nci-cidc-schemas 0.27.22__py2.py3-none-any.whl → 0.27.25__py2.py3-none-any.whl

cidc_schemas/schemas/templates/assays/visium_template.json

@@ -0,0 +1,150 @@
+{    "title": "Visium assay template",
+    "description": "Visium submission.",
+    "prism_template_root_object_schema": "assays/visium_assay.json",
+    "prism_template_root_object_pointer": "/assays/visium/0",
+    "properties":
+    {
+        "worksheets":
+        {
+            "visium":
+            {
+                "preamble_rows":
+                {
+                    "protocol identifier":
+                    {
+                        "merge_pointer": "3/protocol_identifier",
+                        "type_ref": "clinical_trial.json#properties/protocol_identifier"
+                    },
+                    "assay creator":
+                    {
+                        "merge_pointer": "0/assay_creator",
+                        "type_ref": "assays/visium_assay.json#properties/assay_creator"
+                    },
+                    "batch id": {
+                        "merge_pointer": "0/batch_id",
+                        "type_ref": "assays/visium_assay.json#properties/batch_id"
+                    },
+                    "azimuth reference": {
+                        "merge_pointer": "0/azimuth_reference",
+                        "type_ref": "assays/components/scrnaseq_preamble.json#properties/azimuth_reference",
+                        "allow_empty": true
+                    },
+                    "tabula sapiens reference": {
+                        "merge_pointer": "0/tabula_sapiens_reference",
+                        "type_ref": "assays/components/scrnaseq_preamble.json#properties/tabula_sapiens_reference",
+                        "allow_empty": true
+                    },
+                    "spatial gene expression platform": {
+                        "merge_pointer": "0/spatial_gene_expression_platform",
+                        "type_ref": "assays/components/visium_preamble.json#properties/spatial_gene_expression_platform",
+                        "allow_empty": true
+                    },
+                    "human transcriptome probe set version": {
+                        "merge_pointer": "0/human_transcriptome_probe_set_version",
+                        "type_ref": "assays/components/visium_preamble.json#properties/human_transcriptome_probe_set_version",
+                        "allow_empty": true
+                    },
+                    "sample metadata csv": {
+                        "merge_pointer": "0/samples_metadata_csv",
+                        "gcs_uri_format": "{protocol identifier}/visium/{batch id}/samples_metadata.csv",
+                        "is_artifact": 1,
+                        "type_ref": "assays/components/local_file.json#properties/file_path"
+                    }
+                },
+                "prism_data_object_pointer": "/records/-",
+                "data_columns":
+                {
+                    "Samples":
+                    {
+                        "Cimac ID":
+                        {
