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Batch(es) [GET, POST, PUT]

API calls related to batch objects:

Retrieve

Create 

Update

Delete

 

Retrieve


GET /api/v1/vaults/<vault_id>/batches/<id>

Get a single batch.


GET /api/v1/vaults/<vault_id>/batches

Get a collection of batches. 


Query Parameters (all optional):

batches Comma separated list of ids
Cannot be used with other parameters
async Boolean
If true, do an asynchronous export (see Async Export)
Use for large data sets. This is recommended any time you want to download more than page_size results. Note: any page_size parameter used in an API GET call that also uses the async=true parameter will be ignored. The GET call will return all valid data for the given GET call.
no_structures Boolean
If true, omit structure representations for a smaller and faster response.
Default: false
only_ids Boolean
If true, only the Batch IDs are returned, allowing for a smaller and faster response. (Async should still be used when many IDs are expected.)
Default: false
created_before Date (YYYY-MM-DDThh:mm:ss±hh:mm)
created_after Date (YYYY-MM-DDThh:mm:ss±hh:mm)
modified_before Date (YYYY-MM-DDThh:mm:ss±hh:mm)
modified_after Date (YYYY-MM-DDThh:mm:ss±hh:mm)
molecule_created_before Date (YYYY-MM-DDThh:mm:ss±hh:mm)
molecule_created_after Date (YYYY-MM-DDThh:mm:ss±hh:mm)
offset The index of the first object actually returned. Defaults to 0.
page_size The maximum number of objects to return in this call. Default is 50, maximum is 1000. If the response exceeds the page_size, we strongly recommend using the async option instead of downloading multiple chunks. Note: any page_size parameter used in an API GET call that also uses the async=true parameter will be ignored. The GET call will return all valid data for the given GET call.
projects Comma-separated list of project ids
Defaults to all available projects
Limits scope of query
data_sets Comma-separated list of public dataset ids
Defaults to no data sets
Limits scope of query
molecule_batch_identifier A Molecule-Batch ID used to query the Vault. Use this parameter to limit the number of Molecule UDF Fields to return
molecule_fields Array of Molecule field names to include in the resulting JSON
batch_fields Array of Batch field names to include in the resulting JSON. Use this parameter to limit the number of Batch UDF Fields to return
fields_search Array of Batch field names & values
Used to filter Batches returned based on query values

 

Notes on the molecule_fields and batch_fields parameters - returning only specified data (udf) fields when making the GET Batches API call

To instruct the GET Batches API call to return ONLY a subset of Molecule/Batch data fields, you may pass the molecule_fields and/or batch_fields parameters as JSON with the GET Batches API call.  The JSON passed with the GET Batches API call to achieve this should follow this syntax:

GET https://app.collaborativedrug.com/api/v1/vaults/<vault_id>/batches

{   
    "modified_after":"2022-07-13",
    "no_structures":"true",
    "molecule_fields":"Source",
    "batch_fields":"ID"
}

 

As is typical when needing to pass multiple values in a JSON parameter, using the square brackets to pass an array of values is supported.  Using this example JSON, for example, will result in 2 Batch fields (ID and Note) to be returned.

GET https://app.collaborativedrug.com/api/v1/vaults/<vault_id>/batches

{"batch_fields":["ID","Note"]}
 
 

Notes on molecule_batch_identifier parameter - passing Molecule-Batch ID query values via the API

To pass a Molecule-Batch ID query values via the API, you must pass the molecule_batch_identifier parameter as JSON with the GET Batches API call. The molecule_batch_identifier section of the JSON passed with the GET Batches API call should follow this syntax:

   { "molecule_batch_identifier": "DEMO-1000210-001",

   "no_structures": "true}

 

Notes on fields_search parameter - passing Batch field query values via the API

To pass Batch field query values via the API, you must pass the field_search parameters as JSON with the GET Batches API call.  The field_search section of the JSON passed with the GET Batches API call should follow this syntax:

{ "fields_search": [
     { “name”: "<Batch udf field name>", ”<value_type>”: “<value to be searched” },
     { “name”: "<Batch udf field name>", ”<value_type>”: “<value to be searched” }]
}

The allowed values for value_type are:

  • text_value,
  • float_value
  • date_value

As an example, the JSON below will search for Batches created after the date specified that have a Place value of Graceland CRO and an Initial Amount value of 100. Since the no_structure (true) and async (false) parameters are also included, no structural information is returned and the API call is not performed in the background.

 

GET https://app.collaborativedrug.com/api/v1/vaults/<vault_id>/batches

{"created_after":"2022-01-01",
 "no_structures":"true",
 "fields_search":  [{"name""Place""text_value""Graceland CRO"},
   {"name""Initial Amount""float_value"100}],
 "async"false}

 

Notes on Date/Time Formats

The CDD Vault API accepts ISO 8601 date/time formats in any API call that allows a date-type parameter. For example, the full date and timestamp may be used in GET calls that support a date parameter. You may still simply provide a date-only parameter like "created_after=2020-05-20".

You may also specify a date + timestamp, like "created_after= 2020-05-20 14:53:12", to indicate "20 May 2020 14:53:12 PDT" (PDT is based on the user's time zone setting). The timestamp portion can also include a UTC (Coordinated Universal Time) offset, like "created_after= 2020-05-27T14:48:40-07:00" which indicates that the time specified is -7 hours from the UTC time.

