ena-upload-cli 0.7.1__tar.gz → 0.7.2__tar.gz

{ena-upload-cli-0.7.1/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: 0.7.1
+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

ena_upload_cli-0.7.2/ena_upload/_version.py

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

{ena-upload-cli-0.7.1 → 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-0.7.1 → 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>