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Merge pull request #228 from hubmapconsortium/shirey/bulk-registration-specs
Docs/specs for bulk sample/donor registration
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‎bulk-registration/donors-tsv.md‎

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## Donor Bulk Registration
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Donors can be bulk registered by choosing the Bulk Registration -> Donors menu pick in the [Ingest UI](https://ingest.hubmapconsortium.org)
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`insert screen shot showing menu`
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To register multiple donors at once you'll be asked to upload a tsv file with one row of data per donor to be registered. The tsv file has the following columns:
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| Column<br>Name | Required | Neo4j/WS<br>attrib | Description | Validation Rules |
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|-------------|----------|----------|-------------|------------------|
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| lab_id | no | donor.lab_donor_id | An id used by the lab for this donor. This id can be used when searching for the donor in the Ingest UI | Can be blank or an alpha numeric string less than 1024 characters |
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| lab_name | yes | donor.label | A de-identified name used by the lab. This name can be usd when searching for the donor in the Ingest UI | Must be a valid alpha-numeric string greater that 1 and less than 1024 characters |
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| selection_protocol | yes | donor.protocol_url | The doi or doi url to the Protocols IO protocol describing the criteria used when selecting this donor, e.g. 10.17504/protocols.io.bjuxknxn or https://dx.doi.org/10.17504/protocols.io.bjuxknxn | A string that matches either of the patterns<br> - `https://dx.doi.org/##.####/protocols.io.*` <br> - `##.####/protocols.io.*` <br> where # is a numeric character and * matches any characters |
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| description | no | donor.description | A description of this donor | The field can be empty or contain an alphanumeric string less than 10,000 characters |
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‎bulk-registration/example-donor-registrations.tsv‎

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lab_id lab_name selection_protocol description
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test_dn_01 Test Donor 1 ttps://dx.doi.org/10.17504/protocols.io.bjuxknxn Donor 1, Male aged 87
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test_dn_2 Donor 2 ttps://dx.doi.org/10.17504/protocols.io.dkasfkkaadf Liver donor, white female, 65 years old
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test donor 3 Donor 3 10.17504/protocols.io.adskfadfadf surgical donor, skin biopsy
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test donor 4 10.17504/protocols.io.ajdsjafjsdif
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test donor 5 test donor 4 10.17504/protocols.io.kkdjdiudi
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test donor 6 fail invalid lab_name 10.17504/protocols.io.zsdfasdfadf
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test donor 7 fail invalid protocol 10.A7504/protocols.io.adskfadfadf If this were a real description you'd be finding out some relevant information now

‎bulk-registration/example-sample-registrations.tsv‎

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source_id lab_id sample_type organ_type sample_protocol description rui_location
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bfbcdea6a2b709fd0d3aa71b5a47d924 test_smpl_01 organ br https://dx.doi.org/10.17504/protocols.io.bjuxknxn random sample commet
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f083597a5ebb0fae68c17b28bd5b3bc7 test_smpl_01 organ HT https://dx.doi.org/10.17504/protocols.io.bjuxknxn random sample commet
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HBM854.MBMF.586 test_sample_2 biopsy https://dx.doi.org/10.17504/protocols.io.dkasfkkaadf another random comment
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a0572d23c12e18e963f5404292b3d153 test sample 3 blood 10.17504/protocols.io.adskfadfadf
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ff5180d5994eef2526629a710017874f test sample 4 FRESH_TISSUE 10.17504/protocols.io.mjeisdfasdf
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2f9522d5462d7cc22a667417c6b80623 test sample 4a fresh_frozen_oct_block 10.17504/protocols.io.zujdiskshjy {"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084", "@type": "SpatialEntity", "label": "SpatialEntity for Male, Age 21, BMI 21.8", "creator": "Jeff Spraggins", "creator_first_name": "Jeff", "creator_last_name": "Spraggins", "creation_date": "2/12/2020 9:48:13 AM", "ccf_annotations": [], "x_dimension": 23, "y_dimension": 18, "z_dimension": 5, "dimension_units": "millimeter", "placement": {"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084_placement", "@type": "SpatialPlacement", "target": "http://purl.org/ccf/latest/ccf.owl#VHRightKidney", "placement_date": "2/12/2020 9:48:13 AM", "x_scaling": 1, "y_scaling": 1, "z_scaling": 1, "scaling_units": "ratio", "x_rotation": 0, "y_rotation": 0, "z_rotation": 247.9199981689453, "rotation_order": "XYZ", "rotation_units": "degree", "x_translation": -2.729999542236328, "y_translation": 33.220001220703125, "z_translation": -8.940000534057617, "translation_units": "millimeter"}}
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a22c4514e7e40a641d1ea5cdcdb63582 test sample 5 fail invalid organ type fresh_frozen_oct_block LV 10.17504/protocols.io.kkdjdiudi
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HBM265.FCRT.233 test sample 6 fail bad organ code organ bad_code 10.17504/protocols.io.zsdfasdfadf
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ba906793fcba084898ac24e850d5a964 test sample 7 fail bad protocol fresh_frozen_oct_block 10.A7504/protocols.io.adskfadfadf If this were a real description you'd be finding out some relevant information now
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ba5af685d3b266183ec0a903beb0d8dc test-sample-8-missing organ code organ 10.17504/protocols.io.adsdududys
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HBM446.VBGG.933 test-sample-9-missing sample_type 10.17504/protocols.io.dsfsdadf
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75870f9e402e3ac841f1ec78c290bbc9 test-sample-10-bad sample_type zzyx 10.17504/protocols.io.ajdsjafjsdif
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HBX222.1234.938 test-sample-11-misformatted id gdna 10.17504/protocols.io.idsafasdfad
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test-sample-12 fail missing id 10.17504/protocols.io.hfiwkwsdad
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ffd96a39274136284f5x66c7730a4d98 test-sample-13-misformatted id gdna 10.17504/protocols.io.owjwsodffs
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6b955ebeafe9c351831bc36aa086575f test-sample-14 fail incorrect source type gdna 10.17504/protocols.io.siaskasfadsf
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75f837c40c1248e9d53cecf049dc88a6 test-sample-15 fail incorrect source type2 organ RK 10.17504/protocols.io.fiadsfiasdfadf
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fail test_sample_16 missing protocol biopsy
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1222af1638d9bc176f393710cc8b2ebf fail test sample-16 invalid rui json fresh_frozen_oct_block 10.17504/protocols.io.ifjoijrlksfsdf { "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084", "@type": "SpatialEntity", "label": "SpatialEntity for Male, Age 21, BMI 21.8", "creator": "Jeff Spraggins", "creator_first_name": "Jeff", "creator_last_name": "Spraggins", "creation_date": "2/12/2020 9:48:13 AM", "ccf_annotations": [], "x_dimension": 23, "y_dimension": 18, "z_dimension": 5, "dimension_units": "millimeter", "placement": {"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084_placement", "@type": "SpatialPlacement", "target": "http://purl.org/ccf/latest/ccf.owl#VHRightKidney", "placement_date": "2/12/2020 9:48:13 AM", "x_scaling": 1, "y_scaling": 1, "z_scaling": 1, "scaling_units": "ratio", "x_rotation": 0, "y_rotation": 0, "z_rotation": 247.9199981689453, "rotation_order": "XYZ", "rotation_units": "degree", "x_translation": -2.729999542236328, "y_translation": 33.220001220703125, "z_translation": -8.940000534057617, "translation_units": "millimeter"}}"
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0cf6c31efb7463eb036d474369dfec11 fail test sample-17 organ with RUI info organ LK 10.17504/protocols.io.yeuiwwerwe {"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084", "@type": "SpatialEntity", "label": "SpatialEntity for Male, Age 21, BMI 21.8", "creator": "Jeff Spraggins", "creator_first_name": "Jeff", "creator_last_name": "Spraggins", "creation_date": "2/12/2020 9:48:13 AM", "ccf_annotations": [], "x_dimension": 23, "y_dimension": 18, "z_dimension": 5, "dimension_units": "millimeter", "placement": {"@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld", "@id": "http://purl.org/ccf/0.5/c62cd431-dd48-4c1b-9c7b-ca4a683fe084_placement", "@type": "SpatialPlacement", "target": "http://purl.org/ccf/latest/ccf.owl#VHRightKidney", "placement_date": "2/12/2020 9:48:13 AM", "x_scaling": 1, "y_scaling": 1, "z_scaling": 1, "scaling_units": "ratio", "x_rotation": 0, "y_rotation": 0, "z_rotation": 247.9199981689453, "rotation_order": "XYZ", "rotation_units": "degree", "x_translation": -2.729999542236328, "y_translation": 33.220001220703125, "z_translation": -8.940000534057617, "translation_units": "millimeter"}}