 

Example 1 - Search by Batch fields

curl -H X-CDD-Token:apitoken -H "Content-Type: application/json" -X GET -d "@BatchSearch.json" https://app.collaborativedrug.com/api/v1/vaults/4493/batches

File BatchSearch.json:

{
  "created_after":"2022-03-10",
  "no_structures":"true",
  "fields_search":  [{"name": "Place", "text_value": "Graceland CRO"},
{"name": "Date", "date_value": "2022-03-15"}, {"name": "External Identifier", "text_value": "Grace-10-005"}, {"name": "Purity", "float_value": 95}], "async": false }

Returns:

{
    "count": 1,
    "offset": 0,
    "page_size": 50,
    "objects": [
        {
            "id": 114276274,
            "class": "batch",
            "created_at": "2022-03-15T18:15:56.000Z",
            "modified_at": "2022-05-11T15:01:10.000Z",
            "name": "001",
            "molecule_batch_identifier": "DEMO-1000211-001",
            "owner": "Charlie Weatherall",
            "projects": [
                {
                    "name": "CRO Project",
                    "id": 7090
                }
            ],
            "molecule": {
                "id": 107763291,
                "class": "molecule",
                "created_at": "2022-03-15T18:15:56.000Z",
                "modified_at": "2022-05-11T15:01:10.000Z",
                "name": "DEMO-1000211",
                "synonyms": [
                    "DEMO-1000211"
                ],
                "registration_type": "CHEMICAL_STRUCTURE",
                "projects": [
                    {
                        "name": "CRO Project",
                        "id": 7090
                    }
                ],
                "owner": "Charlie Weatherall"
            },
            "salt_name": "Hydrochloride",
            "solvent_of_crystallization_name": "H2O",
            "formula_weight": 252.79500000000002,
            "batch_fields": {
                "Date": "2022-03-15",
                "Person": "Charlie Weatherall",
                "Vendor": "Graceland CRO",
                "External Identifier": "Grace-10-005",
                "Place": "Graceland CRO",
                "Purity": 95.0,
                "Inv Initial Amount": 100.0,
                "Inv Current Amount": 100.0
            },
            "stoichiometry": {
                "core_count": 1,
                "salt_count": 1,
                "solvent_of_crystallization_count": 1
            }
        }
    ]
}

Example 2- Return a single Batch by ID

Note: the use of parameters within the GET Batches url is obsolete - moving forward, create a JSON file containing the parameters you wish to submit with the GET Batches API call (see Example 1 above)

curl -H "X-CDD-Token: $TOKEN" https://app.collaborativedrug.com/api/v1/vaults/489978881/batches/136660530

Returns:

{
  "id": 136660530,
  "class": "batch",
  "owner": "Super User",
  "created_at": "2007-02-04",
  "modified_at": "2007-12-31",
  "projects": [
    {
      "name": "Super User Private Stuff",
      "id": 3870925
    }
  ],
  "molecule": {
    "id": 927454016,
    "class": "molecule",
    "name": "Taurine",
    "synonyms": [
      "Taurine"
    ],
    "projects": [
      {
        "name": "Super User Private Stuff",
        "id": 3870925
      }
    ],
    "collections": [
      {
        "name": "super user hits",
        "id": 90769562
      }
    ],
    "owner": "Super User",
    "created_at": "2010-11-17",
    "modified_at": "2010-11-17",
    "smiles": "NCCS(O)(=O)=O",
    "cxsmiles": "NCCS(O)(=O)=O",
    "inchi": "InChI=1S/C2H7NO3S/c3-1-2-7(4,5)6/h1-3H2,(H,4,5,6)",
    "inchi_key": "XOAAWQZATWQOTB-UHFFFAOYSA-N",
    "iupac_name": "2-aminoethane-1-sulfonic acid",
    "molfile": "taurine\n  Mrv1770 12111714362D      \n\n  7  6  0  0  0  0      999 V2000\n  0.1105   -2.0625  0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  0.1105   -1.2375  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250   -0.8250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250  0.0000  0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250  0.8250  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1.6500   -0.0000  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.0000  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  1  0  0  0  0\n  4  5  1  0  0  0  0\n  4  6  2  0  0  0  0\n  4  7  2  0  0  0  0\nM  END\n",
    "molecular_weight": 125.14,
    "log_p": -2.61469,
    "log_d": -2.61939,
    "log_s": 0.996488,
    "num_h_bond_donors": 2,
    "num_h_bond_acceptors": 4,
    "num_rule_of_5_violations": 0,
    "formula": "C2H7NO3S",
    "isotope_formula": "C2H7NO3S",
    "dot_disconnected_formula": "C2H7NO3S",
    "p_k_a": -1.49,
    "p_k_a_type": "Acidic",
    "exact_mass": 125.014664263,
    "heavy_atom_count": 7,
    "composition": "C (19.2%), H (5.64%), N (11.19%), O (38.35%), S (25.62%)",
    "isotope_composition": "C (19.2%), H (5.64%), N (11.19%), O (38.35%), S (25.62%)",
    "topological_polar_surface_area": 80.39,
    "num_rotatable_bonds": 2,
    "cns_mpo_score": 4.82803,
    "fsp3": 1
  }
}

 

