create_croissant.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The croissant was created with reference to the [mlcroissant-recipes-introduction-notebook](https://github.com/mlcommons/croissant/blob/main/python/mlcroissant/recipes/introduction.ipynb).\n",
    "\n",
    "Install the following packages if necessary (`mlcroissant` requires `python` 3.10+)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# ! pip install mlcroissant charset-normalizer==3.1.0 gitpython"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Locate the path first. Here we use `FileObjects` only."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[FileObject(uuid=\"github-repository\"),\n",
       " FileObject(uuid=\"level-I.csv\"),\n",
       " FileObject(uuid=\"level-IIA.csv\"),\n",
       " FileObject(uuid=\"level-IIB.csv\"),\n",
       " FileObject(uuid=\"level-III.csv\"),\n",
       " FileObject(uuid=\"level-IV.csv\")]"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import mlcroissant as mlc\n",
    "\n",
    "# FileObjects and FileSets define the resources of the dataset.\n",
    "distribution = [\n",
    "    # Hi-TPH is hosted on a GitHub repository:\n",
    "    mlc.FileObject(\n",
    "        id=\"github-repository\",\n",
    "        name=\"github-repository\",\n",
    "        description=\"Hi-TPH repository on GitHub.\",\n",
    "        content_url=\"https://github.com/Jiadong001/Hi-TpH\",\n",
    "        encoding_format=\"git+https\",\n",
    "        sha256=\"main\",\n",
    "    ),\n",
    "    # Within that repository, level I-IV files are csv files with different kinds of columns:\n",
    "    mlc.FileObject(\n",
    "        id=\"level-I.csv\",                           # drop preffix in content_url\n",
    "        name=\"level-I.csv\",\n",
    "        description=\"Hi-TPH level I csv file is hosted on the GitHub repository.\",\n",
    "        content_url=\"data/Hi-TpH-level-I.csv\",      # path = contained_in + content_url\n",
    "        contained_in=[\"github-repository\"],\n",
    "        encoding_format=\"text/csv\",\n",
    "    ),\n",
    "    mlc.FileObject(\n",
    "        id=\"level-IIA.csv\",\n",
    "        name=\"level-IIA.csv\",\n",
    "        description=\"Hi-TPH level II A csv file is hosted on the GitHub repository.\",\n",
    "        content_url=\"data/Hi-TpH-level-IIA.csv\",\n",
    "        contained_in=[\"github-repository\"],\n",
    "        encoding_format=\"text/csv\",\n",
    "    ),\n",
    "    mlc.FileObject(\n",
    "        id=\"level-IIB.csv\",\n",
    "        name=\"level-IIB.csv\",\n",
    "        description=\"Hi-TPH level II B csv file is hosted on the GitHub repository.\",\n",
    "        content_url=\"data/Hi-TpH-level-IIB.csv\",\n",
    "        contained_in=[\"github-repository\"],\n",
    "        encoding_format=\"text/csv\",\n",
    "    ),\n",
    "    mlc.FileObject(\n",
    "        id=\"level-III.csv\",\n",
    "        name=\"level-III.csv\",\n",
    "        description=\"Hi-TPH level III csv file is hosted on the GitHub repository.\",\n",
    "        content_url=\"data/Hi-TpH-level-III.csv\",\n",
    "        contained_in=[\"github-repository\"],\n",
    "        encoding_format=\"text/csv\",\n",
    "    ),\n",
    "    mlc.FileObject(\n",
    "        id=\"level-IV.csv\",\n",
    "        name=\"level-IV.csv\",\n",
    "        description=\"Hi-TPH level IV csv file is hosted on the GitHub repository.\",\n",
    "        content_url=\"data/Hi-TpH-level-IV.csv\",\n",
    "        contained_in=[\"github-repository\"],\n",
    "        encoding_format=\"text/csv\",\n",
    "    )\n",
    "]\n",
    "distribution"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`RecordSet`: Load records from one/many csv files."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "components2desc_dict = {\n",
    "    \"antigen.epitope\": \"Peptide sequence of the antigen epitope.\",\n",
    "\n",
    "    \"alpha.cdr3\": \"Complementarity Determining Region 3 (CDR3) amino acid sequence of TCR alpha chain.\",\n",
    "    \"alpha.v\": \"V gene segment of TCR alpha chain.\",\n",
    "    \"alpha.j\": \"J gene segment of TCR alpha chain.\",\n",
    "    \"alpha.vseq.reconstructed\": \"Reconstructed variable domain sequence of TCR alpha chain using V/J gene annotations and CDR3 sequences.\",\n",
    "\n",
    "    \"beta.cdr3\": \"Complementarity Determining Region 3 (CDR3) amino acid sequence of TCR beta chain.\",\n",
    "    \"beta.v\": \"V gene segment of TCR beta chain.\",\n",