+                            "merge_pointer": "0/cimac_id",
+                            "type_ref": "sample.json#properties/cimac_id"
+                        },
+                        "Lane": {
+                            "merge_pointer": "0/details/lane",
+                            "type": "integer"
+                        },
+                        "Read1 fastq gz": {
+                            "merge_pointer": "0/details/read_1_fastq_gz",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/visium/{batch id}/{cimac id}/fastq/S1_L00{lane}_R1_001.fastq.gz",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        },
+                        "Read2 fastq gz": {
+                            "merge_pointer": "0/details/read_2_fastq_gz",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/visium/{batch id}/{cimac id}/fastq/S1_L00{lane}_R2_001.fastq.gz",
+                            "type_ref": "assays/components/local_file.json#properties/file_path"
+                        },
+                        "Loupe alignment file": {
+                            "merge_pointer": "0/details/loupe_alignment_file",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/visium/{batch id}/{cimac id}/loupe_alignment_file.json",
+                            "type_ref": "assays/components/local_file.json#properties/file_path",
+                            "allow_empty": true
+                        },
+                        "Slide serial code": {
+                            "merge_pointer": "0/details/slide_serial_code",
+                            "type": "string",
+                            "allow_empty": true
+                        },
+                        "Slide capture area": {
+                            "merge_pointer": "0/details/slide_capture_area",
+                            "type": "string",
+                            "allow_empty": true
+                        },
+                        "library yield ng": {
+                            "merge_pointer": "0/details/library_yield_ng",
+                            "type_ref": "assays/components/scrnaseq_input.json#properties/library_yield_ng",
+                            "allow_empty": true
+                        },
+                        "dv200": {
+                            "merge_pointer": "0/details/dv200",
+                            "type_ref": "assays/components/visium_input.json#properties/dv200"
+                        },
+                        "brightfield image": {
+                            "merge_pointer": "0/details/brightfield_image",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/visium/{batch id}/{cimac id}/brightfield.tiff",
+                            "type_ref": "assays/components/local_file.json#properties/file_path",
+                            "allow_empty": true
+                        },
+                        "dark image": {
+                            "merge_pointer": "0/details/dark_image",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/visium/{batch id}/{cimac id}/dark_image.tiff",