Example 3 - Return Batches created before a specified date

Note: the use of parameters within the GET Batches url is obsolete - moving forward, create a JSON file containing the parameters you wish to submit with the GET Batches API call (see Example 1 above)

curl -H "X-CDD-Token: $TOKEN" https://app.collaborativedrug.com/api/v1/vaults/489978881/batches?created_before=2017-12-31

Returns:

{
  "count": 9,
  "offset": 0,
  "page_size": 50,
  "objects": [
    {
      "id": 57473786,
      "class": "batch",
      "owner": "Full-Access User",
      "created_at": "2007-02-04",
      "modified_at": "2007-12-31",
      "projects": [
        {
          "name": "McKerrow Vault",
          "id": 938429932
        }
      ],
      "molecule": {
        "id": 9,
        "class": "molecule",
        "name": "structureless",
        "synonyms": [
          "structureless"
        ],
        "projects": [
          {
            "name": "McKerrow Vault",
            "id": 938429932
          }
        ],
        "collections": [
          {
            "name": "all",
            "id": 557113845
          }
        ],
        "owner": "Full-Access User",
        "created_at": "1999-01-01",
        "modified_at": "1999-01-01"
      }
    },
    {
      "id": 136660530,
      "class": "batch",
      "owner": "Super User",
      "created_at": "2007-02-04",
      "modified_at": "2007-12-31",
      "projects": [
        {
          "name": "Super User Private Stuff",
          "id": 3870925
        }
      ],
      "molecule": {
        "id": 927454016,
        "class": "molecule",
        "name": "Taurine",
        "synonyms": [
          "Taurine"
        ],
        "projects": [
          {
            "name": "Super User Private Stuff",
            "id": 3870925
          }
        ],
        "collections": [
          {
            "name": "super user hits",
            "id": 90769562
          }
        ],
        "owner": "Super User",
        "created_at": "2010-11-17",
        "modified_at": "2010-11-17",
        "smiles": "NCCS(O)(=O)=O",
        "cxsmiles": "NCCS(O)(=O)=O",
        "inchi": "InChI=1S/C2H7NO3S/c3-1-2-7(4,5)6/h1-3H2,(H,4,5,6)",
        "inchi_key": "XOAAWQZATWQOTB-UHFFFAOYSA-N",
        "iupac_name": "2-aminoethane-1-sulfonic acid",
        "molfile": "taurine\n  Mrv1770 12111714502D      \n\n  7  6  0  0  0  0      999 V2000\n  0.1105   -2.0625  0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  0.1105   -1.2375  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250   -0.8250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250  0.0000  0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250  0.8250  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1.6500   -0.0000  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.0000  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  1  0  0  0  0\n  4  5  1  0  0  0  0\n  4  6  2  0  0  0  0\n  4  7  2  0  0  0  0\nM  END\n",
        "molecular_weight": 125.14,
        "log_p": -2.61469,
        "log_d": -2.61939,
        "log_s": 0.996488,
        "num_h_bond_donors": 2,
        "num_h_bond_acceptors": 4,
        "num_rule_of_5_violations": 0,
        "formula": "C2H7NO3S",
        "isotope_formula": "C2H7NO3S",
        "dot_disconnected_formula": "C2H7NO3S",
        "p_k_a": -1.49,
        "p_k_a_type": "Acidic",
        "exact_mass": 125.014664263,
        "heavy_atom_count": 7,
        "composition": "C (19.2%), H (5.64%), N (11.19%), O (38.35%), S (25.62%)",
        "isotope_composition": "C (19.2%), H (5.64%), N (11.19%), O (38.35%), S (25.62%)",
        "topological_polar_surface_area": 80.39,
        "num_rotatable_bonds": 2,
        "cns_mpo_score": 4.82803,
        "fsp3": 1
      }
    },
    {
      "id": 145175681,
      "class": "batch",
      "owner": "Full-Access User",
      "created_at": "2007-02-04",
      "modified_at": "2007-12-31",
      "projects": [
        {
          "name": "McKerrow Vault",
          "id": 938429932
        }
      ],
      "molecule": {
        "id": 7,
        "class": "molecule",
        "name": "Miconazole",
        "synonyms": [
          "Miconazole"
        ],
        "projects": [
          {
            "name": "McKerrow Vault",
            "id": 938429932
          }
        ],
        "collections": [
          {
            "name": "all",
            "id": 557113845
          }
        ],
        "owner": "Full-Access User",
        "created_at": "1999-01-01",
        "modified_at": "1999-01-01",
        "smiles": "ClC1=CC=C(COC(CN2C=CN=C2)C2=CC=C(Cl)C=C2Cl)C(Cl)=C1",
        "cxsmiles": "ClC1=CC=C(COC(CN2C=CN=C2)C2=CC=C(Cl)C=C2Cl)C(Cl)=C1 |c:10,12,20,25,t:1,3,15,17|",
        "inchi": "InChI=1S/C18H14Cl4N2O/c19-13-2-1-12(16(21)7-13)10-25-18(9-24-6-5-23-11-24)15-4-3-14(20)8-17(15)22/h1-8,11,18H,9-10H2",
        "inchi_key": "BYBLEWFAAKGYCD-UHFFFAOYSA-N",
        "iupac_name": "1-[2-(2,4-dichlorophenyl)-2-[(2,4-dichlorophenyl)methoxy]ethyl]-1H-imidazole",