    "    \"beta.j\": \"J gene segment of TCR beta chain.\",\n",
    "    \"beta.vseq.reconstructed\": \"Reconstructed variable domain sequence of TCR beta chain using V/(D/)J gene annotations and CDR3 sequences.\",\n",
    "\n",
    "    \"hla.allele\": \"HLA allele name.\",\n",
    "    \"hla.full.seq\": \"Full HLA protein sequence.\",\n",
    "    \"hla.clip.seq\": \"Amino acid sequence of HLA alpha-1 and alpha-2 domains, which is clipped from the full HLA protein sequence.\",\n",
    "    \"hla.short.seq\": \"HLA pseudo sequence, extracted from HLA alpha-1 and alpha-2 domains.\"\n",
    "}\n",
    "\n",
    "level2components_dict = {\n",
    "    \"level-I\": [\"antigen.epitope\", \"beta.cdr3\"],\n",
    "\n",
    "    \"level-IIA\": [\"antigen.epitope\", \"hla.allele\", \"beta.cdr3\",\n",
    "                \"hla.full.seq\", \"hla.clip.seq\", \"hla.short.seq\"],\n",
    "\n",
    "    \"level-IIB\": [\"antigen.epitope\", \"alpha.cdr3\", \"beta.cdr3\"],\n",
    "\n",
    "    \"level-III\": [\"antigen.epitope\", \"hla.allele\", \"alpha.cdr3\", \"beta.cdr3\",\n",
    "                \"hla.full.seq\", \"hla.clip.seq\", \"hla.short.seq\"],\n",
    "\n",
    "    \"level-IV\": [\"antigen.epitope\", \"hla.allele\", \n",
    "                \"alpha.v\", \"alpha.j\",\"alpha.cdr3\", \n",
    "                \"beta.v\", \"beta.j\", \"beta.cdr3\",\n",
    "                \"alpha.vseq.reconstructed\", \"beta.vseq.reconstructed\",\n",
    "                \"hla.full.seq\", \"hla.clip.seq\", \"hla.short.seq\"],\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[Field(uuid=\"level-I/antigen.epitope\"), Field(uuid=\"level-I/beta.cdr3\")]\n",
      "[Field(uuid=\"level-IIA/antigen.epitope\"), Field(uuid=\"level-IIA/hla.allele\"), Field(uuid=\"level-IIA/beta.cdr3\"), Field(uuid=\"level-IIA/hla.full.seq\"), Field(uuid=\"level-IIA/hla.clip.seq\"), Field(uuid=\"level-IIA/hla.short.seq\")]\n",
      "[Field(uuid=\"level-IIB/antigen.epitope\"), Field(uuid=\"level-IIB/alpha.cdr3\"), Field(uuid=\"level-IIB/beta.cdr3\")]\n",
      "[Field(uuid=\"level-III/antigen.epitope\"), Field(uuid=\"level-III/hla.allele\"), Field(uuid=\"level-III/alpha.cdr3\"), Field(uuid=\"level-III/beta.cdr3\"), Field(uuid=\"level-III/hla.full.seq\"), Field(uuid=\"level-III/hla.clip.seq\"), Field(uuid=\"level-III/hla.short.seq\")]\n",
      "[Field(uuid=\"level-IV/antigen.epitope\"), Field(uuid=\"level-IV/hla.allele\"), Field(uuid=\"level-IV/alpha.v\"), Field(uuid=\"level-IV/alpha.j\"), Field(uuid=\"level-IV/alpha.cdr3\"), Field(uuid=\"level-IV/beta.v\"), Field(uuid=\"level-IV/beta.j\"), Field(uuid=\"level-IV/beta.cdr3\"), Field(uuid=\"level-IV/alpha.vseq.reconstructed\"), Field(uuid=\"level-IV/beta.vseq.reconstructed\"), Field(uuid=\"level-IV/hla.full.seq\"), Field(uuid=\"level-IV/hla.clip.seq\"), Field(uuid=\"level-IV/hla.short.seq\")]\n"
     ]
    }
   ],
   "source": [
    "record_sets = []\n",
    "for level, components in level2components_dict.items():\n",
    "    record_set = mlc.RecordSet(\n",
    "            id=level,\n",
    "            name=level,\n",
    "            # Each record has one or many fields...\n",
    "            fields=[\n",
    "                # Fields can be extracted from the FileObjects/FileSets.\n",
    "                mlc.Field(\n",
    "                    id=f\"{level}/{component}\",              # e.g. \"level-I/antigen.epitope\"\n",
    "                    name=component,\n",
    "                    description=components2desc_dict[component],\n",
    "                    data_types=mlc.DataType.TEXT,\n",
    "                    source=mlc.Source(\n",
    "                        file_object=f\"{level}.csv\",\n",
    "                        # Extract the field from the column of a FileObject/FileSet:\n",
    "                        extract=mlc.Extract(column=component),      \n",
    "                    ),\n",
    "                ) \n",
    "                for component in components\n",
    "            ],\n",
    "        )\n",
    "    print(record_set.fields)\n",
    "    record_sets.append(record_set)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "create metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "metadata = mlc.Metadata(\n",
    "    name=\"Hi-TPH\",\n",
    "    # Descriptions can contain plain text or markdown.\n",
    "    description=(\n",
    "        \"A Large-Scale Hierarchical Dataset for TCR-pHLA Binding Prediction.\"\n",
    "    ),\n",
    "    cite_as=None,                   # None: to be updated\n",