+                            "type_ref": "assays/components/local_file.json#properties/file_path",
+                            "allow_empty": true
+                        },
+                        "colorized image": {
+                            "merge_pointer": "0/details/colorized_image",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/visium/{batch id}/{cimac id}/colorized.tiff",
+                            "type_ref": "assays/components/local_file.json#properties/file_path",
+                            "allow_empty": true
+                        },
+                        "cytassist image": {
+                            "merge_pointer": "0/details/cytassist_image",
+                            "is_artifact": 1,
+                            "gcs_uri_format": "{protocol identifier}/visium/{batch id}/{cimac id}/cytassist.tiff",
+                            "type_ref": "assays/components/local_file.json#properties/file_path",
+                            "allow_empty": true
+                        },
+                        "dapi index": {
+                            "merge_pointer": "0/details/dapi_index",
+                            "type": "integer",
+                            "allow_empty": true
+                        },
+                        "comments": {
+                            "merge_pointer": "0/details/comments",
+                            "type": "string",
+                            "allow_empty": true
+                        }
+
+                    }
+                }
+            }
+        }
+    }
+}

{nci_cidc_schemas-0.27.22.dist-info → nci_cidc_schemas-0.27.25.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_schemas
-Version: 0.27.22
+Version: 0.27.25
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI

{nci_cidc_schemas-0.27.22.dist-info → nci_cidc_schemas-0.27.25.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cidc_schemas/__init__.py,sha256=COii5dEs7h55Xtjv-Tn6FFlgtxB8TrzZLQlVnQXVgwo,136
+cidc_schemas/__init__.py,sha256=E3VX0BIuWNI80Finvf9Ido79vmjwxN7dTo9aTJSsGD8,136
 cidc_schemas/cli.py,sha256=gWiktRlraNH8Q0zNUae9dohKjPwBmcY0BJwdcQ_fIic,4099
 cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
 cidc_schemas/json_validation.py,sha256=spmPsqinib7Ns5GvWOKKa1rc7IrN_s2bqifpTKdaLVU,23288
@@ -11,7 +11,7 @@ cidc_schemas/util.py,sha256=P-889E64I3i9iroxw5qORguzr09Ac7tsgzsoGeGsfwM,4716
 cidc_schemas/metaschema/strict_meta_schema.json,sha256=3FiS0r2dAXgfPsruJwZYbQoQnHhC_yl-3mclX8gfiQU,6428
 cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2,sha256=6no9sFqwzb1T61RZGD-owDt2K5R8G_fPTzflV4fOroo,2832
 cidc_schemas/prism/__init__.py,sha256=J5Tj0X7Di6cyxAjaduOUp2aVyvl8UI67bgxEkgttvcU,530
-cidc_schemas/prism/constants.py,sha256=l_bF54Vn50XbuXi3yKZkKrURt-dwbfOnL_5dGlpuoF8,2397
+cidc_schemas/prism/constants.py,sha256=PevSn-geY8VTGMx1iXdUJ2LgoeuhEdKfIpZYk_LbzwI,4088
 cidc_schemas/prism/core.py,sha256=tXDCCHurvcrxfU11meH3NRAVo9niklup0dpLRoIXwPk,20242
 cidc_schemas/prism/extra_metadata.py,sha256=S9w5EGAT0xwaWMrpYluF7Y1ONsI4wFtxFD8ib6Va_fU,8567
 cidc_schemas/prism/merger.py,sha256=36CKBPVoWecHuvGp3oT9a2d4jWIkvKuS_UofKTEpMYs,13065
