Template:Workflow: Difference between revisions

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T4 reidelbach (talk | contribs)
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T4 reidelbach (talk | contribs)
private
480 edits
 
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Line 158: Line 158:
       (GROUP_CONCAT(DISTINCT ?outputLink; separator=", ") AS ?Output)
       (GROUP_CONCAT(DISTINCT ?outputLink; separator=", ") AS ?Output)
       (GROUP_CONCAT(DISTINCT ?methodLink; separator=", ") AS ?Method)
       (GROUP_CONCAT(DISTINCT ?methodLink; separator=", ") AS ?Method)
       (GROUP_CONCAT(DISTINCT ?environmentLabel; separator=", ") AS ?Environment)
       (GROUP_CONCAT(DISTINCT ?environmentLink; separator=", ") AS ?Environment)
       (GROUP_CONCAT(DISTINCT ?disciplineLink; separator=", ") AS ?Discipline)
       (GROUP_CONCAT(DISTINCT ?disciplineLink; separator=", ") AS ?Discipline)


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     ?environmentID rdfs:label ?environmentLabel.
     ?environmentID rdfs:label ?environmentLabel.
     FILTER (lang(?environmentLabel) = 'en')
     FILTER (lang(?environmentLabel) = 'en')
    BIND(replace( xsd:string(?environmentID),
      'https://portal.mardi4nfdi.de/entity/',
      '') as ?environmentQID)
    BIND (CONCAT('<a href=\'/wiki/Item:',?environmentQID,'\'>',?environmentLabel,'</a>') as ?environmentLink)
   }
   }
    
    
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}}
}}
</div>
</div>
=== Applied methods ===
=== Applied methods ===
<div class='no-pagination no-filter'>
<div class='no-pagination no-filter'>
{{#sparql:
{{#sparql:
SELECT ?ID
SELECT ?Name
      ?Name
       ?Description
       ?Description
       (GROUP_CONCAT(DISTINCT ?stepLink; separator=", ") AS ?ProcessStep)
       (GROUP_CONCAT(DISTINCT ?stepLink; separator=", ") AS ?Process_Step)
       (GROUP_CONCAT(DISTINCT ?softwareLink; separator=", ") AS ?ImplementedBy)
       (GROUP_CONCAT(DISTINCT ?softwareLink; separator=", ") AS ?Implemented_By)
        
        
WHERE {
WHERE {
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<div class='no-pagination no-filter'>
<div class='no-pagination no-filter'>
{{#sparql:
{{#sparql:
SELECT ?ID
SELECT ?Name
      ?Name
       ?Description
       ?Description
       ?Version
       ?Version
       (GROUP_CONCAT(DISTINCT ?plLink; separator=", ") AS ?ProgrammingLanguage)
       (GROUP_CONCAT(DISTINCT ?plLink; separator=", ") AS ?Programming_Language)
       (GROUP_CONCAT(DISTINCT ?dpLink; separator=", ") AS ?Dependencies)
       (GROUP_CONCAT(DISTINCT ?dpLink; separator=", ") AS ?Dependencies)
      ?versioned
      ?published
      ?documented
        
        
WHERE {
WHERE {
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     BIND (CONCAT('<a href=\'/wiki/Item:',?dpQID,'\'>',?dpLabel,'</a>') as ?dpLink)
     BIND (CONCAT('<a href=\'/wiki/Item:',?dpQID,'\'>',?dpLabel,'</a>') as ?dpLink)
   }
   }
 
  # Versioned
  BIND (IF(BOUND(?Version), "Yes", "No") AS ?versioned)
 
  # Published
  OPTIONAL {
    ?softwareID wdt:P339 ?srcREPO.
  }
  BIND (IF(BOUND(?srcREPO), CONCAT('<a href="', STR(?srcREPO), '">Yes</a>'), "No") AS ?published)
 
  # Documented
  OPTIONAL {
    ?softwareID wdt:P340 ?docu.
  }
  BIND (IF(BOUND(?docu), CONCAT('<a href="', STR(?docu), '">Yes</a>'), "No") AS ?documented)
 
