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Merge pull request #40 from microbiomedata/issue-38-tsv-housekeeping
Delete unused sheets_and_friends TSVs
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sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_modifications_long.tsv
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sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_modifications_long_empty.tsv
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sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_validation_converter.tsv
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@@ -1,37 +1,18 @@ | ||
from_val from_type to_type to_val notes tested ; | PMID DOI URL [ time HH date YYYY temporal float {{ - | ||
date linkml range DH datatype xs:date FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE | ||
timestamp value linkml range DH datatype xs:date "^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$" FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE | ||
{timestamp} MIxS string serialization DH datatype xs:date "^([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$" FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE | ||
YYYY-MM-DD MIxS string serialization DH datatype xs:date ^\d{4}\-(0[1-9]|1[012])\-(0[1-9]|[12][0-9]|3[01])$ FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE | ||
double linkml range DH datatype xs:decimal FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE | ||
{float} MIxS string serialization DH datatype xs:decimal [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE | ||
{integer} MIxS string serialization DH datatype xs:nonNegativeInteger why non-negative? FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE | ||
string linkml range DH datatype xs:token FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE | ||
{text} MIxS string serialization DH datatype xs:token FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE | ||
{text}:{text} MIxS string serialization DH pattern regex [^\:\n\r]+\:[^\:\n\r]+ FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE | ||
{text < 20 characters} NMDC string serialization DH pattern regex "^.{1,20}$" | ||
"{time, seconds optional}" NMDC string serialization DH pattern regex ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ | ||
HH:MM:SS MIxS string serialization DH pattern regex ^(2[0-3]|[01]?[0-9]):([0-5]?[0-9])$ FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE | ||
{lat lon} NMDC string serialization DH pattern regex ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ | ||
quantity value linkml range DH pattern regex ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE | ||
{float} {float} MIxS string serialization DH pattern regex ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ not a good validation for lat lon / lat_lon 1.3 4.5 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE | ||
{float} {unit} MIxS string serialization DH pattern regex ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE | ||
{float}|{float}-{float} MIxS string serialization DH pattern regex ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$|^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?-[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE | ||
"{text}: {text}, {text}" NMDC string serialization DH pattern regex "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" | ||
"{date, arbitrary precision}" NMDC string serialization DH pattern regex ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ | ||
{text};{float} {unit} MIxS string serialization DH pattern regex ^\S*;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE | ||
{termLabel} {[termID]}; {timestamp} MIxS string serialization DH pattern regex "^\S+.*\S+ \[ENVO:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$" some words [ENVO:123]; 2022-01-01T10:10:10 TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE | ||
{termLabel} {[termID]};{timestamp} MIxS string serialization DH pattern regex "^\S+.*\S+ \[ENVO:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$" some words [ENVO:123]; 2022-01-01T10:10:10 TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE | ||
{termLabel} {[termID]} MIxS string serialization DH pattern regex ^\S+.*\S+ \[ENVO:\d+\]$ shouldn't really just be for ENVO FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE | ||
{text};{timestamp} MIxS string serialization DH pattern regex "^\S+.*\S+;([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$" some words;2022-01-01T10:10:10 TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE | ||
{text};{float} {unit};{timestamp} MIxS string serialization DH pattern regex "^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$" some words;1.3 mg;2022-01 TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE | ||
{text};{float} {unit};{float} {unit} MIxS string serialization DH pattern regex ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ some words;1.3 mg;1.3 mg TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE | ||
{{text}|{float} {unit}};{float} {unit} MIxS string serialization TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE | ||
{boolean};{Rn/start_time/end_time/duration} MIxS string serialization TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE | ||
{float} {unit};{Rn/start_time/end_time/duration} MIxS string serialization TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE | ||
{PMID}|{DOI}|{URL} MIxS string serialization FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE | ||
{PMID}|{DOI}|{URL}|{text} MIxS string serialization FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE | ||
"{term}: {term}, {text}" MIxS string serialization FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE | ||
{termLabel} {[termID]}|{text} MIxS string serialization FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE | ||
{text};{float} {unit};{Rn/start_time/end_time/duration} MIxS string serialization TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE | ||
{text};{Rn/start_time/end_time/duration} MIxS string serialization TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE | ||
from_val from_type to_type to_val len | ||
{float} MIxS string serialization DH datatype float 5 | ||
{text} MIxS string serialization DH datatype string 6 | ||
{integer} MIxS string serialization DH datatype integer 7 | ||
{text < 20 characters} NMDC string serialization DH pattern regex "^.{1,20}$" 9 | ||
{text}:{text} MIxS string serialization DH pattern regex [^\:\n\r]+\:[^\:\n\r]+ 22 | ||
"{text}: {text}, {text}" NMDC string serialization DH pattern regex "^[^:, ][^:]*: [^:, ][^,]*, [^:, ].*$" 36 | ||
{float} {unit} MIxS string serialization DH pattern regex ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ 44 | ||
"{time, seconds optional}" NMDC string serialization DH pattern regex ^([01]?\d|2[0-3]|24(?=:00?:00?$)):([0-5]\d)(:([0-5]\d))?$ 57 | ||
"{date, arbitrary precision}" NMDC string serialization DH pattern regex ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ 67 | ||
{float} {float} MIxS string serialization DH pattern regex ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ 79 | ||
{lat lon} NMDC string serialization DH pattern regex ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ 86 | ||
{text};{float} {unit};{float} {unit} MIxS string serialization DH pattern regex ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ 96 | ||
{float}|{float}-{float} MIxS string serialization DH pattern regex ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ #REF! | ||
{text};{timestamp} MIxS string serialization DH pattern regex "^\S+.*\S+;([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$" 292 | ||
{termLabel} {[termID]}; {timestamp} MIxS string serialization DH pattern regex "^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$" 314 | ||
{termLabel} {[termID]};{timestamp} MIxS string serialization DH pattern regex "^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\d{4}(?!\d{2}\b))((-?)((0[1-9]|1[0-2])(\3([12]\d|0[1-9]|3[01]))?|W([0-4]\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\d|[12]\d{2}|3([0-5]\d|6[1-6])))([T\s]((([01]\d|2[0-3])((:?)[0-5]\d)?|24\:?00)([\.,]\d+(?!:))?)?(\17[0-5]\d([\.,]\d+)?)?([zZ]|([\+-])([01]\d|2[0-3]):?([0-5]\d)?)?)?)?$" 313 | ||
{text};{float} {unit};{timestamp} MIxS string serialization DH pattern regex .* 2 |
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sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_validation_converter_empty.tsv
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...and_friends/tsv_in/sheets-for-nmdc-submission-schema_validation_converter_no_patterns.tsv
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Original file line number | Diff line number | Diff line change |
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|
@@ -7,3 +7,5 @@ water_data: | |
env_medium: sand [ONTO:1234] | ||
env_package: xyz | ||
depth: 1.5-2.5 | ||
samp_name: xyz | ||
source_mat_id: x:1 |
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -7,3 +7,5 @@ water_data: | |
env_medium: sand [ONTO:1234] | ||
env_package: xyz | ||
rel_to_oxygen: xyz | ||
samp_name: xyz | ||
source_mat_id: x:1 |
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