From f9b5c2b8c4877d6393c5c5850a2faa8ae4745b20 Mon Sep 17 00:00:00 2001 From: Leonardo Laiolo Date: Tue, 6 Feb 2024 15:33:12 +1100 Subject: [PATCH 1/7] bgc_chemistry.dataresource.yaml --- bgc_data/bgc_lfish_countraw.dataresource.yaml | 18 +++++----- bgc_data/bgc_lfish_samples.dataresource.yaml | 35 ++++++++++++------- .../bgc_phyto_changelog.dataresource.yaml | 6 ++-- bgc_data/bgc_phyto_raw.dataresource.yaml | 21 +++++++---- bgc_data/bgc_picoplankton.dataresource.yaml | 18 ++++++---- .../bgc_picoplankton_meta.dataresource.yaml | 24 ++++++++----- bgc_data/bgc_pigments.dataresource.yaml | 14 +++++--- bgc_data/bgc_stationinfo.dataresource.yaml | 23 +++++++----- bgc_data/bgc_trip.dataresource.yaml | 27 +++++++++----- bgc_data/bgc_tss.dataresource.yaml | 12 ++++--- bgc_data/bgc_tss_meta.dataresource.yaml | 15 +++++--- bgc_data/bgc_zoop_changelog.dataresource.yaml | 6 ++-- bgc_data/bgc_zoop_raw.dataresource.yaml | 21 +++++++---- bgc_data/phytoinfo.dataresource.yaml | 6 ++-- bgc_data/zoopinfo.dataresource.yaml | 8 ++--- 15 files changed, 164 insertions(+), 90 deletions(-) diff --git a/bgc_data/bgc_lfish_countraw.dataresource.yaml b/bgc_data/bgc_lfish_countraw.dataresource.yaml index 7201c79..521e25c 100644 --- a/bgc_data/bgc_lfish_countraw.dataresource.yaml +++ b/bgc_data/bgc_lfish_countraw.dataresource.yaml @@ -13,26 +13,28 @@ schema: - name: I_SAMPLE_ID title: "Sample identifier" type: integer - required: true - unique: false + constraints: + required: true - name: TRIP_CODE title: "Identifier for trip" type: string - required: true - unique: false + constraints: + required: true - name: SCIENTIFICNAME title: "Scientific name of taxa" type: string - required: true - unique: false + constraints: + required: true - name: SPCODE title: "Species code for taxa" type: integer - required: true + constraints: + required: true - name: TAXON_COUNT title: "Number of individuals" type: integer - required: true + constraints: + required: true - name: COMMENTS title: "Optional comments" type: string diff --git a/bgc_data/bgc_lfish_samples.dataresource.yaml b/bgc_data/bgc_lfish_samples.dataresource.yaml index 26c4cf3..c882b09 100644 --- a/bgc_data/bgc_lfish_samples.dataresource.yaml +++ b/bgc_data/bgc_lfish_samples.dataresource.yaml @@ -13,23 +13,27 @@ schema: - name: I_SAMPLE_ID title: "Sample identifier" type: integer - required: true - unique: true + constraints: + required: true + unique: true - name: PROJECTNAME title: "Source project name" type: string - required: true + constraints: + required: true - name: TRIP_CODE title: "Identifier for trip" type: string - required: true + constraints: + required: true - name: SAMPLEDATELOCAL title: "Date & time of sample in local time (formatted string)" type: datetime # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: true + constraints: + required: true - name: SAMPLEDATEUTC title: "Date & time of sample in local time (formatted string)" type: datetime @@ -42,13 +46,15 @@ schema: type: number minimum: -90 maximum: 90 - required: true + constraints: + required: true - name: LONGITUDE title: "Longitude of station in decimal degrees East" type: number minimum: -180 maximum: 180 - required: true + constraints: + required: true - name: STATIONNAME title: "Station name" type: string @@ -56,15 +62,18 @@ schema: - name: SAMPVOL_M3 title: "Volume of sample analysed (cubic metres)" type: number - required: true + constraints: + required: true - name: VESSEL title: "Name of sampling vessel" type: string - required: true + constraints: + required: true - name: TOWTYPE title: "Type of tow (e.g. 'Surface', 'Oblong')" type: string - required: true + constraints: + required: true - name: GEARDEPTH_M title: "Depth of gear (metres) - may be a depth range" type: string @@ -72,7 +81,8 @@ schema: - name: GEARMESH_UM title: "Gear mesh descriptor" type: string - required: true + constraints: + required: true - name: DEPTH_M type: number required: false @@ -91,7 +101,8 @@ schema: - name: QC_FLAG title: "Quality control flag value" type: integer - required: true + constraints: + required: true - name: FLAG_COMMENT title: "Optional comments on QC_FLAG" type: string diff --git a/bgc_data/bgc_phyto_changelog.dataresource.yaml b/bgc_data/bgc_phyto_changelog.dataresource.yaml index 02c3cf7..1606959 100644 --- a/bgc_data/bgc_phyto_changelog.dataresource.yaml +++ b/bgc_data/bgc_phyto_changelog.dataresource.yaml @@ -13,12 +13,14 @@ schema: - name: TAXON_NAME title: "Taxonomic name that the species is currently identified as (post startdate)" type: string - required: true + constraints: + required: true - name: STARTDATE title: "Date from which the taxon_name was first consistently used (formatted string: YYYY-MM-DD)" type: date format: "%Y-%m-%d" - required: true + constraints: + required: true - name: PARENT_NAME title: "Taxon name which the species was known by before the start date" type: string diff --git a/bgc_data/bgc_phyto_raw.dataresource.yaml b/bgc_data/bgc_phyto_raw.dataresource.yaml index 790d0c9..5d8cecc 100644 --- a/bgc_data/bgc_phyto_raw.dataresource.yaml +++ b/bgc_data/bgc_phyto_raw.dataresource.yaml @@ -13,15 +13,18 @@ schema: - name: TRIP_CODE title: "Unique identifier for sample" type: string - required: true + constraints: + required: true - name: TAXON_NAME title: "Scientific name of taxa" type: string - required: true + constraints: + required: true - name: TAXON_GROUP title: "Functional group assigned to taxa" type: string - required: true + constraints: + required: true - name: GENUS title: "Genus name of taxa" type: string @@ -37,7 +40,8 @@ schema: - name: CELL_L title: "Abundance of the taxa in cells per litre of water" type: number - required: true + constraints: + required: true - name: BIOVOLUME_UM3L title: "Biovolume of the taxa in um3 per litre of water" type: number @@ -45,11 +49,13 @@ schema: - name: CELL_COUNT title: "Number of the taxa counted in sample" type: number - required: true + constraints: + required: true - name: SAMPVOL_L title: "Volume of sample analysed" type: number - required: true + constraints: + required: true - name: METHODS title: Method code type: string @@ -57,7 +63,8 @@ schema: - name: COMMENTS title: "Comments" type: string - required: true + constraints: + required: true primaryKey: - TRIP_CODE - TAXON_NAME diff --git a/bgc_data/bgc_picoplankton.dataresource.yaml