0,0 +1,86 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?python
+import pandas as pd
+import sys
+def attributetest(row, column):
+    if hasattr(row, column) and pd.notna(row[column]) and not str(row[column]).isspace():
+        return True 
+def mandatorytest(row, column, index):
+    if hasattr(row, column) and pd.notna(row[column]) and not str(row[column]).isspace():
+        return True 
+    else:
+        print("MISSING VALUE ERROR: The mandatory column '"+ str(column) + "' is not filled in at row '" + str(index) + "'" + "\n")
+        sys.exit("This process is terminated")
+?>
+<EXPERIMENT_SET xmlns:py="http://genshi.edgewall.org/"
+    xmlns:xi="http://www.w3.org/2001/XInclude"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:noNamespaceSchemaLocation="ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_6/SRA.experiment.xsd">
+    <py:for each="index, row in df.iterrows()">
+    <EXPERIMENT alias="${row.alias}" center_name="${center}">
+        <py:if test="mandatorytest(row, 'title', index)">
+        <TITLE>${row.title}</TITLE>
+        </py:if>
+        <py:if test="mandatorytest(row, 'study_alias', index)">
+        <STUDY_REF refname="${row.study_alias}"/>
+        </py:if>
+        <DESIGN>
+            <py:if test="mandatorytest(row, 'design_description', index)">
+            <DESIGN_DESCRIPTION>${row.design_description}</DESIGN_DESCRIPTION>
+            </py:if>
+            <py:if test="attributetest(row, 'spot_descriptor')">
+            <SPOT_DESCRIPTOR>${row.spot_descriptor}</SPOT_DESCRIPTOR>
+            </py:if>
+            <py:if test="mandatorytest(row, 'sample_alias', index)">
+            <SAMPLE_DESCRIPTOR refname="${row.sample_alias}"/>
+            </py:if>
+            <LIBRARY_DESCRIPTOR>
+                <py:if test="attributetest(row, 'library_name')">
+                <LIBRARY_NAME>${row.library_name}</LIBRARY_NAME>
+                </py:if>
+                <py:if test="mandatorytest(row, 'library_strategy', index)">
+                <xi:include href="ENA_template_LIBRARY_STRATEGY.xml" />
+                </py:if>
+                <py:if test="mandatorytest(row, 'library_source', index)">
+                <xi:include href="ENA_template_LIBRARY_SOURCE.xml" />
+                </py:if>
+                <py:if test="mandatorytest(row, 'library_selection', index)">
+                <xi:include href="ENA_template_LIBRARY_SELECTION.xml" />
+                </py:if>
+                <py:if test="mandatorytest(row, 'library_layout', index)">
+                <LIBRARY_LAYOUT py:choose="">
+                    <PAIRED py:when="row.library_layout.lower().strip() == 'paired'" NOMINAL_LENGTH="${int(row.insert_size)}" />
+                    <SINGLE py:when="row.library_layout.lower().strip() == 'single'" />
+                </LIBRARY_LAYOUT>
+                </py:if>
+                <py:if test="attributetest(row, 'library_construction_protocol')">
+                <LIBRARY_CONSTRUCTION_PROTOCOL>${row.library_construction_protocol}</LIBRARY_CONSTRUCTION_PROTOCOL>
+                </py:if>
+            </LIBRARY_DESCRIPTOR>
+        </DESIGN>
+        <py:if test="mandatorytest(row, 'platform', index)">
+        <py:if test="mandatorytest(row, 'instrument_model', index)">
+        <xi:include href="ENA_template_PLATFORM.xml" />
+        </py:if>
+        </py:if>
+        <EXPERIMENT_ATTRIBUTES>
+            <py:for each="header, tag in extra_attributes.items()">
+            <py:if test="attributetest(row, header)">
+            <EXPERIMENT_ATTRIBUTE>
+                <TAG>${tag}</TAG>
+                <VALUE>${row[header]}</VALUE>
+            </EXPERIMENT_ATTRIBUTE>
+            </py:if>
+            </py:for>
+            <EXPERIMENT_ATTRIBUTE>
+                <TAG>SUBMISSION_TOOL</TAG>
+                <VALUE>${tool_name}</VALUE>
+            </EXPERIMENT_ATTRIBUTE>
+            <EXPERIMENT_ATTRIBUTE>
+                <TAG>SUBMISSION_TOOL_VERSION</TAG>
+                <VALUE>${tool_version}</VALUE>
+            </EXPERIMENT_ATTRIBUTE>
+        </EXPERIMENT_ATTRIBUTES>
+    </EXPERIMENT>
+    </py:for>
+</EXPERIMENT_SET>

{ena_upload_cli-0.7.5 → ena_upload_cli-0.9.0}/ena_upload/templates/ENA_template_runs.xml

