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ICTV Import #834

Merged
merged 65 commits into from
Mar 21, 2024
Merged

ICTV Import #834

merged 65 commits into from
Mar 21, 2024

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@spiekos spiekos commented Mar 23, 2023

Note: need to add Notes and Caveats as well as commands for running and testing scripts. Also need to add tests and testing files

Note: need to add Notes and Caveats as well as commands for running and testing scripts. Also need to add tests and testing files
@spiekos spiekos requested a review from pradh March 23, 2023 05:03
@spiekos spiekos self-assigned this Mar 23, 2023
@spiekos spiekos changed the title Create README.md ICTV Import Mar 23, 2023
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 23, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 23, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 27, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 27, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 27, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 27, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 27, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 28, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 28, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 28, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 28, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 518973987
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 28, 2023
… and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.” Description from Wikipedia.

The ICTV Master Species List is curated by virology experts, which have established over 100 international study groups, which organize discussions on emerging taxonomic issues in their field, oversee the submission of proposals for new taxonomy, and prepare or revise the relevant chapter(s) in ICTV reports. ICTV is open to submissions of proposals for taxonomic changes from an individual, however in practice proposals are usually submitted by members of the relevant study groups.

The ICTV chooses an exemplar virus for each species and the Virus Metadata Resource provides a list of these exemplars. An exemplar virus serves as an example of a well-characterized virus isolate of that species and includes the GenBank accession number for the genomic sequence of the isolate as well as the virus name, isolate designation, suggested abbreviation, genome composition, and host source.

This import is internally documented including the schema additions [here](https://docs.google.com/document/d/1ELM4XmjyG1bitWqdSrSp6d49EQ2_ya4PpXHc_B0cPIE/edit?resourcekey=0-eefsHcX6YqQ7UqRcwVpaBg#heading=h.qtewylhpzoc9). This import is also being documented on GitHub in datacommonsorg/data [PR #834](datacommonsorg/data#834).

This cleans up the Master Species List and Virus Metadata Resource datasets from ICTV. They are formatted as a  tmcf + csv biomedical import. It also adds schema to represent the data in this import. It passed the tests from Prashanth's json tool and the internal v3 staging tool.

PiperOrigin-RevId: 520131436
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 5, 2024
…the ICTV MSL and VMR datasets to the most current releases. The corresponding code is updated as part of PR #834 (datacommonsorg/data#834)

PiperOrigin-RevId: 612587698
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 5, 2024
…the ICTV MSL and VMR datasets to the most current releases. The corresponding code is updated as part of PR #834 (datacommonsorg/data#834)

PiperOrigin-RevId: 612587698
copybara-service bot pushed a commit to datacommonsorg/schema that referenced this pull request Mar 5, 2024
…the ICTV MSL and VMR datasets to the most current releases. The corresponding code is updated as part of PR #834 (datacommonsorg/data#834)

PiperOrigin-RevId: 612828479
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Thanks for the detailed doc!

I only skimmed through the tests, one main comment on the validation script.

spiekos added 9 commits March 5, 2024 13:48
remove trailing \ in comma separated lists
remove trailing '\' from comma separated lists and directories
remove trailing '\' from comma separated lists and directories
add extra step to download the data commons java test tool
update tests subsection description
update tests subsection description to add assumptions
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Thanks for the updates!

@spiekos spiekos enabled auto-merge (squash) March 7, 2024 00:25
@spiekos spiekos disabled auto-merge March 20, 2024 21:35
@spiekos spiekos enabled auto-merge (squash) March 20, 2024 21:35
@spiekos spiekos merged commit 229d944 into master Mar 21, 2024
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@spiekos spiekos deleted the ICTV_import branch March 21, 2024 23:12
shamimansari1988 pushed a commit to shamimansari1988/data that referenced this pull request Aug 12, 2024
* Create README.md

Note: need to add Notes and Caveats as well as commands for running and testing scripts. Also need to add tests and testing files

* Add VirusMasterSpeciesList.tmcf

* Add tmcf files

* Update title

* Add VMR dataset description

* Mention script formatting taxonomic ranking enums

* format schema list

* update new enumerations lists

* update new schema summary formatting

* update new schema overview formatting

* Add create_virus_taxonomic_ranking_enums.py

* Add formatting scripts

* Update format_virus_metadata_resource.py

Removes error generated in two dcids by removing whitespace

* Add log file

* Update README.md

Add notes and caveats and dcid generation segments. Also add the commands to run data cleaning scripts.

* Create download.sh

* Update command to run download.sh

* update illegal characters subsection

* fix formatting error

* Add header

* Add header

* add header

* Add header

* update header

* Update header

* Update scripts

* Delete log file

* Update script

* Update create_virus_taxonomic_ranking_enums.py

update script to handle new v38 master species list input file

* Update format_virus_master_species_list.py

update script to accommodate new v38 release

* Update format_virus_master_species_list.py

correct file_output description in the header

* Update format_virus_metadata_resource.py

update script to accommodate v38

* Add run.sh

* Update download.sh

* Update format_virus_metadata_resource.log

update log from running script for v38

* Update README.md

* Update run.sh

change taxonomic rank enum schema to be generated from the virus metadata file

* Update create_virus_taxonomic_ranking_enums.py

update so that the virus taxonomic schema is generated from the virus metadata resource file

* Update format_virus_metadata_resource.py

fix new enum added in v38

* Update execution bash files

update download.sh, run.sh, and tests.sh scripts that download, format+clean, and test the import files

* Update README.md

* Rename VirusMasterSpeciesList.tmcf to VirusSpecies.tmcf

* Rename VirusGenomeSegment.tmcf to VirusGenomeSegments.tmcf

* Rename VirusTaxonomy.tmcf to VirusIsolates.tmcf

* Update tmcf links in README.md

* Update bash scripts filepaths in README.md

* Update filepaths in README.md

* Update README.md table of contents

* Update README.md table of contents

* Update README.md Table of Contents

* Update README.md

* Add line creating CSVs directory

* Update create_virus_taxonomic_ranking_enums.py

remove trailing \ in comma separated lists

* Update format_virus_master_species_list.py

remove trailing '\' from comma separated lists and directories

* Update format_virus_metadata_resource.py

remove trailing '\' from comma separated lists and directories

* Update tests.sh

add extra step to download the data commons java test tool

* Update README.md

update tests subsection description

* Update README.md

update tests subsection description to add assumptions

* Update README.md

fix typo

---------

Co-authored-by: Prashanth R <[email protected]>
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2 participants