ena-upload-cli 0.7.4__tar.gz → 0.8.0__tar.gz

{ena_upload_cli-0.7.4 → ena_upload_cli-0.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: ena-upload-cli
-Version: 0.7.4
+Version: 0.8.0
 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
@@ -8,17 +8,28 @@ Author-email: bjoern.gruening@gmail.com
 License: MIT
 Keywords: pip,ena-upload-cli,cli,ENA,upload
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.7
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: genshi==0.7.*
-Requires-Dist: lxml<=5.0.0,>=4.9.3
+Requires-Dist: lxml==5.3.0
 Requires-Dist: pandas<=3.0.0,>=2.0.3
-Requires-Dist: pyyaml==5.3.*
+Requires-Dist: pyyaml==6.0.*
 Requires-Dist: requests<=3.0.0,>=2.31.0
 Requires-Dist: openpyxl<=4.0.0,>=3.1.2
 Requires-Dist: jsonschema>=4.19.1
 Requires-Dist: pytest==7.4.*
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 [![Python application](https://github.com/usegalaxy-eu/ena-upload-cli/workflows/Python%20application/badge.svg)](https://github.com/usegalaxy-eu/ena-upload-cli/actions?query=workflow%3A%22Python+application%22)
 [![BioConda version](https://anaconda.org/bioconda/ena-upload-cli/badges/version.svg)](https://anaconda.org/bioconda/ena-upload-cli)
@@ -51,7 +62,7 @@ After a successful submission, new tsv tables will be generated with the ENA acc
 
 ## Tool dependencies
 
-* python 3.7+ including following packages:
+* python 3.8+ including following packages:
   * Genshi
   * lxml
   * pandas
@@ -130,6 +141,15 @@ 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.
@@ -138,6 +158,13 @@ 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.
+
+#### 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
 
@@ -253,7 +280,7 @@ 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-0.7.4/ena_upload_cli.egg-info/PKG-INFO → ena_upload_cli-0.8.0/README.md

@@ -1,25 +1,3 @@
-Metadata-Version: 2.1
-Name: ena-upload-cli
-Version: 0.7.4
-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
-Author-email: bjoern.gruening@gmail.com
-License: MIT
-Keywords: pip,ena-upload-cli,cli,ENA,upload
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.7
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: genshi==0.7.*
-Requires-Dist: lxml<=5.0.0,>=4.9.3
-Requires-Dist: pandas<=3.0.0,>=2.0.3
-Requires-Dist: pyyaml==5.3.*
-Requires-Dist: requests<=3.0.0,>=2.31.0
-Requires-Dist: openpyxl<=4.0.0,>=3.1.2
-Requires-Dist: jsonschema>=4.19.1
-Requires-Dist: pytest==7.4.*
-
 [![Python application](https://github.com/usegalaxy-eu/ena-upload-cli/workflows/Python%20application/badge.svg)](https://github.com/usegalaxy-eu/ena-upload-cli/actions?query=workflow%3A%22Python+application%22)
 [![BioConda version](https://anaconda.org/bioconda/ena-upload-cli/badges/version.svg)](https://anaconda.org/bioconda/ena-upload-cli)
 [![Pipy version](https://badge.fury.io/py/ena-upload-cli.svg)](https://pypi.org/project/ena-upload-cli/)
@@ -51,7 +29,7 @@ After a successful submission, new tsv tables will be generated with the ENA acc
 
 ## Tool dependencies
 
-* python 3.7+ including following packages:
+* python 3.8+ including following packages:
   * Genshi
   * lxml
   * pandas
@@ -130,6 +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.
@@ -138,6 +125,13 @@ 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.
+
+#### 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
 
@@ -253,7 +247,7 @@ 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-0.8.0/ena_upload/_version.py

@@ -0,0 +1 @@
+__version__ = "0.8.0"