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Merge pull request #231 from cmohl2013/study_docstring
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modified CLI arguments help in IArgParserTemplate
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@HLWeil
HLWeil authored Nov 23, 2023
2 parents f303265 + 3662ce2 commit 8a4bf16
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Showing 2 changed files with 9 additions and 9 deletions.
4 changes: 2 additions & 2 deletions src/ArcCommander/CLIArguments/InvestigationArgs.fs
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Expand Up @@ -88,8 +88,8 @@ module InvestigationContacts =
| Affiliation _ -> "The organization affiliation for a person associated with the investigation"
| ORCID _ -> "The ORCID ID of the person"
| Roles _ -> "Term to classify the role(s) performed by this person in the context of the investigation, which means that the roles reported here do not need to 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 (TAN) and Term Source REF fields below are required."
| RolesTermAccessionNumber _ -> "The accession number from the Term Source associated with the selected term"
| RolesTermSourceREF _ -> "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."
| RolesTermAccessionNumber _ -> "The accession number from the Term Source associated with the selected term. If multiple role terms are defined, multiple accession numbers have to be defined accordingly, separated by a semicolon (“;”)."
| RolesTermSourceREF _ -> "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. If multiple role terms are defined, multiple source REFs have to be defined accordingly, separated by a semicolon (“;”)."
| ReplaceWithEmptyValues _ -> "This flag can be used to delete fields from the person. If this flag is not set, only these fields for which a value was given will be updated."
| AddIfMissing _ -> "If this flag is set, a new person will be registered with the given parameters, if it did not previously exist"

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14 changes: 7 additions & 7 deletions src/ArcCommander/CLIArguments/StudyArgs.fs
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Original file line number Diff line number Diff line change
Expand Up @@ -167,8 +167,8 @@ module StudyContacts =
| Affiliation _ -> "The organization affiliation for a person associated with the study"
| ORCID _ -> "The ORCID ID of the person"
| Roles _ -> "Term to classify the role(s) performed by this person in the context of the study, which means that the roles reported here do not need to 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 _ -> "The accession number from the Term Source associated with the selected term"
| RolesTermSourceREF _ -> "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."
| RolesTermAccessionNumber _ -> "The accession number from the Term Source associated with the selected term. If multiple role terms are defined, multiple accession numbers have to be defined accordingly, separated by a semicolon (“;”)."
| RolesTermSourceREF _ -> "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. If multiple role terms are defined, multiple source REFs have to be defined accordingly, separated by a semicolon (“;”)."


/// CLI arguments for person removal.
Expand Down Expand Up @@ -404,12 +404,12 @@ module StudyProtocols =
| URI _ -> "Pointer to protocol resources external to the ISA-Tab that can be accessed by their Uniform Resource Identifier (URI)"
| Version _ -> "An identifier for the version to ensure protocol tracking"
| ParametersName _ -> "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 _ -> "The accession number from the Term Source associated with the selected term"
| ParametersTermSourceREF _ -> "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."
| ParametersTermAccessionNumber _ -> "A semicolon-delimited (“;”) list of accession numbers from the Term Source associated with the selected terms. "
| ParametersTermSourceREF _ -> "A semicolon-delimited (“;”) list of Source REFs. 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."
| ComponentsName _ -> "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 _ -> "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 (TAN) and Term Source REF fields below are required."
| ComponentsTypeTermAccessionNumber _ -> "The accession number from the Source associated to the selected terms"
| ComponentsTypeTermSourceREF _ -> "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."
| ComponentsType _ -> "A semicolon-delimited (“;”) list of terms 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 (TAN) and Term Source REF fields below are required."
| ComponentsTypeTermAccessionNumber _ -> "A semicolon-delimited (“;”) list of accession numbers from the Source associated to the selected terms"
| ComponentsTypeTermSourceREF _ -> "A semicolon-delimited (“;”) list of Source REFs. 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."
| ReplaceWithEmptyValues _ -> "This flag can be used to delete fields from the protocol. If this flag is not set, only these fields for which a value was given will be updated."
| AddIfMissing _ -> "If this flag is set, a new protocol will be registered with the given parameters, if it did not previously exist"

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