labimotion 1.5.0.rc9 → 2.0.0

data/lib/labimotion/libs/data/mapper/Chemwiki.json

@@ -0,0 +1,236 @@
+{
+  "CHMO:0000025": {
+    "index": ["A", "B", "C", "D", "Q2", "Q3", "G", "H", "Q4", "Q5", "K", "L", "Q6", "N", "O", "P", "Q7", "R", "S", "T", "U", "V", "W", "X", "Q8", "Q9", "Q10"],
+    "mapper": {
+      "A": {
+        "sources": ["inchikey"]
+      },
+      "B": {
+        "sources": ["molfile"]
+      },
+      "C": {
+        "sources": ["concentration"]
+      },
+      "D": {
+        "sources": ["redox"],
+        "separator": ","
+      },
+      "G": {
+        "sources": ["solvent_volume"]
+      },
+      "H": {
+        "sources": ["elect_inchikey"]
+      },
+      "K": {
+        "sources": ["elect_concentration"]
+      },
+      "L": {
+        "sources": ["reference_internal"]
+      },
+      "N": {
+        "sources": ["scan_rate"]
+      },
+      "O": {
+        "sources": ["scan_number"]
+      },
+      "P": {
+        "sources": ["voltage_limit_one", "voltage_limit_two"],
+        "separator": ","
+      },
+      "R": {
+        "sources": ["atmosphere"]
+      },
+      "S": {
+        "sources": ["temperature"]
+      },
+      "T": {
+        "sources": ["condition"]
+      },
+      "U": {
+        "sources": ["we"]
+      },
+      "V": {
+        "sources": ["we_area"]
+      },
+      "W": {
+        "sources": ["ce"]
+      },
+      "X": {
+        "sources": ["re"]
+      },
+      "Q2": {
+        "sources": ["solvent"]
+      },
+      "Q3": {
+        "sources": ["solvent_molfile"]
+      },
+      "Q4": {
+        "sources": ["elect_molfile"]
+      },
+      "Q5": {
+        "sources": ["elect_purity"]
+      },
+      "Q6": {
+        "sources": ["reference_internal_compound_molfile"]
+      },
+      "Q7": {
+        "sources": ["scan_direction"],
+        "separator": ","
+      },
+      "Q8": {
+        "sources": ["details"],
+        "separator": ","
+      },
+      "Q9": {
+        "sources": ["includes"],
+        "separator": ","
+      },
+      "Q10": {
+        "sources": ["base_page"],
+        "separator": ","
+      }
+    },
+    "source": {
+      "concentration": {
+        "title": "Analyte concentration [mM]",
+        "param": "sample_preparation.concentration",
+        "type": "dataset"
+      },
+      "temperature": {
+        "title": "Temperature [°C]",
+        "param": "set.temperature",
+        "type": "dataset"
+      },
+      "condition": {
+        "title": "Condition",
+        "param": "set.conditions",
+        "type": "dataset"
+      },
+      "scan_rate": {
+        "title": "Scan rate [mV/s]",
+        "param": "meas.scan_rate",
+        "type": "dataset"
+      },
+      "atmosphere": {
+        "title": "Gas",
+        "param": "set.atmosphere",
+        "type": "dataset"
+      },
+      "scan_number": {
+        "title": "Scan number",
+        "param": "meas.cycles",
+        "type": "dataset"
+      },
+      "we": {
+        "title": "Working electrode",
+        "param": "electrodes.working",
+        "type": "dataset"
+      },
+      "we_area": {
+        "title": "Working electrode surface area",
+        "param": "electrodes.working_area",
+        "type": "dataset"
+      },
+      "ce": {
+        "title": "Counter electrode",
+        "param": "electrodes.counter",
+        "type": "dataset"
+      },
+      "re": {
+        "title": "Reference electrode",
+        "param": "electrodes.reference",
+        "type": "dataset"
+      },
+      "voltage_limit_one": {
+        "title": "Potential window",
+        "param": "meas.voltage_limit_one",
+        "type": "dataset"
+      },
+      "voltage_limit_two": {
+        "title": "Potential window",
+        "param": "meas.voltage_limit_two",
+        "type": "dataset"
+      },
+      "reference_internal": {
+        "title": "Internal reference compound_inchikey",
+        "param": "meas.reference_internal",
+        "type": "dataset"
+      },
+      "elect_inchikey": {
+        "title": "Electrolyte_inchikey",
+        "param": "sample_preparation.salt",
+        "type": "dataset"
+      },
+      "elect_concentration": {
+        "title": "Electrolyte concentration [M]",
+        "param": "sample_preparation.concentration_salt",
+        "type": "dataset"
+      },
+      "solvent": {
+        "title": "Solvent A_inchikey",
+        "param": "sample_preparation.solvent",
+        "type": "dataset"
+      },
+      "solvent_volume": {
+        "title": "Solvent volume [ml]",
+        "param": "sample_preparation.amount_sol",
+        "type": "dataset"
+      },
+      "solvent_molfile": {
+        "title": "Solvent A_molfile",
+        "param": "n/a",
+        "type": "string"
+      },
+      "scan_direction": {
+        "title": "Scan direction",
+        "param": "n/a",
+        "type": "string"
+      },
+      "reference_internal_compound_molfile": {
+        "title": "Internal reference compound_molfile",
+        "param": "n/a",
+        "type": "string"
+      },
+      "elect_purity": {
+        "title": "Electrolyte purity [%]",
+        "param": "n/a",
+        "type": "string"
+      },
+      "redox": {
+        "title": "Redox-Potential",
+        "param": 6,
+        "type": "spc"
+      },
+      "elect_molfile": {
+        "title": "Electrolyte_inchikey",
+        "param": "n/a",
+        "type": "string"
+      },
+      "inchikey": {
+        "title": "Analyte_inchikey",
+        "param": "inchikey",
+        "type": "molecule"
+      },
+      "molfile": {
+        "title": "Analyte_molfile",
+        "param": "molfile",
+        "type": "sample"
+      },
+      "details": {
+        "title": "Details",
+        "param": "n/a",
+        "type": "string"
+      },
+      "includes": {
+        "title": "Included",
+        "param": "n/a",
+        "type": "string"
+      },
+      "base_page": {
+        "title": "BasePageName",
+        "param": "n/a",
+        "type": "string"
+      }
+    }
+  }
+}

