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− | == Batch importing == | + | == Overview == |
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− | === Required for both ===
| + | See [[App/specimen/batch_loading]] for information on batch loading. |
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− | otu_id
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− | | + | |
− | ''or (both allowed if they match)''
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− | otu_name
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− | | + | |
− | '''OR'''
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− | taxon_name_id
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− | ''or (both allowed if they match)''
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− | taxon_name_string
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− | | + | |
− | === Required for Lots ===
| + | |
− | | + | |
− | count
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− | | + | |
− | === Required for Specimens ===
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− | | + | |
− | identifier
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− | | + | |
− | === Optional for Specimens and Lots ===
| + | |
− | | + | |
− | '''One of'''
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− | | + | |
− | ce_id
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− | verbatim_label
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− | | + | |
− | '''One of'''
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− | | + | |
− | repository_id
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− | repository_coden
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− |
| + | |
− | '''Any of'''
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− | sex
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− | stage
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− | notes
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− | data_entry_by
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− | | + | |
− | === Optional for lots ===
| + | |
− | | + | |
− | identifier
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− | | + | |
− | === Optional for specimens ===
| + | |
− |
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− | '''An additional determination'''
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− | | + | |
− | ''One of''
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− | det_name
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− | det_otu_id
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− | | + | |
− | '' and any of ''
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− | determiner
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− | det_year
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− | det_basis
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− | | + | |
− | '''A type designation'''
| + | |
− | | + | |
− | ''both of''
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− | type
| + | |
− | type_of_taxon_name_id
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− | | + | |
− | == Valid column heads on batch files ==
| + | |
− | | + | |
− | {|
| + | |
− | ! column headers
| + | |
− | ! description
| + | |
− | ! restrictions
| + | |
− | |-
| + | |
− | |ce_id
| + | |
− | |A mx collecting event id.
| + | |
− | |If present in a row then ''verbatim_label'' must be empty.
| + | |
− | |-
| + | |
− | |count
| + | |
− | |Total specimens in a lot.
| + | |
− | |If present in a row then ''identifier'' must be empty.
| + | |
− | |-
| + | |
− | |data_entry_by
| + | |
− | |A mx uses login. If supplied then all creator/updator fields are set to this person. If not supplied the creator is the person logged in.
| + | |
− | |None.
| + | |
− | |-
| + | |
− | |det_basis
| + | |
− | |Free text describing how the specimen. determination was made.
| + | |
− | |Requires ''det_name'' or 'det_otu_id' to be included. Not applicable to lots.
| + | |
− | |-
| + | |
− | |det_name
| + | |
− | |Free text determination of specimen.
| + | |
− | |If present in a row then ''det_otu_id'' must be empty. Not applicable to lots.
| + | |
− | |-
| + | |
− | |det_otu_id
| + | |
− | |An id of an mx OTU that the specimen is determined as.
| + | |
− | |If present in a row then ''det_name'' must be empty. Not applicable to lots.
| + | |
− | |-
| + | |
− | |det_year
| + | |
− | |A year in which a determination is made.
| + | |
− | |Requires ''det_otu_id'' or ''det_name'' to be present. Not applicable to lots.
| + | |
− | |-
| + | |
− | |determiner
| + | |
− | |Free text indicator of determiner.
| + | |
− | |Requires ''det_otu_id'' or ''det_name'' to be present. Not applicable to lots.
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− | |-
| + | |
− | |identifier
| + | |
− | |An identifier in the form of "namespace identifier", like "NCSU 1234".
| + | |
− | |The namespace must be present in mx. Applicable to lots or specimens. Must be unique within given category (lots/specimens).
| + | |
− | |-
| + | |
− | |notes
| + | |
− | |Free text notes.
| + | |
− | |None.
| + | |
− | |-
| + | |
− | |otu_id
| + | |
− | |A mx OTU id to which a specimen or lot is primarily attached.
| + | |
− | |Must match an OTU found by ''otu_name'' if ''otu_name'' is also provided.
| + | |
− | |-
| + | |
− | |otu_name
| + | |
− | |A mx OTU ''name'' (not associated taxon name, manuscript name, nor matrix name) which identifies the specimen.
| + | |
− | |Must match the OTU indicated by ''otu_id'' if ''otu_id'' is also provide. If ''otu_id'' is not provided must be unique for the given project.
| + | |
− | |-
| + | |
− | |repository_coden
| + | |
− | |A mx repository coden, like "NCSU".
| + | |
− | |Must match a coden in repositories. If provided ''repository_id'' must be empty.
| + | |
− | |-
| + | |
− | |repository_id
| + | |
− | |A mx id matching a respository.
| + | |
− | |Must match a coden in repositories. If provided ''repository_coden'' must be empty.
| + | |
− | |-
| + | |
− | |sex
| + | |
− | |Free text determination of sex, standard use is "male" or "female". Applicable to lots or specimens.
| + | |
− | |None.
| + | |
− | |-
| + | |
− | |stage
| + | |
− | |Free text determination of stage. Applicable to lots or specimens.
| + | |
− | |None.
| + | |
− | |-
| + | |
− | |taxon_name_id
| + | |
− | |Mx taxon name id which identifiers a specimen.
| + | |
− | |Must be tied to a single OTU. Applicable to specimens only. Must be empty if ''otu_id'' or ''otu_name'' is provided. Must match ''taxon_name_string'' if ''taxon_name_string'' is provided.
| + | |
− | |-
| + | |
− | |taxon_name_string
| + | |
− | |Mx taxon name which identifiers a specimen.
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− | |Name in mx must be unique, and associated id must be tied to a single OTU. Applicable to specimens only. Must be empty if ''otu_id'' or ''otu_name'' is provided. Must match ''taxon_name_id'' if ''taxon_name_string'' is provided. At present matches only single word string.
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− | |-
| + | |
− | |type
| + | |
− | |The code recognized type status of the specimen. Like "holotype", "paratype", "syntype", "neotype", or "paralectotype". Not for non governed things like "allotype".
| + | |
− | |Applicable to specimens only. Must be used in combination with ''type_of_taxon_name_id''.
| + | |
− | |-
| + | |
− | |type_of_taxon_name_id
| + | |
− | |The mx taxon name id that the ''type'' refers to.
| + | |
− | |Applicable to specimens only. Must be used in combination with ''type''.
| + | |
− | |-
| + | |
− | |verbatim_label
| + | |
− | |The verbatim text of the label(s) of the specimen or lot. Identical ''verbatim_labels'' are tied to a single collecting event in mx. Individual lines can be separated with "||", individual labels can be separated with "++". "||" and '++' will be replaced with one and two new lines respectively.
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− | |Must be empty if ce_id is provided.
| + | |
− | |}
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