Container key values

[khaledk2]

This PR adds two ends points:

• container_keyvalues: This will return all the available values for a key in a container, the user should provide the key and the container name, for example, to return the saved values for a cell line in container id0034, the following should be used:
  https://idr-testing.openmicroscopy.org/searchengine/api/v1/resources/image/container_keyvalues/?container_name=idr0034&key=cell line
  This is the returned results:

[
  {
    "name": "idr0034-kilpinen-hipsci/screenA",
    "results": [
      {
        "key": "cell line",
        "no_image": 324,
        "value": "HPSI0313i-airc_2"
      },
      {
        "key": "cell line",
        "no_image": 324,
        "value": "HPSI0313i-airc_3"
      },
      {
        "key": "cell line",
        "no_image": 324,
        "value": "HPSI0613i-auim_2"
      },
      {
        "key": "cell line",
        "no_image": 324,
        "value": "HPSI0713i-darw_2"
      },
      {
        "key": "cell line",
        "no_image": 324,
        "value": "HPSI0713i-kaks_2"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0413i-ougl_1"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0413i-ougl_3"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0513i-coio_1"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0513i-coio_2"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0513i-cuau_2"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0513i-euir_1"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0513i-leeh_2"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0613i-riiv_1"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0713i-darw_1"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0713i-qimz_1"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0713i-ruyv_1"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0713i-ruyv_3"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0813i-meqo_2"
      },
      {
        "key": "cell line",
        "no_image": 243,
        "value": "HPSI0813i-meqo_3"
      },
      {
        "key": "cell line",
        "no_image": 162,
        "value": "HPSI0513i-cuau_1"
      },
      {
        "key": "cell line",
        "no_image": 162,
        "value": "HPSI0513i-euir_2"
      },
      {
        "key": "cell line",
        "no_image": 162,
        "value": "HPSI0513i-leeh_3"
      },
      {
        "key": "cell line",
        "no_image": 162,
        "value": "HPSI0713i-kaks_3"
      },
      {
        "key": "cell line",
        "no_image": 162,
        "value": "HPSI0713i-qimz_2"
      },
      {
        "key": "cell line",
        "no_image": 81,
        "value": "HPSI0413i-iakz_1"
      },
      {
        "key": "cell line",
        "no_image": 81,
        "value": "HPSI0413i-iakz_2"
      },
      {
        "key": "cell line",
        "no_image": 81,
        "value": "HPSI0613i-auim_3"
      },
      {
        "key": "cell line",
        "no_image": 81,
        "value": "HPSI0613i-riiv_3"
      }
    ],
    "type": "screen"
  }
]

• container_keys, this endpoint will return the available attributes with a container, for example, to return the available attributes for the idr0034 container, this should be used:
  https://idr-testing.openmicroscopy.org/searchengine/api/v1/resources/image/container_keys/?container_name=idr0034
  This is the returned results:

[
  {
    "name": "idr0034-kilpinen-hipsci/screenA",
    "results": [
      {
        "key": "biosamples identifier",
        "no_image": 6156
      },
      {
        "key": "biosamples identifier url",
        "no_image": 6156
      },
      {
        "key": "cell line",
        "no_image": 6156
      },
      {
        "key": "cell line url",
        "no_image": 6156
      },
      {
        "key": "cell type",
        "no_image": 6156
      },
      {
        "key": "channels",
        "no_image": 6156
      },
      {
        "key": "disease state",
        "no_image": 6156
      },
      {
        "key": "donor identifier",
        "no_image": 6156
      },
      {
        "key": "operetta measurement",
        "no_image": 6156
      },
      {
        "key": "operetta plate name",
        "no_image": 6156
      },
      {
        "key": "organism",
        "no_image": 6156
      },
      {
        "key": "progenitor cell type",
        "no_image": 6156
      },
      {
        "key": "results measurements",
        "no_image": 6156
      },
      {
        "key": "results summary",
        "no_image": 6156
      },
      {
        "key": "sex",
        "no_image": 6156
      },
      {
        "key": "chembl identifier",
        "no_image": 5994
      },
      {
        "key": "chembl identifier url",
        "no_image": 5994
      },
      {
        "key": "compound name",
        "no_image": 5994
      },
      {
        "key": "compound name url",
        "no_image": 5994
      },
      {
        "key": "dose",
        "no_image": 5994
      },
      {
        "key": "age",
        "no_image": 972
      },
      {
        "key": "ethnicity",
        "no_image": 972
      }
    ],
    "type": "screen"
  }
]

[jburel]

@khaledk2 have you considered passing multiple containers name e.g. idr0034, idr0035?

[khaledk2]

It searches using the contains operator (for the container name ). So, if idr003 is used as the container name, it will return all the containers in the IDR whose names contain this term, including idr0034 and idr0035.

[jburel]

yes but it will also contain idr0036 etc. which is potentially more that one will need.
That's okay

[khaledk2]

This PR has been deployed in idr-testing.

[jburel]

Thanks

[jburel]

Using this PR to retrieve gene identifier associated to a given study.
I have not yet used the CSV export option

[khaledk2]

CSV export option is now available in idr-testing

The following example is to export a CSV file for the available values for the gene identifier inside container idr0114
https://idr-testing.openmicroscopy.org/searchengine//api/v1/resources/image/container_keyvalues/?container_name=idr0114&key=gene identifier&csv=true

This example is to export a CSV file for the available keys inside container idr0114
https://idr-testing.openmicroscopy.org/searchengine//api/v1/resources/image/container_keys/?container_name=idr0114&csv=true

[khaledk2]

I fixed that and pushed the changes.

[jburel]

typo in file name conatiner_key_values.py => container_key_values.py

[khaledk2]

@jburel I have fixed the file name typo.

[khaledk2]

@jburel do you have any other comments?

[jburel]

Sorry for the delay