You will need Universal Unreal Engine 4 Unlocker to use the console.

Check out the mission select mod to get all items without using the console.
https://www.nexusmods.com/vampyr/mods/29?tab=description

Edit: Added a second option if you have issues with the container near the door.
Use exec allitems.txt this will put all items in the medical cabinet near the locker also use 
Set GP_LootDef_Gen_Hos_003_Med_C_C bGenerated False as below.

This mod will put all items in two different containers in Jonathan's office at Pembroke Hospital.

The container closest to the door will have weapons and the other lootable container near the locker will have items.

If your not sure which lootable containers look at the uploaded images.

One of the included weapons is a debug machete with 9999 damage. Don't try to upgrade this weapon as you will downgrade it.

Place AVGame folder in the root of your Vampyr install location.

In the console type exec items.txt for items and exec weapons.txt for weapons.

If you have already looted the chest first use exec commands then use these codes 
Set GP_LootDef_Gen_Hos_088_Res_C_C bGenerated False and Set GP_LootDef_Gen_Hos_003_Med_C_C bGenerated False

Rest at the bed (press confirm) if the chest isn't closed return to the main menu and reload your save file.
It's a bit tricky to get the chest to respawn, it's probably better to start a new game.

Any weapons you already have will not be upgraded to level 5. The weapons you get from the chest are only at base level 5 you still need to put the other
upgrades on them.

Since the crossbows only hold 6 bolts use this code for unlimited ammo Set AVGame.AVWeaponRanged iAmmoConsumedByEachShot 0

If you would like Jonathan to run like a vampire should run use this Set PlayerPawnDefault_Start_C_0.PostureWalkComp fSprintAnimSpeed 1500.000000


If you want all weapons and items in one container use the old version.