        "molfile": "\n  Mrv1770 12111714502D      \n\n 25 27  0  0  0  0      999 V2000\n   -1.4289  0.8250  0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7145  0.4125  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.8250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.7145  0.4125  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.7145   -0.4125  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1.4289   -0.8250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1.4289   -1.6500  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  2.1434   -2.0625  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  2.8579   -1.6500  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  3.5724   -2.0625  0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  4.3260   -1.7269  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  4.8781   -2.3400  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  4.4656   -3.0545  0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  3.6586   -2.8830  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  2.1434   -2.8875  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  2.8579   -3.3000  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  2.8579   -4.1250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  2.1434   -4.5375  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  2.1434   -5.3625  0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n  1.4289   -4.1250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1.4289   -3.3000  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.7145   -2.8875  0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000   -0.8250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000   -1.6500  0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n   -0.7145   -0.4125  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  2  3  2  0  0  0  0\n  3  4  1  0  0  0  0\n  4  5  2  0  0  0  0\n  5  6  1  0  0  0  0\n  6  7  1  0  0  0  0\n  7  8  1  0  0  0  0\n  8  9  1  0  0  0  0\n  9 10  1  0  0  0  0\n 10 11  1  0  0  0  0\n 11 12  2  0  0  0  0\n 12 13  1  0  0  0  0\n 13 14  2  0  0  0  0\n 10 14  1  0  0  0  0\n  8 15  1  0  0  0  0\n 15 16  2  0  0  0  0\n 16 17  1  0  0  0  0\n 17 18  2  0  0  0  0\n 18 19  1  0  0  0  0\n 18 20  1  0  0  0  0\n 20 21  2  0  0  0  0\n 15 21  1  0  0  0  0\n 21 22  1  0  0  0  0\n  5 23  1  0  0  0  0\n 23 24  1  0  0  0  0\n 23 25  2  0  0  0  0\n  2 25  1  0  0  0  0\nM  END\n",
        "molecular_weight": 416.12,
        "log_p": 5.95637,
        "log_d": 5.92051,
        "log_s": -6.08948,
        "num_h_bond_donors": 0,
        "num_h_bond_acceptors": 2,
        "num_rule_of_5_violations": 1,
        "formula": "C18H14Cl4N2O",
        "isotope_formula": "C18H14Cl4N2O",
        "dot_disconnected_formula": "C18H14Cl4N2O",
        "p_k_a": 6.48,
        "p_k_a_type": "Basic",
        "exact_mass": 413.9860239,
        "heavy_atom_count": 25,
        "composition": "C (51.96%), H (3.39%), Cl (34.08%), N (6.73%), O (3.84%)",
        "isotope_composition": "C (51.96%), H (3.39%), Cl (34.08%), N (6.73%), O (3.84%)",
        "topological_polar_surface_area": 27.05,
        "num_rotatable_bonds": 6,
        "cns_mpo_score": 2.95164,
        "fsp3": 0.166667
      }
    },
    {
      "id": 373670577,
      "class": "batch",
      "owner": "Super User",
      "created_at": "2007-02-04",
      "modified_at": "2007-12-31",
      "projects": [
        {
          "name": "Super User Private Stuff",
          "id": 3870925
        }
      ],
      "molecule": {
        "id": 971541720,
        "class": "molecule",
        "name": "Secret",
        "synonyms": [
          "Secret"
        ],
        "projects": [
          {
            "name": "Super User Private Stuff",
            "id": 3870925
          }
        ],
        "owner": "Super User",
        "created_at": "2010-11-17",
        "modified_at": "2010-11-17"
      }
    },
    {
      "id": 618771089,
      "class": "batch",
      "name": "KGB-51AD88",
      "owner": "Full-Access User",
      "created_at": "2007-02-04",
      "modified_at": "2007-12-31",
      "projects": [
        {
          "name": "McKerrow Vault",
          "id": 938429932
        }
      ],
      "molecule": {
        "id": 3,
        "class": "molecule",
        "name": "Cyanide",
        "synonyms": [
          "Cyanide"
        ],
        "cdd_registry_number": 3,
        "projects": [
          {
            "name": "McKerrow Vault",
            "id": 938429932
          }
        ],
        "collections": [
          {
            "name": "super user hits",
            "id": 90769562
          },
          {
            "name": "all",
            "id": 557113845
          }
        ],
        "owner": "Full-Access User",
        "created_at": "1999-01-01",
        "modified_at": "1999-01-01",
        "smiles": "C#N",
        "cxsmiles": "C#N",
        "inchi": "InChI=1S/CHN/c1-2/h1H",
        "inchi_key": "LELOWRISYMNNSU-UHFFFAOYSA-N",
        "iupac_name": "formonitrile",
        "molfile": "\n  Mrv1770 12111714502D      \n\n  2  1  0  0  0  0      999 V2000\n  0.8250  0.0000  0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.0000  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  3  0  0  0  0\nM  END\n",
        "molecular_weight": 27.026,
        "log_p": -0.346198,
        "log_d": -0.339047,
        "log_s": 0.321662,
        "num_h_bond_donors": 0,
        "num_h_bond_acceptors": 1,
        "num_rule_of_5_violations": 0,
        "formula": "CHN",
        "isotope_formula": "CHN",
        "dot_disconnected_formula": "CHN",
        "p_k_a": 9.5,
        "p_k_a_type": "Acidic",
        "exact_mass": 27.010899036,
        "heavy_atom_count": 2,
        "composition": "C (44.44%), H (3.73%), N (51.83%)",
        "isotope_composition": "C (44.44%), H (3.73%), N (51.83%)",
        "topological_polar_surface_area": 23.79,
        "num_rotatable_bonds": 0,
        "cns_mpo_score": 5.1895,
        "fsp3": 0
