Updates graphql tags that are not within an object literal and not standalone expressions to be wrapped in an object similar to what the Relay babel plugin used to do before simplifying the logic there.

fix-graphql.js

'use strict';

// To be used with jscodeshift: https://github.com/facebook/jscodeshift

export default function transformer(file, api) {
  const j = api.jscodeshift;

  if (!file.source.includes('graphql`')) {
    return;
  }

  source = j(source)
    .find(j.TaggedTemplateExpression, {
      tag: {type: 'Identifier', name: 'graphql'},
    })
    .filter(path => getAssignedObjectPropertyName(path) == null)
    .filter(path => path.parentPath.node.type !== 'ExpressionStatement')
    .forEach(path => {
      const text = path.node.quasi.quasis[0].value.raw;
      const fragmentNameMatch = text
        .replace(/#.*/g, '')
        .match(/fragment (\w+)/);
      if (!fragmentNameMatch) {
        return;
      }
      const fragmentName = fragmentNameMatch[1];

      const [, propName] = getFragmentNameParts(fragmentName);

      j(path).replaceWith(
        j.objectExpression([
          j.objectProperty(j.identifier(propName), path.node),
        ]),
      );
    })
    .toSource();

  return source;
}

function getAssignedObjectPropertyName(path) {
  var property = path;
  while (property) {
    if (property.node.type === 'Property' && property.node.key.name) {
      return property.node.key.name;
    }
    property = property.parentPath;
  }
}

function getFragmentNameParts(fragmentName) {
  const match = fragmentName.match(
    /^([a-zA-Z][a-zA-Z0-9]*)(?:_([a-zA-Z][_a-zA-Z0-9]*))?$/,
  );
  if (!match) {
    throw new Error(
      'BabelPluginGraphQL: Fragments should be named ' +
        '`ModuleName_fragmentName`, got `' +
        fragmentName +
        '`.',
    );
  }
  const module = match[1];
  const propName = match[2] || '@nocommit';
  return [module, propName];
}

Thank you a lot but The codemod is not useful when we have multiple fragments inside one graphql tag.
I have modified it to support this situation:

// To be used with jscodeshift: https://github.com/facebook/jscodeshift

export default function transformer(file, api) {
    const j = api.jscodeshift;

    if (!file.source.includes('graphql`')) {
      return;
    }

    function getAssignedObjectPropertyName(path) {
        var property = path;
        while (property) {
            if (property.node.type === 'Property' && property.node.key.name) {
                return property.node.key.name;
            }
            property = property.parentPath;
        }
    }

    function getFragmentNameParts(fragmentName) {
        const match = fragmentName.match(
            /^([a-zA-Z][a-zA-Z0-9]*)(?:_([a-zA-Z][_a-zA-Z0-9]*))?$/,
        );
        if (!match) {
            throw new Error(
                'BabelPluginGraphQL: Fragments should be named ' +
                '`ModuleName_fragmentName`, got `' +
                fragmentName +
                '`.',
            );
        }
        const module = match[1];
        const propName = match[2] || "data";
        return [module, propName];
    }

    return j(file.source)
    .find(j.TaggedTemplateExpression, { tag: { type: 'Identifier', name: 'graphql' } })
    .filter(path => getAssignedObjectPropertyName(path) == null)
    .filter(path => path.parentPath.node.type !== 'ExpressionStatement')
    .forEach(path => {
        const text = path.node.quasi.quasis[0].value.raw;
        if (!text.includes('fragment ')) {
          return;
        }

        const fragmentStrings = text.replace(/#.*/g, '')
          .split('fragment ')
          .map(item => item.trim())
          .filter(item => item !== '' && !item.startsWith('query') && !item.startsWith('mutation'))
          .map(item => `fragment ${item}`);

        const expressions = fragmentStrings.map((fragmentString) => {
          const fragmentNameMatch =  fragmentString.match(/fragment\s+(\w+)/);
          if (!fragmentNameMatch) {
            return;
          }

          const fragmentName = fragmentNameMatch[1];
          const [, propName] = getFragmentNameParts(fragmentName);

          const key = j.identifier(propName);
          const value = j.taggedTemplateExpression(
              j.identifier('graphql'),
              j.templateLiteral([
                j.templateElement({ cooked: fragmentString, raw: fragmentString }, true ),
              ], []),
            );

          return j.objectProperty(key, value);
        }).filter(Boolean)

        if (expressions.length > 0) {
          j(path).replaceWith(j.objectExpression(expressions));
        }
    })
    .toSource();
}