  }
  }
GROUP BY ?ID ?Name ?Description ?Version
GROUP BY ?ID ?Name ?Description ?Version ?versioned ?published ?documented
| chart=bordercloud.visualization.DataTable
| chart=bordercloud.visualization.DataTable
| options=width=100%!
| options=width=100%!
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<div class='no-pagination no-filter'>
<div class='no-pagination no-filter'>
{{#sparql:
{{#sparql:
SELECT ?ID
SELECT ?Name
      ?Name
       ?Description
       ?Description
       (GROUP_CONCAT(DISTINCT ?processorLink; separator=", ") AS ?Processor)
       (GROUP_CONCAT(DISTINCT ?processorLink; separator=", ") AS ?Processor)
       (GROUP_CONCAT(DISTINCT ?nodes; separator=", ") AS ?NumberOfNodes)
       (GROUP_CONCAT(DISTINCT ?nodes; separator=", ") AS ?Node_Number)
       (GROUP_CONCAT(DISTINCT ?cores; separator=", ") AS ?NumberOfCores)
       (GROUP_CONCAT(DISTINCT ?cores; separator=", ") AS ?Core_Number)
        
        
WHERE {
WHERE {
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=== Input data ===
=== Input data ===
<div class="no-pagination no-filter">
{{#sparql:
SELECT ?Name
      ?Size
      (?DataStructure AS ?Data_Structure)
      (?ExchangeFormat AS ?Exchange_Format)
      (?BinaryOrText AS ?Binary_Text)
      ?Proprietary
      (?toPublish AS ?to_Publish)
      (?toArchive AS ?to_Archive)
     
WHERE {
 
  # Get Step
  wd:{{#invoke:Wd|label|raw|}} p:P557 ?mainStatement.
  ?mainStatement ps:P557 ?stepID.
  ?stepID wdt:P31 wd:Q6486603.           
 
  # Get Data
  OPTIONAL {
    ?stepID wdt:P1605 ?inputID.
    ?inputID rdfs:label ?NameLabel.
    FILTER (lang(?NameLabel) = 'en')
   
    BIND(replace( xsd:string(?inputID),
      'https://portal.mardi4nfdi.de/entity/',
      '') as ?qid)
   
    BIND(CONCAT('mardi:','<a href=\'/wiki/Item:',?qid,'\'>',?qid,'</a>') as ?ID)
    BIND(CONCAT('<a href=\'/wiki/Item:',?qid,'\'>',?NameLabel,'</a>') as ?Name)
  # Data Size (maps to Size if File etc size is provided)
  OPTIONAL {
    ?inputID p:P1542 ?statementNode.         
    ?statementNode psv:P1542 ?valueNode.     
    ?valueNode wikibase:quantityAmount ?size;
              wikibase:quantityUnit ?unit.
    ?unit rdfs:label ?unitlabel.
    FILTER (lang(?unitlabel) = 'en')
    BIND(CONCAT(STR(?size), ' ', STR(?unitlabel)) AS ?Size)
}
 
  # Number of Records (maps to Size if Number of Entries in a Database etc is provided=
  OPTIONAL {
    ?inputID wdt:P139 ?Sizeraw
    BIND(CONCAT(STR(?Sizeraw),' Items') as ?Size)
  }
 
  # Data Structure
  OPTIONAL {
    ?inputID wdt:P1193 ?DataStructure
    }
   
  # Exchange Format
  OPTIONAL {
    ?inputID wdt:P921 ?ExchangeFormat
    }
 
  # Binary or Text
  BIND(IF(EXISTS { ?inputID wdt:P31 wd:Q6480276 }, "binary", IF(EXISTS { ?inputID wdt:P31 wd:Q6534207 }, "text", "" )) AS ?BinaryOrText)
 
  # Proprietary
  BIND(IF(EXISTS { ?inputID wdt:P31 wd:Q6480367 }, "yes", IF(EXISTS { ?inputID wdt:P31 wd:Q6480313 }, "no", "" )) AS ?Proprietary)
 
  # Bind DOI and URL if they exist
  OPTIONAL { ?inputID wdt:P23 ?doi. }
  OPTIONAL { ?inputID wdt:P188 ?url. }
 
  # Data Publishing
  BIND(
  IF(EXISTS { ?inputID wdt:P1563 wd:Q6480291 },
    IF(EXISTS { ?inputID wdt:P27 ?doi },
        CONCAT('<a href="', 'https://dx.doi.org', STR(?doi), '">yes</a>'),
        IF(EXISTS { ?inputID wdt:P188 ?url },
          CONCAT('<a href="', STR(?url), '">yes</a>'),
          "yes"
        )
    ),
    "no"
  ) AS ?toPublish
)
# Data Archiving
  OPTIONAL {
  ?inputID p:P1563 ?statementNode.
  ?statementNode ps:P1563 wd:Q6480370.
  OPTIONAL {
    ?statementNode pq:P411 ?endTime.
  }
}
BIND(
  IF(BOUND(?statementNode),
    IF(BOUND(?endTime),
        SUBSTR(STR(?endTime), 1, 4),
        "yes"
    ),
    "no"
  ) AS ?toArchive
)
   
