diff --git a/README.md b/README.md index 8d3f4c6..d60cdd1 100644 --- a/README.md +++ b/README.md @@ -2,95 +2,6 @@ ArcCommander is a command line tool to create, manage and share your ARCs. - - -- [Install and start](#install-and-start) -- [Develop](#develop) - - [Prerequisites](#prerequisites) - - [Build](#build) - - [via dotnet cli](#via-dotnet-cli) - - [using the shell scripts](#using-the-shell-scripts) -- [Usage](#usage) - - [General cli structure](#general-cli-structure) - - [Subcommand verbs](#subcommand-verbs) - - [CLI argument help](#cli-argument-help) - - [Top level:](#top-level) - - [init:](#init) - - [investigation:](#investigation) - - [investigation create](#investigation-create) - - [investigation update](#investigation-update) - - [investigation delete](#investigation-delete) - - [investigation person](#investigation-person) - - [investigation person update](#investigation-person-update) - - [investigation person edit](#investigation-person-edit) - - [investigation person register](#investigation-person-register) - - [investigation person unregister](#investigation-person-unregister) - - [investigation person get](#investigation-person-get) - - [investigation publication](#investigation-publication) - - [investigation publication update](#investigation-publication-update) - - [investigation publication edit](#investigation-publication-edit) - - [investigation publication register](#investigation-publication-register) - - [investigation publication unregister](#investigation-publication-unregister) - - [investigation publication get](#investigation-publication-get) - - [study:](#study) - - [study init](#study-init) - - [study register](#study-register) - - [study add](#study-add) - - [study delete](#study-delete) - - [study unregister](#study-unregister) - - [study remove](#study-remove) - - [study update](#study-update) - - [study edit](#study-edit) - - [study get](#study-get) - - [study person](#study-person) - - [study person update](#study-person-update) - - [study person edit](#study-person-edit) - - [study person register](#study-person-register) - - [study person unregister](#study-person-unregister) - - [study person get](#study-person-get) - - [study publication](#study-publication) - - [study publication update](#study-publication-update) - - [study publication edit](#study-publication-edit) - - [study publication register](#study-publication-register) - - [study publication unregister](#study-publication-unregister) - - [study publication get](#study-publication-get) - - [study design](#study-design) - - [study design update](#study-design-update) - - [study design edit](#study-design-edit) - - [study design register](#study-design-register) - - [study design unregister](#study-design-unregister) - - [study design get](#study-design-get) - - [study factor](#study-factor) - - [study factor update](#study-factor-update) - - [study factor edit](#study-factor-edit) - - [study factor register](#study-factor-register) - - [study factor unregister](#study-factor-unregister) - - [study factor get](#study-factor-get) - - [study protocol](#study-protocol) - - [study protocol update](#study-protocol-update) - - [study protocol edit](#study-protocol-edit) - - [study protocol register](#study-protocol-register) - - [study protocol unregister](#study-protocol-unregister) - - [study protocol get](#study-protocol-get) - - [assay:](#assay) - - [assay init](#assay-init) - - [assay register](#assay-register) - - [assay add](#assay-add) - - [assay delete](#assay-delete) - - [assay unregister](#assay-unregister) - - [assay remove](#assay-remove) - - [assay update](#assay-update) - - [assay edit](#assay-edit) - - [assay move](#assay-move) - - [assay get](#assay-get) - - [configuration:](#configuration) - - [configuration list](#configuration-list) - - [configuration edit](#configuration-edit) - - [configuration set](#configuration-set) - - [configuration unset](#configuration-unset) - - - ## Install and start Head over to [Releases](https://github.com/nfdi4plants/arcCommander/releases). Download the newest release for the OS you use. Extract the .zip into a folder of your choice. @@ -100,6 +11,8 @@ We strongly recommend to read the in-depth guide to the ArcCommander in this rep ## Develop +The following part addresses all who want to contribute to the ArcCommander. + ### Prerequisites - .NET SDK >= 3.1.00 (should roll forward to .net 5 if you are using that) @@ -150,1757 +63,4 @@ build.sh -t prerelease #### testing the binary -After running the default build target, binaries of the arcCommander tool will lie in ./bin/ArcCommander. To run the binary, either use the `ArcCommander.exe` file on windows or `dotnet ArcCommander.dll` on linux - -## Usage - -### General cli structure - -The general command line structure is designed as either - -```powershell -arc -``` - -e.g. - -```powershell -arc init -``` - -or - -```powershell -arc -``` - -where `` is one of the following: - - - `assay` - - `study` or its sub-objects - - `investigation` or its sub-objects - - `configuration` - -and `` models what to do with the object, e.g - -```powershell -arc study init -``` - -will initialize a new empty study in the ARC. - -### Subcommand verbs - -while not all object subcommands support all verbs, here is a list of the verbs and what to expect when they are applicable for an ``: - -- arc `` **init** : will initialize a new empty `` in the ARC. -- arc `` **create** will create a new `` with the passed arguments in the ARC. -- arc `` **update** will update the registration of an existing `` with the passed arguments. -- arc `` **edit** will open an existing `` with a text editor, allowing editing the registration of the ``. -- arc `` **register** will register an existing `` in the ARC with the passed arguments. -- arc `` **add** is the combination of create/init+update and register, meaning it will create a new `` in the ARC and subsequently register it with the passed arguments -- arc `` **delete** will delete the `` from the arc file structure. -- arc `` **unregister** will remove the `` from the ARC's register. -- arc `` **remove** is the combination of delete and unregister, meaning it will delete the `` from the ARC file structure and the ARC's registry -- arc `` **move** will move the `` from source to target register. -- arc `` **list** will print all `s` registered in the ARC. -- arc `` **set** will set a single value in the ``. -- arc `` **unset** will remove a single value from the ``. - -### CLI argument help - -Here is the current help dump from the command line tool: - -#### Top level: - -```powershell -USAGE: ArcCommander.exe [--help] [--workingdir ] [--verbosity ] - [ []] - -SUBCOMMANDS: - - init Initializes basic folder structure - investigation, i - Investigation file functions - study, s - Study functions - assay, a - Assay functions - configuration, config - Configuration editing - - Use 'ArcCommander.exe --help' for additional information. - -OPTIONS: - - --workingdir, -p - Set the base directory of your ARC - --verbosity, -v - Sets the amount of additional printed information: 0->No information, 1 (Default) -> Basic - Information, 2 -> Additional information - --help display this list of options. -``` - -#### init: - -```powershell -USAGE: ArcCommander.exe init [--help] [--owner ] [--repositoryadress ] [--editorpath ] - -OPTIONS: - - --owner Owner of the arc - --repositoryadress - Github adress - --editorpath - The path leading to the editor used for text prompts (Default in Windows is notepad) - --help display this list of options. -``` -
- -#### investigation: - -```powershell -USAGE: ArcCommander.exe investigation [--help] [ []] - -SUBCOMMANDS: - - create Create a new investigation with the given metadata - update Update the arc's investigation with the given metdadata - edit Open an editor window to directly edit the arc's investigation file - delete Delete the arc's investigation file (danger zone!) - person Person functions - publication - Publication functions - - Use 'ArcCommander.exe --help' for additional information. - -OPTIONS: - - --help display this list of options. -``` - -##### investigation create - -```powershell -USAGE: ArcCommander.exe investigation create [--help] --identifier [--title ] - [--description <description>] [--submissiondate <submission date>] - [--publicreleasedate <public release date>] - -OPTIONS: - - --identifier <investigation identifier> - A identifier or an accession number provided by a repository. This SHOULD be locally unique. - --title <title> A concise name given to the investigation. - --description <description> - A textual description of the investigation. - --submissiondate <submission date> - The date on which the investigation was reported to the repository. - --publicreleasedate <public release date> - The date on which the investigation was released publicly. - --help display this list of options. -``` - -##### investigation update - -```powershell -USAGE: ArcCommander.exe investigation update [--help] --identifier <investigation identifier> [--title <title>] - [--description <description>] [--submissiondate <submission date>] - [--publicreleasedate <public release date>] - -OPTIONS: - - --identifier <investigation identifier> - A identifier