@@ -40,22 +40,30 @@ cidc_schemas/schemas/artifacts/artifact_fcs.json,sha256=8Pa9sq1oqdK5_bVoc0s6smwh
 cidc_schemas/schemas/artifacts/artifact_file.json,sha256=DLY3Gipxpw9N20OJE2t_upAo5G6w4XOr3aeyN32ZNNY,1668
 cidc_schemas/schemas/artifacts/artifact_gz.json,sha256=mtUUc2n3npxhp_JhM-W-6wqVSvMT3nvIv9HJP_R37wg,1649
 cidc_schemas/schemas/artifacts/artifact_h5ad.json,sha256=JaDerbzmR0ABxqaNyWZlHy4rEK3L62e0W-O3Y4xvf6E,1657
+cidc_schemas/schemas/artifacts/artifact_html.json,sha256=qzJJ5W4X1SaLvU-uDdhsmLNbCRRzfSlEHpYkjSLpEyk,1657
 cidc_schemas/schemas/artifacts/artifact_image.json,sha256=y8uY4DqfzeM8cHVkI-aH5BMrbJ3QbbBinJOqudlrlPI,2015
 cidc_schemas/schemas/artifacts/artifact_jpg.json,sha256=Z4-FxEdoiQ7MzzC7uEqkakjaHjoph5rULrBnlQhls5M,1653
 cidc_schemas/schemas/artifacts/artifact_json.json,sha256=dE2ch8Ycs6ORJ3bdDD8Yyp-ixI3OjFHuabZ5pbQVeSU,1657
 cidc_schemas/schemas/artifacts/artifact_junction.json,sha256=KRRlU5Lanmho5u9gOz1dBbOhCtAiT7_JnDFuB0f7wEQ,1775
 cidc_schemas/schemas/artifacts/artifact_log.json,sha256=TvHQLsxAfnB9WbnHt-otYObKn7J0IuylxWYQOHHDzGk,1755
 cidc_schemas/schemas/artifacts/artifact_maf.json,sha256=MyJOs8A0aHrl8i9l5Q1m4ADm8dqcTyJ_YtUJDS48Bjk,1653
+cidc_schemas/schemas/artifacts/artifact_mtx.json,sha256=S3WRaHXTYfzIK8Xo_C1H48Gflt3MFRL4-EYt7f86oRY,1653
 cidc_schemas/schemas/artifacts/artifact_narrowPeak.json,sha256=EOGIAmpo46qZdSzZj3Gi7WKLS81OH1xUTJzeu7_I75c,1681
 cidc_schemas/schemas/artifacts/artifact_npx.json,sha256=I0o8C9ilOrbLBmLpTOQ1ARFyQHyaSd321mPjuJMGUUw,2134
 cidc_schemas/schemas/artifacts/artifact_ome_tiff.json,sha256=wSIQPf2mi00BwikFlz8qL3wmVvtYWhuOxrHLc3ngzS0,1673
+cidc_schemas/schemas/artifacts/artifact_out.json,sha256=hgFfI9up7dYoQ33XpyILZgffL2H1dp-vi-F-Nx--SqU,1653
 cidc_schemas/schemas/artifacts/artifact_pdf.json,sha256=t-RR4gftGD-wjB7t40lb1TbnKLosPQCDyP-SL1V5dWc,1674
 cidc_schemas/schemas/artifacts/artifact_png.json,sha256=cGzHZQg3qbungIkxvLh6TY8iqKjtutBU2XmBnRyiijQ,1653
 cidc_schemas/schemas/artifacts/artifact_rcc.json,sha256=IyqqsxPdFZjRoFuBpnkBKBLbc-SoWvrQoqFWeNLU_as,1704
 cidc_schemas/schemas/artifacts/artifact_rdata.json,sha256=rnaukVGTKrqJAW9aLEyITTTOZnMB3mbZ1T76BbhokpA,1661
+cidc_schemas/schemas/artifacts/artifact_rds.json,sha256=3FB5jp24uZQ_q8v7L1vGHakujp7oMKInVt6ZH6bD4xE,1653
+cidc_schemas/schemas/artifacts/artifact_stats.json,sha256=VO6AIfYwyUmPzLezdBzHEwYDOlDpQ_MYGz58pirG7lI,1661
+cidc_schemas/schemas/artifacts/artifact_tab.json,sha256=3Q0YhbO0AvLoduqd6BtrnK83hrbjcjqIerza6-QvlBY,1653
 cidc_schemas/schemas/artifacts/artifact_tbi.json,sha256=FXZyiAeU6ot-gR-ML8iDi7zcFa0UwkO8Ym-ip4yAEm4,1661
 cidc_schemas/schemas/artifacts/artifact_text.json,sha256=8srLHRfM3g9EyxgNgdANZy8C13xcnkby8amM01dDFhc,1657
+cidc_schemas/schemas/artifacts/artifact_tiff.json,sha256=-jToUDt06TOUFOAVQ_lfdmvITgPDFioZAzCvFgg8_-Q,1657
 cidc_schemas/schemas/artifacts/artifact_tsv.json,sha256=ITRJhHOWTeSmutQOrFZ4hzyWQ7XWUev7rT-LMhfUp6E,1663
+cidc_schemas/schemas/artifacts/artifact_txt.json,sha256=DesonWRCKx56yxrXAM4GTKoz2VR4xc4Dx3Q4yPvmOLQ,1653
 cidc_schemas/schemas/artifacts/artifact_vcf.json,sha256=qNQwt7ReS_hAK3TUNUqbG_IARI83tW_94oQeTXPAF7Y,1653
