removed provider_sample_id references

7 files changed, 8 insertions, 11 deletions

diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html
index aea74ad..2651f85 100644
--- a/doc/blog/using-covid-19-pubseq-part3.html
+++ b/doc/blog/using-covid-19-pubseq-part3.html
@@ -358,8 +358,8 @@ the web form. Here we add some extra information.
 <p>
 This is a string field that defines a unique sample identifier by the
 submitter. In addition to sample_id we also have host_id,
-provider_sample_id and submitter_sample_id where host is the host the
-sample came from, provider sample is the institution sample id and
+provider and submitter_sample_id where host is the host the
+sample came from, provider sample is the institution id and
 submitter is the submitting individual id. host_id is important when
 multiple sequences come from the same host. Make sure not to have
 spaces in the sample_id.
@@ -599,7 +599,7 @@ submitter:
     submitter_address: John Doe's address
     originating_lab: John Doe kitchen
     lab_address: John Doe's address
-    provider_sample_id: XXX<span style="color: #8bc34a;">1</span>
+    provider: XXX<span style="color: #8bc34a;">1</span>
     submitter_sample_id: XXX<span style="color: #8bc34a;">2</span>
     publication: PMID<span style="color: #8bc34a;">00001113</span>
     submitter_orcid: [https://orcid.org/<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>,https://orcid.org/<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0001</span>]
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index 7336cf6..307a87a 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -83,8 +83,8 @@ the web form. Here we add some extra information.
 
 This is a string field that defines a unique sample identifier by the
 submitter. In addition to sample_id we also have host_id,
-provider_sample_id and submitter_sample_id where host is the host the
-sample came from, provider sample is the institution sample id and
+provider and submitter_sample_id where host is the host the
+sample came from, provider sample is the institution id and
 submitter is the submitting individual id. host_id is important when
 multiple sequences come from the same host. Make sure not to have
 spaces in the sample_id.
@@ -245,7 +245,7 @@ a more elaborate example (note most fields are optional) may look like
       submitter_address: John Doe's address
       originating_lab: John Doe kitchen
       lab_address: John Doe's address
-      provider_sample_id: XXX1
+      provider: XXX1
       submitter_sample_id: XXX2
       publication: PMID00001113
       submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001]
diff --git a/example/esr_example.yaml b/example/esr_example.yaml
index 693aff3..c97d0bf 100644
--- a/example/esr_example.yaml
+++ b/example/esr_example.yaml
@@ -33,7 +33,6 @@ submitter:
     submitter_name: [Joep de Ligt]
     submitter_address: "PO Box 50348,  Porirua 5240, New Zealand"
     originating_lab: ESR
-    provider_sample_id: "20VR0174"
     submitter_sample_id: "PRJNA648792"
     submitted_to: https://www.ncbi.nlm.nih.gov/biosample
     publication: https://doi.org/10.1101/2020.08.05.20168930
diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml
index cd8890d..8bc08de 100644
--- a/example/maximum_metadata_example.yaml
+++ b/example/maximum_metadata_example.yaml
@@ -45,7 +45,7 @@ submitter:
     submitter_address: John Doe's address
     originating_lab: John Doe kitchen
     lab_address: John Doe's address
-    provider_sample_id: XXX1
+    provider: XXX1
     submitter_sample_id: XXX2
     publication: PMID00001113
     submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001]
diff --git a/example/uthsc_example.yaml b/example/uthsc_example.yaml
index 2384114..661cf60 100644
--- a/example/uthsc_example.yaml
+++ b/example/uthsc_example.yaml
@@ -33,7 +33,7 @@ submitter:
     submitter_name: [Mariah Taylor]
     submitter_address: UTHSC, Memphis, Tennessee 38163, USA
     originating_lab: Regional Biocontainment Laboratory
-    provider_sample_id: XXX1
+    provider: XXX1
     submitter_sample_id: XXX2
     publication: PMID00001113
     submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001]
diff --git a/scripts/uthsc_samples/template.yaml b/scripts/uthsc_samples/template.yaml
index dab8634..9f5efd2 100644
--- a/scripts/uthsc_samples/template.yaml
+++ b/scripts/uthsc_samples/template.yaml
@@ -31,6 +31,5 @@ submitter:
     submitter_name: [Mariah Taylor, Colleen B. Jonsson, Pjotr Prins]
     submitter_address: UTHSC, Memphis, Tennessee 38163, USA
     originating_lab: Regional Biocontainment Laboratory, Memphis, TN
-    provider_sample_id: $sample_id
     submitter_sample_id: $sample_id
     submitter_orcid: [https://orcid.org/0000-0002-2640-7672,https://orcid.org/0000-0002-8021-9162]
diff --git a/test/data/input/TN_UT2.yaml b/test/data/input/TN_UT2.yaml
index f2f190b..55a7591 100644
--- a/test/data/input/TN_UT2.yaml
+++ b/test/data/input/TN_UT2.yaml
@@ -31,6 +31,5 @@ submitter:
     submitter_name: [Mariah Taylor, Colleen B. Jonsson, Pjotr Prins]
     submitter_address: UTHSC, Memphis, Tennessee 38163, USA
     originating_lab: Regional Biocontainment Laboratory, Memphis, TN
-    provider_sample_id: TN_UT2
     submitter_sample_id: TN_UT2
     submitter_orcid: [https://orcid.org/0000-0002-2640-7672,https://orcid.org/0000-0002-8021-9162]