  }
} GROUP BY ?ID ?Name ?Size ?DataStructure ?ExchangeFormat ?BinaryOrText ?Proprietary ?toPublish ?toArchive
| chart=bordercloud.visualization.DataTable
| options=width=100%!
| endpoint=https://query.portal.mardi4nfdi.de/proxy/wdqs/bigdata/namespace/wdq/sparql
}}
</div>


=== Output data ===
=== Output data ===
<div class="no-pagination no-filter">
{{#sparql:
SELECT ?Name
      ?Size
      (?DataStructure AS ?Data_Structure)
      (?ExchangeFormat AS ?Exchange_Format)
      (?BinaryOrText AS ?Binary_Text)
      ?Proprietary
      (?toPublish AS ?to_Publish)
      (?toArchive AS ?to_Archive)
     
WHERE {
 
  # Get Step
  wd:{{#invoke:Wd|label|raw|}} p:P557 ?mainStatement.
  ?mainStatement ps:P557 ?stepID.
  ?stepID wdt:P31 wd:Q6486603.           
 
  # Get Data
  OPTIONAL {
    ?stepID wdt:P1606 ?outputID.
    ?outputID rdfs:label ?NameLabel.
    FILTER (lang(?NameLabel) = 'en')
   
    BIND(replace( xsd:string(?outputID),
      'https://portal.mardi4nfdi.de/entity/',
      '') as ?qid)
   
    BIND(CONCAT('mardi:','<a href=\'/wiki/Item:',?qid,'\'>',?qid,'</a>') as ?ID)
    BIND(CONCAT('<a href=\'/wiki/Item:',?qid,'\'>',?NameLabel,'</a>') as ?Name)
  # Data Size (maps to Size if File etc size is provided)
  OPTIONAL {
    ?outputID p:P1542 ?statementNode.         
    ?statementNode psv:P1542 ?valueNode.     
    ?valueNode wikibase:quantityAmount ?size;
              wikibase:quantityUnit ?unit.
    ?unit rdfs:label ?unitlabel.
    FILTER (lang(?unitlabel) = 'en')
    BIND(CONCAT(STR(?size), ' ', STR(?unitlabel)) AS ?Size)
}
 
  # Number of Records (maps to Size if Number of Entries in a Database etc is provided=
  OPTIONAL {
    ?outputID wdt:P139 ?Sizeraw
    BIND(CONCAT(STR(?Sizeraw),' Items') as ?Size)
  }
 
  # Data Structure
  OPTIONAL {
    ?outputID wdt:P1193 ?DataStructure
    }
   
  # Exchange Format
  OPTIONAL {
    ?outputID wdt:P921 ?ExchangeFormat
    }
 
  # Binary or Text
  BIND(IF(EXISTS { ?outputID wdt:P31 wd:Q6480276 }, "binary", IF(EXISTS { ?outputID wdt:P31 wd:Q6534207 }, "text", "" )) AS ?BinaryOrText)
 
  # Proprietary
  BIND(IF(EXISTS { ?outputID wdt:P31 wd:Q6480367 }, "yes", IF(EXISTS { ?outputID wdt:P31 wd:Q6480313 }, "no", "" )) AS ?Proprietary)
 
  # Bind DOI and URL if they exist
  OPTIONAL { ?outputID wdt:P23 ?doi. }
  OPTIONAL { ?outputID wdt:P188 ?url. }
 
  # Data Publishing
  BIND(
  IF(EXISTS { ?outputID wdt:P1563 wd:Q6480291 },
    IF(EXISTS { ?outputID wdt:P27 ?doi },
        CONCAT('<a href="', 'https://dx.doi.org', STR(?doi), '">yes</a>'),
        IF(EXISTS { ?outputID wdt:P188 ?url },
          CONCAT('<a href="', STR(?url), '">yes</a>'),
          "yes"
        )
    ),
    "no"
  ) AS ?toPublish
)
# Data Archiving
  OPTIONAL {
  ?outputID p:P1563 ?statementNode.
  ?statementNode ps:P1563 wd:Q6480370.
  OPTIONAL {
    ?statementNode pq:P411 ?endTime.
  }
}
BIND(
  IF(BOUND(?statementNode),
    IF(BOUND(?endTime),
        SUBSTR(STR(?endTime), 1, 4),
        "yes"
    ),
    "no"
  ) AS ?toArchive
)
   