      },
      "formula_weight": 27.026
    },
    {
      "id": 700861902,
      "class": "batch",
      "name": "Will's bottle of benzene",
      "owner": "Readadd User",
      "created_at": "2007-02-04",
      "modified_at": "2007-12-31",
      "projects": [
        {
          "name": "McKerrow Vault",
          "id": 938429932
        },
        {
          "name": "Super User Private Stuff",
          "id": 3870925
        }
      ],
      "molecule": {
        "id": 1,
        "class": "molecule",
        "name": "Benzene",
        "synonyms": [
          "Benzene",
          "benzene-002"
        ],
        "cdd_registry_number": 1,
        "projects": [
          {
            "name": "McKerrow Vault",
            "id": 938429932
          },
          {
            "name": "Super User Private Stuff",
            "id": 3870925
          }
        ],
        "collections": [
          {
            "name": "all",
            "id": 557113845
          }
        ],
        "owner": "Full-Access User",
        "created_at": "1999-01-01",
        "modified_at": "1999-01-01",
        "smiles": "C1=CC=CC=C1",
        "cxsmiles": "C1=CC=CC=C1 |c:0,2,4|",
        "inchi": "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H",
        "inchi_key": "UHOVQNZJYSORNB-UHFFFAOYSA-N",
        "iupac_name": "benzene",
        "molfile": "\n  Mrv1770 12111714502D      \n\n  6  6  0  0  0  0      999 V2000\n  0.7145  1.2375  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1.4289  0.8250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1.4289   -0.0000  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.7145   -0.4125  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.0000  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.8250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  2  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  1  6  1  0  0  0  0\nM  END\n",
        "molecular_weight": 78.114,
        "log_p": 1.97325,
        "log_d": 1.97325,
        "log_s": -1.26596,
        "num_h_bond_donors": 0,
        "num_h_bond_acceptors": 0,
        "num_rule_of_5_violations": 0,
        "formula": "C6H6",
        "isotope_formula": "C6H6",
        "dot_disconnected_formula": "C6H6",
        "exact_mass": 78.0469501932,
        "heavy_atom_count": 6,
        "composition": "C (92.26%), H (7.74%)",
        "isotope_composition": "C (92.26%), H (7.74%)",
        "topological_polar_surface_area": 0,
        "num_rotatable_bonds": 0,
        "cns_mpo_score": 5,
        "fsp3": 0,
        "udfs": {
          "Color": "colorless",
          "Taste": "very bitter",
          "Smell": "sweet"
        }
      },
      "formula_weight": 78.114,
      "batch_fields": {
        "Date": "2006-01-01",
        "Person": "Will",
        "Place": "The kitchen",
        "Note": "50% water"
      }
    },
    {
      "id": 787637732,
      "class": "batch",
      "name": "Sigma-Aldrich #2451",
      "owner": "Full-Access User",
      "created_at": "2007-02-04",
      "modified_at": "2007-12-31",
      "projects": [
        {
          "name": "McKerrow Vault",
          "id": 938429932
        }
      ],
      "molecule": {
        "id": 2,
        "class": "molecule",
        "name": "Water",
        "synonyms": [
          "Water"
        ],
        "cdd_registry_number": 2,
        "projects": [
          {
            "name": "McKerrow Vault",
            "id": 938429932
          }
        ],
        "collections": [
          {
            "name": "super user hits",
            "id": 90769562
          },
          {
            "name": "all",
            "id": 557113845
          }
        ],
        "owner": "Full-Access User",
        "created_at": "1999-01-01",
        "modified_at": "1999-01-01",
        "smiles": "O",
        "cxsmiles": "O",
        "inchi": "InChI=1S/H2O/h1H2",
        "inchi_key": "XLYOFNOQVPJJNP-UHFFFAOYSA-N",
        "iupac_name": "water",
        "molfile": "\n  Mrv1770 12111714502D      \n\n  1  0  0  0  0  0      999 V2000\n  0.0000  0.0000  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\nM  END\n",
        "molecular_weight": 18.015,
        "log_p": -0.652,
        "log_d": -0.652,
        "log_s": 0.530744,
        "num_h_bond_donors": 1,
        "num_h_bond_acceptors": 1,
        "num_rule_of_5_violations": 0,
        "formula": "H2O",
        "isotope_formula": "H2O",
        "dot_disconnected_formula": "H2O",
        "p_k_a": 15.7,
        "p_k_a_type": "Acidic",
        "exact_mass": 18.010564684,
        "heavy_atom_count": 1,
        "composition": "H (11.19%), O (88.81%)",
        "isotope_composition": "H (11.19%), O (88.81%)",
        "topological_polar_surface_area": 25.3,
        "num_rotatable_bonds": 0,
        "cns_mpo_score": 5.09833,
        "udfs": {
          "Literature Reference": "Aqueous et al. 2009",
          "Description": "water is the source of life"
        }
      },
      "formula_weight": 18.015,
      "batch_fields": {
        "Person": "Will",
        "Place": "The kitchen",
        "Date": "2007-02-04",
        "Note": "note taken"
      }
    },
    {
      "id": 812057525,
      "class": "batch",
      "owner": "Super User",
      "created_at": "2007-02-04",
      "modified_at": "2007-12-31",
      "projects": [
        {
          "name": "Super User Private Stuff",
          "id": 3870925
        }
      ],
      "molecule": {
        "id": 246113948,
        "class": "molecule",
        "name": "Glucose",