data/lib/labimotion/libs/data/mapper/Source.json

@@ -0,0 +1,78 @@
+{
+  "sourceMap": {
+    "sourceSelector": [
+      "parm",
+      "acqus",
+      "procs"
+    ],
+    "acqus": {
+      "file": "acqus",
+      "parameters": [
+        "DATE",
+        "D1",
+        "INSTRUM",
+        "NS",
+        "NUC1",
+        "NUC2",
+        "PROBHD",
+        "PULPROG",
+        "SFO1",
+        "SFO2",
+        "SOLVENT",
+        "SW",
+        "TD",
+        "TE",
+        "TITLE"
+      ]
+    },
+    "procs": {
+      "file": "pdata/1/procs",
+      "parameters": [
+        "SI",
+        "SF",
+        "WDW",
+        "LB",
+        "GB"
+      ]
+    },
+    "parm": {
+      "file": "pdata/1/parm.txt",
+      "parameters": [
+        "Date_",
+        "Time",
+        "INSTRUM",
+        "PROBHD",
+        "SOLVENT",
+        "TE",
+        "NS",
+        "PULPROG",
+        "TD",
+        "D1",
+        "SF",
+        "SFO1",
+        "SFO2",
+        "NUC1",
+        "NUC2"
+      ]
+    },
+    "parameters": {
+      "DATE": "general.date",
+      "D1": "set.done",
+      "INSTRUM": "instrument.instrument",
+      "NS": "set.ns",
+      "NUC1": "set.nucone",
+      "NUC2": "set.nuctwo",
+      "SF": "set.sf",
+      "SFO1": "set.sfoone",
+      "SFO2": "set.sfotwo",
+      "PROBHD": "equipment.probehead",
+      "PULPROG": "set.PULPROG",
+      "SOLVENT": "sample_preparation.solvent",
+      "TD": "set.td",
+      "TE": "set.temperature",
+      "TITLE": "software.Name",
+      "Version": "software.Version",
+      "Time": "general.time"
+    }
+  }
+}

data/lib/labimotion/libs/data/vocab/Standard.json

@@ -1,6 +1,6 @@
 [
   {
-      "identifier": "atmosphere",
+      "identifier": "std-atmosphere",
       "name": "atmosphere",
       "label": "Atmosphere",
       "field_type": "text",
@@ -20,7 +20,7 @@
       "source": "Standard"
   },
   {
-      "identifier": "calibration",
+      "identifier": "std-calibration",
       "name": "calibration",
       "label": "Calibration",
       "field_type": "text",
@@ -40,7 +40,7 @@
       "source": "Standard"
   },
   {
-      "identifier": "coating",
+      "identifier": "std-coating",
       "name": "coating",
       "label": "Coating",
       "field_type": "text",
@@ -60,7 +60,7 @@
       "source": "Standard"
   },
   {
-      "identifier": "coating_material",
+      "identifier": "std-coating_material",
       "name": "coating_material",
       "label": "Coating Material",
       "field_type": "text",
@@ -80,7 +80,7 @@
       "source": "Standard"
   },
   {
-      "identifier": "wavelength",
+      "identifier": "std-wavelength",
       "name": "wavelength",
       "label": "Wavelength",
       "field_type": "text",