@@ -2,6 +2,9 @@
 <?python
 import pandas as pd
 import sys
+def attributetest(row, column):
+    if hasattr(row, column) and pd.notna(row[column]) and not str(row[column]).isspace():
+        return True
 def mandatorytest(row, column, index):
     if hasattr(row, column) and pd.notna(row[column]) and not str(row[column]).isspace():
         return True 
@@ -20,7 +23,14 @@ def mandatorytest(row, column, index):
             <FILES>
                 <py:for each="index, row in file_groups.get_group(alias).iterrows()">
                 <py:if test="mandatorytest(row, 'file_type', index)">
-                <xi:include href="ENA_template_FILE.xml" />
+                <py:choose xmlns:py="http://genshi.edgewall.org/" test="">
+                    <py:when test="row.file_type.lower().strip() == 'fastq'">
+                         <xi:include href="ENA_template_FASTQFILE.xml" />
+                    </py:when>
+                    <py:otherwise>
+                        <xi:include href="ENA_template_FILE.xml" />
+                    </py:otherwise>
+                </py:choose>
                 </py:if>
                 </py:for>
             </FILES>

{ena_upload_cli-0.7.5 → ena_upload_cli-0.9.0}/ena_upload/templates/ENA_template_samples_ERC000011.xml

@@ -87,12 +87,6 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['collection date']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="attributetest(row, 'geographic location (region and locality)')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (region and locality)</TAG>
@@ -123,6 +117,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sex']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'lab_host')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>lab_host</TAG>
@@ -213,6 +213,14 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['strain']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:for each="header, tag in extra_attributes.items()">
+            <py:if test="attributetest(row, header)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>${tag}</TAG>
+                <VALUE>${row[header]}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            </py:for>
             <SAMPLE_ATTRIBUTE>
                 <TAG>SUBMISSION_TOOL</TAG>
                 <VALUE>${tool_name}</VALUE>

{ena_upload_cli-0.7.5 → ena_upload_cli-0.9.0}/ena_upload/templates/ENA_template_samples_ERC000012.xml

@@ -179,12 +179,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -262,6 +256,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'host disease status')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>host disease status</TAG>
@@ -516,6 +516,14 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['chemical administration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:for each="header, tag in extra_attributes.items()">
+            <py:if test="attributetest(row, header)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>${tag}</TAG>
+                <VALUE>${row[header]}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            </py:for>
             <SAMPLE_ATTRIBUTE>
                 <TAG>SUBMISSION_TOOL</TAG>
                 <VALUE>${tool_name}</VALUE>

{ena_upload_cli-0.7.5 → ena_upload_cli-0.9.0}/ena_upload/templates/ENA_template_samples_ERC000013.xml

@@ -203,12 +203,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -285,6 +279,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'host disease status')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>host disease status</TAG>
@@ -645,6 +645,14 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['chemical administration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:for each="header, tag in extra_attributes.items()">
+            <py:if test="attributetest(row, header)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>${tag}</TAG>
+                <VALUE>${row[header]}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            </py:for>
             <SAMPLE_ATTRIBUTE>
                 <TAG>SUBMISSION_TOOL</TAG>
                 <VALUE>${tool_name}</VALUE>

{ena_upload_cli-0.7.5 → ena_upload_cli-0.9.0}/ena_upload/templates/ENA_template_samples_ERC000014.xml

@@ -203,12 +203,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -273,6 +267,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'nose/mouth/teeth/throat disorder')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>nose/mouth/teeth/throat disorder</TAG>
@@ -667,6 +667,14 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['chemical administration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:for each="header, tag in extra_attributes.items()">
+            <py:if test="attributetest(row, header)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>${tag}</TAG>
+                <VALUE>${row[header]}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            </py:for>
             <SAMPLE_ATTRIBUTE>
                 <TAG>SUBMISSION_TOOL</TAG>
                 <VALUE>${tool_name}</VALUE>

{ena_upload_cli-0.7.5 → ena_upload_cli-0.9.0}/ena_upload/templates/ENA_template_samples_ERC000015.xml

@@ -191,12 +191,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -261,6 +255,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'gastrointestinal tract disorder')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>gastrointestinal tract disorder</TAG>
@@ -564,6 +564,14 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['chemical administration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:for each="header, tag in extra_attributes.items()">
+            <py:if test="attributetest(row, header)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>${tag}</TAG>
+                <VALUE>${row[header]}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            </py:for>
             <SAMPLE_ATTRIBUTE>
                 <TAG>SUBMISSION_TOOL</TAG>
                 <VALUE>${tool_name}</VALUE>

{ena_upload_cli-0.7.5 → ena_upload_cli-0.9.0}/ena_upload/templates/ENA_template_samples_ERC000016.xml

@@ -197,12 +197,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>geographic location (country and/or sea)</TAG>
-                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'geographic location (latitude)', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>
@@ -267,6 +261,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['sample storage duration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="mandatorytest(row, 'geographic location (country and/or sea)', index)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'nose/mouth/teeth/throat disorder')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>nose/mouth/teeth/throat disorder</TAG>
@@ -565,6 +565,14 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['chemical administration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:for each="header, tag in extra_attributes.items()">
+            <py:if test="attributetest(row, header)">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>${tag}</TAG>
+                <VALUE>${row[header]}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            </py:for>
             <SAMPLE_ATTRIBUTE>
                 <TAG>SUBMISSION_TOOL</TAG>
                 <VALUE>${tool_name}</VALUE>