        "synonyms": [
          "Glucose"
        ],
        "projects": [
          {
            "name": "Super User Private Stuff",
            "id": 3870925
          }
        ],
        "collections": [
          {
            "name": "super user hits",
            "id": 90769562
          }
        ],
        "owner": "Super User",
        "created_at": "2010-11-17",
        "modified_at": "2010-11-17",
        "smiles": "OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O",
        "cxsmiles": "OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O",
        "inchi": "InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1",
        "inchi_key": "WQZGKKKJIJFFOK-GASJEMHNSA-N",
        "iupac_name": "(3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol",
        "molfile": "glucose\n  Mrv1770 12111714502D      \n\n 12 12  0  0  1  0      999 V2000\n  0.0000  2.4750  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  0.7145  2.0625  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.7145  1.2375  0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0\n  1.4289  0.8250  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1.4289   -0.0000  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  2.1434   -0.4125  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  0.7145   -0.4125  0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0\n  0.7145   -1.2375  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.0000  0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0\n   -0.7145   -0.4125  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.8250  0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0\n   -0.7145  1.2375  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  3  2  1  1  0  0  0\n  3  4  1  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  1  0  0  0  0\n  5  7  1  0  0  0  0\n  7  8  1  6  0  0  0\n  7  9  1  0  0  0  0\n  9 10  1  1  0  0  0\n  9 11  1  0  0  0  0\n  3 11  1  0  0  0  0\n 11 12  1  6  0  0  0\nM  END\n",
        "molecular_weight": 180.156,
        "log_p": -2.93254,
        "log_d": -2.93259,
        "log_s": 0.351011,
        "num_h_bond_donors": 5,
        "num_h_bond_acceptors": 6,
        "num_rule_of_5_violations": 0,
        "formula": "C6H12O6",
        "isotope_formula": "C6H12O6",
        "dot_disconnected_formula": "C6H12O6",
        "p_k_a": 11.3,
        "p_k_a_type": "Acidic",
        "exact_mass": 180.063388106,
        "heavy_atom_count": 12,
        "composition": "C (40%), H (6.71%), O (53.28%)",
        "isotope_composition": "C (40%), H (6.71%), O (53.28%)",
        "topological_polar_surface_area": 110.38,
        "num_rotatable_bonds": 1,
        "cns_mpo_score": 4.32067,
        "fsp3": 1
      }
    },
    {
      "id": 858251680,
      "class": "batch",
      "name": "Joey's bottle of benzene",
      "owner": "Full-Access User",
      "created_at": "2010-02-04",
      "modified_at": "2010-12-31",
      "projects": [
        {
          "name": "McKerrow Vault",
          "id": 938429932
        }
      ],
      "molecule": {
        "id": 1,
        "class": "molecule",
        "name": "Benzene",
        "synonyms": [
          "Benzene",
          "benzene-002"
        ],
        "cdd_registry_number": 1,
        "projects": [
          {
            "name": "McKerrow Vault",
            "id": 938429932
          },
          {
            "name": "Super User Private Stuff",
            "id": 3870925
          }
        ],
        "collections": [
          {
            "name": "all",
            "id": 557113845
          }
        ],
        "owner": "Full-Access User",
        "created_at": "1999-01-01",
        "modified_at": "1999-01-01",
        "smiles": "C1=CC=CC=C1",
        "cxsmiles": "C1=CC=CC=C1 |c:0,2,4|",
        "inchi": "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H",
        "inchi_key": "UHOVQNZJYSORNB-UHFFFAOYSA-N",
        "iupac_name": "benzene",
        "molfile": "\n  Mrv1770 12111714502D      \n\n  6  6  0  0  0  0      999 V2000\n  0.7145  1.2375  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1.4289  0.8250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1.4289   -0.0000  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.7145   -0.4125  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.0000  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.8250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  2  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  1  6  1  0  0  0  0\nM  END\n",
        "molecular_weight": 78.114,
        "log_p": 1.97325,
        "log_d": 1.97325,
        "log_s": -1.26596,
        "num_h_bond_donors": 0,
        "num_h_bond_acceptors": 0,
        "num_rule_of_5_violations": 0,
        "formula": "C6H6",
        "isotope_formula": "C6H6",
        "dot_disconnected_formula": "C6H6",
        "exact_mass": 78.0469501932,
        "heavy_atom_count": 6,
        "composition": "C (92.26%), H (7.74%)",
        "isotope_composition": "C (92.26%), H (7.74%)",
        "topological_polar_surface_area": 0,
        "num_rotatable_bonds": 0,
        "cns_mpo_score": 5,
        "fsp3": 0,
        "udfs": {
          "Color": "colorless",
          "Taste": "very bitter",
          "Smell": "sweet"
        }
      },
      "formula_weight": 78.114,
      "batch_fields": {
        "Date": "2009-01-01",
        "Person": "Joey",
        "Note": "in between the Jack and the Grey Goose",
        "Place": "The bar"
      }
    }
  ]
}