    "    license=\"https://creativecommons.org/licenses/by-nc/4.0/\",\n",
    "    version=None,\n",
    "    date_published=None,\n",
    "    url=\"https://github.com/Jiadong001/Hi-TpH\",\n",
    "    distribution=distribution,\n",
    "    record_sets=record_sets,\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found the following 3 warning(s) during the validation:\n",
      "  -  [Metadata(Hi-TPH)] Property \"http://mlcommons.org/croissant/citeAs\" is recommended, but does not exist.\n",
      "  -  [Metadata(Hi-TPH)] Property \"https://schema.org/datePublished\" is recommended, but does not exist.\n",
      "  -  [Metadata(Hi-TPH)] Property \"https://schema.org/version\" is recommended, but does not exist.\n"
     ]
    }
   ],
   "source": [
    "print(metadata.issues.report())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Save croissant (metadata)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"@context\": {\n",
      "    \"@language\": \"en\",\n",
      "    \"@vocab\": \"https://schema.org/\",\n",
      "    \"citeAs\": \"cr:citeAs\",\n",
      "    \"column\": \"cr:column\",\n",
      "    \"conformsTo\": \"dct:conformsTo\",\n",
      "    \"cr\": \"http://mlcommons.org/croissant/\",\n",
      "    \"rai\": \"http://mlcommons.org/croissant/RAI/\",\n",
      "    \"data\": {\n",
      "      \"@id\": \"cr:data\",\n",
      "      \"@type\": \"@json\"\n",
      "    },\n",
      "    \"dataType\": {\n",
      "      \"@id\": \"cr:dataType\",\n",
      "      \"@type\": \"@vocab\"\n",
      "    },\n",
      "    \"dct\": \"http://purl.org/dc/terms/\",\n",
      "    \"examples\": {\n",
      "      \"@id\": \"cr:examples\",\n",
      "      \"@type\": \"@json\"\n",
      "    },\n",
      "    \"extract\": \"cr:extract\",\n",
      "    \"field\": \"cr:field\",\n",
      "    \"fileProperty\": \"cr:fileProperty\",\n",
      "    \"fileObject\": \"cr:fileObject\",\n",
      "    \"fileSet\": \"cr:fileSet\",\n",
      "    \"format\": \"cr:format\",\n",
      "    \"includes\": \"cr:includes\",\n",
      "    \"isLiveDataset\": \"cr:isLiveDataset\",\n",
      "    \"jsonPath\": \"cr:jsonPath\",\n",
      "    \"key\": \"cr:key\",\n",
      "    \"md5\": \"cr:md5\",\n",
      "    \"parentField\": \"cr:parentField\",\n",
      "    \"path\": \"cr:path\",\n",
      "    \"recordSet\": \"cr:recordSet\",\n",
      "    \"references\": \"cr:references\",\n",
      "    \"regex\": \"cr:regex\",\n",
      "    \"repeated\": \"cr:repeated\",\n",
      "    \"replace\": \"cr:replace\",\n",
      "    \"sc\": \"https://schema.org/\",\n",
      "    \"separator\": \"cr:separator\",\n",
      "    \"source\": \"cr:source\",\n",
      "    \"subField\": \"cr:subField\",\n",
      "    \"transform\": \"cr:transform\"\n",
      "  },\n",
      "  \"@type\": \"sc:Dataset\",\n",
      "  \"name\": \"Hi-TPH\",\n",
      "  \"description\": \"A Large-Scale Hierarchical Dataset for TCR-pHLA Binding Prediction.\",\n",
      "  \"conformsTo\": \"http://mlcommons.org/croissant/1.0\",\n",
      "  \"license\": \"https://creativecommons.org/licenses/by-nc/4.0/\",\n",
      "  \"url\": \"https://github.com/Jiadong001/Hi-TpH\",\n",
      "  \"distribution\": [\n",
      "    {\n",
      "      \"@type\": \"cr:FileObject\",\n",
      "      \"@id\": \"github-repository\",\n",
      "      \"name\": \"github-repository\",\n",
      "      \"description\": \"Hi-TPH repository on GitHub.\",\n",
      "      \"contentUrl\": \"https://github.com/Jiadong001/Hi-TpH\",\n",
      "      \"encodingFormat\": \"git+https\",\n",
      "      \"sha256\": \"main\"\n",
      "    },\n",
      "    {\n",
      "      \"@type\": \"cr:FileObject\",\n",
      "      \"@id\": \"level-I.csv\",\n",
      "      \"name\": \"level-I.csv\",\n",
      "      \"description\": \"Hi-TPH level I csv file is hosted on the GitHub repository.\",\n",
      "      \"containedIn\": {\n",
      "        \"@id\": \"github-repository\"\n",
      "      },\n",
      "      \"contentUrl\": \"data/Hi-TpH-level-I.csv\",\n",
      "      \"encodingFormat\": \"text/csv\"\n",
      "    },\n",
      "    {\n",
      "      \"@type\": \"cr:FileObject\",\n",
      "      \"@id\": \"level-IIA.csv\",\n",
      "      \"name\": \"level-IIA.csv\",\n",
      "      \"description\": \"Hi-TPH level II A csv file is hosted on the GitHub repository.\",\n",
      "      \"containedIn\": {\n",
      "        \"@id\": \"github-repository\"\n",
      "      },\n",
