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| # Databricks notebook source | ||
| ###### This code contains the up to date version of the ODM schema that is in production. | ||
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| # COMMAND ---------- | ||
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| ###### Aggregate tables - Derived based on ODM table | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,allSites - The table that contains information about ww daily signal average per replicate level assocaited with a given site | ||
| allSites { | ||
| collDT | ||
| name | ||
| healthReg | ||
| measID | ||
| fractionID | ||
| dataID | ||
| valavg | ||
| sampleID | ||
| MA7 | ||
| confidence | ||
| siteID | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,allSitesAdj- The table that contains information about the adjusted (based on Quality Flag) ww daily signal average per replicate level assocaited with a given site | ||
| allSitesAdj { | ||
| collDT | ||
| name | ||
| healthReg | ||
| measID | ||
| fractionID | ||
| dataID | ||
| valavg | ||
| sampleID | ||
| MA7 | ||
| confidence | ||
| siteID | ||
| } | ||
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| # COMMAND ---------- | ||
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| ###### ODM tables | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,Dataset - A report table for capturing details about data’s parental data set and data custodians. Supplying attribution for data collectors. | ||
| datasets { | ||
| parDatasetID | ||
| datasetID | ||
| name | ||
| license | ||
| descr | ||
| refLink | ||
| langID | ||
| funderCont | ||
| custodyCont | ||
| funderID | ||
| custodyID | ||
| notes | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,Infobase - subset of allsite table that is publishing on public health infobase | ||
| Infobase { | ||
| Date | ||
| Location | ||
| region | ||
| measureid | ||
| fractionid | ||
| viral_load | ||
| seven_day_rolling_avg | ||
| pruid | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,InfobaseTrend- The table that contains information about the trend flag assocaited with a given site | ||
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| InfobaseTrend { | ||
| fractionid | ||
| region | ||
| Location | ||
| measureid | ||
| LatestTrend | ||
| pruid | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1, measures - The table that contains information and details about a given measure adapt from verson 1 documentation | ||
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| measures { | ||
| measureRepID | ||
| protocolID | ||
| sampleID | ||
| purposeID | ||
| polygonID | ||
| siteID | ||
| datasetID | ||
| measureSetRepID | ||
| compartment | ||
| specimenID | ||
| fraction | ||
| group | ||
| class | ||
| measure | ||
| value | ||
| unit | ||
| aggregation | ||
| nomenclature | ||
| index | ||
| measureLic | ||
| reportable | ||
| organizationID | ||
| contactID | ||
| refLink | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,samples - The table that contains information about a sample. A sample is defined as a representative volume of wastewater (or other forms of water or liquid), air, or surface area taken from a site. Samples can be combined, split, stored and reused. | ||
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| samples { | ||
| sampleID | ||
| protocolID | ||
| organizationID | ||
| contactID | ||
| siteID | ||
| purposeID | ||
| saMaterial | ||
| datasetID | ||
| origin | ||
| repType | ||
| collType | ||
| collPer | ||
| collNum | ||
| pooled | ||
| collDT | ||
| collDTStart | ||
| collDTEnd | ||
| sentDate | ||
| recDate | ||
| reportable | ||
| lastEdited | ||
| notes | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,qualityReports - The table for recording the various quality metrics and indicators for samples and measures. | ||
| qualityReports { | ||
| quality | ||
| measureRepID | ||
| sampleID | ||
| measureSetRepID | ||
| qualityFlag | ||
| severity | ||
| notes | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,sites - The table that contains information about a site; the location where an environmental sample was taken. The site of an eviromental sample. Information in the site table does not regularly change. Consider using the MeasureReport table if the infomation changes often. | ||
| sites { | ||
| parSiteID | ||
| siteID | ||
| datasetID | ||
| polygonID | ||
| siteType | ||
| sampleShed | ||
| addressID | ||
| organizationID | ||
| contactID | ||
| name | ||
| descr | ||
| repOrg1 | ||
| repOrg2 | ||
| healthReg | ||