  

Create

 

POST /api/v1/vaults/<vault_id>/batches

Creates a new batch.

 

The body of the POST must contain a JSON structure specifying the molecule attributes. The structure is roughly the same format as what is returned by a GET call but with some restrictions and additions.

 

The HTTP response contains the full JSON representation of the new batch (as would be returned from a GET).

 

Allowed JSON keys for batches:

class

Optional. If present, must be “batch”

molecule

See Create Molecule if creating a new molecule in a Vault without a registration system enabled. 

Use the following when creating a new small molecule:

  • {"registration_type":"CHEMICAL_STRUCTURE"}

Also include one of the following when creating a new molecule:

  • {"id": <number>}

  • {"name": <name>}

  • {"structure": <structure>}

  • {“smiles”: <smiles>}

  • {“cxsmiles”: <cxsmiles>}

Use the following when creating a new amino acid:

  • {"registration_type":"AMINO_ACID"}

Also include one of the following when creating a new amino acid:

  • {"amino_acid":<amino acid code>}

Use the following when creating a new nucleotide:

  • {"registration_type":"NUCLEOTIDE"}

Also include one of the following when creating a new nucleotide:

  • {"nucleotide":<nucleotide code>}

name

String

projects

An array of project ids and/or names

batch_fields

Each vault has its own settings on the minimum information required to create a new Batch (for a Vault Administrator, see Settings > Vault > Batch Fields, to change which Batch fields are required).

{<batch_field_name>: <batch_field_value>, ... }

salt_name

(Registration Vaults Only)

A two-letter code or Salt vendor string as listed in the All Available Salts table.  The salt is determined automatically when the salt is included in the molecular structure.

solvent_of_crystallization_name

(Registration Vaults Only)

 Name of the solvent.  Click here to the view the available solvents

stoichiometry

(Registration Vaults Only)

{
  "core_count": <integer>,
  "salt_count": <integer>,
  "solvent_of_crystallization_count": <integer>
}

 

Note that in a registration vault, POST batch is the only way to create a new molecule, since the registration of a new molecule must be accompanied by a first batch. In this case, the JSON describing the batch will include a "molecule" field with detailed information on the new molecule.

Example

curl -H "X-CDD-Token: $TOKEN" -X POST -H "Content-Type: application/json" -d "@data.json" https://app.collaborativedrug.com/api/v1/vaults/489978881/batches

File data.json:

{
  "molecule":{"registration_type":"CHEMICAL_STRUCTURE","smiles":"ccc"},
  "projects": [938429932, "Super User Private Stuff"],
  "batch_fields": {
    "Date": "2017-01-01",
    "Person": "Colonel Mustard",
    "Place": "Foyer",
    "Note": "With a Candlestick"
  }
}

Returns:

{
  "id": 1043808269,
  "class": "batch",
  "owner": "Super User",
  "created_at": "2017-12-11",
  "modified_at": "2017-12-11",
  "projects": [
    {
      "name": "Some Vault Name",
      "id": 938429932
    },
    {
      "name": "Super User Private Stuff",
      "id": 3870925
    }
  ],
  "molecule": {
    "id": 927454016,
    "class": "molecule",
    "name": "Taurine",
    "synonyms": [
      "Taurine"
    ],
    "projects": [
      {
        "name": "McKerrow Vault",
        "id": 938429932
      },
      {
        "name": "Super User Private Stuff",
        "id": 3870925
      }
    ],
    "collections": [
      {
        "name": "super user hits",
        "id": 90769562
      }
    ],
    "owner": "Super User",
    "created_at": "2010-11-17",
    "modified_at": "2017-12-11",
    "smiles": "NCCS(O)(=O)=O",
    "cxsmiles": "NCCS(O)(=O)=O",
    "inchi": "InChI=1S/C2H7NO3S/c3-1-2-7(4,5)6/h1-3H2,(H,4,5,6)",
    "inchi_key": "XOAAWQZATWQOTB-UHFFFAOYSA-N",
    "iupac_name": "2-aminoethane-1-sulfonic acid",
    "molfile": "taurine\n  Mrv1770 12111716072D      \n\n  7  6  0  0  0  0      999 V2000\n  0.1105   -2.0625  0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  0.1105   -1.2375  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250   -0.8250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250  0.0000  0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250  0.8250  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1.6500   -0.0000  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.0000  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  1  0  0  0  0\n  4  5  1  0  0  0  0\n  4  6  2  0  0  0  0\n  4  7  2  0  0  0  0\nM  END\n",
    "molecular_weight": 125.14,
    "log_p": -2.61469,
    "log_d": -2.61939,
    "log_s": 0.996488,
    "num_h_bond_donors": 2,
    "num_h_bond_acceptors": 4,
    "num_rule_of_5_violations": 0,
    "formula": "C2H7NO3S",
    "isotope_formula": "C2H7NO3S",
    "dot_disconnected_formula": "C2H7NO3S",
    "p_k_a": -1.49,
    "p_k_a_type": "Acidic",
    "exact_mass": 125.014664263,
    "heavy_atom_count": 7,
    "composition": "C (19.2%), H (5.64%), N (11.19%), O (38.35%), S (25.62%)",
    "isotope_composition": "C (19.2%), H (5.64%), N (11.19%), O (38.35%), S (25.62%)",
    "topological_polar_surface_area": 80.39,
    "num_rotatable_bonds": 2,
    "cns_mpo_score": 4.82803,
    "fsp3": 1
  },
  "formula_weight": 125.14,
  "batch_fields": {
    "Date": "2017-01-01",
    "Person": "Colonel Mustard",
    "Place": "Foyer",
    "Note": "With a Candlestick"
  }
}