      "      \"contentUrl\": \"data/Hi-TpH-level-IIA.csv\",\n",
      "      \"encodingFormat\": \"text/csv\"\n",
      "    },\n",
      "    {\n",
      "      \"@type\": \"cr:FileObject\",\n",
      "      \"@id\": \"level-IIB.csv\",\n",
      "      \"name\": \"level-IIB.csv\",\n",
      "      \"description\": \"Hi-TPH level II B csv file is hosted on the GitHub repository.\",\n",
      "      \"containedIn\": {\n",
      "        \"@id\": \"github-repository\"\n",
      "      },\n",
      "      \"contentUrl\": \"data/Hi-TpH-level-IIB.csv\",\n",
      "      \"encodingFormat\": \"text/csv\"\n",
      "    },\n",
      "    {\n",
      "      \"@type\": \"cr:FileObject\",\n",
      "      \"@id\": \"level-III.csv\",\n",
      "      \"name\": \"level-III.csv\",\n",
      "      \"description\": \"Hi-TPH level III csv file is hosted on the GitHub repository.\",\n",
      "      \"containedIn\": {\n",
      "        \"@id\": \"github-repository\"\n",
      "      },\n",
      "      \"contentUrl\": \"data/Hi-TpH-level-III.csv\",\n",
      "      \"encodingFormat\": \"text/csv\"\n",
      "    },\n",
      "    {\n",
      "      \"@type\": \"cr:FileObject\",\n",
      "      \"@id\": \"level-IV.csv\",\n",
      "      \"name\": \"level-IV.csv\",\n",
      "      \"description\": \"Hi-TPH level IV csv file is hosted on the GitHub repository.\",\n",
      "      \"containedIn\": {\n",
      "        \"@id\": \"github-repository\"\n",
      "      },\n",
      "      \"contentUrl\": \"data/Hi-TpH-level-IV.csv\",\n",
      "      \"encodingFormat\": \"text/csv\"\n",
      "    }\n",
      "  ],\n",
      "  \"recordSet\": [\n",
      "    {\n",
      "      \"@type\": \"cr:RecordSet\",\n",
      "      \"@id\": \"level-I\",\n",
      "      \"name\": \"level-I\",\n",
      "      \"field\": [\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-I/antigen.epitope\",\n",
      "          \"name\": \"antigen.epitope\",\n",
      "          \"description\": \"Peptide sequence of the antigen epitope.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-I.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"antigen.epitope\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-I/beta.cdr3\",\n",
      "          \"name\": \"beta.cdr3\",\n",
      "          \"description\": \"Complementarity Determining Region 3 (CDR3) amino acid sequence of TCR beta chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-I.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"beta.cdr3\"\n",
      "            }\n",
      "          }\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"@type\": \"cr:RecordSet\",\n",
      "      \"@id\": \"level-IIA\",\n",
      "      \"name\": \"level-IIA\",\n",
      "      \"field\": [\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IIA/antigen.epitope\",\n",
      "          \"name\": \"antigen.epitope\",\n",
      "          \"description\": \"Peptide sequence of the antigen epitope.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IIA.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"antigen.epitope\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IIA/hla.allele\",\n",
      "          \"name\": \"hla.allele\",\n",
      "          \"description\": \"HLA allele name.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IIA.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.allele\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IIA/beta.cdr3\",\n",
      "          \"name\": \"beta.cdr3\",\n",
      "          \"description\": \"Complementarity Determining Region 3 (CDR3) amino acid sequence of TCR beta chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IIA.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"beta.cdr3\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IIA/hla.full.seq\",\n",
      "          \"name\": \"hla.full.seq\",\n",
      "          \"description\": \"Full HLA protein sequence.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IIA.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.full.seq\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IIA/hla.clip.seq\",\n",
      "          \"name\": \"hla.clip.seq\",\n",
      "          \"description\": \"Amino acid sequence of HLA alpha-1 and alpha-2 domains, which is clipped from the full HLA protein sequence.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IIA.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.clip.seq\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IIA/hla.short.seq\",\n",