or an accession number provided by a repository. This SHOULD be locally unique. - --title <title> A concise name given to the investigation. - --description <description> - A textual description of the investigation. - --submissiondate <submission date> - The date on which the investigation was reported to the repository. - --publicreleasedate <public release date> - The date on which the investigation was released publicly. - --help display this list of options. -``` - -##### investigation delete - -```powershell -USAGE: ArcCommander.exe investigation delete [--help] --identifier <investigation identifier> - -OPTIONS: - - --identifier <investigation identifier> - DangerZone: In order to delete this investigation file please provide its identifier here. - --help display this list of options. -``` - -<br> - -##### investigation person - -```powershell -USAGE: ArcCommander.exe investigation person [--help] [<subcommand> [<options>]] - -SUBCOMMANDS: - - update <update args> Update an existing person in the arc investigation with the given person metadata. The person is - identified by the full name (first name, last name, mid initials) - edit <edit args> Open and edit an existing person in the arc investigation with a text editor. The person is - identified by the full name (first name, last name, mid initials) - register <register args> - Register a person in the arc investigation with the given assay metadata. - unregister <remove args> - Unregister a person from the given investigation. The person is identified by the full name (first - name, last name, mid initials). - get <get args> Get the metadata of a person registered in the arc investigation - list List all persons registered in the arc investigation - - Use 'ArcCommander.exe <subcommand> --help' for additional information. - -OPTIONS: - - --help display this list of options. -``` - -##### investigation person update - -```powershell -OPTIONS: - - --lastname, -l <last name> - The last name of a person associated with the investigation. - --firstname, -f <first name> - The first name of a person associated with the investigation. - --midinitials, -m <mid initials> - The middle initials of a person associated with the investigation. - --email <e mail> The email address of a person associated with the investigation. - --phone <phone number> - The telephone number of a person associated with the investigation. - --fax <fax number> The fax number of a person associated with the investigation. - --address <adress> The address of a person associated with the investigation. - --affiliation <affiliation> - The organization affiliation for a person associated with the investigation. - --roles <roles> Term to classify the role(s) performed by this person in the context of the investigation, which - means that the roles reported here need not correspond to roles held withing their affiliated - organization. Multiple annotations or values attached to one person can be provided by using a - semicolon (";") Unicode (U0003+B) as a separator (e.g.: submitter;funder;sponsor). The term can be - free text or from, for example, a controlled vocabulary or an ontology. If the latter source is used - the Term Accession Number and Term Source REF fields below are required. - --rolestermaccessionnumber <roles term accession number> - The accession number from the Term Source associated with the selected term. - --rolestermsourceref <roles term source ref> - dentifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Names declared in the Ontology Source Reference section. - --help display this list of options. -``` - - -##### investigation person edit - -```powershell -USAGE: ArcCommander.exe investigation person edit [--help] --lastname <last name> --firstname <first name> - [--midinitials <mid initials>] - -OPTIONS: - - --lastname, -l <last name> - The last name of a person associated with the investigation. - --firstname, -f <first name> - The first name of a person associated with the investigation. - --midinitials, -m <mid initials> - The middle initials of a person associated with the investigation. - --help display this list of options. -``` - - -##### investigation person register - -```powershell -USAGE: ArcCommander.exe investigation person register [--help] --lastname <last name> --firstname <first name> - [--midinitials <mid initials>] [--email <e mail>] - [--phone <phone number>] [--fax <fax number>] [--address <adress>] - [--affiliation <affiliation>] [--roles <roles>] - [--rolestermaccessionnumber <roles term accession number>] - [--rolestermsourceref <roles term source ref>] - -OPTIONS: - - --lastname, -l <last name> - The last name of a person associated with the investigation. - --firstname, -f <first name> - The first name of a person associated with the investigation. - --midinitials, -m <mid initials> - The middle initials of a person associated with the investigation. - --email <e mail> The email address of a person associated with the investigation. - --phone <phone number> - The telephone number of a person associated with the investigation. - --fax <fax number> The fax number of a person associated with the investigation. - --address <adress> The address of a person associated with the investigation. - --affiliation <affiliation> - The organization affiliation for a person associated with the investigation. - --roles <roles> Term to classify the role(s) performed by this person in the context of the investigation, which - means that the roles reported here need not correspond to roles held withing their affiliated - organization. Multiple annotations or values attached to one person can be provided by using a - semicolon (";") Unicode (U0003+B) as a separator (e.g.: submitter;funder;sponsor). The term can be - free text or from, for example, a controlled vocabulary or an ontology. If the latter source is used - the Term Accession Number and Term Source REF fields below are required. - --rolestermaccessionnumber <roles term accession number> - The accession number from the Term Source associated with the selected term. - --rolestermsourceref <roles term source ref> - dentifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Names declared in the Ontology Source Reference section. - --help display this list of options. -``` - - -##### investigation person unregister - -```powershell -USAGE: ArcCommander.exe investigation person register [--help] --lastname <last name> --firstname <first name> - [--midinitials <mid initials>] [--email <e mail>] - [--phone <phone number>] [--fax <fax number>] [--address <adress>] - [--affiliation <affiliation>] [--roles <roles>] - [--rolestermaccessionnumber <roles term accession number>] - [--rolestermsourceref <roles term source ref>] - -OPTIONS: - - --lastname, -l <last name> - The last name of a person associated with the investigation. - --firstname, -f <first name> - The first name of a person associated with the investigation. - --midinitials, -m <mid initials> - The middle initials of a person associated with the investigation. - --email <e mail> The email address of a person associated with the investigation. - --phone <phone number> - The telephone number of a person associated with the investigation. - --fax <fax number> The fax number of a person associated with the investigation. - --address <adress> The address of a person associated with the investigation. - --affiliation <affiliation> - The organization affiliation for a person associated with the investigation. - --roles <roles> Term to classify the role(s) performed by this person in the context of the investigation, which - means that the roles reported here need not correspond to roles held withing their affiliated - organization. Multiple annotations or values attached to one person can be provided by using a - semicolon (";") Unicode (U0003+B) as a separator (e.g.: submitter;funder;sponsor). The term can be - free text or from, for example, a controlled vocabulary or an ontology. If the latter source is used - the Term Accession Number and Term Source REF fields below are required. - --rolestermaccessionnumber <roles term accession number> - The accession number from the Term Source associated with the selected term. - --rolestermsourceref <roles term source ref> - dentifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Names declared in the Ontology Source Reference section. - --help display this list of options. -``` - -##### investigation person get - -```powershell -USAGE: ArcCommander.exe investigation person get [--help] --lastname <last name> --firstname <first name> - [--midinitials <mid initials>] - -OPTIONS: - - --lastname, -l <last name> - The last name of a person associated with the investigation. - --firstname, -f <first name> - The first name of a person associated with the investigation. - --midinitials, -m <mid initials> - The middle initials of a person associated with the investigation. - --help display this list of options. -``` - -<br> - -##### investigation publication - -```powershell -USAGE: ArcCommander.exe investigation publication [--help] [<subcommand> [<options>]] - -SUBCOMMANDS: - - update <update args> Update an existing publication in the arc investigation with the given publication metadata. The - publication is identified by the doi - edit <edit args> Open and edit an existing publication in the arc investigation with a text editor. The publication - is identified by the doi - register <register args> - Register a publication in the arc investigation with the given assay metadata. - unregister <remove args> - Unregister a publication from the given investigation. The publication is identified by the doi - get <get args> Get the metadata of a publication registered in the arc investigation - list List all publication registered in the arc investigation - - Use 'ArcCommander.exe <subcommand> --help' for additional information. - -OPTIONS: - - --help display this list of options. -``` - -##### investigation publication update - -```powershell -USAGE: ArcCommander.exe investigation publication update [--help] --doi <doi> [--pubmedid <pubmed id>] - [--authorlist <author list>] [--title <publication title>] - [--status <publication status>] - [--statustermaccessionnumber <publication status term accession number>] - [--statustermsourceref <publication status term source ref>] - -OPTIONS: - - --doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available). - --pubmedid, -p <pubmed id> - The PubMed IDs of the described publication(s) associated with this investigation. - --authorlist <author list> - The list of authors associated with that publication. - --title <publication title> - The title of publication associated with the investigation. - --status <publication status> - A term describing the status of that publication (i.e. submitted, in preparation, published). - --statustermaccessionnumber <publication status term accession number> - The accession number from the Term Source associated with the selected term. - --statustermsourceref <publication status term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one the Term Source Name declared in the in the Ontology Source Reference section. - --help display this list of options. -``` - -##### investigation publication edit - -```powershell -USAGE: ArcCommander.exe investigation publication edit [--help] --doi <doi> - -OPTIONS: - - --doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available). - --help display this list of options. -``` - -##### investigation publication register - -```powershell -USAGE: ArcCommander.exe investigation publication register [--help] --doi <doi> [--pubmedid <pubmed id>] - [--authorlist <author list>] [--title <publication title>] - [--status <publication status>] - [--statustermaccessionnumber <publication status term accession number>] - [--statustermsourceref <publication status term source ref>] - -OPTIONS: - - --doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available). - --pubmedid, -p <pubmed id> - The PubMed IDs of the described publication(s) associated with this investigation. - --authorlist <author list> - The list of authors associated with that publication. - --title <publication title> - The title of publication associated with the investigation. - --status <publication status> - A term describing the status of that publication (i.e. submitted, in preparation, published). - --statustermaccessionnumber <publication status term accession number> - The accession number from the Term Source associated with the selected term. - --statustermsourceref <publication status term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one the Term Source Name declared in the in the Ontology Source Reference section. - --help display this list of options. -``` - -##### investigation publication unregister - -```powershell -USAGE: ArcCommander.exe investigation publication unregister [--help] --doi <doi> - -OPTIONS: - - --doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available). - --help display this list of options. -``` - -##### investigation publication get - -```powershell -USAGE: ArcCommander.exe investigation publication get [--help] --doi <doi> - -OPTIONS: - - --doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available). - --help display this list of options. -``` - -<br> - -#### study: - -```powershell -USAGE: ArcCommander.exe study [--help] [<subcommand> [<options>]] - -SUBCOMMANDS: - - init <init args> Initialize a new empty study file in the arc - register <register args> - Register an existing study in the arc with the given assay metadata. - add <add args> Create a new study file in the arc and subsequently register it with the given study metadata - delete <delete args> Delete a study from the arc file structure - unregister <unregister args> - Unregister a study from the arc investigation file - remove <remove args> Remove a study from the arc - update <update args> Update an existing study in the arc with the given study metadata - edit <edit args> Open and edit an existing study in the arc with a text editor. Arguments passed for this command - will be pre-set in the editor. - get <get args> Get the values of a study - list List all studies registered in the arc - person <person verbs> Person functions - publication <publication verbs> - Publication functions - design <design verbs> Design functions - factor <factor verbs> Factor functions - protocol <protocol verbs> - Protocol functions - - Use 'ArcCommander.exe <subcommand> --help' for additional information. - -OPTIONS: - - --help display this list of options. -``` - -##### study init - -```powershell -USAGE: ArcCommander.exe study init [--help] --identifier <study identifier> - -OPTIONS: - - --identifier <study identifier> - A unique identifier, either a temporary identifier supplied by users or one generated by a - repository or other database. For example, it could be an identifier complying with the LSID - specification. - --help display this list of options. -``` - -##### study register - -```powershell -USAGE: ArcCommander.exe study register [--help] --identifier <study identifier> [--title <title>] [--description <description>] - [--submissiondate <submission date>] [--publicreleasedate <public release date>] - -OPTIONS: - - --identifier <study identifier> - A unique identifier, either a temporary identifier supplied by users or one generated by a - repository or other database. For example, it could be an identifier complying with the LSID - specification. - --title <title> A concise phrase used to encapsulate the purpose and goal of the study. - --description <description> - A textual description of the study, with components such as objective or goals. - --submissiondate <submission date> - The date on which the study is submitted to an archive. - --publicreleasedate <public release date> - The date on which the study SHOULD be released publicly. - --help display this list of options. -``` - -##### study add - -```powershell -USAGE: ArcCommander.exe study add [--help] --identifier <study identifier> [--title <title>] [--description <description>] - [--submissiondate <submission date>] [--publicreleasedate <public release date>] - -OPTIONS: - - --identifier <study identifier> - A unique identifier, either a temporary identifier supplied by users or one generated by a - repository or other database. For example, it could be an identifier complying with the LSID - specification. - --title <title> A concise phrase used to encapsulate the purpose and goal of the study. - --description <description> - A textual description of the study, with components such as objective or goals. - --submissiondate <submission date> - The date on which the study is submitted to an archive. - --publicreleasedate <public release date> - The date on which the study SHOULD be released publicly. - --help display this list of options. -``` - -##### study delete - -```powershell -USAGE: ArcCommander.exe study delete [--help] --identifier <study identifier> - -OPTIONS: - - --identifier <study identifier> - A unique identifier, either a temporary identifier supplied by users or one generated by a - repository or other database. For example, it could be an identifier complying with the LSID - specification. - --help display this list of options. -``` - -##### study unregister - -```powershell -USAGE: ArcCommander.exe study unregister [--help] --identifier <study identifier> - -OPTIONS: - - --identifier <study identifier> - A unique identifier, either a temporary identifier supplied by users or one generated by a - repository or other database. For example, it could be an identifier complying with the LSID - specification. - --help display this list of options. -``` - -##### study remove - -```powershell -USAGE: ArcCommander.exe study remove [--help] --identifier <study identifier> - -OPTIONS: - - --identifier <study identifier> - A unique identifier, either a temporary identifier supplied by users or one generated by a - repository or other database. For example, it could be an identifier complying with the LSID - specification. - --help display this list of options. -``` - -##### study update - -```powershell -USAGE: ArcCommander.exe study update [--help] --identifier <study identifier> [--title <title>] [--description <description>] - [--submissiondate <submission date>] [--publicreleasedate <public release date>] - -OPTIONS: - - --identifier <study identifier> - A unique identifier, either a temporary identifier supplied by users or