| popServ | ||
| geoLat | ||
| geoLong | ||
| geoEPSG | ||
| lastEdited | ||
| notes | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,StandardCurve - Table that contains the std curve information along with Lot number that serve for quantification | ||
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| StandardCurve { | ||
| sampleID | ||
| N2_Curve_ID | ||
| PMMV_Curve_ID | ||
| CDCA_Curve_ID | ||
| CDCB_Curve_ID | ||
| RSVA_Curve_ID | ||
| RSVB_Curve_ID | ||
| LotNumber | ||
| } | ||
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| # COMMAND ---------- | ||
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| ###### ODM Dictionary tables - Theses tables are pulled from the ODM working group osfhome or page | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,parts - Look up table containing all parts in of the data model. Contains all parts, including self-referential parts. | ||
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| parts { | ||
| partID | ||
| partLabel | ||
| partType | ||
| shortName | ||
| partDesc | ||
| partInstr | ||
| domain | ||
| specimenSet | ||
| compartmentSet | ||
| group | ||
| class | ||
| nomenclature | ||
| ontologyRef | ||
| latExp | ||
| mmaSet | ||
| unitSet | ||
| aggreationScale | ||
| aggregationSet | ||
| qualitySet | ||
| missingnessSet | ||
| status | ||
| changes | ||
| protocolSteps | ||
| protocolStepsRequired | ||
| protocolStepsOrder | ||
| protocolRelationships | ||
| protocolRelationshipsRequired | ||
| protocolRelationshipsOrder | ||
| measures | ||
| measuresRequired | ||
| measuresOrder | ||
| measureSets | ||
| measureSetsRequired | ||
| measureSetsOrder | ||
| datasets | ||
| datasetsRequired | ||
| datasetsOrder | ||
| sites | ||
| sitesRequired | ||
| sitesOrder | ||
| samples | ||
| samplesRequired | ||
| samplesOrder | ||
| addresses | ||
| addressesRequired | ||
| addressesOrder | ||
| contacts | ||
| contactsRequired | ||
| contactsOrder | ||
| organizations | ||
| organizationsRequired | ||
| organizationsOrder | ||
| instruments | ||
| instrumentsRequired | ||
| instrumentsOrder | ||
| polygons | ||
| polygonsRequired | ||
| polygonsOrder | ||
| languages | ||
| languagesRequired | ||
| languagesOrder | ||
| translations | ||
| translationsRequired | ||
| translationsOrder | ||
| parts | ||
| partsRequired | ||
| partsOrder | ||
| sets | ||
| setsRquired | ||
| setsOrder | ||
| qualityReports | ||
| qualityReportsRequired | ||
| qualityReportsOrder | ||
| sampleRelationships | ||
| sampleRelationshipsRequired | ||
| sampleRelationshipsOrder | ||
| protocols | ||
| protocolsRequired | ||
| protocolsOrder | ||
| countries | ||
| countriesRequired | ||
| countriesOrder | ||
| zones | ||
| zonesRequired | ||
| zonesOrder | ||
| refLink | ||
| dataType | ||
| minValue | ||
| maxValue | ||
| minLength | ||
| maxLength | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,countries - Look up table for the possible country inputs. | ||
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| countries { | ||
| isoCode | ||
| isoCodeX | ||
| numCode | ||
| tld | ||
| nameEngl | ||
| nameOffical | ||
| sovereignity | ||
| countryExonym | ||
| capitalExonym | ||
| countryEndonym | ||
| capitalEndonym | ||
| langScript | ||
| phone | ||
| utc | ||
| utcDST | ||
| } | ||
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| # COMMAND ---------- | ||
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| sets { | ||
| setID | ||
| setType | ||
| partID | ||
| partLabel | ||
| status | ||
| changes | ||
| notes | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,translations - Look up table for translations of the description, label, and instruction for all parts. The default language if a translation is not specified is English. | ||
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| translations { | ||
| lang | ||
| part | ||
| partLabel | ||
| partDesc | ||
| partInstr | ||
| changes | ||
| notes | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,zones - Look up table for the possible sub-national region or zone inputs. | ||
| zones { | ||
| isoCode | ||
| isoZone | ||
| zoneName | ||
| } | ||
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| # COMMAND ---------- | ||
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| # DBTITLE 1,languages - Look up table for all languages, used to give structure to the translation table. | ||
| languages { | ||
| lang | ||
| langFam | ||
| langName | ||
| natName | ||
| ISO6391 | ||
| ISO6392B | ||
| ISO6392T | ||
| ISO6393 | ||
| ISO6396 | ||
| changes | ||
| notes | ||
| } |