ena-upload-cli 0.7.0__tar.gz → 0.7.2__tar.gz

{ena-upload-cli-0.7.0/ena_upload_cli.egg-info → ena_upload_cli-0.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ena-upload-cli
-Version: 0.7.0
+Version: 0.7.2
 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
@@ -8,7 +8,7 @@ Author-email: bjoern.gruening@gmail.com
 License: MIT
 Keywords: pip,ena-upload-cli,cli,ENA,upload
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.5
+Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: genshi==0.7.*
@@ -29,7 +29,7 @@ Requires-Dist: pytest==7.4.*
 
 # ENA upload tool
 
-This command line tool (CLI) allows easy submission of experimental data and respective metadata to the European Nucleotide Archive (ENA) using tabular files or one of the excel spreadsheets that can be found on this [template repo](https://github.com/ELIXIR-Belgium/ENA-metadata-templates). The supported metadata that can be submitted includes study, sample, run and experiment info so you can use the tool for programmatic submission of everything ENA needs without the need of logging in to the Webin interface. This also includes client side validation using ENA checklists and releasing the ENA objects. This command line tool is also available as a [Galaxy tool](https://toolshed.g2.bx.psu.edu/view/iuc/ena_upload/) and can be added to you own Galaxy instance or you can make use of one of the existing Galaxy instances, like [usegalaxy.eu](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload).
+This command line tool (CLI) allows easy submission of experimental data and respective metadata to the European Nucleotide Archive (ENA) using tabular files or one of the excel spreadsheets that can be found on this [template repo](https://github.com/ELIXIR-Belgium/ENA-metadata-templates). The supported metadata that can be submitted includes study, sample, run and experiment info so you can use the tool for programmatic submission of everything ENA needs without the need of logging in to the Webin interface. This also includes client side validation using ENA checklists and releasing the ENA objects. This command line tool is also available as a [Galaxy tool](https://toolshed.g2.bx.psu.edu/view/iuc/ena_upload/) and can be added to you own Galaxy instance or you can make use of one of the existing Galaxy instances, like [usegalaxy.eu](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload) or [usegalaxy.be](https://usegalaxy.be/?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload). 
 
 ## Overview
 

{ena-upload-cli-0.7.0 → ena_upload_cli-0.7.2}/README.md

@@ -7,7 +7,7 @@
 
 # ENA upload tool
 
-This command line tool (CLI) allows easy submission of experimental data and respective metadata to the European Nucleotide Archive (ENA) using tabular files or one of the excel spreadsheets that can be found on this [template repo](https://github.com/ELIXIR-Belgium/ENA-metadata-templates). The supported metadata that can be submitted includes study, sample, run and experiment info so you can use the tool for programmatic submission of everything ENA needs without the need of logging in to the Webin interface. This also includes client side validation using ENA checklists and releasing the ENA objects. This command line tool is also available as a [Galaxy tool](https://toolshed.g2.bx.psu.edu/view/iuc/ena_upload/) and can be added to you own Galaxy instance or you can make use of one of the existing Galaxy instances, like [usegalaxy.eu](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload).
+This command line tool (CLI) allows easy submission of experimental data and respective metadata to the European Nucleotide Archive (ENA) using tabular files or one of the excel spreadsheets that can be found on this [template repo](https://github.com/ELIXIR-Belgium/ENA-metadata-templates). The supported metadata that can be submitted includes study, sample, run and experiment info so you can use the tool for programmatic submission of everything ENA needs without the need of logging in to the Webin interface. This also includes client side validation using ENA checklists and releasing the ENA objects. This command line tool is also available as a [Galaxy tool](https://toolshed.g2.bx.psu.edu/view/iuc/ena_upload/) and can be added to you own Galaxy instance or you can make use of one of the existing Galaxy instances, like [usegalaxy.eu](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload) or [usegalaxy.be](https://usegalaxy.be/?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload). 
 