 

Example JSON used for registering a new Amino Acid might resemble:

{
"molecule": {"registration_type":"AMINO_ACID","amino_acid":"AAZNRXXNA"},
"projects": ["Test"]
}

 

Example JSON used for registering a new Nucleotide might resemble:

{
"molecule": {"registration_type":"NUCLEOTIDE","nucleotide":"GATTACA"},
"projects": ["Test"]
}

 

Update

 

PUT /api/v1/vaults/<vault_id>/batches/id

Update an existing batch.

 

See Create for valid fields.  (An exception to this is the Molecule field - this PUT Batches call should not be used to update the chemical structure of the parent Molecule - use the PUT Molecules API call to achieve this.) Fields not specified in the JSON are not changed.

To delete a Batch, simply submit with an empty projects array. (For safety/security purposes, Batches which have data associated with them cannot be deleted via this PUT Batches API call. Data (such as rows of readout data in a Protocol Run) must be removed prior to using the PUT Batches API call to delete a Batch.)

 

Note that the ID for the batch is specified as part of the URL, not in the JSON (the JSON can contain an ID field as long as its value matches the URL).

 

Examples

curl -H "X-CDD-Token: $TOKEN" -X PUT -H "Content-Type: application/json" -d "@data.json" https://app.collaborativedrug.com/api/v1/vaults/489978881/batches/1043808269

File data.json:

{
  "batch_fields": {
    "Person": "Mrs. Peacock"
  }
}

Returns:

{
  "id": 1043808269,
  "class": "batch",
  "name": "tmp API batch",
  "owner": "Super User",
  "created_at": "2017-12-11",
  "modified_at": "2017-12-11",
  "projects": [
    {
      "name": "McKerrow Vault",
      "id": 938429932
    },
    {
      "name": "Super User Private Stuff",
      "id": 3870925
    }
  ],
  "molecule": {
    "id": 927454016,
    "class": "molecule",
    "name": "Taurine",
    "synonyms": [
      "Taurine"
    ],
    "projects": [
      {
        "name": "McKerrow Vault",
        "id": 938429932
      },
      {
        "name": "Super User Private Stuff",
        "id": 3870925
      }
    ],
    "collections": [
      {
        "name": "super user hits",
        "id": 90769562
      }
    ],
    "owner": "Super User",
    "created_at": "2010-11-17",
    "modified_at": "2017-12-11",
    "smiles": "NCCS(O)(=O)=O",
    "cxsmiles": "NCCS(O)(=O)=O",
    "inchi": "InChI=1S/C2H7NO3S/c3-1-2-7(4,5)6/h1-3H2,(H,4,5,6)",
    "inchi_key": "XOAAWQZATWQOTB-UHFFFAOYSA-N",
    "iupac_name": "2-aminoethane-1-sulfonic acid",
    "molfile": "taurine\n  Mrv1770 12111716072D      \n\n  7  6  0  0  0  0      999 V2000\n  0.1105   -2.0625  0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n  0.1105   -1.2375  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250   -0.8250  0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250  0.0000  0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n  0.8250  0.8250  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1.6500   -0.0000  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  0.0000  0.0000  0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  1  0  0  0  0\n  4  5  1  0  0  0  0\n  4  6  2  0  0  0  0\n  4  7  2  0  0  0  0\nM  END\n",
    "molecular_weight": 125.14,
    "log_p": -2.61469,
    "log_d": -2.61939,
    "log_s": 0.996488,
    "num_h_bond_donors": 2,
    "num_h_bond_acceptors": 4,
    "num_rule_of_5_violations": 0,
    "formula": "C2H7NO3S",
    "isotope_formula": "C2H7NO3S",
    "dot_disconnected_formula": "C2H7NO3S",
    "p_k_a": -1.49,
    "p_k_a_type": "Acidic",
    "exact_mass": 125.014664263,
    "heavy_atom_count": 7,
    "composition": "C (19.2%), H (5.64%), N (11.19%), O (38.35%), S (25.62%)",
    "isotope_composition": "C (19.2%), H (5.64%), N (11.19%), O (38.35%), S (25.62%)",
    "topological_polar_surface_area": 80.39,
    "num_rotatable_bonds": 2,
    "cns_mpo_score": 4.82803,
    "fsp3": 1
  },
  "formula_weight": 125.14,
  "batch_fields": {
    "Date": "2017-01-01",
    "Person": "Mrs. Peacock",
    "Place": "Foyer",
    "Note": "With a Candlestick"
  }
}

  

curl -H "X-CDD-Token: $TOKEN" -X PUT -H "Content-Type: application/json" -d "@data.json" https://app.collaborativedrug.com/api/v1/vaults/489978881/batches/1043808269

File data.json:

{
  "projects": []
}

Returns:

{
"message": "Object has been removed from all projects, so it has been deleted"
}