‎bulk-registration/samples-tsv.md‎

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## Sample Donor Registration
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(Tissue) Samples can be bulk registered by choosing the Bulk Registration -> Samples menu pick in the [Ingest UI](https://ingest.hubmapconsortium.org)
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`insert screen shot showing menu`
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To register multiple samples at once you'll be asked to upload a tsv file with one row of data per donor to be registered. The tsv file has the following columns:
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| Column<br>Name | Required | entity-api<br>attrib | Description | Validation Rules |
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|-------------|----------|----------|-------------|------------------|
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| source_id | yes | sample.direct_ancestor_uuid | The id of the source/parent of the new sample, can be a UUID, HuBMAP ID or HuBMAP Sample ID per [this](https://portal.hubmapconsortium.org/docs/apis) | - This is required and should fit the format of a hubmap uuid, hubmap id, or hubmap submission id<br> - should be checked against the uuid-api for existance<br> - if sample_type == organ it must point to a donor<br> - if sample_type != organ it must point to a sample<br> -If rui_location is not blank cannot be the id of a donor |
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| lab_id | yes | sample.lab_tissue_sample_id |An id used by the lab for this sample. This id can be used when searching for the donor in the Ingest UI | Must be an alpha numeric string less than 1024 characters |
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| sample_type | yes | specimen.specimen_type | The code specifying the type of sample | -Must be a code listed in the [tissue sample types file](https://github.com/hubmapconsortium/search-api/blob/master/src/search-schema/data/definitions/enums/tissue_sample_types.yaml) via case insensitive compare<br> -If rui_location is not blank cannot be 'organ' |
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| organ_type | maybe | specimen.organ | The code specifying the type of organ that the sample is | -if sample_type == organ must be a code from the [organ types file](https://github.com/hubmapconsortium/search-api/blob/master/src/search-schema/data/definitions/enums/organ_types.yaml) via case insensitive compare <br> -if sample_type != organ must be empty |
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| sample_protocol | yes | sample.protocol_url | The doi or doi url to the Protocols IO protocol describing how the sample was procured, e.g. 10.17504/protocols.io.bjuxknxn or https://dx.doi.org/10.17504/protocols.io.bjuxknxn | A string that matches either of the patterns<br> - `https://dx.doi.org/##.####/protocols.io.*` <br> - `##.####/protocols.io.*` <br> where # is a numeric character and * matches any characters |
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| description | no | sample.description | A description of this sample | The field can be empty or contain an alphanumeric string less than 10,000 characters |
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| rui_location | no | sample.rui_location | The json output from the RUI location registration interface. Must not include any line breaks. | - Can be blan <br> - If not blank must be a valid json string |

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