 ## Overview
 

ena_upload_cli-0.7.2/ena_upload/_version.py

@@ -0,0 +1 @@
+__version__ = "0.7.2"

{ena-upload-cli-0.7.0 → ena_upload_cli-0.7.2}/ena_upload/ena_upload.py

@@ -39,6 +39,12 @@ class MyFTP_TLS(ftplib.FTP_TLS):
             conn = self.context.wrap_socket(conn,
                                             server_hostname=self.host,
                                             session=self.sock.session)
+            # fix reuse of ssl socket:
+            # https://stackoverflow.com/a/53456626/10971151 and
+            # https://stackoverflow.com/a/70830916/10971151
+            def custom_unwrap():
+                pass
+            conn.unwrap = custom_unwrap
         return conn, size
 
 
@@ -407,7 +413,7 @@ def submit_data(file_paths, password, webin_id):
 
     print("\nConnecting to ftp.webin2.ebi.ac.uk....")
     try:
-        ftps = MyFTP_TLS(timeout=10)
+        ftps = MyFTP_TLS(timeout=120)
         ftps.context.set_ciphers('HIGH:!DH:!aNULL')
         ftps.connect(ftp_host, port=21)
         ftps.auth()

{ena-upload-cli-0.7.0 → ena_upload_cli-0.7.2}/ena_upload/json_parsing/characteristic.py

@@ -11,8 +11,8 @@ class IsaBase:
 
     @classmethod
     def validate_json(self, isa_json: Dict[str, str], schema):
-        schema_path = os.path.join(os.curdir, "ena_upload", "json_parsing", "json_schemas", schema)
-
+        base_path = os.path.abspath(os.path.dirname(__file__))
+        schema_path = os.path.join(base_path, 'json_schemas', schema)
         json_file = open(schema_path)
         json_schema = json.load(json_file)
 

{ena-upload-cli-0.7.0 → ena_upload_cli-0.7.2}/ena_upload/templates/ENA.project.xsd

@@ -157,15 +157,7 @@
                         </xs:annotation>
                         <xs:complexType>
                             <xs:sequence maxOccurs="unbounded" minOccurs="1">
-                                <xs:element name="PROJECT_LINK">
-                                    <xs:complexType>
-                                        <xs:choice>
-                                            <xs:element name="XREF_LINK" type="com:XRefType"/>
-                                            <xs:element name="URL_LINK" type="com:URLType">
-                                            </xs:element>
-                                        </xs:choice>
-                                    </xs:complexType>
-                                </xs:element>
+                                <xs:element name="PROJECT_LINK" type="com:LinkType" />
                             </xs:sequence>
                         </xs:complexType>
                     </xs:element>

{ena-upload-cli-0.7.0 → ena_upload_cli-0.7.2}/ena_upload/templates/ENA_template_PLATFORM.xml

@@ -111,4 +111,24 @@
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'ug 100'">UG 100</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'unspecified'">unspecified</INSTRUMENT_MODEL>
 </ULTIMA>
+<VELA_DIAGNOSTICS py:when="row.platform.lower().strip() == 'vela_diagnostics'" py:choose="">
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'sentosa sq301'">Sentosa SQ301</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'unspecified'">unspecified</INSTRUMENT_MODEL>
+</VELA_DIAGNOSTICS>
+<GENAPSYS py:when="row.platform.lower().strip() == 'genapsys'" py:choose="">
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'genius'">GENIUS</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'genapsys sequencer'">Genapsys Sequencer</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'gs111'">GS111</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'unspecified'">unspecified</INSTRUMENT_MODEL>
+</GENAPSYS>
+<GENEMIND py:when="row.platform.lower().strip() == 'genemind'" py:choose="">
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'genocare 1600'">GenoCare 1600</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'genolab m'">GenoLab M</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'fastaseq 300'">FASTASeq 300</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'unspecified'">unspecified</INSTRUMENT_MODEL>
+</GENEMIND>
+<TAPESTRI py:when="row.platform.lower().strip() == 'tapestri'" py:choose="">
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'tapestri'">Tapestri</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'unspecified'">unspecified</INSTRUMENT_MODEL>
+</TAPESTRI>
 </PLATFORM>