data/lib/labimotion/libs/data/vocab/System.json

@@ -1,8 +1,8 @@
 [
   {
     "id": 1,
-    "identifier": "dateTime.create",
-    "name": "Create Time",
+    "identifier": "dateTime-create",
+    "name": "create_time",
     "label": "Create Time",
     "field_type": "datetime",
     "opid": 9,
@@ -27,8 +27,8 @@
   },
   {
     "id": 2,
-    "identifier": "dateTime.update",
-    "name": "Update Time",
+    "identifier": "dateTime-update",
+    "name": "update_time",
     "label": "Update Time",
     "field_type": "datetime",
     "opid": 9,
@@ -53,9 +53,9 @@
   },
   {
     "id": 4,
-    "identifier": "user.name",
+    "identifier": "user-name",
     "name": "creator",
-    "label": "creator",
+    "label": "Creator",
     "field_type": "text",
     "opid": 9,
     "term_id": "NCIT_C42628",
@@ -79,8 +79,8 @@
   },
   {
     "id": 2,
-    "identifier": "element.id",
-    "name": "Element Id",
+    "identifier": "element-id",
+    "name": "element_id",
     "label": "Element Id",
     "field_type": "text",
     "opid": 9,
@@ -92,8 +92,8 @@
   },
   {
     "id": 5,
-    "identifier": "element.name",
-    "name": "Element Name",
+    "identifier": "element-name",
+    "name": "element_name",
     "label": "Element Name",
     "field_type": "text",
     "opid": 8,
@@ -105,8 +105,8 @@
   },
   {
     "id": 3,
-    "identifier": "element.short_label",
-    "name": "Element Short Label",
+    "identifier": "element-short_label",
+    "name": "element_short_label",
     "label": "Element Short Label",
     "field_type": "text",
     "opid": 9,
@@ -118,8 +118,8 @@
   },
   {
     "id": 3,
-    "identifier": "element.class",
-    "name": "Element Class",
+    "identifier": "element-class",
+    "name": "element_class",
     "label": "Element Class",
     "field_type": "text",
     "opid": 9,

data/lib/labimotion/libs/dataset_builder.rb

@@ -0,0 +1,70 @@
+# frozen_string_literal: true
+
+require 'labimotion/utils/utils'
+require 'labimotion/version'
+
+module Labimotion
+  class DatasetBuilder
+    def self.build(container, content)
+      return unless valid_input?(container, content)
+
+      create_dataset_with_metadata(container, content)
+    end
+
+    private
+
+    def self.valid_input?(container, content)
+      container.present? &&
+        content.present? &&
+        content[:ols].present? &&
+        content[:metadata].present?
+    end
+
+    def self.create_dataset_with_metadata(container, content)
+      klass = find_dataset_klass(content[:ols])
+      return unless klass
+
+      dataset = create_dataset(container, klass)
+      build_result(dataset, content)
+    end
+
+    def self.find_dataset_klass(ols_term_id)
+      Labimotion::DatasetKlass.find_by(ols_term_id: ols_term_id)
+    end
+
+    def self.create_dataset(container, klass)
+      uuid = SecureRandom.uuid
+      props = prepare_properties(klass, uuid)
+
+      Labimotion::Dataset.create!(
+        uuid: uuid,
+        dataset_klass_id: klass.id,
+        element_type: 'Container',
+        element_id: container.id,
+        properties: props,
+        properties_release: klass.properties_release,
+        klass_uuid: klass.uuid
+      )
+    end
+
+    def self.prepare_properties(klass, uuid)
+      props = klass.properties_release
+      props['uuid'] = uuid
+      props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
+      props['klass'] = 'Dataset'
+      props
+    end
+
+    def self.build_result(dataset, content)
+      {
+        dataset: dataset,
+        metadata: content[:metadata],
+        ols: content[:ols],
+        parameters: content[:parameters]
+      }
+    end
+
+    private_class_method :valid_input?, :create_dataset_with_metadata, :find_dataset_klass, :create_dataset,
+                         :prepare_properties, :build_result
+  end
+end