one generated by a - repository or other database. For example, it could be an identifier complying with the LSID - specification. - --title <title> A concise phrase used to encapsulate the purpose and goal of the study. - --description <description> - A textual description of the study, with components such as objective or goals. - --submissiondate <submission date> - The date on which the study is submitted to an archive. - --publicreleasedate <public release date> - The date on which the study SHOULD be released publicly. - --help display this list of options. -``` - -##### study edit - -```powershell -USAGE: ArcCommander.exe study edit [--help] --identifier <study identifier> - -OPTIONS: - - --identifier <study identifier> - A unique identifier, either a temporary identifier supplied by users or one generated by a - repository or other database. For example, it could be an identifier complying with the LSID - specification. - --help display this list of options. - -``` - -##### study get - -```powershell -USAGE: ArcCommander.exe study get [--help] --identifier <study identifier> - -OPTIONS: - - --identifier <study identifier> - A unique identifier, either a temporary identifier supplied by users or one generated by a - repository or other database. For example, it could be an identifier complying with the LSID - specification. - --help display this list of options. -``` - -<br> - -##### study person - -```powershell -USAGE: ArcCommander.exe study person [--help] [<subcommand> [<options>]] - -SUBCOMMANDS: - - update <update args> Update an existing person in the arc investigation study with the given person metadata. The person - is identified by the full name (first name, last name, mid initials) - edit <edit args> Open and edit an existing person in the arc investigation study with a text editor. The person is - identified by the full name (first name, last name, mid initials) - register <register args> - Register a person in the arc investigation study with the given assay metadata. - unregister <remove args> - Unregister a person from the given investigation study. The person is identified by the full name - (first name, last name, mid initials). - get <get args> Get the metadata of a person registered in the arc investigation study - list List all persons registered in the arc investigation - - Use 'ArcCommander.exe <subcommand> --help' for additional information. - -OPTIONS: - - --help display this list of options. -``` - - -##### study person update - -```powershell -USAGE: ArcCommander.exe study person update [--help] --studyidentifier <string> --lastname <last name> --firstname <first name> - [--midinitials <mid initials>] [--email <e mail>] [--phone <phone number>] - [--fax <fax number>] [--address <adress>] [--affiliation <affiliation>] - [--roles <roles>] [--rolestermaccessionnumber <roles term accession number>] - [--rolestermsourceref <roles term source ref>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the person is associated with - --lastname, -l <last name> - The last name of a person associated with the study. - --firstname, -f <first name> - The first name of a person associated with the study. - --midinitials, -m <mid initials> - The middle initials of a person associated with the study. - --email <e mail> The email address of a person associated with the study. - --phone <phone number> - The telephone number of a person associated with the study. - --fax <fax number> The fax number of a person associated with the study. - --address <adress> The address of a person associated with the study. - --affiliation <affiliation> - The organization affiliation for a person associated with the study. - --roles <roles> Term to classify the role(s) performed by this person in the context of the study, which means that - the roles reported here need not correspond to roles held withing their affiliated organization. - Multiple annotations or values attached to one person can be provided by using a semicolon (";") - Unicode (U0003+B) as a separator (e.g.: submitter;funder;sponsor) .The term can be free text or - from, for example, a controlled vocabulary or an ontology. If the latter source is used the Term - Accession Number and Term Source REF fields below are required. - --rolestermaccessionnumber <roles term accession number> - The accession number from the Term Source associated with the selected term. - --rolestermsourceref <roles term source ref> - dentifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Names declared in the Ontology Source Reference section. - --help display this list of options. -``` - - -##### study person edit - -```powershell -USAGE: ArcCommander.exe study person edit [--help] --studyidentifier <string> --lastname <last name> --firstname <first name> - [--midinitials <mid initials>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the person is associated with - --lastname, -l <last name> - The last name of a person associated with the study. - --firstname, -f <first name> - The first name of a person associated with the study. - --midinitials, -m <mid initials> - The middle initials of a person associated with the study. - --help display this list of options. -``` - - -##### study person register - -```powershell -USAGE: ArcCommander.exe study person register [--help] --studyidentifier <string> --lastname <last name> - --firstname <first name> [--midinitials <mid initials>] [--email <e mail>] - [--phone <phone number>] [--fax <fax number>] [--address <adress>] - [--affiliation <affiliation>] [--roles <roles>] - [--rolestermaccessionnumber <roles term accession number>] - [--rolestermsourceref <roles term source ref>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the person is associated with - --lastname, -l <last name> - The last name of a person associated with the study. - --firstname, -f <first name> - The first name of a person associated with the study. - --midinitials, -m <mid initials> - The middle initials of a person associated with the study. - --email <e mail> The email address of a person associated with the study. - --phone <phone number> - The telephone number of a person associated with the study. - --fax <fax number> The fax number of a person associated with the study. - --address <adress> The address of a person associated with the study. - --affiliation <affiliation> - The organization affiliation for a person associated with the study. - --roles <roles> Term to classify the role(s) performed by this person in the context of the study, which means that - the roles reported here need not correspond to roles held withing their affiliated organization. - Multiple annotations or values attached to one person can be provided by using a semicolon (";") - Unicode (U0003+B) as a separator (e.g.: submitter;funder;sponsor) .The term can be free text or - from, for example, a controlled vocabulary or an ontology. If the latter source is used the Term - Accession Number and Term Source REF fields below are required. - --rolestermaccessionnumber <roles term accession number> - The accession number from the Term Source associated with the selected term. - --rolestermsourceref <roles term source ref> - dentifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Names declared in the Ontology Source Reference section. - --help display this list of options. -``` - - -##### study person unregister - -```powershell -USAGE: ArcCommander.exe study person unregister [--help] --studyidentifier <string> --lastname <last name> - --firstname <first name> [--midinitials <mid initials>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the person is associated with - --lastname, -l <last name> - The last name of a person associated with the study. - --firstname, -f <first name> - The first name of a person associated with the study. - --midinitials, -m <mid initials> - The middle initials of a person associated with the study. - --help display this list of options. -``` - - -##### study person get - -```powershell -USAGE: ArcCommander.exe study person get [--help] --studyidentifier <string> --lastname <last name> --firstname <first name> - [--midinitials <mid initials>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the person is associated with - --lastname, -l <last name> - The last name of a person associated with the study. - --firstname, -f <first name> - The first name of a person associated with the study. - --midinitials, -m <mid initials> - The middle initials of a person associated with the study. - --help display this list of options. -``` -<br> - -##### study publication - -```powershell -USAGE: ArcCommander.exe study publication [--help] [<subcommand> [<options>]] - -SUBCOMMANDS: - - update <update args> Update an existing publication in the arc investigation study with the given publication metadata. - The publication is identified by the doi - edit <edit args> Open and edit an existing publication in the arc investigation study with a text editor. The - publication is identified by the doi - register <register args> - Register a publication in the arc investigation study with the given assay metadata. - unregister <remove args> - Unregister a publication from the given investigation study. The publication is identified by the doi - get <get args> Get the metadata of a publication registered in the arc investigation study - list List all publication registered in the arc investigation study - - Use 'ArcCommander.exe <subcommand> --help' for additional information. - -OPTIONS: - - --help display this list of options. -``` - -##### study publication update - -```powershell -USAGE: ArcCommander.exe study publication update [--help] --studyidentifier <string> --doi <doi> [--pubmedid <pubmed id>] - [--authorlist <author list>] [--title <publication title>] - [--status <publication status>] - [--statustermaccessionnumber <publication status term accession number>] - [--statustermsourceref <publication status term source ref>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the publication is associated with - --doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available). - --pubmedid, -p <pubmed id> - The PubMed IDs of the described publication(s) associated with this study. - --authorlist <author list> - The list of authors associated with that publication. - --title <publication title> - The title of publication associated with the study. - --status <publication status> - A term describing the status of that publication (i.e. submitted, in preparation, published). - --statustermaccessionnumber <publication status term accession number> - The accession number from the Term Source associated with the selected term. - --statustermsourceref <publication status term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one the Term Source Name declared in the in the Ontology Source Reference section. - --help display this list of options. -``` - -##### study publication edit - -```powershell -USAGE: ArcCommander.exe study publication edit [--help] --studyidentifier <string> --doi <doi> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the publication is associated with - --doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available). - --help display this list of options. -``` - -##### study publication register - -```powershell -USAGE: ArcCommander.exe study publication register [--help] --studyidentifier <string> --doi <doi> [--pubmedid <pubmed id>] - [--authorlist <author list>] [--title <publication title>] - [--status <publication status>] - [--statustermaccessionnumber <publication status term accession number>] - [--statustermsourceref <publication status term source ref>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the publication is associated with - --doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available). - --pubmedid, -p <pubmed id> - The PubMed IDs of the described publication(s) associated with this study. - --authorlist <author list> - The list of authors associated with that publication. - --title <publication title> - The title of publication associated with the study. - --status <publication status> - A term describing the status of that publication (i.e. submitted, in preparation, published). - --statustermaccessionnumber <publication status term accession number> - The accession number from the Term Source associated with the selected term. - --statustermsourceref <publication status term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one the Term Source Name declared in the in the Ontology Source Reference section. - --help display this list of options. -``` - -##### study publication unregister - -```powershell -USAGE: ArcCommander.exe study publication unregister [--help] --studyidentifier <string> --doi <doi> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the publication is associated with - --doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available). - --help display this list of options. -``` - -##### study publication get - -```powershell -USAGE: ArcCommander.exe study publication get [--help] --studyidentifier <string> --doi <doi> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the publication is associated with - --doi, -d <doi> A Digital Object Identifier (DOI) for that publication (where available). - --help display this list of options. -``` - - -<br> - -##### study design - -```powershell -USAGE: ArcCommander.exe study design [--help] [<subcommand> [<options>]] - -SUBCOMMANDS: - - update <update args> Update an existing design in the arc investigation study with the given publication metadata. The - publication is identified by the design type - edit <edit args> Open and edit an existing design in the arc investigation study with a text editor. The publication - is identified by the design type - register <register args> - Register a design in the arc investigation study with the given assay metadata. - unregister <remove args> - Unregister a design from the given investigation study. The publication is identified by the design - type - get <get args> Get the metadata of a design registered in the arc investigation study - list List all design registered in the arc investigation study - - Use 'ArcCommander.exe <subcommand> --help' for additional information. - -OPTIONS: - - --help display this list of options. -``` - -##### study design update - -```powershell -USAGE: ArcCommander.exe study design update [--help] --studyidentifier <string> --designtype <design type> - [--typetermaccessionnumber <type term accession number>] - [--typetermsourceref <type term source ref>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --designtype, -d <design type> - A term allowing the classification of the study based on the overall experimental design, e.g - cross-over design or parallel group design. The term can be free text or from, for example, a - controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and - Term Source REF fields below are required. - --typetermaccessionnumber <type term accession number> - The accession number from the Term Source associated with the selected term. - --typetermsourceref <type term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Study Design Term - Source REF has to match one the Term Source Name declared in the Ontology Source Reference section. - --help display this list of options. -``` - -##### study design edit - -```powershell -USAGE: ArcCommander.exe study design edit [--help] --studyidentifier <string> --designtype <design type> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --designtype, -d <design type> - A term allowing the classification of the study based on the overall experimental design, e.g - cross-over design or parallel group design. The term can be free text or from, for example, a - controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and - Term Source REF fields below are required. - --help display this list of options. -``` - -##### study design register - -```powershell -USAGE: ArcCommander.exe study design register [--help] --studyidentifier <string> --designtype <design type> - [--typetermaccessionnumber <type term accession number>] - [--typetermsourceref <type term source ref>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --designtype, -d <design type> - A term allowing the classification of the study based on the overall experimental design, e.g - cross-over design or parallel group design. The term can be free text or from, for example, a - controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and - Term Source REF fields below are required. - --typetermaccessionnumber <type term accession number> - The accession number from the Term Source associated with the selected term. - --typetermsourceref <type term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Study Design Term - Source REF has to match one the Term Source Name declared in the Ontology Source Reference section. - --help display this list of options. -``` - -##### study design unregister - -```powershell -USAGE: ArcCommander.exe study design unregister [--help] --studyidentifier <string> --designtype <design type> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --designtype, -d <design type> - A term allowing the classification of the study based on the overall experimental design, e.g - cross-over design or parallel group design. The term can be free text or from, for example, a - controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and - Term Source REF fields below are required. - --help display this list of options. -``` - -##### study design get - -```powershell -USAGE: ArcCommander.exe study design get [--help] --studyidentifier <string> --designtype <design type> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --designtype, -d <design type> - A term allowing the classification of the study based on the overall experimental design, e.g - cross-over design or parallel group design. The term can be free text or from, for example, a - controlled vocabulary or an ontology. If the latter source is used the Term Accession Number and - Term Source REF fields below are required. - --help display this list of options. -``` -<br> - -##### study factor - -```powershell -USAGE: ArcCommander.exe study factor [--help] [<subcommand> [<options>]] - -SUBCOMMANDS: - - update <update args> Update an existing factor in the arc investigation study with the given publication metadata. The - publication is identified by name - edit <edit args> Open and edit an existing factor in the arc investigation