{ena-upload-cli-0.7.0 → ena_upload_cli-0.7.2}/ena_upload/templates/ENA_template_samples_ERC000012.xml

@@ -33,101 +33,95 @@ def mandatorytest(row, column, index):
         <DESCRIPTION>${row.sample_description}</DESCRIPTION>
         </py:if>
         <SAMPLE_ATTRIBUTES>
-            <py:if test="mandatorytest(row, 'project name', index)">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>project name</TAG>
-                <VALUE>${row['project name']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
-            <py:if test="attributetest(row, 'experimental factor')">
+            <py:if test="attributetest(row, 'trophic level')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>experimental factor</TAG>
-                <VALUE>${row['experimental factor']}</VALUE>
+                <TAG>trophic level</TAG>
+                <VALUE>${row['trophic level']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'ploidy')">
+            <py:if test="attributetest(row, 'observed biotic relationship')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>ploidy</TAG>
-                <VALUE>${row['ploidy']}</VALUE>
+                <TAG>observed biotic relationship</TAG>
+                <VALUE>${row['observed biotic relationship']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'number of replicons')">
+            <py:if test="attributetest(row, 'known pathogenicity')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>number of replicons</TAG>
-                <VALUE>${row['number of replicons']}</VALUE>
+                <TAG>known pathogenicity</TAG>
+                <VALUE>${row['known pathogenicity']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'extrachromosomal elements')">
+            <py:if test="attributetest(row, 'relationship to oxygen')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>extrachromosomal elements</TAG>
-                <VALUE>${row['extrachromosomal elements']}</VALUE>
+                <TAG>relationship to oxygen</TAG>
+                <VALUE>${row['relationship to oxygen']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'estimated size')">
+            <py:if test="attributetest(row, 'propagation')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>estimated size</TAG>
-                <VALUE>${row['estimated size']}</VALUE>
+                <TAG>propagation</TAG>
+                <VALUE>${row['propagation']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'reference for biomaterial')">
+            <py:if test="attributetest(row, 'sample collection device')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>reference for biomaterial</TAG>
-                <VALUE>${row['reference for biomaterial']}</VALUE>
+                <TAG>sample collection device</TAG>
+                <VALUE>${row['sample collection device']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'annotation source')">
+            <py:if test="attributetest(row, 'sample collection method')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>annotation source</TAG>
-                <VALUE>${row['annotation source']}</VALUE>
+                <TAG>sample collection method</TAG>
+                <VALUE>${row['sample collection method']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'sample volume or weight for DNA extraction')">
+            <py:if test="attributetest(row, 'sample storage temperature')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>sample volume or weight for DNA extraction</TAG>
-                <VALUE>${row['sample volume or weight for DNA extraction']}</VALUE>
-                <UNITS>ng</UNITS>
+                <TAG>sample storage temperature</TAG>
+                <VALUE>${row['sample storage temperature']}</VALUE>
+                <UNITS>°C</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'nucleic acid extraction')">
+            <py:if test="attributetest(row, 'sample storage location')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>nucleic acid extraction</TAG>
-                <VALUE>${row['nucleic acid extraction']}</VALUE>
+                <TAG>sample storage location</TAG>
+                <VALUE>${row['sample storage location']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'nucleic acid amplification')">
+            <py:if test="attributetest(row, 'oxygenation status of sample')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>nucleic acid amplification</TAG>
-                <VALUE>${row['nucleic acid amplification']}</VALUE>
+                <TAG>oxygenation status of sample</TAG>
+                <VALUE>${row['oxygenation status of sample']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'library size')">
+            <py:if test="mandatorytest(row, 'project name', index)">
             <SAMPLE_ATTRIBUTE>
-                <TAG>library size</TAG>
-                <VALUE>${row['library size']}</VALUE>
+                <TAG>project name</TAG>
+                <VALUE>${row['project name']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'library reads sequenced')">
+            <py:if test="attributetest(row, 'ploidy')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>library reads sequenced</TAG>
-                <VALUE>${row['library reads sequenced']}</VALUE>
+                <TAG>ploidy</TAG>
+                <VALUE>${row['ploidy']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'library construction method')">
+            <py:if test="attributetest(row, 'number of replicons')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>library construction method</TAG>
-                <VALUE>${row['library construction method']}</VALUE>
+                <TAG>number of replicons</TAG>
+                <VALUE>${row['number of replicons']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'library vector')">
+            <py:if test="attributetest(row, 'extrachromosomal elements')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>library vector</TAG>
-                <VALUE>${row['library vector']}</VALUE>
+                <TAG>extrachromosomal elements</TAG>
+                <VALUE>${row['extrachromosomal elements']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'library screening strategy')">
