Merge pull request #80 from microbiomedata/nmdc-dh-issue-156

Remove dna/rna organisms and collect_site slots
microbiomedata · Mar 28, 2023 · 8ac3953 · 8ac3953
2 parents 0848c54 + ebf2301
commit 8ac3953
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Showing 13 changed files with 1,619 additions and 1,592 deletions.
diff --git a/schema_sheets/populated_tsv/slot_usage_minimal.tsv b/schema_sheets/populated_tsv/slot_usage_minimal.tsv
diff --git a/schema_sheets/tsv_in/sheets-for-nmdc-submission-schema_classes.tsv b/schema_sheets/tsv_in/sheets-for-nmdc-submission-schema_classes.tsv
@@ -8,8 +8,8 @@ EmslInterface	Emsl	emsl dh_interface		DhInterface		DhMultiviewCommonColumnsMixin
 HcrCoresInterface	Hcr Cores	hcr_cores dh_interface		DhInterface		DhMultiviewCommonColumnsMixin	
 HcrFluidsSwabsInterface	Hcr Fluids Swabs	hcr_fluids_swabs dh_interface		DhInterface		DhMultiviewCommonColumnsMixin	
 HostAssociatedInterface	Host Associated	host_associated dh_interface		DhInterface		DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin	
-JgiMgInterface	JGI MG	jgi_mg dh_interface		DhInterface		DhMultiviewCommonColumnsMixin	dna_absorb1|dna_absorb2|dna_collect_site|dna_concentration|dna_cont_type|dna_cont_well|dna_container_id|dna_dnase|dna_isolate_meth|dna_organisms|dna_project_contact|dna_samp_id|dna_sample_format|dna_sample_name|dna_seq_project|dna_seq_project_name|dna_seq_project_pi|dna_volume|proposal_dna
-JgiMtInterface	JGI MT	jgi_mt dh_interface		DhInterface		DhMultiviewCommonColumnsMixin	dnase_rna|proposal_rna|rna_absorb1|rna_absorb2|rna_collect_site|rna_concentration|rna_cont_type|rna_cont_well|rna_container_id|rna_isolate_meth|rna_organisms|rna_project_contact|rna_samp_id|rna_sample_format|rna_sample_name|rna_seq_project|rna_seq_project_name|rna_seq_project_pi|rna_volume
+JgiMgInterface	JGI MG	jgi_mg dh_interface		DhInterface		DhMultiviewCommonColumnsMixin	dna_absorb1|dna_absorb2|dna_concentration|dna_cont_type|dna_cont_well|dna_container_id|dna_dnase|dna_isolate_meth|dna_project_contact|dna_samp_id|dna_sample_format|dna_sample_name|dna_seq_project|dna_seq_project_name|dna_seq_project_pi|dna_volume|proposal_dna
+JgiMtInterface	JGI MT	jgi_mt dh_interface		DhInterface		DhMultiviewCommonColumnsMixin	dnase_rna|proposal_rna|rna_absorb1|rna_absorb2|rna_concentration|rna_cont_type|rna_cont_well|rna_container_id|rna_isolate_meth|rna_project_contact|rna_samp_id|rna_sample_format|rna_sample_name|rna_seq_project|rna_seq_project_name|rna_seq_project_pi|rna_volume
 MiscEnvsInterface	Misc Envs	misc_envs dh_interface		DhInterface		DhMultiviewCommonColumnsMixin	
 PlantAssociatedInterface	Plant Associated	plant_associated dh_interface		DhInterface		DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin	
 SedimentInterface	Sediment	sediment dh_interface		DhInterface		DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin	

diff --git a/sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_import_slots_regardless.tsv b/sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_import_slots_regardless.tsv
diff --git a/...nd_friends/tsv_in/sheets-for-nmdc-submission-schema_modifications_long-dont-mod-water.tsv b/...nd_friends/tsv_in/sheets-for-nmdc-submission-schema_modifications_long-dont-mod-water.tsv
diff --git a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_type.yaml b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_type.yaml
@@ -2,7 +2,6 @@ jgi_mg_data:
   - analysis_type:
       - metagenomics
       - metatranscriptomics
-    dna_collect_site: xxx
     dna_concentration: 1.23
     dna_cont_type: bucket
     dna_cont_well: H3