study with a text editor. The publication - is identified by name - register <register args> - Register a factor in the arc investigation study with the given assay metadata. - unregister <remove args> - Unregister a factor from the given investigation study. The publication is identified by name - get <get args> Get the metadata of a factor registered in the arc investigation study - list List all factor registered in the arc investigation study - - Use 'ArcCommander.exe <subcommand> --help' for additional information. - -OPTIONS: - - --help display this list of options. -``` - - -##### study factor update - -```powershell -USAGE: ArcCommander.exe study factor update [--help] --studyidentifier <string> --name <name> [--factortype <factor type>] - [--typetermaccessionnumber <type term accession number>] - [--typetermsourceref <type term source ref>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent - variable manipulated by the experimentalist with the intention to affect biological systems in a way - that can be measured by an assay. The value of a factor is given in the Study or Assay file, - accordingly. If both Study and Assay have a Factor Value, these must be different. - --factortype <factor type> - A term allowing the classification of this factor into categories. The term can be free text or - from, for example, a controlled vocabulary or an ontology. If the latter source is used the Term - Accession Number and Term Source REF fields below are required. - --typetermaccessionnumber <type term accession number> - The accession number from the Term Source associated with the selected term. - --typetermsourceref <type term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Name declared in the Ontology Source Reference section. - --help display this list of options. -``` - - -##### study factor edit - -```powershell -USAGE: ArcCommander.exe study factor edit [--help] --studyidentifier <string> --name <name> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent - variable manipulated by the experimentalist with the intention to affect biological systems in a way - that can be measured by an assay. The value of a factor is given in the Study or Assay file, - accordingly. If both Study and Assay have a Factor Value, these must be different. - --help display this list of options. -``` - - -##### study factor register - -```powershell -USAGE: ArcCommander.exe study factor register [--help] --studyidentifier <string> --name <name> [--factortype <factor type>] - [--typetermaccessionnumber <type term accession number>] - [--typetermsourceref <type term source ref>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent - variable manipulated by the experimentalist with the intention to affect biological systems in a way - that can be measured by an assay. The value of a factor is given in the Study or Assay file, - accordingly. If both Study and Assay have a Factor Value, these must be different. - --factortype <factor type> - A term allowing the classification of this factor into categories. The term can be free text or - from, for example, a controlled vocabulary or an ontology. If the latter source is used the Term - Accession Number and Term Source REF fields below are required. - --typetermaccessionnumber <type term accession number> - The accession number from the Term Source associated with the selected term. - --typetermsourceref <type term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Name declared in the Ontology Source Reference section. - --help display this list of options. -``` - - -##### study factor unregister - -```powershell -USAGE: ArcCommander.exe study factor unregister [--help] --studyidentifier <string> --name <name> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent - variable manipulated by the experimentalist with the intention to affect biological systems in a way - that can be measured by an assay. The value of a factor is given in the Study or Assay file, - accordingly. If both Study and Assay have a Factor Value, these must be different. - --help display this list of options. -``` - - -##### study factor get - -```powershell -USAGE: ArcCommander.exe study factor get [--help] --studyidentifier <string> --name <name> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent - variable manipulated by the experimentalist with the intention to affect biological systems in a way - that can be measured by an assay. The value of a factor is given in the Study or Assay file, - accordingly. If both Study and Assay have a Factor Value, these must be different. - --help display this list of options. -``` -<br> - -##### study protocol - -```powershell -USAGE: ArcCommander.exe study protocol [--help] [<subcommand> [<options>]] - -SUBCOMMANDS: - - update <update args> Update an existing protocol in the arc investigation study with the given publication metadata. The - publication is identified by name - edit <edit args> Open and edit an existing protocol in the arc investigation study with a text editor. The - publication is identified by name - register <register args> - Register a protocol in the arc investigation study with the given assay metadata. - unregister <remove args> - Unregister a protocol from the given investigation study. The publication is identified by name - get <get args> Get the metadata of a protocol registered in the arc investigation study - list List all protocol registered in the arc investigation study - - Use 'ArcCommander.exe <subcommand> --help' for additional information. - -OPTIONS: - - --help display this list of options. -``` - -##### study protocol update - -```powershell -USAGE: ArcCommander.exe study protocol update [--help] --studyidentifier <string> --name <name> - [--protocoltype <protocol type>] - [--typetermaccessionnumber <type term accession number>] - [--typetermsourceref <type term source ref>] [--description <description>] - [--uri <uri>] [--version <version>] [--parametersname <parameters name>] - [--parameterstermaccessionnumber <parameters term accession number>] - [--parameterstermsourceref <parameters term source ref>] - [--componentsname <compoments name>] [--componentstype <compoments type>] - [--componentstypetermaccessionnumber <compoments type accession number>] - [--componentstypetermsourceref <compoments type term source ref>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --name, -n <name> The name of the protocols used within the ISA-Tab document. The names are used as identifiers within - the ISA-Tab document and will be referenced in the Study and Assay files in the Protocol REF - columns. Names can be either local identifiers, unique within the ISA Archive which contains them, - or fully qualified external accession numbers. - --protocoltype <protocol type> - Term to classify the protocol. The term can be free text or from, for example, a controlled - vocabulary or an ontology. If the latter source is used the Term Accession Number and Term Source - REF fields below are required. - --typetermaccessionnumber <type term accession number> - The accession number from the Term Source associated with the selected term. - --typetermsourceref <type term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Name declared in the Ontology Source Reference section. - --description <description> - A free-text description of the protocol. - --uri <uri> Pointer to protocol resources external to the ISA-Tab that can be accessed by their Uniform Resource - Identifier (URI). - --version <version> An identifier for the version to ensure protocol tracking. - --parametersname <parameters name> - A semicolon-delimited (";") list of parameter names, used as an identifier within the ISA-Tab - document. These names are used in the Study and Assay files (in the "Parameter Value []" column - heading) to list the values used for each protocol parameter. Refer to section Multiple values - fields in the Investigation File on how to encode multiple values in one field and match term sources - --parameterstermaccessionnumber <parameters term accession number> - The accession number from the Term Source associated with the selected term. - --parameterstermsourceref <parameters term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Name declared in the Ontology Source Reference section. - --componentsname <compoments name> - A semicolon-delimited (";") list of a protocol's components; e.g. instrument names, software names, - and reagents names. Refer to section Multiple values fields in the Investigation File on how to - encode multiple components in one field and match term sources. - --componentstype <compoments type> - Term to classify the protocol components listed for example, instrument, software, detector or - reagent. The term can be free text or from, for example, a controlled vocabulary or an ontology. If - the latter source is used the Term Accession Number and Term Source REF fields below are required. - --componentstypetermaccessionnumber <compoments type accession number> - The accession number from the Source associated to the selected terms. - --componentstypetermsourceref <compoments type term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match a Term Source Name previously declared in the ontology section. - --help