+            <py:if test="attributetest(row, 'estimated size')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>library screening strategy</TAG>
-                <VALUE>${row['library screening strategy']}</VALUE>
+                <TAG>estimated size</TAG>
+                <VALUE>${row['estimated size']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
             <py:if test="attributetest(row, 'target gene')">
@@ -142,36 +136,12 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['target subfragment']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'pcr primers')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>pcr primers</TAG>
-                <VALUE>${row['pcr primers']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="attributetest(row, 'multiplex identifiers')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>multiplex identifiers</TAG>
                 <VALUE>${row['multiplex identifiers']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'adapters')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>adapters</TAG>
-                <VALUE>${row['adapters']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
-            <py:if test="attributetest(row, 'pcr conditions')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>pcr conditions</TAG>
-                <VALUE>${row['pcr conditions']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
-            <py:if test="attributetest(row, 'sequencing method')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>sequencing method</TAG>
-                <VALUE>${row['sequencing method']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="attributetest(row, 'sequence quality check')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>sequence quality check</TAG>
@@ -196,18 +166,6 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['relevant standard operating procedures']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'negative control type')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>negative control type</TAG>
-                <VALUE>${row['negative control type']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
-            <py:if test="attributetest(row, 'positive control type')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>positive control type</TAG>
-                <VALUE>${row['positive control type']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="mandatorytest(row, 'collection date', index)">
             <SAMPLE_ATTRIBUTE>
                 <TAG>collection date</TAG>
@@ -285,30 +243,6 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['ventilation type']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'source material identifiers')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>source material identifiers</TAG>
-                <VALUE>${row['source material identifiers']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
-            <py:if test="attributetest(row, 'sample material processing')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>sample material processing</TAG>
-                <VALUE>${row['sample material processing']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
-            <py:if test="attributetest(row, 'isolation and growth condition')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>isolation and growth condition</TAG>
-                <VALUE>${row['isolation and growth condition']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
-            <py:if test="attributetest(row, 'propagation')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>propagation</TAG>
-                <VALUE>${row['propagation']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="attributetest(row, 'amount or size of sample collected')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>amount or size of sample collected</TAG>
@@ -316,12 +250,6 @@ def mandatorytest(row, column, index):
                 <UNITS>m3</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'oxygenation status of sample')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>oxygenation status of sample</TAG>
-                <VALUE>${row['oxygenation status of sample']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="attributetest(row, 'organism count')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>organism count</TAG>
@@ -332,32 +260,6 @@ def mandatorytest(row, column, index):
             <SAMPLE_ATTRIBUTE>
                 <TAG>sample storage duration</TAG>
                 <VALUE>${row['sample storage duration']}</VALUE>
-                <UNITS>years</UNITS>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
-            <py:if test="attributetest(row, 'sample storage temperature')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>sample storage temperature</TAG>
-                <VALUE>${row['sample storage temperature']}</VALUE>
-                <UNITS>°C</UNITS>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
-            <py:if test="attributetest(row, 'sample storage location')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>sample storage location</TAG>
-                <VALUE>${row['sample storage location']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
-            <py:if test="attributetest(row, 'sample collection device')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>sample collection device</TAG>
-                <VALUE>${row['sample collection device']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
-            <py:if test="attributetest(row, 'sample collection method')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>sample collection method</TAG>
-                <VALUE>${row['sample collection method']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
             <py:if test="attributetest(row, 'host disease status')">
@@ -469,28 +371,34 @@ def mandatorytest(row, column, index):
                 <UNITS>psu</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'subspecific genetic lineage')">
+            <py:if test="attributetest(row, 'source material identifiers')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>subspecific genetic lineage</TAG>
-                <VALUE>${row['subspecific genetic lineage']}</VALUE>
+                <TAG>source material identifiers</TAG>