 cidc_schemas/schemas/artifacts/artifact_vcf_gz.json,sha256=R37aMZQCorDCqEJQBVB6fIeMW1fLAuocdHZ2G4o0QzU,1675
 cidc_schemas/schemas/artifacts/artifact_xlsx.json,sha256=PmQ3NY_8ywS3iFa4vvLzcXbewdY41jxa6isnPrWfWUQ,1659
@@ -77,17 +85,20 @@ cidc_schemas/schemas/assays/nanostring_assay.json,sha256=XAL6n80sxaAwUcNrx-pgA_Y
 cidc_schemas/schemas/assays/olink_assay.json,sha256=kQrUPjDKLKYyWpXoauiNDa0FANxPH_1bOfHeQEY-qAQ,5193
 cidc_schemas/schemas/assays/rna_assay-v0.json,sha256=skNGXbVVDY-6RpPosTHweQYtLntvo0bAiXcOxVSeh1s,3043
 cidc_schemas/schemas/assays/rna_assay.json,sha256=Gh47rRWYJSUIoLK3vvOb8_kFXhlISScrtA7nWasoBZI,409
+cidc_schemas/schemas/assays/scrnaseq_analysis.json,sha256=SasSpvclv1lllqLbym1zyyoTJJJxvvJ7CL-rDmfhlqI,4495
 cidc_schemas/schemas/assays/scrnaseq_assay.json,sha256=zZSt1AsP5l8DkObi5tsD3oSh1s1aRwr5xUmTRYOLbeQ,2657
 cidc_schemas/schemas/assays/tcr_analysis.json,sha256=Sj8a4A3NpKl4PVu69_3Q0pAsRvIlgT7ltbIFHB7bHZQ,2380
 cidc_schemas/schemas/assays/tcr_assay.json,sha256=lQm_f-3UUT_nqctc4ARjYNPKjpDfmfGzUkgRJf4m36k,4691
+cidc_schemas/schemas/assays/visium_analysis.json,sha256=5WDhZy26OuAB3z8OlT19k_vMDlopj9t6S6dcEyhZ50Q,2032
+cidc_schemas/schemas/assays/visium_assay.json,sha256=iSVYjVLougLaT9YUwpPD3j2NviTRw9F6b-YshLzBRUg,2396
 cidc_schemas/schemas/assays/wes_analysis.json,sha256=4RAnkqtCj5-txc189KmwNHJaxjrtIUIbpihFrAJFeIw,2771
 cidc_schemas/schemas/assays/wes_assay.json,sha256=vk9iK8FOiT3wU_RF3PXDV6IJqvNRbteebYGF8EfalfY,3776
 cidc_schemas/schemas/assays/wes_core.json,sha256=dwAe2Hi-K5G0rm_icSbFUEIhDNG7HkESYKEGhV9L7wM,12858
 cidc_schemas/schemas/assays/wes_tumor_only_analysis.json,sha256=dU3oaeBbPnEv2Xjym7ikWr5ywwolnVbWDu1Weq2m8Wg,2018
 cidc_schemas/schemas/assays/components/antibody.json,sha256=vfLxXkXIcaJ1BXeUjCaJehrRCdVrBW3gxibwrD7zzd4,960
 cidc_schemas/schemas/assays/components/assay_core.json,sha256=QGuLiArVb7lEF2t1Ml4Qt7g4SXY58WuGBPFVgvOLI5w,485
-cidc_schemas/schemas/assays/components/available_assays.json,sha256=XEzfK_ocbR17loALDqLPNtkG6aLcfYQLxqbl_AFvoW8,4034
-cidc_schemas/schemas/assays/components/available_ngs_analyses.json,sha256=dmC10wI7roGVwbf5T8DxIW1geIjks-Sl-GHJkJXc6eQ,1163
+cidc_schemas/schemas/assays/components/available_assays.json,sha256=5H637v-NAAO9_RRcLyE7LlTmTfdvyQen4lstAWZTcWs,4281
+cidc_schemas/schemas/assays/components/available_ngs_analyses.json,sha256=Y_CL6A5hg4w57En9q1TsLH5ZBdlFeEpE6ggb3-dIIDk,1732
 cidc_schemas/schemas/assays/components/composite_image.json,sha256=k9EaBG3y9j-lvg3nQNZbfVpo9fK_gUz1-9iTwjlTDfE,733
 cidc_schemas/schemas/assays/components/controls.json,sha256=_Wxz7W2msTGJ2Ei4XZg0Qy1t8A5_rLSHNvdPurC073E,458
 cidc_schemas/schemas/assays/components/enrichment_core.json,sha256=zC5G7q-QyNrdynCOoPCCSfOuSKq8TiDH-Pl6gITNfVQ,813
@@ -108,6 +119,8 @@ cidc_schemas/schemas/assays/components/reads_core.json,sha256=p5RWN2TEGefenpz6pZ
 cidc_schemas/schemas/assays/components/reads_with_index.json,sha256=pg3wMQYMawCb1ZxJwiH_yCH3TAYu29EIZnB18AevzmM,1091
 cidc_schemas/schemas/assays/components/scrnaseq_input.json,sha256=fIvV_xJPXDCoYajbsu21ISdhLaQVYjbPg_3nR_Jo7cE,1003
 cidc_schemas/schemas/assays/components/scrnaseq_preamble.json,sha256=himJMT53FS2XdDZ81u_eW2tYVS212AqZuxdGKWgSwXU,2251