  }
} GROUP BY ?ID ?Name ?Size ?DataStructure ?ExchangeFormat ?BinaryOrText ?Proprietary ?toPublish ?toArchive
| chart=bordercloud.visualization.DataTable
| options=width=100%!
| endpoint=https://query.portal.mardi4nfdi.de/proxy/wdqs/bigdata/namespace/wdq/sparql
}}
</div>
== Reproducibility ==
<div class='no-pagination no-filter'>
{{#sparql:
SELECT ?Mathematically
      ?Runtime
      ?Result
      (?OriginalPlatform AS ?Original_Platform)
      (?CrossPlatform AS ?Cross_Platform)
      ?Transferability
     
WHERE {
  # Mathematical Reproducibility
  OPTIONAL {
    wd:{{#invoke:Wd|label|raw|}} p:P31 ?math_statement.
    ?math_statement ps:P31 wd:Q6534210.
    BIND("Yes" AS ?math_hasTriple)
    OPTIONAL {
      ?math_statement pq:P8 ?math_text.
      BIND(CONCAT("Yes: ", STR(?math_text)) AS ?math_result)
      }
  }
  BIND(IF(BOUND(?math_result), ?math_result, IF(BOUND(?math_hasTriple), "Yes", "No")) AS ?Mathematically)
 
  # Runtime Reproducibility
  OPTIONAL {
    wd:{{#invoke:Wd|label|raw|}} p:P31 ?run_statement.
    ?run_statement ps:P31 wd:Q6534211.
    BIND("Yes" AS ?run_hasTriple)
    OPTIONAL {
      ?run_statement pq:P8 ?run_text.
      BIND(CONCAT("Yes: ", STR(?run_text)) AS ?run_result)
      }
  }
  BIND(IF(BOUND(?run_result), ?run_result, IF(BOUND(?run_hasTriple), "Yes", "No")) AS ?Runtime)
 
  # Result Reproducibility
  OPTIONAL {
    wd:{{#invoke:Wd|label|raw|}} p:P31 ?res_statement.
    ?res_statement ps:P31 wd:Q6534212.
    BIND("Yes" AS ?res_hasTriple)
    OPTIONAL {
      ?res_statement pq:P8 ?res_text.
      BIND(CONCAT("Yes: ", STR(?res_text)) AS ?res_result)
      }
  }
  BIND(IF(BOUND(?res_result), ?res_result, IF(BOUND(?res_hasTriple), "Yes", "No")) AS ?Result)
 
  # Original Platform Reproducibility
  OPTIONAL {
    wd:{{#invoke:Wd|label|raw|}} p:P31 ?plat_statement.
    ?plat_statement ps:P31 wd:Q6534213.
    BIND("Yes" AS ?plat_hasTriple)
    OPTIONAL {
      ?plat_statement pq:P8 ?plat_text.
      BIND(CONCAT("Yes: ", STR(?plat_text)) AS ?plat_result)
      }
  }
  BIND(IF(BOUND(?plat_result), ?plat_result, IF(BOUND(?plat_hasTriple), "Yes", "No")) AS ?OriginalPlatform)
 
  # Cross Platform Reproducibility
  OPTIONAL {
    wd:{{#invoke:Wd|label|raw|}} p:P31 ?xplat_statement.
    ?xplat_statement ps:P31 wd:Q6534214.
    BIND("Yes" AS ?xplat_hasTriple)
    OPTIONAL {
      ?xplat_statement pq:P8 ?xplat_text.
      BIND(CONCAT("Yes: ", STR(?xplat_text)) AS ?xplat_result)
      }
  }
  BIND(IF(BOUND(?xplat_result), ?xplat_result, IF(BOUND(?xplat_hasTriple), "Yes", "No")) AS ?CrossPlatform)
 
  # Transferability
  OPTIONAL {
    wd:{{#invoke:Wd|label|raw|}} p:P31 ?trans_statement.
    ?trans_statement ps:P31 wd:Q6534215.
    BIND("Yes" AS ?trans_hasTriple)
    OPTIONAL {
      ?trans_statement pq:P8 ?trans_text.
      BIND(CONCAT("Yes: ", STR(?trans_text)) AS ?trans_result)
      }
  }
  BIND(IF(BOUND(?trans_result), ?trans_result, IF(BOUND(?trans_hasTriple), "Yes", "No")) AS ?Transferability)
}
GROUP BY ?Mathematically ?Runtime ?Result ?OriginalPlatform ?CrossPlatform ?Transferability
| chart=bordercloud.visualization.DataTable
| options=width=100%!
| endpoint=https://query.portal.mardi4nfdi.de/proxy/wdqs/bigdata/namespace/wdq/sparql
}}
</div>

Latest revision as of 10:22, 19 December 2024


Available identifiers

Problem statement

Object of research and objective

Involved disciplines

    Model

    Variables

    Parameters

    Process information

    Process steps

    Applied methods

    Software used

    Hardware

    Input data

    Output data

    Reproducibility

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