b/bgc_data/bgc_picoplankton.dataresource.yaml index 30a8504..853d7e5 100644 --- a/bgc_data/bgc_picoplankton.dataresource.yaml +++ b/bgc_data/bgc_picoplankton.dataresource.yaml @@ -13,18 +13,21 @@ schema: - name: TRIP_CODE title: "Identifier for trip" type: string - required: true + constraints: + required: true - name: SAMPLEDEPTH_M title: "Depth (m) that sample was obtained, or 'WC' if combined water-column sample" type: string - required: true + constraints: + required: true - name: SAMPLEDATELOCAL title: "Date & time of sample in local time (formatted string)" type: datetime # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: true + constraints: + required: true - name: PROCHLOROCOCCUS_CELLSML type: number required: false @@ -42,13 +45,16 @@ schema: required: false - name: PROCHLOROCOCCUS_FLAG type: integer - required: true + constraints: + required: true - name: SYNECOCHOCCUS_FLAG type: integer - required: true + constraints: + required: true - name: PICOEUKARYOTES_FLAG type: integer - required: true + constraints: + required: true - name: BACTERIA_FLAG type: integer required: false diff --git a/bgc_data/bgc_picoplankton_meta.dataresource.yaml b/bgc_data/bgc_picoplankton_meta.dataresource.yaml index ae5fc58..993355e 100644 --- a/bgc_data/bgc_picoplankton_meta.dataresource.yaml +++ b/bgc_data/bgc_picoplankton_meta.dataresource.yaml @@ -13,25 +13,30 @@ schema: - name: TRIP_CODE title: "Identifier for trip" type: string - required: true + constraints: + required: true - name: SAMPLE_CODE title: "Unique identifier for sample" type: string - required: true + constraints: + required: true - name: SAMPLEDEPTH_M title: "Depth (m) that sample was obtained, or 'WC' if combined water-column sample" type: string - required: true + constraints: + required: true - name: SAMPLEDATELOCAL title: "Date & time of sample in local time (formatted string)" type: datetime # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: true + constraints: + required: true - name: REPLICATE type: integer - required: true + constraints: + required: true - name: PROCHLOROCOCCUS_CELLSML type: number required: false @@ -49,13 +54,16 @@ schema: required: false - name: PROCHLOROCOCCUS_FLAG type: integer - required: true + constraints: + required: true - name: SYNECOCHOCCUS_FLAG type: integer - required: true + constraints: + required: true - name: PICOEUKARYOTES_FLAG type: integer - required: true + constraints: + required: true - name: BACTERIA_FLAG type: integer required: false diff --git a/bgc_data/bgc_pigments.dataresource.yaml b/bgc_data/bgc_pigments.dataresource.yaml index 93918d3..10aefe1 100644 --- a/bgc_data/bgc_pigments.dataresource.yaml +++ b/bgc_data/bgc_pigments.dataresource.yaml @@ -13,19 +13,22 @@ schema: - name: TRIP_CODE title: "Identifier for trip" type: string - required: true - unique: true + constraints: + required: true + unique: true - name: SAMPLEDATELOCAL title: "Date & time of sample in local time (formatted string)" type: datetime # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: true + constraints: + required: true - name: SAMPLEDEPTH_M title: "Depth (m) that sample was obtained, or 'WC' if combined water-column sample" type: string - required: true + constraints: + required: true - name: CPHL_C3 type: number required: false @@ -154,7 +157,8 @@ schema: required: false - name: PIGMENTS_FLAG type: integer - required: true + constraints: + required: true - name: PIGMENTS_COMMENTS type: string required: false diff --git a/bgc_data/bgc_stationinfo.dataresource.yaml b/bgc_data/bgc_stationinfo.dataresource.yaml index e0a8412..8491aa0 100644 --- a/bgc_data/bgc_stationinfo.dataresource.yaml +++ b/bgc_data/bgc_stationinfo.dataresource.yaml @@ -13,24 +13,29 @@ schema: - name: PROJECTNAME title: "Source project name" type: string - required: true + constraints: + required: true - name: STATIONCODE title: "Station code used to build trip code" type: string - required: true + constraints: + required: true - name: STATIONNAME title: "Long station name" type: string - required: true - unique: true + constraints: + required: true + unique: true - name: NODE title: "Name of relevant IMOS node" type: string - required: true + constraints: + required: true - name: STATECODE title: "State code for station location" type: string - required: true + constraints: + required: true - name: LONGITUDE title: "Longitude of station in decimal degrees East" type: number @@ -49,7 +54,8 @@ schema: # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d" - required: true + constraints: + required: true - name: STATIONDEPTH_M title: "Depth of station location in metres" type: number @@ -57,7 +63,8 @@ schema: - name: SAMPLINGEFFORT title: "Frequency of sampling at station" type: string - required: true + constraints: + required: true - name: IMCRA title: "The IMCRA bioregion" type: string diff --git a/bgc_data/bgc_trip.dataresource.yaml b/bgc_data/bgc_trip.dataresource.yaml index 7ca2f43..6b8185e 100644 --- a/bgc_data/bgc_trip.dataresource.yaml +++ b/bgc_data/bgc_trip.dataresource.yaml @@ -13,39 +13,47 @@ schema: - name: PROJECTNAME title: "Source project name" type: string - required: true + constraints: + required: true - name: TRIP_CODE title: "Unique identifier for trip" type: string - required: true + constraints: + required: true - name: STATIONNAME title: "Station name sample was taken at" type: string - required: true + constraints: + required: true - name: STATIONCODE title: "Station code (used to build trip code)" type: string - required: true + constraints: + required: true - name: LONGITUDE title: "Longitude of mid point of segment in decimal degrees East" type: number minimum: -180 maximum: 180 - required: true + constraints: + required: true - name: LATITUDE title: "Latitude of mid point of segment in decimal degrees North" type: number - required: true + constraints: + required: true minimum: -90 maximum: 90 - name: ZOOPSAMPLEDEPTH_M title: "Depth (m) that zooplankton sample was obtained" type: number - required: true + constraints: + required: true - name: PHYTOSAMPLEDEPTH_M title: "Depth (m) that phytoplankton sample was obtained" type: number - required: true + constraints: + required: true - name: SAMPLEDATELOCAL title: "Date & time of sample in local time (formatted string)" type: datetime @@ -59,7 +67,8 @@ schema: # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: true + constraints: + required: true - name: BIOMASS_MGM3 title: Biomass in mg per m3 for Trip type: number diff --git a/bgc_data/bgc_tss.dataresource.yaml b/bgc_data/bgc_tss.dataresource.yaml index 7404335..dfd4c05 100644 --- a/bgc_data/bgc_tss.dataresource.yaml +++ b/bgc_data/bgc_tss.dataresource.yaml @@ -13,18 +13,21 @@ schema: - name: TRIP_CODE title: "Identifier for trip" type: string - required: true + constraints: + required: true - name: SAMPLEDATELOCAL title: "Date & time of sample in local time (formatted string)" type: datetime # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: true + constraints: + required: true - name: SAMPLEDEPTH_M title: "Depth (m) that sample was obtained, or 'WC' if combined water-column sample" type: string - required: true + constraints: + required: true - name: TSS_MGL type: number required: false @@ -36,7 +39,8 @@ schema: required: false - name: TSS_FLAG type: integer - required: true + constraints: + required: true primaryKey: - TRIP_CODE - SAMPLEDEPTH_M diff --git a/bgc_data/bgc_tss_meta.dataresource.yaml b/bgc_data/bgc_tss_meta.dataresource.yaml index 0b26d75..d2298f8 100644 --- a/bgc_data/bgc_tss_meta.dataresource.yaml +++ b/bgc_data/bgc_tss_meta.dataresource.yaml @@ -13,22 +13,26 @@ schema: - name: TRIP_CODE title: "Identifier for trip" type: string - required: true + constraints: + required: true - name: SAMPLEDATELOCAL title: "Date & time of sample in local time (formatted string)" type: datetime # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: true + constraints: + required: true - name: SAMPLEDEPTH_M title: "Depth (m) that sample was obtained, or 'WC' if combined water-column sample" type: string - required: true + constraints: + required: true - name: REPLICATE title: "Sample replicate" type: integer - required: true + constraints: + required: true - name: TSS_MGL type: number required: false @@ -40,7 +44,8 @@ schema: required: false - name: TSS_FLAG type: integer - required: true + constraints: + required: true - name: TSS_COMMENTS type: string required: false diff --git a/bgc_data/bgc_zoop_changelog.dataresource.yaml b/bgc_data/bgc_zoop_changelog.dataresource.yaml index 0bd49ee..d3a9878 100644 --- a/bgc_data/bgc_zoop_changelog.dataresource.yaml +++ b/bgc_data/bgc_zoop_changelog.dataresource.yaml @@ -13,12 +13,14 @@ schema: - name: TAXON_NAME title: "Taxonomic name that the species is currently identified as (post startdate)" type: string - required: true + constraints: + required: true - name: STARTDATE title: "Date from which the taxon_name was first consistently used (formatted string: YYYY-MM-DD)" type: date format: "%Y-%m-%d" - required: true + constraints: + required: true - name: PARENT_NAME title: "Taxon name which the species was known by before the start date" type: string diff --git a/bgc_data/bgc_zoop_raw.dataresource.yaml b/bgc_data/bgc_zoop_raw.dataresource.yaml index fdedc35..b399964 100644 --- a/bgc_data/bgc_zoop_raw.dataresource.yaml +++ b/bgc_data/bgc_zoop_raw.dataresource.yaml @@ -13,19 +13,23 @@ schema: - name: TRIP_CODE title: "Unique identifier for sample" type: string - required: true + constraints: + required: true - name: TAXON_NAME title: "Scientific name of taxa" type: string - required: true + constraints: + required: true - name: COPEPOD title: "Taxonomic category assigned to taxa (e.g. COPEPOD, NON-COPEPOD, NOCTILUCA)" type: string - required: true + constraints: + required: true - name: TAXON_GROUP title: "Functional group assigned to taxa" type: string - required: true + constraints: + required: true - name: GENUS title: "Genus name of taxa" type: string @@ -41,15 +45,18 @@ schema: - name: ZOOP_ABUNDANCE_M3 title: "Abundance of the taxa in individuals per m3 of water" type: number - required: true + constraints: + required: true - name: TAXON_COUNT title: "Number of individuals counted in sample" type: number - required: true + constraints: + required: true - name: SAMPVOL_M3 title: "Volume of sample analysed" type: number - required: true + constraints: + required: true primaryKey: - TRIP_CODE - TAXON_NAME diff --git a/bgc_data/phytoinfo.dataresource.yaml b/bgc_data/phytoinfo.dataresource.yaml index 4edca72..3bb811c 100644 --- a/bgc_data/phytoinfo.dataresource.yaml +++ b/bgc_data/phytoinfo.dataresource.yaml @@ -14,12 +14,12 @@ schema: title: "Species code for taxa AphiaID Worms" type: integer required: false - unique: false - name: TAXON_NAME title: "Name of taxa" type: string - required: true - unique: true + constraints: + required: true + unique: true - name: BV_CELL type: number required: false diff --git a/bgc_data/zoopinfo.dataresource.yaml b/bgc_data/zoopinfo.dataresource.yaml index ad4ef49..ec9802a 100644 --- a/bgc_data/zoopinfo.dataresource.yaml +++ b/bgc_data/zoopinfo.dataresource.yaml @@ -13,8 +13,9 @@ schema: - name: TAXON_NAME title: "Name of taxa" type: string - required: true - unique: true + constraints: + required: true + unique: true - name: SUBGENERA type: string required: false @@ -31,7 +32,6 @@ schema: title: "Species code for taxa AphiaID Worms" type: integer required: false - unique: false - name: LENGTH_MM type: number required: false @@ -45,4 +45,4 @@ schema: licenses: - name: CC-BY-4.0 title: Creative Commons Attribution 4.0 - path: https://creativecommons.org/licenses/by/4.0/ \ No newline at end of file + path: https://creativecommons.org/licenses/by/4.0/ From 3bf41262f6d9268de80b5c3e7062075458678bc4 Mon Sep 17 00:00:00 2001 From: Leonardo Laiolo Date: Tue, 6 Feb 2024 15:33:47 +1100 Subject: [PATCH 2/7] update bgc --- bgc_data/bgc_chemistry.dataresource.yaml | 36 ++++++++++++++++-------- 1 file changed, 24 insertions(+), 12 deletions(-) diff --git a/bgc_data/bgc_chemistry.dataresource.yaml b/bgc_data/bgc_chemistry.dataresource.yaml index 5eed9d0..54676f1 100644 --- a/bgc_data/bgc_chemistry.dataresource.yaml +++ b/bgc_data/bgc_chemistry.dataresource.yaml @@ -13,18 +13,21 @@ schema: - name: TRIP_CODE title: "Identifier for trip" type: string - required: true + constraints: + required: true - name: SAMPLEDEPTH_M title: "Depth (m) that sample was obtained" type: number - required: true + constraints: + required: true - name: SAMPLEDATELOCAL title: "Date & time of sample in local time (formatted string)" type: datetime # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: true + constraints: + required: true - name: SALINITY_PSU title: "Salinity PSU value" type: number @@ -32,7 +35,8 @@ schema: - name: SALINITY_FLAG title: "FLAG value" type: integer - required: true + constraints: + required: true - name: SILICATE_UMOLL title: "Silicate umoll" type: number @@ -40,56 +44,64 @@ schema: - name: SILICATE_FLAG title: "FLAG value" type: integer - required: true + constraints: + required: true - name: NITRATE_UMOLL type: number required: false - name: NITRATE_FLAG title: "FLAG value" type: integer - required: true + constraints: + required: true - name: PHOSPHATE_UMOLL type: number required: false - name: PHOSPHATE_FLAG title: "FLAG value" type: integer - required: true + constraints: + required: true - name: AMMONIUM_UMOLL type: number required: false - name: AMMONIUM_FLAG title: "FLAG value" type: integer - required: true + constraints: + required: true - name: NITRITE_UMOLL type: number required: false - name: NITRITE_FLAG title: "FLAG value" type: integer - required: true + constraints: + required: true - name: DIC_UMOLKG type: number required: false - name: CARBON_FLAG title: "FLAG value" type: integer - required: true + constraints: + required: true - name: TALKALINITY_UMOLKG type: number required: false - name: ALKALINITY_FLAG title: "FLAG value" type: integer - required: true + constraints: + required: true - name: OXYGEN_UMOLL type: number required: false - name: OXYGEN_FLAG title: "FLAG value" type: integer - required: true + constraints: + required: true - name: MICROBIOMESAMPLE_ID title: "Microbiomesample_id" type: string From 43a448d0a7a7819240cf52968082d386ae978f05 Mon Sep 17 00:00:00 2001 From: Leonardo Laiolo Date: Thu, 8 Feb 2024 08:38:55 +1100 Subject: [PATCH 3/7] fix not necessary constrain for bgc_pigments --- bgc_data/bgc_pigments.dataresource.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/bgc_data/bgc_pigments.dataresource.yaml b/bgc_data/bgc_pigments.dataresource.yaml index 10aefe1..6d0a4d4 100644 --- a/bgc_data/bgc_pigments.dataresource.yaml +++ b/bgc_data/bgc_pigments.dataresource.yaml @@ -15,7 +15,6 @@ schema: type: string constraints: required: true - unique: true - name: SAMPLEDATELOCAL title: "Date & time of sample in local time (formatted string)" type: datetime From a44020e5f4100bf64034d98aa20925d2a726b9b6 Mon Sep 17 00:00:00 2001 From: Leonardo Laiolo Date: Thu, 8 Feb 2024 08:50:47 +1100 Subject: [PATCH 4/7] update cpr --- .../cpr_phyto_changelog.dataresource.yaml | 6 ++++-- cpr_data/cpr_phyto_raw.dataresource.yaml | 18 ++++++++++------ cpr_data/cpr_samp.dataresource.yaml | 21 ++++++++++++------- cpr_data/cpr_zoop_changelog.dataresource.yaml | 6 ++++-- cpr_data/cpr_zoop_raw.dataresource.yaml | 21 ++++++++++++------- 5 files changed, 48 insertions(+), 24 deletions(-) diff --git a/cpr_data/cpr_phyto_changelog.dataresource.yaml b/cpr_data/cpr_phyto_changelog.dataresource.yaml index 0855dad..c82ab5e 100644 --- a/cpr_data/cpr_phyto_changelog.dataresource.yaml +++ b/cpr_data/cpr_phyto_changelog.dataresource.yaml @@ -13,12 +13,14 @@ schema: - name: TAXON_NAME title: "Taxonomic name that the species is currently identified as (post startdate)" type: string - required: true + constraints: + required: true - name: STARTDATE title: "Date from which the taxon_name was first consistently used (formatted string: YYYY-MM-DD)" type: date format: "%Y-%m-%d" - required: true + constraints: + required: true - name: PARENT_NAME title: "Taxon name which the species was known by before the start date" type: string diff --git a/cpr_data/cpr_phyto_raw.dataresource.yaml b/cpr_data/cpr_phyto_raw.dataresource.yaml index bbb8877..c7002ed 100644 --- a/cpr_data/cpr_phyto_raw.dataresource.yaml +++ b/cpr_data/cpr_phyto_raw.dataresource.yaml @@ -13,15 +13,18 @@ schema: - name: SAMPLE title: "Unique identifier for sample" type: string - required: true + constraints: + required: true - name: TAXON_NAME title: "Scientific name of taxa" type: string - required: true + constraints: + required: true - name: TAXON_GROUP title: "Functional group assigned to taxa" type: string - required: true + constraints: + required: true - name: GENUS title: "Genus name of taxa" type: string @@ -37,7 +40,8 @@ schema: - name: PHYTO_ABUNDANCE_M3 title: "Abundance of the taxa in cells per litre of water" type: number - required: true + constraints: + required: true - name: BIOVOL_UM3M3 title: "Biovolume of the taxa in um3 per cubic metre of water" type: number @@ -45,11 +49,13 @@ schema: - name: FOV_COUNT title: "Number of the taxa counted" type: number - required: true + constraints: + required: true - name: SAMPVOL_M3 title: "Volume of sample analysed (cubic metres)" type: number - required: true + constraints: + required: true primaryKey: - SAMPLE - TAXON_NAME diff --git a/cpr_data/cpr_samp.dataresource.yaml b/cpr_data/cpr_samp.dataresource.yaml index 81ce0be..2569650 100644 --- a/cpr_data/cpr_samp.dataresource.yaml +++ b/cpr_data/cpr_samp.dataresource.yaml @@ -13,19 +13,23 @@ schema: - name: TRIP_CODE title: "Unique identifier for trip" type: string - required: true + constraints: + required: true - name: SAMPLE title: "Unique sample identifier" type: string - required: true + constraints: + required: true - name: REGION title: "Region identifier" type: string - required: true + constraints: + required: true - name: LATITUDE title: "Latitude of sampling in decimal degrees North" type: number - required: true + constraints: + required: true minimum: -90 maximum: 90 - name: LONGITUDE @@ -33,14 +37,16 @@ schema: type: number minimum: -180 maximum: 180 - required: true + constraints: + required: true - name: SAMPLEDATEUTC title: "Date & time of sample in UTC time (formatted string)" type: datetime # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: true + constraints: + required: true - name: SAMPLEDATELOCAL title: "Date & time of sample in local time (formatted string)" type: datetime @@ -59,7 +65,8 @@ schema: - name: SAMPLETYPE title: "sample type code" type: string - required: true + constraints: + required: true - name: GHRSST_6D_DEGC title: "IMOS L3S Day and Night gridded multiple-sensor multiple-swath Australian region HRPT AVHRR foundation SST" type: number diff --git a/cpr_data/cpr_zoop_changelog.dataresource.yaml b/cpr_data/cpr_zoop_changelog.dataresource.yaml index 