+cidc_schemas/schemas/assays/components/visium_input.json,sha256=ESJRVNC1MJD4YgM5DXbHufT6Evz7n6BNrsFG9rSvQtU,1710
+cidc_schemas/schemas/assays/components/visium_preamble.json,sha256=h66kdSdFt5J1wr81JcbBsHQTqriWKIjwjA-SigyN8XE,843
 cidc_schemas/schemas/assays/components/imaging/mif_entry.json,sha256=0jYCSMD3j5r_u7Z-TJRV2ZLt7C4r7KuTtH8lMB6O9rU,546
 cidc_schemas/schemas/assays/components/imaging/mif_export.json,sha256=CVGCpIVcHkTnIQvBibU4HkdYcm2lYzGYu3pXGm4bUa8,1728
 cidc_schemas/schemas/assays/components/imaging/mif_input.json,sha256=Hf1PKkk6pHRLcGGJrVmkhC6SApOA5pD6XJFRscM9ee0,1000
@@ -128,7 +141,9 @@ cidc_schemas/schemas/assays/components/ngs/rna/trust4.json,sha256=o-fxkTL-1Tho1k
 cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json,sha256=7vBdwVD6HEd9Pj8AkEoa34fQjIynztsNaKvfn2KoFFc,5403
 cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json,sha256=d6qOGbYXXx1c8rb-saM4D_tMuK8n4ydbyW9_xaW6xhk,6381
 cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json,sha256=vMHXSQNZz8sFxwiBUnRXb5o08GxgbKZjMu8ZPjNn4TI,15944
+cidc_schemas/schemas/templates/analyses/scrnaseq_analysis_template.json,sha256=_eBhwRmw3g_Cd6ye9E2ZQkm9WntYF1iX5EmSIyJ63bA,12868
 cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json,sha256=ai5KUp6q5GGTxDybOHBaseOnvQCVqIRh4SurETz5Vx0,3054
+cidc_schemas/schemas/templates/analyses/visium_analysis_template.json,sha256=zF_VLfR-kLuXxsAUQpj_dDTNwkq_tlrh4spovD_OQ4I,4438
 cidc_schemas/schemas/templates/analyses/wes_analysis_template.json,sha256=kvnbC6nYrwqfGKfvHwZs1d4rePW_BOLzV6oRvrMkiD4,35297
 cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json,sha256=hhWA6mBPVBIM9QFg0C7CkimD9fcFXXtFSSkvo0lvnro,16264
 cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json,sha256=7WygawkxnhFu5xBAuIhSOBD8TwCqDgINjC-HIYeCf4Q,3928
@@ -150,6 +165,7 @@ cidc_schemas/schemas/templates/assays/rna_fastq_template.json,sha256=ZSKfzQ38Skp
 cidc_schemas/schemas/templates/assays/scrnaseq_template.json,sha256=H_xU32U-1S7HCqZanaSqWb6KJ97jMQIBjwO_zsxDsfg,4843
 cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json,sha256=Hb8ngxw6XHjIqtA9W1eLfO3ciH18VfRTKOQvipX14Dg,3269
 cidc_schemas/schemas/templates/assays/tcr_fastq_template.json,sha256=7Qq4ssI8ErDrHy5RIxjPcNiDf2IBHG42JcngDFKxqlE,3457
+cidc_schemas/schemas/templates/assays/visium_template.json,sha256=H_UhJBGxPyGWq4HSPsn4SpKMmb3xTC1e5DMz3XlXAu4,7898
 cidc_schemas/schemas/templates/assays/wes_bam_template.json,sha256=nxbb_lNPi-5cdAlwmSBvn7cS_8gMjROOz7wBWk6ev0Y,2724
 cidc_schemas/schemas/templates/assays/wes_fastq_template.json,sha256=vuwuIpqXyqpGxCunpjbHKaBQhfKFnr2R-wMkXDiJdKM,3143
 cidc_schemas/schemas/templates/manifests/h_and_e_template.json,sha256=8fbhWxKWhITds1KkbEdQxHHoeoKB2Tm40plzsxz3_FE,18009
@@ -162,9 +178,9 @@ cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=q2GmO
 cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json,sha256=lVJrGb28n-vyfjGBzhrzjn1lMKw1b4HXXmWtwA603v0,2797
 cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json,sha256=LpaoDXDS11NCa-Dv37N-tzEGomswQrx5fypkUcG7xJk,18956
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