      "          \"name\": \"hla.short.seq\",\n",
      "          \"description\": \"HLA pseudo sequence, extracted from HLA alpha-1 and alpha-2 domains.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IIA.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.short.seq\"\n",
      "            }\n",
      "          }\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"@type\": \"cr:RecordSet\",\n",
      "      \"@id\": \"level-IIB\",\n",
      "      \"name\": \"level-IIB\",\n",
      "      \"field\": [\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IIB/antigen.epitope\",\n",
      "          \"name\": \"antigen.epitope\",\n",
      "          \"description\": \"Peptide sequence of the antigen epitope.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IIB.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"antigen.epitope\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IIB/alpha.cdr3\",\n",
      "          \"name\": \"alpha.cdr3\",\n",
      "          \"description\": \"Complementarity Determining Region 3 (CDR3) amino acid sequence of TCR alpha chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IIB.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"alpha.cdr3\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IIB/beta.cdr3\",\n",
      "          \"name\": \"beta.cdr3\",\n",
      "          \"description\": \"Complementarity Determining Region 3 (CDR3) amino acid sequence of TCR beta chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IIB.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"beta.cdr3\"\n",
      "            }\n",
      "          }\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"@type\": \"cr:RecordSet\",\n",
      "      \"@id\": \"level-III\",\n",
      "      \"name\": \"level-III\",\n",
      "      \"field\": [\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-III/antigen.epitope\",\n",
      "          \"name\": \"antigen.epitope\",\n",
      "          \"description\": \"Peptide sequence of the antigen epitope.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-III.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"antigen.epitope\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-III/hla.allele\",\n",
      "          \"name\": \"hla.allele\",\n",
      "          \"description\": \"HLA allele name.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-III.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.allele\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-III/alpha.cdr3\",\n",
      "          \"name\": \"alpha.cdr3\",\n",
      "          \"description\": \"Complementarity Determining Region 3 (CDR3) amino acid sequence of TCR alpha chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-III.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"alpha.cdr3\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-III/beta.cdr3\",\n",
      "          \"name\": \"beta.cdr3\",\n",
      "          \"description\": \"Complementarity Determining Region 3 (CDR3) amino acid sequence of TCR beta chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-III.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"beta.cdr3\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-III/hla.full.seq\",\n",
      "          \"name\": \"hla.full.seq\",\n",
      "          \"description\": \"Full HLA protein sequence.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-III.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.full.seq\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-III/hla.clip.seq\",\n",
      "          \"name\": \"hla.clip.seq\",\n",
      "          \"description\": \"Amino acid sequence of HLA alpha-1 and alpha-2 domains, which is clipped from the full HLA protein sequence.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-III.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.clip.seq\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-III/hla.short.seq\",\n",
      "          \"name\": \"hla.short.seq\",\n",
      "          \"description\": \"HLA pseudo sequence, extracted from HLA alpha-1 and alpha-2 domains.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-III.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.short.seq\"\n",
      "            }\n",
      "          }\n",
      "        }\n",
      "      ]\n",
      "    },\n",
      "    {\n",
      "      \"@type\": \"cr:RecordSet\",\n",
      "      \"@id\": \"level-IV\",\n",
      "      \"name\": \"level-IV\",\n",
      "      \"field\": [\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/antigen.epitope\",\n",