display this list of options. -``` - -##### study protocol edit - -```powershell -USAGE: ArcCommander.exe study protocol edit [--help] --studyidentifier <string> --name <name> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent - variable manipulated by the experimentalist with the intention to affect biological systems in a way - that can be measured by an assay. The value of a factor is given in the Study or Assay file, - accordingly. If both Study and Assay have a Factor Value, these must be different. - --help display this list of options. -``` - -##### study protocol register - -```powershell -USAGE: ArcCommander.exe study protocol register [--help] --studyidentifier <string> --name <name> - [--protocoltype <protocol type>] - [--typetermaccessionnumber <type term accession number>] - [--typetermsourceref <type term source ref>] [--description <description>] - [--uri <uri>] [--version <version>] [--parametersname <parameters name>] - [--parameterstermaccessionnumber <parameters term accession number>] - [--parameterstermsourceref <parameters term source ref>] - [--componentsname <compoments name>] [--componentstype <compoments type>] - [--componentstypetermaccessionnumber <compoments type accession number>] - [--componentstypetermsourceref <compoments type term source ref>] - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --name, -n <name> The name of the protocols used within the ISA-Tab document. The names are used as identifiers within - the ISA-Tab document and will be referenced in the Study and Assay files in the Protocol REF - columns. Names can be either local identifiers, unique within the ISA Archive which contains them, - or fully qualified external accession numbers. - --protocoltype <protocol type> - Term to classify the protocol. The term can be free text or from, for example, a controlled - vocabulary or an ontology. If the latter source is used the Term Accession Number and Term Source - REF fields below are required. - --typetermaccessionnumber <type term accession number> - The accession number from the Term Source associated with the selected term. - --typetermsourceref <type term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Name declared in the Ontology Source Reference section. - --description <description> - A free-text description of the protocol. - --uri <uri> Pointer to protocol resources external to the ISA-Tab that can be accessed by their Uniform Resource - Identifier (URI). - --version <version> An identifier for the version to ensure protocol tracking. - --parametersname <parameters name> - A semicolon-delimited (";") list of parameter names, used as an identifier within the ISA-Tab - document. These names are used in the Study and Assay files (in the "Parameter Value []" column - heading) to list the values used for each protocol parameter. Refer to section Multiple values - fields in the Investigation File on how to encode multiple values in one field and match term sources - --parameterstermaccessionnumber <parameters term accession number> - The accession number from the Term Source associated with the selected term. - --parameterstermsourceref <parameters term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Name declared in the Ontology Source Reference section. - --componentsname <compoments name> - A semicolon-delimited (";") list of a protocol's components; e.g. instrument names, software names, - and reagents names. Refer to section Multiple values fields in the Investigation File on how to - encode multiple components in one field and match term sources. - --componentstype <compoments type> - Term to classify the protocol components listed for example, instrument, software, detector or - reagent. The term can be free text or from, for example, a controlled vocabulary or an ontology. If - the latter source is used the Term Accession Number and Term Source REF fields below are required. - --componentstypetermaccessionnumber <compoments type accession number> - The accession number from the Source associated to the selected terms. - --componentstypetermsourceref <compoments type term source ref> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match a Term Source Name previously declared in the ontology section. - --help display this list of options. -``` - -##### study protocol unregister - -```powershell -USAGE: ArcCommander.exe study protocol unregister [--help] --studyidentifier <string> --name <name> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent - variable manipulated by the experimentalist with the intention to affect biological systems in a way - that can be measured by an assay. The value of a factor is given in the Study or Assay file, - accordingly. If both Study and Assay have a Factor Value, these must be different. - --help display this list of options. -``` - -##### study protocol get - -```powershell -USAGE: ArcCommander.exe study protocol get [--help] --studyidentifier <string> --name <name> - -OPTIONS: - - --studyidentifier, -s <string> - Identifier of the study the design is associated with - --name, -n <name> The name of one factor used in the Study and/or Assay files. A factor corresponds to an independent - variable manipulated by the experimentalist with the intention to affect biological systems in a way - that can be measured by an assay. The value of a factor is given in the Study or Assay file, - accordingly. If both Study and Assay have a Factor Value, these must be different. - --help display this list of options. -``` - - -<br> - -#### assay: - -```powershell -USAGE: ArcCommander.exe assay [--help] [<subcommand> [<options>]] - -SUBCOMMANDS: - - init <init args> Initialize a new empty assay and associated folder structure in the arc. - register <register args> - Register an existing assay in the arc with the given assay metadata. - add <add args> Create a new assay file and associated folder structure in the arc and subsequently register it with - the given assay metadata - delete <delete args> Delete the given assays folder and its underlying file structure - unregister <unregister args> - Unregister an assay from the given studys' assay register in the investigation file - remove <remove args> Both unregister and assay from the investigation file and delete its folders and files - update <update args> Update an existing assay in the arc with the given assay metadata - edit <edit args> Open and edit an existing assay in the arc with a text editor. Arguments passed for this command - will be pre-set in the editor. - move <move args> Move an assay from one study to another - get <get args> Gets the values of an existing assay - list List all assays registered in the arc - - Use 'ArcCommander.exe <subcommand> --help' for additional information. - -OPTIONS: - - --help display this list of options. -``` - -##### assay init - -```powershell -USAGE: ArcCommander.exe assay init [--help] --assayidentifier <assay identifier> - -OPTIONS: - - --assayidentifier, -a <assay identifier> - Identifier of the assay, will be used as name of the root folder of the new assay folder structure - --help display this list of options. -``` - - -##### assay register - -```powershell -USAGE: ArcCommander.exe assay register [--help] [--studyidentifier <string>] --assayidentifier <string> - [--measurementtype <measurement type>] - [--measurementtypetermaccessionnumber <measurement type accession>] - [--measurementtypetermsourceref <measurement type term source>] - [--technologytype <technology type>] - [--technologytypetermaccessionnumber <technology type accession>] - [--technologytypetermsourceref <technology type term source>] - [--technologyplatform <technology platform>] - -OPTIONS: - - --studyidentifier, -s <string> - Name of the study in which the assay is situated - --assayidentifier, -a <string> - Name of the assay of interest - --measurementtype <measurement type> - A term to qualify the endpoint, or what is being measured (e.g. gene expression profiling or protein - identification). The term can be free text or from, for example, a controlled vocabulary or an - ontology. If the latter source is used the Term Accession Number and Term Source REF fields below - are required. - --measurementtypetermaccessionnumber <measurement type accession> - The accession number from the Term Source associated with the selected term. - --measurementtypetermsourceref <measurement type term source> - The Source REF has to match one of the Term Source Name declared in the Ontology Source Reference - section. - --technologytype <technology type> - Term to identify the technology used to perform the measurement, e.g. DNA microarray, mass - spectrometry. The term can be free text or from, for example, a controlled vocabulary or an - ontology. If the latter source is used the Term Accession Number and Term Source REF fields below - are required. - --technologytypetermaccessionnumber <technology type accession> - The accession number from the Term Source associated with the selected term. - --technologytypetermsourceref <technology type term source> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Names declared in the Ontology Source Reference section. - --technologyplatform <technology platform> - Manufacturer and platform