03f7c9b..b703e05 100644 --- a/cpr_data/cpr_zoop_changelog.dataresource.yaml +++ b/cpr_data/cpr_zoop_changelog.dataresource.yaml @@ -13,12 +13,14 @@ schema: - name: TAXON_NAME title: "Taxonomic name that the species is currently identified as (post startdate)" type: string - required: true + constraints: + required: true - name: STARTDATE title: "Date from which the taxon_name was first consistently used (formatted string: YYYY-MM-DD)" type: date format: "%Y-%m-%d" - required: true + constraints: + required: true - name: PARENT_NAME title: "Taxon name which the species was known by before the start date" type: string diff --git a/cpr_data/cpr_zoop_raw.dataresource.yaml b/cpr_data/cpr_zoop_raw.dataresource.yaml index e183f97..7752eed 100644 --- a/cpr_data/cpr_zoop_raw.dataresource.yaml +++ b/cpr_data/cpr_zoop_raw.dataresource.yaml @@ -13,19 +13,23 @@ schema: - name: SAMPLE title: "Unique identifier for sample" type: string - required: true + constraints: + required: true - name: TAXON_NAME title: "Scientific name of taxa" type: string - required: true + constraints: + required: true - name: COPEPOD title: "Taxonomic flag value" type: string - required: true + constraints: + required: true - name: TAXON_GROUP title: "Functional group assigned to taxa" type: string - required: true + constraints: + required: true - name: GENUS title: "Genus name of taxa" type: string @@ -41,15 +45,18 @@ schema: - name: TAXON_COUNT title: "Number of the taxa counted" type: number - required: true + constraints: + required: true - name: SAMPVOL_M3 title: "Volume of sample analysed (cubic metres)" type: number - required: true + constraints: + required: true - name: ZOOP_ABUNDANCE_M3 title: "Abundance of the taxa per cubic metre of water" type: number - required: true + constraints: + required: true primaryKey: - SAMPLE From 402ddb4926a4e8b7c12fc09ee03cb485a608aa4d Mon Sep 17 00:00:00 2001 From: Leonardo Laiolo Date: Thu, 8 Feb 2024 09:54:57 +1100 Subject: [PATCH 5/7] remove required:false from cpr --- cpr_data/cpr_phyto_changelog.dataresource.yaml | 3 --- cpr_data/cpr_phyto_raw.dataresource.yaml | 4 ---- cpr_data/cpr_samp.dataresource.yaml | 5 ----- cpr_data/cpr_zoop_changelog.dataresource.yaml | 3 --- cpr_data/cpr_zoop_raw.dataresource.yaml | 3 --- 5 files changed, 18 deletions(-) diff --git a/cpr_data/cpr_phyto_changelog.dataresource.yaml b/cpr_data/cpr_phyto_changelog.dataresource.yaml index c82ab5e..e01f398 100644 --- a/cpr_data/cpr_phyto_changelog.dataresource.yaml +++ b/cpr_data/cpr_phyto_changelog.dataresource.yaml @@ -24,15 +24,12 @@ schema: - name: PARENT_NAME title: "Taxon name which the species was known by before the start date" type: string - required: false - name: TRAINING title: "Training from which the taxon_name was first consistently used" type: string - required: false - name: COMMENTS title: "Comments" type: string - required: false primaryKey: - TAXON_NAME licenses: diff --git a/cpr_data/cpr_phyto_raw.dataresource.yaml b/cpr_data/cpr_phyto_raw.dataresource.yaml index c7002ed..03514f0 100644 --- a/cpr_data/cpr_phyto_raw.dataresource.yaml +++ b/cpr_data/cpr_phyto_raw.dataresource.yaml @@ -28,15 +28,12 @@ schema: - name: GENUS title: "Genus name of taxa" type: string - required: false - name: SPECIES title: "Species name of taxa" type: string - required: false - name: SPCODE title: "Species code for taxa AphiaID Worms" type: integer - required: false - name: PHYTO_ABUNDANCE_M3 title: "Abundance of the taxa in cells per litre of water" type: number @@ -45,7 +42,6 @@ schema: - name: BIOVOL_UM3M3 title: "Biovolume of the taxa in um3 per cubic metre of water" type: number - required: false - name: FOV_COUNT title: "Number of the taxa counted" type: number diff --git a/cpr_data/cpr_samp.dataresource.yaml b/cpr_data/cpr_samp.dataresource.yaml index 2569650..4489859 100644 --- a/cpr_data/cpr_samp.dataresource.yaml +++ b/cpr_data/cpr_samp.dataresource.yaml @@ -53,15 +53,12 @@ schema: # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: false - name: PCI title: "pci" type: number - required: false - name: BIOMASS_MGM3 title: "biomass (mg/mg3)" type: number - required: false - name: SAMPLETYPE title: "sample type code" type: string @@ -70,11 +67,9 @@ schema: - name: GHRSST_6D_DEGC title: "IMOS L3S Day and Night gridded multiple-sensor multiple-swath Australian region HRPT AVHRR foundation SST" type: number - required: false - name: CHLOC3_MGM3 title: "Chlorophyll concentration mgm3 OC3 algorithm available at: https://thredds.aodn.org.au/thredds/catalog/IMOS/SRS/OC/gridded/aqua/P1D/catalog.html" type: number - required: false primaryKey: SAMPLE licenses: - name: CC-BY-4.0 diff --git a/cpr_data/cpr_zoop_changelog.dataresource.yaml b/cpr_data/cpr_zoop_changelog.dataresource.yaml index b703e05..58f997a 100644 --- a/cpr_data/cpr_zoop_changelog.dataresource.yaml +++ b/cpr_data/cpr_zoop_changelog.dataresource.yaml @@ -24,15 +24,12 @@ schema: - name: PARENT_NAME title: "Taxon name which the species was known by before the start date" type: string - required: false - name: TRAINING title: "Training from which the taxon_name was first consistently used" type: string - required: false - name: COMMENTS title: "Comments" type: string - required: false primaryKey: - TAXON_NAME licenses: diff --git a/cpr_data/cpr_zoop_raw.dataresource.yaml b/cpr_data/cpr_zoop_raw.dataresource.yaml index 7752eed..af5c727 100644 --- a/cpr_data/cpr_zoop_raw.dataresource.yaml +++ b/cpr_data/cpr_zoop_raw.dataresource.yaml @@ -33,15 +33,12 @@ schema: - name: GENUS title: "Genus name of taxa" type: string - required: false - name: SPECIES title: "Species name of taxa" type: string - required: false - name: SPCODE title: "Species code for taxa AphiaID Worms" type: integer - required: false - name: TAXON_COUNT title: "Number of the taxa counted" type: number From f957279a7b949119e84cc2d5eef1e432fa258a67 Mon Sep 17 00:00:00 2001 From: Leonardo Laiolo Date: Thu, 8 Feb 2024 10:09:00 +1100 Subject: [PATCH 6/7] remove required:false from bgc --- bgc_data/bgc_chemistry.dataresource.yaml | 10 ----- bgc_data/bgc_lfish_countraw.dataresource.yaml | 1 - bgc_data/bgc_lfish_samples.dataresource.yaml | 8 ---- .../bgc_phyto_changelog.dataresource.yaml | 3 -- bgc_data/bgc_phyto_raw.dataresource.yaml | 5 --- bgc_data/bgc_picoplankton.dataresource.yaml | 7 --- .../bgc_picoplankton_meta.dataresource.yaml | 21 --------- bgc_data/bgc_pigments.dataresource.yaml | 43 ------------------- bgc_data/bgc_stationinfo.dataresource.yaml | 6 --- bgc_data/bgc_trip.dataresource.yaml | 5 --- bgc_data/bgc_tss.dataresource.yaml | 3 -- bgc_data/bgc_tss_meta.dataresource.yaml | 5 --- bgc_data/bgc_zoop_changelog.dataresource.yaml | 3 -- bgc_data/bgc_zoop_raw.dataresource.yaml | 3 -- bgc_data/phytoinfo.dataresource.yaml | 6 --- bgc_data/zoopinfo.dataresource.yaml | 8 ---- 16 files changed, 137 deletions(-) diff --git a/bgc_data/bgc_chemistry.dataresource.yaml b/bgc_data/bgc_chemistry.dataresource.yaml index 54676f1..10b09b6 100644 --- a/bgc_data/bgc_chemistry.dataresource.yaml +++ b/bgc_data/bgc_chemistry.dataresource.yaml @@ -31,7 +31,6 @@ schema: - name: SALINITY_PSU title: "Salinity PSU value" type: number - required: false - name: SALINITY_FLAG title: "FLAG value" type: integer @@ -40,7 +39,6 @@ schema: - name: SILICATE_UMOLL title: "Silicate umoll" type: number - required: false - name: SILICATE_FLAG title: "FLAG value" type: integer @@ -48,7 +46,6 @@ schema: required: true - name: NITRATE_UMOLL type: number - required: false - name: NITRATE_FLAG title: "FLAG value" type: integer @@ -56,7 +53,6 @@ schema: required: true - name: PHOSPHATE_UMOLL type: number - required: false - name: PHOSPHATE_FLAG title: "FLAG value" type: integer @@ -64,7 +60,6 @@ schema: required: true - name: AMMONIUM_UMOLL type: number - required: false - name: AMMONIUM_FLAG title: "FLAG value" type: integer @@ -72,7 +67,6 @@ schema: required: true - name: NITRITE_UMOLL type: number - required: false - name: NITRITE_FLAG title: "FLAG value" type: integer @@ -80,7 +74,6 @@ schema: required: true - name: DIC_UMOLKG type: number - required: false - name: CARBON_FLAG title: "FLAG value" type: integer @@ -88,7 +81,6 @@ schema: required: true - name: TALKALINITY_UMOLKG type: number - required: false - name: ALKALINITY_FLAG title: "FLAG value" type: integer @@ -96,7 +88,6 @@ schema: required: true - name: OXYGEN_UMOLL type: number - required: false - name: OXYGEN_FLAG title: "FLAG value" type: integer @@ -105,7 +96,6 @@ schema: - name: MICROBIOMESAMPLE_ID title: "Microbiomesample_id" type: string - required: false primaryKey: - TRIP_CODE - SAMPLEDEPTH_M diff --git a/bgc_data/bgc_lfish_countraw.dataresource.yaml b/bgc_data/bgc_lfish_countraw.dataresource.yaml index 521e25c..4c514e4 100644 --- a/bgc_data/bgc_lfish_countraw.dataresource.yaml +++ b/bgc_data/bgc_lfish_countraw.dataresource.yaml @@ -38,7 +38,6 @@ schema: - name: COMMENTS title: "Optional comments" type: string - required: false primaryKey: - I_SAMPLE_ID - SCIENTIFICNAME diff --git a/bgc_data/bgc_lfish_samples.dataresource.yaml b/bgc_data/bgc_lfish_samples.dataresource.yaml index c882b09..35bfc6f 100644 --- a/bgc_data/bgc_lfish_samples.dataresource.yaml +++ b/bgc_data/bgc_lfish_samples.dataresource.yaml @@ -40,7 +40,6 @@ schema: # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: false - name: LATITUDE title: "Latitude of station in decimal degrees North" type: number @@ -58,7 +57,6 @@ schema: - name: STATIONNAME title: "Station name" type: string - required: false - name: SAMPVOL_M3 title: "Volume of sample analysed (cubic metres)" type: number @@ -77,7 +75,6 @@ schema: - name: GEARDEPTH_M title: "Depth of gear (metres) - may be a depth range" type: string - required: false - name: GEARMESH_UM title: "Gear mesh descriptor" type: string @@ -85,19 +82,15 @@ schema: required: true - name: DEPTH_M type: number - required: false - name: TEMPERATURE_C title: "Temperature (deg C)" type: number - required: false - name: SALINITY_PSU title: "Salinity" type: number - required: false - name: COMMENTS title: "Comments (optional)" type: string - required: false - name: QC_FLAG title: "Quality control flag value" type: integer @@ -106,7 +99,6 @@ schema: - name: FLAG_COMMENT title: "Optional comments on QC_FLAG" type: string - required: false primaryKey: I_SAMPLE_ID licenses: - name: CC-BY-4.0 diff --git a/bgc_data/bgc_phyto_changelog.dataresource.yaml b/bgc_data/bgc_phyto_changelog.dataresource.yaml index 1606959..ae44957 100644 --- a/bgc_data/bgc_phyto_changelog.dataresource.yaml +++ b/bgc_data/bgc_phyto_changelog.dataresource.yaml @@ -24,15 +24,12 @@ schema: - name: PARENT_NAME title: "Taxon name which the species was known by before the start date" type: string - required: false - name: TRAINING title: "Training from which the taxon_name was first consistently used" type: string - required: false - name: COMMENTS title: "Comments" type: string - required: false primaryKey: - TAXON_NAME licenses: diff --git a/bgc_data/bgc_phyto_raw.dataresource.yaml b/bgc_data/bgc_phyto_raw.dataresource.yaml index 5d8cecc..84784a2 100644 --- a/bgc_data/bgc_phyto_raw.dataresource.yaml +++ b/bgc_data/bgc_phyto_raw.dataresource.yaml @@ -28,15 +28,12 @@ schema: - name: GENUS title: "Genus name of taxa" type: string - required: false - name: SPECIES title: "Species name of taxa" type: string - required: false - name: SPCODE title: "Species code for taxa AphiaID Worms" type: integer - required: false - name: CELL_L title: "Abundance of the taxa in cells per litre of water" type: number @@ -45,7 +42,6 @@ schema: - name: BIOVOLUME_UM3L title: "Biovolume of the taxa in um3 per litre of water" type: number - required: false - name: CELL_COUNT title: "Number of the taxa counted in sample" type: number @@ -59,7 +55,6 @@ schema: - name: METHODS title: Method code type: string - required: false - name: COMMENTS title: "Comments" type: string diff --git a/bgc_data/bgc_picoplankton.dataresource.yaml b/bgc_data/bgc_picoplankton.dataresource.yaml index 853d7e5..f316d53 100644 --- a/bgc_data/bgc_picoplankton.dataresource.yaml +++ b/bgc_data/bgc_picoplankton.dataresource.yaml @@ -30,19 +30,14 @@ schema: required: true - name: PROCHLOROCOCCUS_CELLSML type: number - required: false - name: SYNECOCHOCCUS_CELLSML type: number - required: false - name: PICOEUKARYOTES_CELLSML type: number - required: false - name: BACTERIA_CELLSML type: number - required: false - name: VIRUS_CELLSML type: number - required: false - name: PROCHLOROCOCCUS_FLAG type: integer constraints: @@ -57,10 +52,8 @@ schema: required: true - name: BACTERIA_FLAG type: integer - required: false - name: VIRUS_FLAG type: integer - required: false primaryKey: - TRIP_CODE - SAMPLEDEPTH_M diff --git a/bgc_data/bgc_picoplankton_meta.dataresource.yaml b/bgc_data/bgc_picoplankton_meta.dataresource.yaml index 993355e..5ab9725 100644 --- a/bgc_data/bgc_picoplankton_meta.dataresource.yaml +++ b/bgc_data/bgc_picoplankton_meta.dataresource.yaml @@ -39,19 +39,14 @@ schema: required: true - name: PROCHLOROCOCCUS_CELLSML type: number - required: false - name: SYNECOCHOCCUS_CELLSML type: number - required: false - name: PICOEUKARYOTES_CELLSML type: number - required: false - name: BACTERIA_CELLSML type: number - required: false - name: VIRUS_CELLSML type: number - required: false - name: PROCHLOROCOCCUS_FLAG type: integer constraints: @@ -66,61 +61,45 @@ schema: required: true - name: BACTERIA_FLAG type: integer - required: false - name: VIRUS_FLAG type: integer - required: false - name: PICO_COMMENTS title: "Comments" type: string - required: false - name: ANALYSIS_LOCATION title: "Site where sample was analysed" type: string - required: false - name: ANALYSIS_DATE title: "Date that sample was analysed (formatted string: YYYY-MM-DD)" type: date format: "%Y-%m-%d" - required: false - name: ANALYST_NAME type: string - required: false - name: TEMP_THAWED_DEGC type: number - required: false - name: INTERNAL_STANDARD type: string - required: false - name: INSTRUMENT_BRAND_MODEL title: "Comments" type: string - required: false - name: INSTRUMENT_SERIAL_NUMBER title: "Comments" type: string - required: false - name: LASER_NM title: "Comments" type: string - required: false - name: MODE_TYPE title: "Comments" type: string - required: false - name: ANALYSIS_VOLUME_UL type: number - required: false - name: FLOW_RATE_UL_PER_MIN type: integer - required: false - name: ANALYSIS_TIME_MINUTES type: integer - required: false - name: BATCH_COMMENTS title: "Optional comments on batch process" type: string - required: false primaryKey: SAMPLE_CODE licenses: - name: CC-BY-4.0 diff --git a/bgc_data/bgc_pigments.dataresource.yaml b/bgc_data/bgc_pigments.dataresource.yaml index 6d0a4d4..22e48f5 100644 --- a/bgc_data/bgc_pigments.dataresource.yaml +++ b/bgc_data/bgc_pigments.dataresource.yaml @@ -30,137 +30,94 @@ schema: required: true - name: CPHL_C3 type: number - required: false - name: MG_DVP type: number - required: false - name: CPHL_C2 type: number - required: false - name: CPHL_C1 type: number - required: false - name: CPHL_C1C2 type: number - required: false - name: CPHLIDE_A type: number - required: false - name: PHIDE_A type: number - required: false - name: PERID type: number - required: false - name: PYROPHIDE_A type: number - required: false - name: BUT_FUCO type: number - required: false - name: FUCO type: number - required: false - name: NEO type: number - required: false - name: KETO_HEX_FUCO type: number - required: false - name: PRAS type: number - required: false - name: VIOLA type: number - required: false - name: HEX_FUCO type: number - required: false - name: ASTA type: number - required: false - name: DIADCHR type: number - required: false - name: DIADINO type: number - required: false - name: DINO type: number - required: false - name: ANTH type: number - required: false - name: ALLO type: number - required: false - name: MYXO type: number - required: false - name: DIATO type: number - required: false - name: ZEA type: number - required: false - name: LUT type: number - required: false - name: CANTHA type: number - required: false - name: GYRO type: number - required: false - name: DV_CPHL_B type: number - required: false - name: CPHL_B type: number - required: false - name: DV_CPHL_B_AND_CPHL_B type: number - required: false - name: DV_CPHL_A type: number - required: false - name: CPHL_A type: number - required: false - name: DV_CPHL_A_AND_CPHL_A type: number - required: false - name: ECHIN type: number - required: false - name: PHYTIN_B type: number - required: false - name: PHYTIN_A type: number - required: false - name: LYCO type: number - required: false - name: BETA_EPI_CAR type: number - required: false - name: BETA_BETA_CAR type: number - required: false - name: ALPHA_BETA_CAR type: number - required: false - name: PYROPHYTIN_A type: number - required: false - name: PIGMENTS_FLAG type: integer constraints: required: true - name: PIGMENTS_COMMENTS type: string - required: false primaryKey: - TRIP_CODE - SAMPLEDEPTH_M diff --git a/bgc_data/bgc_stationinfo.dataresource.yaml b/bgc_data/bgc_stationinfo.dataresource.yaml index 8491aa0..67a16b5 100644 --- a/bgc_data/bgc_stationinfo.dataresource.yaml +++ b/bgc_data/bgc_stationinfo.dataresource.yaml @@ -41,11 +41,9 @@ schema: type: number minimum: -180 maximum: 180 - required: false - name: LATITUDE title: "Latitude of station in decimal degrees North" type: number - required: false minimum: -90 maximum: 90 - name: STATIONSTARTDATE @@ -59,7 +57,6 @@ schema: - name: STATIONDEPTH_M title: "Depth of station location in metres" type: number - required: false - name: SAMPLINGEFFORT title: "Frequency of sampling at station" type: string @@ -68,15 +65,12 @@ schema: - name: IMCRA title: "The IMCRA bioregion" type: string - required: false - name: IMCRA_PB title: "The larger IMCRA bioregion" type: string - required: false - name: MANAGEMENTREGION title: "The bioregion as defined by Dept of Environment" type: string - required: false primaryKey: STATIONCODE licenses: - name: CC-BY-4.0 diff --git a/bgc_data/bgc_trip.dataresource.yaml b/bgc_data/bgc_trip.dataresource.yaml index 6b8185e..c580738 100644 --- a/bgc_data/bgc_trip.dataresource.yaml +++ b/bgc_data/bgc_trip.dataresource.yaml @@ -60,7 +60,6 @@ schema: # format string *must* be specified using standard Python/C strptime specification # https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior format: "%Y-%m-%d %H:%M:%S" - required: false - name: SAMPLEDATEUTC title: "Date & time of sample in UTC time (formatted string)" type: datetime @@ -72,19 +71,15 @@ schema: - name: BIOMASS_MGM3 title: Biomass in mg per m3 for Trip type: number - required: false - name: ASHFREEBIOMASS_MGM3 title: Ash Free Biomass in mg per m3 for Trip type: number - required: false - name: SECCHI_M title: Secchi depth in m for Trip type: number - required: false - name: SAMPLETYPE title: Code for which analysis is available for that segment type: string - required: false primaryKey: TRIP_CODE licenses: - name: CC-BY-4.0 