+                <VALUE>${row['source material identifiers']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'trophic level')">
+            <py:if test="attributetest(row, 'perturbation')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>trophic level</TAG>
-                <VALUE>${row['trophic level']}</VALUE>
+                <TAG>perturbation</TAG>
+                <VALUE>${row['perturbation']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'relationship to oxygen')">
+            <py:if test="attributetest(row, 'negative control type')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>relationship to oxygen</TAG>
-                <VALUE>${row['relationship to oxygen']}</VALUE>
+                <TAG>negative control type</TAG>
+                <VALUE>${row['negative control type']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'known pathogenicity')">
+            <py:if test="attributetest(row, 'positive control type')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>known pathogenicity</TAG>
-                <VALUE>${row['known pathogenicity']}</VALUE>
+                <TAG>positive control type</TAG>
+                <VALUE>${row['positive control type']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'experimental factor')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>experimental factor</TAG>
+                <VALUE>${row['experimental factor']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
             <py:if test="attributetest(row, 'encoded traits')">
@@ -499,22 +407,113 @@ def mandatorytest(row, column, index):
                 <VALUE>${row['encoded traits']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'observed biotic relationship')">
+            <py:if test="attributetest(row, 'subspecific genetic lineage')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>observed biotic relationship</TAG>
-                <VALUE>${row['observed biotic relationship']}</VALUE>
+                <TAG>subspecific genetic lineage</TAG>
+                <VALUE>${row['subspecific genetic lineage']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'chemical administration')">
+            <py:if test="attributetest(row, 'taxonomic classification')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>chemical administration</TAG>
-                <VALUE>${row['chemical administration']}</VALUE>
+                <TAG>taxonomic classification</TAG>
+                <VALUE>${row['taxonomic classification']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'perturbation')">
+            <py:if test="attributetest(row, 'isolation and growth condition')">
             <SAMPLE_ATTRIBUTE>
-                <TAG>perturbation</TAG>
-                <VALUE>${row['perturbation']}</VALUE>
+                <TAG>isolation and growth condition</TAG>
+                <VALUE>${row['isolation and growth condition']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'annotation source')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>annotation source</TAG>
+                <VALUE>${row['annotation source']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'reference for biomaterial')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>reference for biomaterial</TAG>
+                <VALUE>${row['reference for biomaterial']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'sample material processing')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>sample material processing</TAG>
+                <VALUE>${row['sample material processing']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'sample volume or weight for DNA extraction')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>sample volume or weight for DNA extraction</TAG>
+                <VALUE>${row['sample volume or weight for DNA extraction']}</VALUE>
+                <UNITS>ng</UNITS>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'nucleic acid extraction')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>nucleic acid extraction</TAG>
+                <VALUE>${row['nucleic acid extraction']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'nucleic acid amplification')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>nucleic acid amplification</TAG>
+                <VALUE>${row['nucleic acid amplification']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'library size')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>library size</TAG>
+                <VALUE>${row['library size']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'library reads sequenced')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>library reads sequenced</TAG>
+                <VALUE>${row['library reads sequenced']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'library construction method')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>library construction method</TAG>
+                <VALUE>${row['library construction method']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'library vector')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>library vector</TAG>
+                <VALUE>${row['library vector']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'library screening strategy')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>library screening strategy</TAG>
+                <VALUE>${row['library screening strategy']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'pcr conditions')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>pcr conditions</TAG>
+                <VALUE>${row['pcr conditions']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'pcr primers')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>pcr primers</TAG>
+                <VALUE>${row['pcr primers']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'adapters')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>adapters</TAG>
+                <VALUE>${row['adapters']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'chemical administration')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>chemical administration</TAG>
+                <VALUE>${row['chemical administration']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
             <SAMPLE_ATTRIBUTE>