name, e.g. Bruker AVANCE - --help display this list of options. -``` - - -##### assay add - -```powershell -USAGE: ArcCommander.exe assay add [--help] [--studyidentifier <string>] --assayidentifier <string> - [--measurementtype <measurement type>] - [--measurementtypetermaccessionnumber <measurement type accession>] - [--measurementtypetermsourceref <measurement type term source>] - [--technologytype <technology type>] - [--technologytypetermaccessionnumber <technology type accession>] - [--technologytypetermsourceref <technology type term source>] - [--technologyplatform <technology platform>] - -OPTIONS: - - --studyidentifier, -s <string> - Name of the study in which the assay is situated - --assayidentifier, -a <string> - Name of the assay of interest - --measurementtype <measurement type> - A term to qualify the endpoint, or what is being measured (e.g. gene expression profiling or protein - identification). The term can be free text or from, for example, a controlled vocabulary or an - ontology. If the latter source is used the Term Accession Number and Term Source REF fields below - are required. - --measurementtypetermaccessionnumber <measurement type accession> - The accession number from the Term Source associated with the selected term. - --measurementtypetermsourceref <measurement type term source> - The Source REF has to match one of the Term Source Name declared in the Ontology Source Reference - section. - --technologytype <technology type> - Term to identify the technology used to perform the measurement, e.g. DNA microarray, mass - spectrometry. The term can be free text or from, for example, a controlled vocabulary or an - ontology. If the latter source is used the Term Accession Number and Term Source REF fields below - are required. - --technologytypetermaccessionnumber <technology type accession> - The accession number from the Term Source associated with the selected term. - --technologytypetermsourceref <technology type term source> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Names declared in the Ontology Source Reference section. - --technologyplatform <technology platform> - Manufacturer and platform name, e.g. Bruker AVANCE - --help display this list of options. -``` - - -##### assay delete - -```powershell -USAGE: ArcCommander.exe assay delete [--help] --assayidentifier <assay identifier> - -OPTIONS: - - --assayidentifier, -a <assay identifier> - Identifier of the assay, will be used as name of the root folder of the new assay folder structure - --help display this list of options. -``` - - -##### assay unregister - -```powershell -USAGE: ArcCommander.exe assay unregister [--help] [--studyidentifier <study identifier>] --assayidentifier <assay identifier> - -OPTIONS: - - --studyidentifier, -s <study identifier> - Identifier of the study in which the assay is registered - --assayidentifier, -a <assay identifier> - Identifier of the assay of interest - --help display this list of options. -``` - - -##### assay remove - -```powershell -USAGE: ArcCommander.exe assay remove [--help] [--studyidentifier <study identifier>] --assayidentifier <assay identifier> - -OPTIONS: - - --studyidentifier, -s <study identifier> - Identifier of the study in which the assay is registered - --assayidentifier, -a <assay identifier> - Identifier of the assay of interest - --help display this list of options. -``` - - -##### assay update - -```powershell -USAGE: ArcCommander.exe assay update [--help] [--studyidentifier <string>] --assayidentifier <string> - [--measurementtype <measurement type>] - [--measurementtypetermaccessionnumber <measurement type accession>] - [--measurementtypetermsourceref <measurement type term source>] - [--technologytype <technology type>] - [--technologytypetermaccessionnumber <technology type accession>] - [--technologytypetermsourceref <technology type term source>] - [--technologyplatform <technology platform>] - -OPTIONS: - - --studyidentifier, -s <string> - Name of the study in which the assay is situated - --assayidentifier, -a <string> - Name of the assay of interest - --measurementtype <measurement type> - A term to qualify the endpoint, or what is being measured (e.g. gene expression profiling or protein - identification). The term can be free text or from, for example, a controlled vocabulary or an - ontology. If the latter source is used the Term Accession Number and Term Source REF fields below - are required. - --measurementtypetermaccessionnumber <measurement type accession> - The accession number from the Term Source associated with the selected term. - --measurementtypetermsourceref <measurement type term source> - The Source REF has to match one of the Term Source Name declared in the Ontology Source Reference - section. - --technologytype <technology type> - Term to identify the technology used to perform the measurement, e.g. DNA microarray, mass - spectrometry. The term can be free text or from, for example, a controlled vocabulary or an - ontology. If the latter source is used the Term Accession Number and Term Source REF fields below - are required. - --technologytypetermaccessionnumber <technology type accession> - The accession number from the Term Source associated with the selected term. - --technologytypetermsourceref <technology type term source> - Identifies the controlled vocabulary or ontology that this term comes from. The Source REF has to - match one of the Term Source Names declared in the Ontology Source Reference section. - --technologyplatform <technology platform> - Manufacturer and platform name, e.g. Bruker AVANCE - --help display this list of options. -``` - - -##### assay edit - -```powershell -USAGE: ArcCommander.exe assay edit [--help] [--studyidentifier <study identifier>] --assayidentifier <assay identifier> - -OPTIONS: - - --studyidentifier, -s <study identifier> - Identifier of the study in which the assay is registered - --assayidentifier, -a <assay identifier> - Identifier of the assay of interest - --help display this list of options. -``` - -##### assay move - -```powershell -USAGE: ArcCommander.exe assay move [--help] --studyidentifier <study identifier> --assayidentifier <assay identifier> - --targetstudyidentifier <target study identifier> - -OPTIONS: - - --studyidentifier, -s <study identifier> - Name of the study in which the assay is situated - --assayidentifier, -a <assay identifier> - Name of the assay of interest - --targetstudyidentifier, -t <target study identifier> - Target study to which the assay should be moved - --help display this list of options. -``` - -##### assay get - -```powershell -USAGE: ArcCommander.exe assay get [--help] [--studyidentifier <study identifier>] --assayidentifier <assay identifier> - -OPTIONS: - - --studyidentifier, -s <study identifier> - Identifier of the study in which the assay is registered - --assayidentifier, -a <assay identifier> - Identifier of the assay of interest - --help display this list of options. -``` -<br> - -#### configuration: - -```powershell -USAGE: ArcCommander.exe configuration [--help] [<subcommand> [<options>]] - -SUBCOMMANDS: - - edit <edit args> Open and edit an existing assay in the arc with a text editor. Arguments passed for this command - will be pre-set in the editor. - list <list args> List all assays registered in the arc. - set <set args> Assign the given value to the given name. - unset <unset args> Remove the value bound to the given name. - - Use 'ArcCommander.exe <subcommand> --help' for additional information. - -OPTIONS: - - --help display this list of options. -``` - -##### configuration list - -```powershell -USAGE: ArcCommander.exe configuration list [--help] [--local] [--global] - -OPTIONS: - - --local, -l Lists the local settings for this arc - --global, -g Lists the global settings of the arccommander - --help display this list of options. -``` - -##### configuration edit - -```powershell -USAGE: ArcCommander.exe configuration edit [--help] [--local] [--global] - -OPTIONS: - - --local, -l Edit the local settings for this arc - --global, -g Edit the global settings of the arccommander - --help display this list of options. -``` - -##### configuration set - -```powershell -USAGE: ArcCommander.exe configuration set [--help] [--local] [--global] --name <string> --value <string> - -OPTIONS: - - --local, -l Set the the value of the name locally for this arc - --global, -g Set the the value of the name globally for the arccommander - --name, -n <string> The name of the setting in 'Section.Key' format - --value, -v <string> The new value of the setting - --help display this list of options. -``` - -##### configuration unset - -```powershell -USAGE: ArcCommander.exe configuration unset [--help] [--local] [--global] --name <string> - -OPTIONS: - - --local, -l Unset the the value of the name locally for this arc - --global, -g Unset the the value of the name globally for the arccommander - --name, -n <string> The name of the setting in 'Section.Key' format - --help display this list of options. -``` +After running the default build target, binaries of the arcCommander tool will lie in ./bin/ArcCommander. To run the binary, either use the `ArcCommander.exe` file on windows or `dotnet ArcCommander.dll` on linux. \ No newline at end of file