diff --git a/bgc_data/bgc_tss.dataresource.yaml b/bgc_data/bgc_tss.dataresource.yaml index dfd4c05..184ba1b 100644 --- a/bgc_data/bgc_tss.dataresource.yaml +++ b/bgc_data/bgc_tss.dataresource.yaml @@ -30,13 +30,10 @@ schema: required: true - name: TSS_MGL type: number - required: false - name: INORGANICFRACTION_MGL type: number - required: false - name: ORGANICFRACTION_MGL type: number - required: false - name: TSS_FLAG type: integer constraints: diff --git a/bgc_data/bgc_tss_meta.dataresource.yaml b/bgc_data/bgc_tss_meta.dataresource.yaml index d2298f8..9f95231 100644 --- a/bgc_data/bgc_tss_meta.dataresource.yaml +++ b/bgc_data/bgc_tss_meta.dataresource.yaml @@ -35,23 +35,18 @@ schema: required: true - name: TSS_MGL type: number - required: false - name: INORGANICFRACTION_MGL type: number - required: false - name: ORGANICFRACTION_MGL type: number - required: false - name: TSS_FLAG type: integer constraints: required: true - name: TSS_COMMENTS type: string - required: false - name: BLANKADJUSTAVAILABLE type: string - required: false primaryKey: - TRIP_CODE - SAMPLEDEPTH_M diff --git a/bgc_data/bgc_zoop_changelog.dataresource.yaml b/bgc_data/bgc_zoop_changelog.dataresource.yaml index d3a9878..e44adf8 100644 --- a/bgc_data/bgc_zoop_changelog.dataresource.yaml +++ b/bgc_data/bgc_zoop_changelog.dataresource.yaml @@ -24,15 +24,12 @@ schema: - name: PARENT_NAME title: "Taxon name which the species was known by before the start date" type: string - required: false - name: TRAINING title: "Training from which the taxon_name was first consistently used" type: string - required: false - name: COMMENTS title: "Comments" type: string - required: false primaryKey: - TAXON_NAME licenses: diff --git a/bgc_data/bgc_zoop_raw.dataresource.yaml b/bgc_data/bgc_zoop_raw.dataresource.yaml index b399964..0cc4ad7 100644 --- a/bgc_data/bgc_zoop_raw.dataresource.yaml +++ b/bgc_data/bgc_zoop_raw.dataresource.yaml @@ -33,15 +33,12 @@ schema: - name: GENUS title: "Genus name of taxa" type: string - required: false - name: SPECIES title: "Species name of taxa" type: string - required: false - name: SPCODE title: "Species code for taxa AphiaID Worms" type: string - required: false - name: ZOOP_ABUNDANCE_M3 title: "Abundance of the taxa in individuals per m3 of water" type: number diff --git a/bgc_data/phytoinfo.dataresource.yaml b/bgc_data/phytoinfo.dataresource.yaml index 3bb811c..926d7ab 100644 --- a/bgc_data/phytoinfo.dataresource.yaml +++ b/bgc_data/phytoinfo.dataresource.yaml @@ -13,7 +13,6 @@ schema: - name: SPCODE title: "Species code for taxa AphiaID Worms" type: integer - required: false - name: TAXON_NAME title: "Name of taxa" type: string @@ -22,19 +21,14 @@ schema: unique: true - name: BV_CELL type: number - required: false - name: FUNCTIONALGROUP type: string - required: false - name: MONT2001PGN_CELL type: number - required: false - name: PGC_CELL type: number - required: false - name: TROPHY type: string - required: false primaryKey: TAXON_NAME licenses: - name: CC-BY-4.0 diff --git a/bgc_data/zoopinfo.dataresource.yaml b/bgc_data/zoopinfo.dataresource.yaml index ec9802a..c981036 100644 --- a/bgc_data/zoopinfo.dataresource.yaml +++ b/bgc_data/zoopinfo.dataresource.yaml @@ -18,29 +18,21 @@ schema: unique: true - name: SUBGENERA type: string - required: false - name: FUNCTIONALGROUP type: string - required: false - name: GENUS type: string - required: false - name: SPECIES type: string - required: false - name: SPCODE title: "Species code for taxa AphiaID Worms" type: integer - required: false - name: LENGTH_MM type: number - required: false - name: SIZEREFERENCE type: string - required: false - name: DIET type: string - required: false primaryKey: TAXON_NAME licenses: - name: CC-BY-4.0 From 249449cd36d17b2feb38dbb26eb376d67fab2811 Mon Sep 17 00:00:00 2001 From: Leonardo Laiolo Date: Thu, 8 Feb 2024 15:06:26 +1100 Subject: [PATCH 7/7] Claire feedback update --- bgc_data/bgc_picoplankton.dataresource.yaml | 6 ------ bgc_data/bgc_picoplankton_meta.dataresource.yaml | 6 ------ bgc_data/bgc_trip.dataresource.yaml | 4 ---- cpr_data/cpr_samp.dataresource.yaml | 2 -- 4 files changed, 18 deletions(-) diff --git a/bgc_data/bgc_picoplankton.dataresource.yaml b/bgc_data/bgc_picoplankton.dataresource.yaml index f316d53..ae3eaa5 100644 --- a/bgc_data/bgc_picoplankton.dataresource.yaml +++ b/bgc_data/bgc_picoplankton.dataresource.yaml @@ -40,16 +40,10 @@ schema: type: number - name: PROCHLOROCOCCUS_FLAG type: integer - constraints: - required: true - name: SYNECOCHOCCUS_FLAG type: integer - constraints: - required: true - name: PICOEUKARYOTES_FLAG type: integer - constraints: - required: true - name: BACTERIA_FLAG type: integer - name: VIRUS_FLAG diff --git a/bgc_data/bgc_picoplankton_meta.dataresource.yaml b/bgc_data/bgc_picoplankton_meta.dataresource.yaml index 5ab9725..3522810 100644 --- a/bgc_data/bgc_picoplankton_meta.dataresource.yaml +++ b/bgc_data/bgc_picoplankton_meta.dataresource.yaml @@ -49,16 +49,10 @@ schema: type: number - name: PROCHLOROCOCCUS_FLAG type: integer - constraints: - required: true - name: SYNECOCHOCCUS_FLAG type: integer - constraints: - required: true - name: PICOEUKARYOTES_FLAG type: integer - constraints: - required: true - name: BACTERIA_FLAG type: integer - name: VIRUS_FLAG diff --git a/bgc_data/bgc_trip.dataresource.yaml b/bgc_data/bgc_trip.dataresource.yaml index c580738..b6d4f33 100644 --- a/bgc_data/bgc_trip.dataresource.yaml +++ b/bgc_data/bgc_trip.dataresource.yaml @@ -47,13 +47,9 @@ schema: - name: ZOOPSAMPLEDEPTH_M title: "Depth (m) that zooplankton sample was obtained" type: number - constraints: - required: true - name: PHYTOSAMPLEDEPTH_M title: "Depth (m) that phytoplankton sample was obtained" type: number - constraints: - required: true - name: SAMPLEDATELOCAL title: "Date & time of sample in local time (formatted string)" type: datetime diff --git a/cpr_data/cpr_samp.dataresource.yaml b/cpr_data/cpr_samp.dataresource.yaml index 4489859..61db4be 100644 --- a/cpr_data/cpr_samp.dataresource.yaml +++ b/cpr_data/cpr_samp.dataresource.yaml @@ -62,8 +62,6 @@ schema: - name: SAMPLETYPE title: "sample type code" type: string - constraints: - required: true - name: GHRSST_6D_DEGC title: "IMOS L3S Day and Night gridded multiple-sensor multiple-swath Australian region HRPT AVHRR foundation SST" type: number