      "          \"name\": \"antigen.epitope\",\n",
      "          \"description\": \"Peptide sequence of the antigen epitope.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"antigen.epitope\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/hla.allele\",\n",
      "          \"name\": \"hla.allele\",\n",
      "          \"description\": \"HLA allele name.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.allele\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/alpha.v\",\n",
      "          \"name\": \"alpha.v\",\n",
      "          \"description\": \"V gene segment of TCR alpha chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"alpha.v\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/alpha.j\",\n",
      "          \"name\": \"alpha.j\",\n",
      "          \"description\": \"J gene segment of TCR alpha chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"alpha.j\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/alpha.cdr3\",\n",
      "          \"name\": \"alpha.cdr3\",\n",
      "          \"description\": \"Complementarity Determining Region 3 (CDR3) amino acid sequence of TCR alpha chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"alpha.cdr3\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/beta.v\",\n",
      "          \"name\": \"beta.v\",\n",
      "          \"description\": \"V gene segment of TCR beta chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"beta.v\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/beta.j\",\n",
      "          \"name\": \"beta.j\",\n",
      "          \"description\": \"J gene segment of TCR beta chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"beta.j\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/beta.cdr3\",\n",
      "          \"name\": \"beta.cdr3\",\n",
      "          \"description\": \"Complementarity Determining Region 3 (CDR3) amino acid sequence of TCR beta chain.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"beta.cdr3\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/alpha.vseq.reconstructed\",\n",
      "          \"name\": \"alpha.vseq.reconstructed\",\n",
      "          \"description\": \"Reconstructed variable domain sequence of TCR alpha chain using V/J gene annotations and CDR3 sequences.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"alpha.vseq.reconstructed\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/beta.vseq.reconstructed\",\n",
      "          \"name\": \"beta.vseq.reconstructed\",\n",
      "          \"description\": \"Reconstructed variable domain sequence of TCR beta chain using V/(D/)J gene annotations and CDR3 sequences.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"beta.vseq.reconstructed\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/hla.full.seq\",\n",
      "          \"name\": \"hla.full.seq\",\n",
      "          \"description\": \"Full HLA protein sequence.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.full.seq\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/hla.clip.seq\",\n",
      "          \"name\": \"hla.clip.seq\",\n",
      "          \"description\": \"Amino acid sequence of HLA alpha-1 and alpha-2 domains, which is clipped from the full HLA protein sequence.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.clip.seq\"\n",
      "            }\n",
      "          }\n",
      "        },\n",
      "        {\n",
      "          \"@type\": \"cr:Field\",\n",
      "          \"@id\": \"level-IV/hla.short.seq\",\n",
      "          \"name\": \"hla.short.seq\",\n",
      "          \"description\": \"HLA pseudo sequence, extracted from HLA alpha-1 and alpha-2 domains.\",\n",
      "          \"dataType\": \"sc:Text\",\n",
      "          \"source\": {\n",
      "            \"fileObject\": {\n",
      "              \"@id\": \"level-IV.csv\"\n",
      "            },\n",
      "            \"extract\": {\n",
      "              \"column\": \"hla.short.seq\"\n",
      "            }\n",
      "          }\n",
      "        }\n",
      "      ]\n",
      "    }\n",
      "  ]\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "import json\n",
    "\n",
    "with open(\"croissant.json\", \"w\") as f:\n",
    "    content = metadata.to_json()\n",
    "    content = json.dumps(content, indent=2)\n",
    "    print(content)\n",
    "    f.write(content)\n",
    "    f.write(\"\\n\")       # Terminate file with newline"
   ]
  }
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