diff --git a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_well.yaml b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_well.yaml
@@ -2,7 +2,6 @@ jgi_mg_data:
   - analysis_type:
       - metagenomics
       - metatranscriptomics
-    dna_collect_site: xxx
     dna_concentration: 1.23
     dna_cont_type: plate
     dna_cont_well: Z99

diff --git a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_dnase.yaml b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_dnase.yaml
@@ -2,7 +2,6 @@ jgi_mg_data:
   - analysis_type:
       - metagenomics
       - metatranscriptomics
-    dna_collect_site: xxx
     dna_concentration: 1.23
     dna_cont_type: plate
     dna_cont_well: C3

diff --git a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_sample_format.yaml b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_sample_format.yaml
@@ -2,7 +2,6 @@ jgi_mg_data:
   - analysis_type:
       - metagenomics
       - metatranscriptomics
-    dna_collect_site: xxx
     dna_concentration: 1.23
     dna_cont_type: plate
     dna_cont_well: C3

diff --git a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_volume.yaml b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_volume.yaml
@@ -2,7 +2,6 @@ jgi_mg_data:
   - analysis_type:
       - metagenomics
       - metatranscriptomics
-    dna_collect_site: xxx
     dna_concentration: 1.23
     dna_cont_type: plate
     dna_cont_well: C3

diff --git a/src/data/invalid/SampleData-jgi_mg_data-dna_collect_site.yaml b/src/data/invalid/SampleData-jgi_mg_data-dna_collect_site.yaml
@@ -0,0 +1,23 @@
+jgi_mg_data:
+  - analysis_type:
+      - metagenomics
+      - metatranscriptomics
+    dna_collect_site: xxx
+    dna_concentration: 1.23
+    dna_cont_type: plate
+    dna_cont_well: C3
+    dna_container_id: xxx
+    dna_dnase: "no"
+    dna_isolate_meth: xxx
+    dna_project_contact: xxx
+    dna_samp_id: xxx
+    dna_sample_format: DNAStable
+    dna_sample_name: xxx
+    dna_seq_project: xxx
+    dna_seq_project_name: xxx
+    dna_seq_project_pi: xxx
+    dna_volume: 999
+    proposal_dna: xxx
+    samp_name: xxx
+    source_mat_id: x:1
+
diff --git a/src/data/invalid/SampleData-jgi_mg_data-dna_organisms.yaml b/src/data/invalid/SampleData-jgi_mg_data-dna_organisms.yaml
@@ -0,0 +1,22 @@
+jgi_mg_data:
+  - analysis_type:
+      - metagenomics
+      - metatranscriptomics
+    dna_concentration: 1.23
+    dna_cont_type: plate
+    dna_cont_well: C3
+    dna_container_id: xxx
+    dna_dnase: "no"
+    dna_isolate_meth: xxx
+    dna_project_contact: xxx
+    dna_samp_id: xxx
+    dna_sample_format: DNAStable
+    dna_sample_name: xxx
+    dna_seq_project: xxx
+    dna_seq_project_name: xxx
+    dna_seq_project_pi: xxx
+    dna_volume: 999
+    proposal_dna: xxx
+    samp_name: xxx
+    source_mat_id: x:1
+    dna_organisms: xxx
diff --git a/src/data/valid/SampleData-jgi_mg_data-exhaustive.yaml b/src/data/valid/SampleData-jgi_mg_data-exhaustive.yaml
@@ -4,14 +4,14 @@ jgi_mg_data:
       - metatranscriptomics
     dna_absorb1: 1.23
     dna_absorb2: 1.23
-    dna_collect_site: xxx
+#    dna_collect_site: xxx
     dna_concentration: 1.23
     dna_cont_type: plate
     dna_cont_well: C3
     dna_container_id: xxx
     dna_dnase: "no"
     dna_isolate_meth: xxx
-    dna_organisms: xxx
+#    dna_organisms: xxx
     dna_project_contact: xxx
     dna_samp_id: xxx
     dna_sample_format: DNAStable

diff --git a/src/data/valid/SampleData-jgi_mg_data-minimal.yaml b/src/data/valid/SampleData-jgi_mg_data-minimal.yaml
@@ -2,7 +2,6 @@ jgi_mg_data:
   - analysis_type:
       - metagenomics
       - metatranscriptomics
-    dna_collect_site: xxx
     dna_concentration: 1.23
     dna_cont_type: plate
     dna_cont_well: C3